Starting phenix.real_space_refine on Thu Mar 21 10:05:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rqc_4980/03_2024/6rqc_4980_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rqc_4980/03_2024/6rqc_4980.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rqc_4980/03_2024/6rqc_4980.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rqc_4980/03_2024/6rqc_4980.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rqc_4980/03_2024/6rqc_4980_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rqc_4980/03_2024/6rqc_4980_trim_updated.pdb" } resolution = 4.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians Zn 5 6.06 5 P 192 5.49 5 Mg 3 5.21 5 S 228 5.16 5 C 33205 2.51 5 N 9167 2.21 5 O 10445 1.98 5 H 51978 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 406": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 423": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 452": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 453": "OE1" <-> "OE2" Residue "A PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 491": "OE1" <-> "OE2" Residue "A GLU 495": "OE1" <-> "OE2" Residue "A GLU 512": "OE1" <-> "OE2" Residue "A GLU 535": "OE1" <-> "OE2" Residue "A PHE 548": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 577": "OD1" <-> "OD2" Residue "A PHE 582": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 603": "OD1" <-> "OD2" Residue "A ARG 607": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 616": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A PHE 619": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 637": "OD1" <-> "OD2" Residue "A ASP 676": "OD1" <-> "OD2" Residue "A ARG 683": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ASP 687": "OD1" <-> "OD2" Residue "A GLU 718": "OE1" <-> "OE2" Residue "A TYR 727": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 784": "OE1" <-> "OE2" Residue "A ARG 796": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A PHE 804": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 821": "OE1" <-> "OE2" Residue "A GLU 844": "OE1" <-> "OE2" Residue "A GLU 859": "OE1" <-> "OE2" Residue "A ARG 862": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A PHE 868": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 888": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 899": "OE1" <-> "OE2" Residue "A ARG 912": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B PHE 243": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 246": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 260": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B PHE 281": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 316": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 317": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 323": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B TYR 333": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 390": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B TYR 395": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 411": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 433": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B PHE 437": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 466": "OD1" <-> "OD2" Residue "B PHE 477": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 484": "OE1" <-> "OE2" Residue "B GLU 489": "OE1" <-> "OE2" Residue "C TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 55": "OE1" <-> "OE2" Residue "C ASP 77": "OD1" <-> "OD2" Residue "C GLU 86": "OE1" <-> "OE2" Residue "C ASP 89": "OD1" <-> "OD2" Residue "C ARG 99": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 100": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 117": "OE1" <-> "OE2" Residue "C ASP 120": "OD1" <-> "OD2" Residue "C GLU 135": "OE1" <-> "OE2" Residue "C ARG 144": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C GLU 189": "OE1" <-> "OE2" Residue "C ASP 198": "OD1" <-> "OD2" Residue "C PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 213": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 217": "OD1" <-> "OD2" Residue "C ASP 286": "OD1" <-> "OD2" Residue "C ASP 289": "OD1" <-> "OD2" Residue "C PHE 298": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 301": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 330": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 337": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 339": "OD1" <-> "OD2" Residue "C ASP 348": "OD1" <-> "OD2" Residue "C ASP 349": "OD1" <-> "OD2" Residue "C ASP 375": "OD1" <-> "OD2" Residue "C ARG 386": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C GLU 390": "OE1" <-> "OE2" Residue "C GLU 394": "OE1" <-> "OE2" Residue "C PHE 395": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 408": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 455": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 459": "OD1" <-> "OD2" Residue "C TYR 483": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 504": "OE1" <-> "OE2" Residue "C ARG 529": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C PHE 556": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 589": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 599": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 614": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 55": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ARG 84": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D TYR 123": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 181": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 217": "OD1" <-> "OD2" Residue "D GLU 218": "OE1" <-> "OE2" Residue "D PHE 248": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 258": "OE1" <-> "OE2" Residue "D TYR 259": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ARG 295": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D GLU 312": "OE1" <-> "OE2" Residue "D ARG 317": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D PHE 363": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 365": "OD1" <-> "OD2" Residue "D ARG 400": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D TYR 415": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ARG 425": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D GLU 461": "OE1" <-> "OE2" Residue "D GLU 471": "OE1" <-> "OE2" Residue "D ARG 478": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D TYR 504": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 512": "OE1" <-> "OE2" Residue "D ARG 515": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E GLU 7": "OE1" <-> "OE2" Residue "E ARG 11": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 63": "OE1" <-> "OE2" Residue "E TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 104": "OE1" <-> "OE2" Residue "E ASP 136": "OD1" <-> "OD2" Residue "E ASP 140": "OD1" <-> "OD2" Residue "E TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 166": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 172": "OE1" <-> "OE2" Residue "E PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ARG 178": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E TYR 179": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 189": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 196": "OE1" <-> "OE2" Residue "E GLU 211": "OE1" <-> "OE2" Residue "E GLU 221": "OE1" <-> "OE2" Residue "E ASP 230": "OD1" <-> "OD2" Residue "E PHE 239": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ARG 272": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E PHE 292": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 322": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 340": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 342": "OE1" <-> "OE2" Residue "E ASP 346": "OD1" <-> "OD2" Residue "E ARG 365": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 366": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 374": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E GLU 401": "OE1" <-> "OE2" Residue "E ARG 409": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E PHE 421": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ASP 442": "OD1" <-> "OD2" Residue "E TYR 443": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 461": "OE1" <-> "OE2" Residue "E PHE 468": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 473": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ASP 476": "OD1" <-> "OD2" Residue "F TYR 63": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F GLU 71": "OE1" <-> "OE2" Residue "F TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ARG 287": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F GLU 297": "OE1" <-> "OE2" Residue "F ASP 304": "OD1" <-> "OD2" Residue "F ARG 312": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F PHE 332": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ARG 336": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ASP 360": "OD1" <-> "OD2" Residue "F ASP 361": "OD1" <-> "OD2" Residue "F ARG 380": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 385": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F TYR 386": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ASP 388": "OD1" <-> "OD2" Residue "F GLU 396": "OE1" <-> "OE2" Residue "2 ASP 220": "OD1" <-> "OD2" Residue "2 ARG 224": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "2 GLU 240": "OE1" <-> "OE2" Residue "2 GLU 266": "OE1" <-> "OE2" Residue "2 ASP 272": "OD1" <-> "OD2" Residue "2 TYR 283": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "2 ASP 299": "OD1" <-> "OD2" Residue "2 ARG 319": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "2 ARG 326": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "2 TYR 336": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "2 PHE 339": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "2 PHE 363": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "2 TYR 382": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "2 TYR 434": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "2 ASP 435": "OD1" <-> "OD2" Residue "2 ARG 489": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "2 ASP 495": "OD1" <-> "OD2" Residue "2 TYR 506": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "2 ARG 509": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "2 PHE 520": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "2 ARG 534": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "2 PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "2 GLU 588": "OE1" <-> "OE2" Residue "2 ARG 656": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "2 ASP 685": "OD1" <-> "OD2" Residue "2 TYR 766": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "2 TYR 775": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "2 ASP 782": "OD1" <-> "OD2" Residue "2 ARG 794": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "2 ARG 808": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "2 ARG 824": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "2 PHE 828": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "2 PHE 845": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "2 ARG 854": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "2 ARG 859": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "2 TYR 864": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "3 PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "3 PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "3 ARG 39": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "3 ASP 40": "OD1" <-> "OD2" Residue "3 ASP 58": "OD1" <-> "OD2" Residue "3 ASP 59": "OD1" <-> "OD2" Residue "3 ASP 61": "OD1" <-> "OD2" Residue "3 PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "3 ARG 108": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "3 TYR 120": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "3 PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "3 ASP 138": "OD1" <-> "OD2" Residue "3 ARG 208": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "3 TYR 214": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "3 ARG 224": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "3 PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "3 ASP 284": "OD1" <-> "OD2" Residue "3 ASP 290": "OD1" <-> "OD2" Residue "3 ARG 291": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "3 PHE 317": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "3 ARG 339": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "3 ASP 344": "OD1" <-> "OD2" Residue "3 ARG 420": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "3 ARG 435": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "3 GLU 451": "OE1" <-> "OE2" Residue "3 GLU 458": "OE1" <-> "OE2" Residue "3 ASP 466": "OD1" <-> "OD2" Residue "3 ARG 467": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "3 ASP 473": "OD1" <-> "OD2" Residue "3 ASP 482": "OD1" <-> "OD2" Residue "3 ARG 483": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "3 ARG 509": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "3 PHE 520": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "3 ASP 551": "OD1" <-> "OD2" Residue "3 ASP 552": "OD1" <-> "OD2" 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 "4 ARG 178": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "4 TYR 203": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "4 ASP 210": "OD1" <-> "OD2" Residue "4 GLU 211": "OE1" <-> "OE2" Residue "4 TYR 226": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "4 GLU 232": "OE1" <-> "OE2" Residue "4 ARG 234": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "4 GLU 235": "OE1" <-> "OE2" Residue "4 ASP 278": "OD1" <-> "OD2" Residue "4 ARG 388": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "4 ASP 404": "OD1" <-> "OD2" Residue "4 ASP 421": "OD1" <-> "OD2" Residue "4 GLU 422": "OE1" <-> "OE2" Residue "4 ASP 471": "OD1" <-> "OD2" Residue "4 ARG 473": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "4 ASP 475": "OD1" <-> "OD2" Residue "4 GLU 484": "OE1" <-> "OE2" Residue "4 ASP 491": "OD1" <-> "OD2" Residue "4 GLU 494": "OE1" <-> "OE2" Residue "4 ARG 524": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "4 PHE 545": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "4 ARG 557": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "4 ARG 559": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "4 ASP 569": "OD1" <-> "OD2" Residue "4 ARG 607": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "4 ASP 608": "OD1" <-> "OD2" Residue "4 ASP 625": "OD1" <-> "OD2" Residue "4 ARG 681": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "4 ASP 693": "OD1" <-> "OD2" Residue "4 ASP 703": "OD1" <-> "OD2" Residue "4 TYR 706": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "4 TYR 728": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "4 ASP 739": "OD1" <-> "OD2" Residue "4 GLU 756": "OE1" <-> "OE2" Residue "4 ARG 796": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "4 ARG 827": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "4 TYR 836": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "5 ASP 41": "OD1" <-> "OD2" Residue "5 GLU 66": "OE1" <-> "OE2" Residue "5 ASP 74": "OD1" <-> "OD2" Residue "5 ASP 85": "OD1" <-> "OD2" Residue "5 ARG 106": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "5 PHE 197": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "5 ASP 239": "OD1" <-> "OD2" Residue "5 PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "5 GLU 269": "OE1" <-> "OE2" Residue "5 TYR 301": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "5 ASP 336": "OD1" <-> "OD2" Residue "5 PHE 379": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "5 ARG 407": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "5 ASP 409": "OD1" <-> "OD2" Residue "5 GLU 430": "OE1" <-> "OE2" Residue "5 ARG 455": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "5 ARG 460": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "5 TYR 463": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "5 PHE 482": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "5 ASP 487": "OD1" <-> "OD2" Residue "5 TYR 527": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "5 ASP 559": "OD1" <-> "OD2" Residue "5 ASP 565": "OD1" <-> "OD2" Residue "5 ARG 651": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "5 ASP 678": "OD1" <-> "OD2" Residue "6 ASP 105": "OD1" <-> "OD2" Residue "6 ARG 112": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "6 ASP 121": "OD1" <-> "OD2" Residue "6 ASP 128": "OD1" <-> "OD2" Residue "6 TYR 136": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "6 ARG 137": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "6 ASP 147": "OD1" <-> "OD2" Residue "6 TYR 174": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "6 ARG 176": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "6 ARG 186": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "6 ARG 187": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "6 ARG 190": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "6 PHE 263": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" 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 296": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "6 PHE 309": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "6 PHE 343": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "6 ARG 375": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "6 ARG 382": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "6 ASP 384": "OD1" <-> "OD2" Residue "6 ASP 393": "OD1" <-> "OD2" Residue "6 PHE 397": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "6 ASP 406": "OD1" <-> "OD2" Residue "6 ARG 424": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "6 ARG 441": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "6 ARG 446": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "6 TYR 450": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "6 GLU 512": "OE1" <-> "OE2" Residue "6 TYR 526": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "6 ARG 531": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "6 TYR 597": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "6 ARG 614": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "6 GLU 616": "OE1" <-> "OE2" Residue "6 ASP 620": "OD1" <-> "OD2" Residue "6 TYR 621": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "6 ASP 632": "OD1" <-> "OD2" Residue "6 ASP 639": "OD1" <-> "OD2" Residue "6 PHE 641": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "6 ASP 645": "OD1" <-> "OD2" Residue "6 ARG 691": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "6 ARG 708": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "6 PHE 712": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "6 PHE 746": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "6 TYR 757": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "6 ARG 781": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "6 ASP 783": "OD1" <-> "OD2" Residue "6 ARG 790": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "6 GLU 801": "OE1" <-> "OE2" Residue "6 ASP 839": "OD1" <-> "OD2" Residue "7 TYR 14": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "7 PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "7 ASP 136": "OD1" <-> "OD2" Residue "7 ARG 198": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "7 ARG 199": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "7 PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "7 ARG 214": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "7 ASP 263": "OD1" <-> "OD2" Residue "7 TYR 267": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "7 GLU 283": "OE1" <-> "OE2" Residue "7 ARG 303": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "7 ASP 350": "OD1" <-> "OD2" Residue "7 PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "7 ARG 400": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "7 ASP 409": "OD1" <-> "OD2" Residue "7 ASP 427": "OD1" <-> "OD2" Residue "7 ASP 441": "OD1" <-> "OD2" Residue "7 ARG 451": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "7 TYR 482": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "7 ARG 573": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "7 TYR 574": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "7 ARG 577": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "7 PHE 598": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "7 ASP 607": "OD1" <-> "OD2" Residue "7 ASP 608": "OD1" <-> "OD2" Residue "7 ASP 627": "OD1" <-> "OD2" Residue "7 ARG 639": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "7 TYR 641": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "7 GLU 654": "OE1" <-> "OE2" Residue "7 ARG 673": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "7 PHE 679": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" 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" Time to flip residues: 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 105223 Number of models: 1 Model: "" Number of chains: 23 Chain: "A" Number of atoms: 8028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 494, 8028 Classifications: {'peptide': 494} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 484} Chain breaks: 3 Chain: "B" Number of atoms: 4067 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 4067 Classifications: {'peptide': 247} Link IDs: {'PTRANS': 11, 'TRANS': 235} Chain breaks: 1 Chain: "C" Number of atoms: 9579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 582, 9579 Classifications: {'peptide': 582} Link IDs: {'PTRANS': 16, 'TRANS': 565} Chain breaks: 1 Chain: "D" Number of atoms: 7193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 7193 Classifications: {'peptide': 437} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 424} Chain breaks: 3 Chain: "E" Number of atoms: 7529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 459, 7529 Classifications: {'peptide': 459} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 21, 'TRANS': 437} Chain breaks: 1 Chain: "F" Number of atoms: 4046 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 4046 Classifications: {'peptide': 242} Link IDs: {'PTRANS': 6, 'TRANS': 235} Chain breaks: 3 Chain: "2" Number of atoms: 9573 Number of conformers: 1 Conformer: "" Number of residues, atoms: 601, 9573 Classifications: {'peptide': 601} Link IDs: {'PTRANS': 23, 'TRANS': 577} Chain breaks: 2 Chain: "3" Number of atoms: 9448 Number of conformers: 1 Conformer: "" Number of residues, atoms: 599, 9448 Classifications: {'peptide': 599} Link IDs: {'PTRANS': 24, 'TRANS': 574} Chain breaks: 4 Chain: "4" Number of atoms: 10282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 641, 10282 Classifications: {'peptide': 641} Link IDs: {'PTRANS': 23, 'TRANS': 617} Chain breaks: 2 Chain: "5" Number of atoms: 9532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 602, 9532 Classifications: {'peptide': 602} Link IDs: {'PTRANS': 24, 'TRANS': 577} Chain breaks: 5 Chain: "6" Number of atoms: 9782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 616, 9782 Classifications: {'peptide': 616} Link IDs: {'PTRANS': 22, 'TRANS': 593} Chain breaks: 3 Chain: "7" Number of atoms: 10353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 654, 10353 Classifications: {'peptide': 654} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 30, 'TRANS': 623} Chain breaks: 3 Chain: "X" Number of atoms: 2806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 2806 Classifications: {'DNA': 88} Modifications used: {'3*END': 1, '5*END': 1} Link IDs: {'rna3p': 87} Chain: "Y" Number of atoms: 2796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 2796 Classifications: {'DNA': 88} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 87} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "2" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' ZN': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "3" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' ZN': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' ZN': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 62207 SG CYS 4 349 85.225 128.448 95.493 1.00142.75 S ATOM 62247 SG CYS 4 352 85.412 132.467 96.030 1.00154.24 S ATOM 62536 SG CYS 4 371 86.968 127.904 98.291 1.00141.61 S ATOM 62616 SG CYS 4 376 86.637 131.288 99.007 1.00144.77 S ATOM 72051 SG CYS 5 183 97.158 77.132 120.118 1.00131.80 S ATOM 72100 SG CYS 5 186 97.978 78.297 123.692 1.00134.74 S ATOM 72413 SG CYS 5 211 94.232 79.751 124.387 1.00139.90 S ATOM 81646 SG CYS 6 311 74.834 115.796 112.064 1.00143.57 S ATOM 81991 SG CYS 6 333 75.263 119.914 110.979 1.00153.30 S ATOM 82054 SG CYS 6 338 78.535 117.854 113.435 1.00171.80 S ATOM 92146 SG CYS 7 265 112.337 117.021 91.765 1.00150.09 S ATOM 92439 SG CYS 7 284 108.564 114.351 92.094 1.00163.20 S ATOM 92504 SG CYS 7 289 109.760 117.191 93.976 1.00169.26 S Time building chain proxies: 35.47, per 1000 atoms: 0.34 Number of scatterers: 105223 At special positions: 0 Unit cell: (157.32, 158.7, 306.36, 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 228 16.00 P 192 15.00 Mg 3 11.99 O 10445 8.00 N 9167 7.00 C 33205 6.00 H 51978 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: 72.91 Conformation dependent library (CDL) restraints added in 7.9 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN 41001 " pdb="ZN ZN 41001 " - pdb=" SG CYS 4 349 " pdb="ZN ZN 41001 " - pdb=" SG CYS 4 376 " pdb="ZN ZN 41001 " - pdb=" SG CYS 4 371 " pdb="ZN ZN 41001 " - pdb=" SG CYS 4 352 " pdb=" ZN 5 802 " pdb="ZN ZN 5 802 " - pdb=" SG CYS 5 186 " pdb="ZN ZN 5 802 " - pdb=" SG CYS 5 183 " pdb="ZN ZN 5 802 " - pdb=" SG CYS 5 211 " pdb=" ZN 61101 " pdb="ZN ZN 61101 " - pdb=" SG CYS 6 333 " pdb="ZN ZN 61101 " - pdb=" SG CYS 6 338 " pdb="ZN ZN 61101 " - pdb=" SG CYS 6 311 " pdb=" ZN 7 902 " pdb="ZN ZN 7 902 " - pdb=" SG CYS 7 265 " pdb="ZN ZN 7 902 " - pdb=" SG CYS 7 284 " pdb="ZN ZN 7 902 " - pdb=" SG CYS 7 289 " Number of angles added : 6 12176 Ramachandran restraints generated. 6088 Oldfield, 0 Emsley, 6088 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11834 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: 258 helices and 56 sheets defined 53.2% alpha, 12.4% beta 83 base pairs and 152 stacking pairs defined. Time for finding SS restraints: 72.61 Creating SS restraints... Processing helix chain 'A' and resid 374 through 380 removed outlier: 4.449A pdb=" N ARG A 378 " --> pdb=" O PRO A 374 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N PHE A 379 " --> pdb=" O PHE A 375 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N LYS A 380 " --> pdb=" O SER A 376 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 374 through 380' Processing helix chain 'A' and resid 387 through 392 removed outlier: 4.002A pdb=" N LEU A 391 " --> pdb=" O ASP A 387 " (cutoff:3.500A) Proline residue: A 392 - end of helix No H-bonds generated for 'chain 'A' and resid 387 through 392' Processing helix chain 'A' and resid 398 through 406 removed outlier: 4.397A pdb=" N MET A 402 " --> pdb=" O SER A 398 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N PHE A 406 " --> pdb=" O MET A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 423 through 431 Processing helix chain 'A' and resid 452 through 470 removed outlier: 4.491A pdb=" N PHE A 456 " --> pdb=" O ARG A 452 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N LEU A 461 " --> pdb=" O ALA A 457 " (cutoff:3.500A) Processing helix chain 'A' and resid 484 through 503 removed outlier: 3.998A pdb=" N ARG A 503 " --> pdb=" O SER A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 514 through 519 removed outlier: 4.363A pdb=" N VAL A 519 " --> pdb=" O GLY A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 533 removed outlier: 3.852A pdb=" N GLU A 526 " --> pdb=" O THR A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 551 removed outlier: 5.174A pdb=" N GLU A 544 " --> pdb=" O ALA A 540 " (cutoff:3.500A) Processing helix chain 'A' and resid 567 through 573 removed outlier: 4.310A pdb=" N MET A 571 " --> pdb=" O GLU A 567 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N VAL A 572 " --> pdb=" O LEU A 568 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N THR A 573 " --> pdb=" O ASP A 569 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 567 through 573' Processing helix chain 'A' and resid 576 through 587 removed outlier: 4.254A pdb=" N THR A 587 " --> pdb=" O PHE A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 609 removed outlier: 3.751A pdb=" N LEU A 609 " --> pdb=" O PRO A 605 " (cutoff:3.500A) Processing helix chain 'A' and resid 610 through 618 removed outlier: 3.891A pdb=" N THR A 614 " --> pdb=" O GLY A 610 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLY A 618 " --> pdb=" O THR A 614 " (cutoff:3.500A) Processing helix chain 'A' and resid 628 through 641 removed outlier: 3.618A pdb=" N LEU A 640 " --> pdb=" O ILE A 636 " (cutoff:3.500A) Processing helix chain 'A' and resid 685 through 700 removed outlier: 3.649A pdb=" N VAL A 696 " --> pdb=" O ALA A 692 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N SER A 698 " --> pdb=" O ARG A 694 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N VAL A 699 " --> pdb=" O LYS A 695 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N SER A 700 " --> pdb=" O VAL A 696 " (cutoff:3.500A) Processing helix chain 'A' and resid 702 through 726 removed outlier: 3.755A pdb=" N HIS A 725 " --> pdb=" O TYR A 721 " (cutoff:3.500A) Processing helix chain 'A' and resid 774 through 787 removed outlier: 3.822A pdb=" N GLU A 784 " --> pdb=" O LYS A 780 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N THR A 785 " --> pdb=" O ALA A 781 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N LEU A 786 " --> pdb=" O LEU A 782 " (cutoff:3.500A) Processing helix chain 'A' and resid 789 through 798 removed outlier: 6.239A pdb=" N SER A 798 " --> pdb=" O MET A 794 " (cutoff:3.500A) Processing helix chain 'A' and resid 799 through 816 Processing helix chain 'A' and resid 821 through 837 removed outlier: 3.918A pdb=" N ILE A 825 " --> pdb=" O GLU A 821 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ASN A 836 " --> pdb=" O LEU A 832 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLY A 837 " --> pdb=" O ILE A 833 " (cutoff:3.500A) Processing helix chain 'A' and resid 839 through 846 removed outlier: 3.841A pdb=" N ALA A 846 " --> pdb=" O VAL A 842 " (cutoff:3.500A) Processing helix chain 'A' and resid 865 through 877 Processing helix chain 'A' and resid 897 through 908 removed outlier: 4.011A pdb=" N ALA A 901 " --> pdb=" O SER A 897 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N GLU A 907 " --> pdb=" O ARG A 903 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ASP A 908 " --> pdb=" O ALA A 904 " (cutoff:3.500A) Processing helix chain 'A' and resid 909 through 914 removed outlier: 4.338A pdb=" N ASN A 913 " --> pdb=" O GLU A 909 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LEU A 914 " --> pdb=" O THR A 910 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 909 through 914' Processing helix chain 'B' and resid 242 through 251 removed outlier: 4.498A pdb=" N LYS B 251 " --> pdb=" O PHE B 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 259 removed outlier: 4.086A pdb=" N LYS B 258 " --> pdb=" O ARG B 254 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N SER B 259 " --> pdb=" O THR B 255 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 254 through 259' Processing helix chain 'B' and resid 262 through 267 removed outlier: 4.692A pdb=" N ALA B 266 " --> pdb=" O THR B 262 " (cutoff:3.500A) Proline residue: B 267 - end of helix No H-bonds generated for 'chain 'B' and resid 262 through 267' Processing helix chain 'B' and resid 270 through 285 removed outlier: 3.736A pdb=" N PHE B 274 " --> pdb=" O THR B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 311 removed outlier: 3.604A pdb=" N ARG B 290 " --> pdb=" O GLN B 286 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N LYS B 298 " --> pdb=" O PHE B 294 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N LYS B 299 " --> pdb=" O GLU B 295 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N MET B 300 " --> pdb=" O ILE B 296 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N PHE B 301 " --> pdb=" O GLN B 297 " (cutoff:3.500A) Proline residue: B 302 - end of helix removed outlier: 3.704A pdb=" N GLN B 310 " --> pdb=" O PHE B 306 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLY B 311 " --> pdb=" O GLU B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 332 removed outlier: 4.641A pdb=" N LEU B 326 " --> pdb=" O LYS B 322 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N GLU B 328 " --> pdb=" O ASN B 324 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ILE B 331 " --> pdb=" O GLU B 327 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ASP B 332 " --> pdb=" O GLU B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 343 removed outlier: 3.998A pdb=" N LEU B 343 " --> pdb=" O ALA B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 383 removed outlier: 4.632A pdb=" N VAL B 375 " --> pdb=" O ASN B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 389 through 394 removed outlier: 4.470A pdb=" N THR B 393 " --> pdb=" O THR B 389 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N LYS B 394 " --> pdb=" O ARG B 390 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 389 through 394' Processing helix chain 'B' and resid 398 through 413 removed outlier: 3.557A pdb=" N LEU B 402 " --> pdb=" O ASN B 398 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ASP B 409 " --> pdb=" O GLN B 405 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N ASN B 413 " --> pdb=" O ASP B 409 " (cutoff:3.500A) Processing helix chain 'B' and resid 434 through 446 removed outlier: 4.324A pdb=" N SER B 445 " --> pdb=" O LEU B 441 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N VAL B 446 " --> pdb=" O SER B 442 " (cutoff:3.500A) Processing helix chain 'B' and resid 460 through 465 removed outlier: 3.979A pdb=" N LEU B 464 " --> pdb=" O TYR B 460 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N TRP B 465 " --> pdb=" O ALA B 461 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 460 through 465' Processing helix chain 'B' and resid 466 through 474 Processing helix chain 'B' and resid 486 through 491 removed outlier: 3.760A pdb=" N SER B 490 " --> pdb=" O SER B 486 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N THR B 491 " --> pdb=" O THR B 487 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 486 through 491' Processing helix chain 'C' and resid 50 through 94 removed outlier: 3.864A pdb=" N GLN C 71 " --> pdb=" O HIS C 67 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLU C 80 " --> pdb=" O ILE C 76 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N TYR C 92 " --> pdb=" O SER C 88 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N SER C 93 " --> pdb=" O ASP C 89 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N GLU C 94 " --> pdb=" O LEU C 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 137 removed outlier: 3.797A pdb=" N SER C 136 " --> pdb=" O THR C 132 " (cutoff:3.500A) Proline residue: C 137 - end of helix No H-bonds generated for 'chain 'C' and resid 132 through 137' Processing helix chain 'C' and resid 138 through 159 removed outlier: 4.280A pdb=" N MET C 142 " --> pdb=" O ASN C 138 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N ALA C 156 " --> pdb=" O SER C 152 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N GLU C 157 " --> pdb=" O ALA C 153 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N GLU C 158 " --> pdb=" O ALA C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 184 through 191 removed outlier: 4.226A pdb=" N VAL C 188 " --> pdb=" O ASP C 184 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLU C 189 " --> pdb=" O LEU C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 212 through 226 removed outlier: 4.096A pdb=" N SER C 225 " --> pdb=" O ILE C 221 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N ALA C 226 " --> pdb=" O LEU C 222 " (cutoff:3.500A) Processing helix chain 'C' and resid 243 through 252 removed outlier: 3.986A pdb=" N ILE C 247 " --> pdb=" O ASN C 243 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N LYS C 249 " --> pdb=" O SER C 245 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N ASN C 250 " --> pdb=" O ASN C 246 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N ARG C 252 " --> pdb=" O GLU C 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 263 removed outlier: 4.920A pdb=" N LEU C 258 " --> pdb=" O SER C 254 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LEU C 259 " --> pdb=" O THR C 255 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ARG C 261 " --> pdb=" O ARG C 257 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N ASN C 262 " --> pdb=" O LEU C 258 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N TYR C 263 " --> pdb=" O LEU C 259 " (cutoff:3.500A) Processing helix chain 'C' and resid 274 through 289 removed outlier: 4.802A pdb=" N GLN C 279 " --> pdb=" O LYS C 275 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N VAL C 288 " --> pdb=" O PHE C 284 " (cutoff:3.500A) Processing helix chain 'C' and resid 295 through 310 removed outlier: 3.604A pdb=" N VAL C 299 " --> pdb=" O SER C 295 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N ALA C 307 " --> pdb=" O LEU C 303 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ASN C 308 " --> pdb=" O SER C 304 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N ASN C 309 " --> pdb=" O LYS C 305 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N THR C 310 " --> pdb=" O MET C 306 " (cutoff:3.500A) Processing helix chain 'C' and resid 312 through 332 removed outlier: 5.623A pdb=" N LEU C 316 " --> pdb=" O HIS C 312 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU C 317 " --> pdb=" O ASN C 313 " (cutoff:3.500A) Processing helix chain 'C' and resid 339 through 344 removed outlier: 4.172A pdb=" N VAL C 343 " --> pdb=" O ASP C 339 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N ASP C 344 " --> pdb=" O PRO C 340 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 339 through 344' Processing helix chain 'C' and resid 347 through 357 removed outlier: 3.794A pdb=" N ARG C 356 " --> pdb=" O LYS C 352 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N CYS C 357 " --> pdb=" O ILE C 353 " (cutoff:3.500A) Processing helix chain 'C' and resid 358 through 372 removed outlier: 4.277A pdb=" N ALA C 372 " --> pdb=" O ILE C 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 374 through 381 removed outlier: 3.719A pdb=" N LEU C 378 " --> pdb=" O ALA C 374 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 398 removed outlier: 3.795A pdb=" N LEU C 388 " --> pdb=" O LYS C 384 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N ARG C 398 " --> pdb=" O GLU C 394 " (cutoff:3.500A) Processing helix chain 'C' and resid 400 through 416 removed outlier: 4.046A pdb=" N GLY C 404 " --> pdb=" O ASN C 400 " (cutoff:3.500A) Processing helix chain 'C' and resid 423 through 434 removed outlier: 4.367A pdb=" N LEU C 427 " --> pdb=" O ASN C 423 " (cutoff:3.500A) Processing helix chain 'C' and resid 435 through 444 removed outlier: 4.345A pdb=" N ARG C 442 " --> pdb=" O SER C 438 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N TRP C 443 " --> pdb=" O TYR C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 449 through 454 Processing helix chain 'C' and resid 462 through 467 removed outlier: 4.124A pdb=" N PHE C 466 " --> pdb=" O PHE C 462 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N THR C 467 " --> pdb=" O GLN C 463 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 462 through 467' Processing helix chain 'C' and resid 473 through 479 removed outlier: 4.849A pdb=" N GLN C 477 " --> pdb=" O GLY C 473 " (cutoff:3.500A) Processing helix chain 'C' and resid 482 through 494 removed outlier: 3.837A pdb=" N ASN C 490 " --> pdb=" O ASN C 486 " (cutoff:3.500A) Processing helix chain 'C' and resid 504 through 509 removed outlier: 3.779A pdb=" N THR C 508 " --> pdb=" O GLU C 504 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N LEU C 509 " --> pdb=" O ASN C 505 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 504 through 509' Processing helix chain 'C' and resid 510 through 517 removed outlier: 4.691A pdb=" N LYS C 515 " --> pdb=" O GLY C 511 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N ILE C 516 " --> pdb=" O ASP C 512 " (cutoff:3.500A) Processing helix chain 'C' and resid 519 through 531 removed outlier: 4.033A pdb=" N GLN C 523 " --> pdb=" O PRO C 519 " (cutoff:3.500A) Processing helix chain 'C' and resid 537 through 548 removed outlier: 4.456A pdb=" N THR C 547 " --> pdb=" O ALA C 543 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N LEU C 548 " --> pdb=" O PHE C 544 " (cutoff:3.500A) Processing helix chain 'C' and resid 549 through 561 removed outlier: 3.852A pdb=" N ILE C 553 " --> pdb=" O PRO C 549 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ASP C 560 " --> pdb=" O PHE C 556 " (cutoff:3.500A) Proline residue: C 561 - end of helix Processing helix chain 'C' and resid 563 through 572 removed outlier: 4.434A pdb=" N THR C 572 " --> pdb=" O GLU C 568 " (cutoff:3.500A) Processing helix chain 'C' and resid 573 through 595 removed outlier: 4.352A pdb=" N ASP C 577 " --> pdb=" O PRO C 573 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ASN C 593 " --> pdb=" O PHE C 589 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N MET C 594 " --> pdb=" O ALA C 590 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLY C 595 " --> pdb=" O PHE C 591 " (cutoff:3.500A) Processing helix chain 'C' and resid 333 through 338 removed outlier: 3.975A pdb=" N VAL C 336 " --> pdb=" O ALA C 333 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ILE C 338 " --> pdb=" O SER C 335 " (cutoff:3.500A) Processing helix chain 'D' and resid 46 through 62 Processing helix chain 'D' and resid 72 through 91 removed outlier: 4.399A pdb=" N ASP D 77 " --> pdb=" O THR D 73 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N CYS D 78 " --> pdb=" O TYR D 74 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N ARG D 84 " --> pdb=" O GLN D 80 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N SER D 89 " --> pdb=" O ILE D 85 " (cutoff:3.500A) Processing helix chain 'D' and resid 107 through 123 removed outlier: 4.547A pdb=" N LEU D 111 " --> pdb=" O TYR D 107 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N GLN D 121 " --> pdb=" O SER D 117 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N SER D 122 " --> pdb=" O LEU D 118 " (cutoff:3.500A) Processing helix chain 'D' and resid 139 through 158 removed outlier: 5.363A pdb=" N ILE D 143 " --> pdb=" O GLU D 139 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ASN D 144 " --> pdb=" O GLN D 140 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LEU D 154 " --> pdb=" O LEU D 150 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLN D 155 " --> pdb=" O GLU D 151 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N LYS D 156 " --> pdb=" O GLN D 152 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ILE D 157 " --> pdb=" O GLN D 153 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 189 Processing helix chain 'D' and resid 218 through 224 removed outlier: 4.443A pdb=" N PHE D 222 " --> pdb=" O GLU D 218 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N GLY D 224 " --> pdb=" O ASP D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 228 through 241 removed outlier: 3.952A pdb=" N TYR D 232 " --> pdb=" O GLN D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 255 through 260 removed outlier: 4.863A pdb=" N TYR D 259 " --> pdb=" O ASN D 255 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N LEU D 260 " --> pdb=" O ILE D 256 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 255 through 260' Processing helix chain 'D' and resid 261 through 268 removed outlier: 3.522A pdb=" N LYS D 265 " --> pdb=" O GLU D 261 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 293 removed outlier: 4.032A pdb=" N MET D 284 " --> pdb=" O ASN D 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 316 removed outlier: 3.812A pdb=" N ASP D 315 " --> pdb=" O LYS D 311 " (cutoff:3.500A) Proline residue: D 316 - end of helix Processing helix chain 'D' and resid 318 through 330 Processing helix chain 'D' and resid 333 through 348 removed outlier: 4.315A pdb=" N LEU D 337 " --> pdb=" O SER D 333 " (cutoff:3.500A) Proline residue: D 343 - end of helix Processing helix chain 'D' and resid 350 through 361 Processing helix chain 'D' and resid 362 through 373 removed outlier: 3.555A pdb=" N ILE D 366 " --> pdb=" O SER D 362 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N LEU D 372 " --> pdb=" O ASN D 368 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N SER D 373 " --> pdb=" O LYS D 369 " (cutoff:3.500A) Processing helix chain 'D' and resid 375 through 383 removed outlier: 6.222A pdb=" N ARG D 379 " --> pdb=" O ASN D 375 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N LEU D 380 " --> pdb=" O LEU D 376 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N LEU D 383 " --> pdb=" O ARG D 379 " (cutoff:3.500A) Processing helix chain 'D' and resid 384 through 402 removed outlier: 3.516A pdb=" N LEU D 388 " --> pdb=" O SER D 384 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N VAL D 397 " --> pdb=" O SER D 393 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N LYS D 402 " --> pdb=" O ALA D 398 " (cutoff:3.500A) Processing helix chain 'D' and resid 407 through 426 removed outlier: 3.526A pdb=" N ALA D 411 " --> pdb=" O ASN D 407 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ILE D 426 " --> pdb=" O ILE D 422 " (cutoff:3.500A) Processing helix chain 'D' and resid 452 through 467 removed outlier: 3.695A pdb=" N ASN D 458 " --> pdb=" O LYS D 454 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N VAL D 459 " --> pdb=" O ASP D 455 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N GLU D 461 " --> pdb=" O LYS D 457 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASN D 462 " --> pdb=" O ASN D 458 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU D 466 " --> pdb=" O ASN D 462 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ASP D 467 " --> pdb=" O LEU D 463 " (cutoff:3.500A) Processing helix chain 'D' and resid 480 through 491 removed outlier: 3.568A pdb=" N SER D 488 " --> pdb=" O ALA D 484 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N GLN D 491 " --> pdb=" O ALA D 487 " (cutoff:3.500A) Processing helix chain 'D' and resid 492 through 497 Processing helix chain 'D' and resid 509 through 517 Processing helix chain 'D' and resid 523 through 528 removed outlier: 3.611A pdb=" N THR D 527 " --> pdb=" O TYR D 523 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N GLN D 528 " --> pdb=" O TYR D 524 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 523 through 528' Processing helix chain 'D' and resid 133 through 138 removed outlier: 5.004A pdb=" N SER D 138 " --> pdb=" O ASN D 133 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 133 through 138' Processing helix chain 'E' and resid 11 through 23 removed outlier: 5.567A pdb=" N SER E 23 " --> pdb=" O ALA E 19 " (cutoff:3.500A) Processing helix chain 'E' and resid 25 through 30 removed outlier: 4.206A pdb=" N THR E 29 " --> pdb=" O ASP E 25 " (cutoff:3.500A) Proline residue: E 30 - end of helix No H-bonds generated for 'chain 'E' and resid 25 through 30' Processing helix chain 'E' and resid 42 through 55 removed outlier: 3.733A pdb=" N LYS E 48 " --> pdb=" O THR E 44 " (cutoff:3.500A) Proline residue: E 55 - end of helix Processing helix chain 'E' and resid 63 through 68 removed outlier: 4.097A pdb=" N LEU E 67 " --> pdb=" O GLU E 63 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N VAL E 68 " --> pdb=" O PRO E 64 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 63 through 68' Processing helix chain 'E' and resid 69 through 90 removed outlier: 4.101A pdb=" N LEU E 73 " --> pdb=" O SER E 69 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N GLN E 82 " --> pdb=" O ALA E 78 " (cutoff:3.500A) Proline residue: E 90 - end of helix Processing helix chain 'E' and resid 104 through 120 Processing helix chain 'E' and resid 145 through 157 removed outlier: 3.583A pdb=" N TYR E 149 " --> pdb=" O LEU E 145 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N LEU E 152 " --> pdb=" O LYS E 148 " (cutoff:3.500A) removed outlier: 5.520A pdb=" N ASN E 153 " --> pdb=" O TYR E 149 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N GLU E 154 " --> pdb=" O ILE E 150 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU E 155 " --> pdb=" O LYS E 151 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU E 156 " --> pdb=" O LEU E 152 " (cutoff:3.500A) Proline residue: E 157 - end of helix Processing helix chain 'E' and resid 172 through 181 removed outlier: 6.772A pdb=" N LEU E 176 " --> pdb=" O GLU E 172 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N TYR E 179 " --> pdb=" O PHE E 175 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N SER E 180 " --> pdb=" O LEU E 176 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N THR E 181 " --> pdb=" O GLN E 177 " (cutoff:3.500A) Processing helix chain 'E' and resid 193 through 212 removed outlier: 4.359A pdb=" N CYS E 206 " --> pdb=" O VAL E 202 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N GLY E 207 " --> pdb=" O MET E 203 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N GLU E 208 " --> pdb=" O SER E 204 " (cutoff:3.500A) Processing helix chain 'E' and resid 213 through 223 removed outlier: 4.317A pdb=" N ILE E 220 " --> pdb=" O ARG E 216 " (cutoff:3.500A) Processing helix chain 'E' and resid 228 through 252 removed outlier: 5.575A pdb=" N SER E 249 " --> pdb=" O GLN E 245 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N TYR E 250 " --> pdb=" O ALA E 246 " (cutoff:3.500A) Processing helix chain 'E' and resid 254 through 274 removed outlier: 5.552A pdb=" N LEU E 258 " --> pdb=" O ASP E 254 " (cutoff:3.500A) Proline residue: E 267 - end of helix removed outlier: 5.679A pdb=" N THR E 274 " --> pdb=" O VAL E 270 " (cutoff:3.500A) Processing helix chain 'E' and resid 275 through 281 Proline residue: E 281 - end of helix Processing helix chain 'E' and resid 282 through 295 removed outlier: 5.174A pdb=" N LYS E 290 " --> pdb=" O LYS E 286 " (cutoff:3.500A) removed outlier: 7.636A pdb=" N LEU E 291 " --> pdb=" O SER E 287 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N PHE E 292 " --> pdb=" O ALA E 288 " (cutoff:3.500A) Processing helix chain 'E' and resid 325 through 341 removed outlier: 3.679A pdb=" N LYS E 329 " --> pdb=" O SER E 325 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LEU E 332 " --> pdb=" O SER E 328 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ILE E 333 " --> pdb=" O LYS E 329 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ALA E 334 " --> pdb=" O TYR E 330 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N SER E 335 " --> pdb=" O LEU E 331 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N TYR E 336 " --> pdb=" O LEU E 332 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ILE E 337 " --> pdb=" O ILE E 333 " (cutoff:3.500A) Processing helix chain 'E' and resid 342 through 351 removed outlier: 4.089A pdb=" N ASP E 346 " --> pdb=" O GLU E 342 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N ALA E 347 " --> pdb=" O PRO E 343 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N SER E 348 " --> pdb=" O ARG E 344 " (cutoff:3.500A) removed outlier: 5.529A pdb=" N ILE E 349 " --> pdb=" O TYR E 345 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N SER E 351 " --> pdb=" O ALA E 347 " (cutoff:3.500A) Processing helix chain 'E' and resid 372 through 377 removed outlier: 4.753A pdb=" N LEU E 376 " --> pdb=" O ASN E 372 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N GLN E 377 " --> pdb=" O PRO E 373 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 372 through 377' Processing helix chain 'E' and resid 382 through 394 removed outlier: 4.301A pdb=" N LEU E 386 " --> pdb=" O ALA E 382 " (cutoff:3.500A) Processing helix chain 'E' and resid 405 through 410 removed outlier: 4.002A pdb=" N ARG E 409 " --> pdb=" O LEU E 405 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLU E 410 " --> pdb=" O SER E 406 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 405 through 410' Processing helix chain 'E' and resid 417 through 431 removed outlier: 4.438A pdb=" N PHE E 421 " --> pdb=" O ASN E 417 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N LEU E 427 " --> pdb=" O ASN E 423 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N HIS E 428 " --> pdb=" O LEU E 424 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N THR E 429 " --> pdb=" O SER E 425 " (cutoff:3.500A) Processing helix chain 'E' and resid 455 through 467 removed outlier: 3.751A pdb=" N ILE E 459 " --> pdb=" O PRO E 455 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ILE E 462 " --> pdb=" O ILE E 458 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N SER E 463 " --> pdb=" O ILE E 459 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N GLU E 464 " --> pdb=" O LYS E 460 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N SER E 465 " --> pdb=" O GLU E 461 " (cutoff:3.500A) Processing helix chain 'E' and resid 470 through 476 removed outlier: 3.748A pdb=" N PHE E 474 " --> pdb=" O ILE E 470 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N ASP E 476 " --> pdb=" O ASP E 472 " (cutoff:3.500A) Processing helix chain 'E' and resid 98 through 103 removed outlier: 5.018A pdb=" N GLU E 103 " --> pdb=" O LEU E 100 " (cutoff:3.500A) Processing helix chain 'F' and resid 7 through 17 removed outlier: 4.087A pdb=" N ASP F 17 " --> pdb=" O VAL F 13 " (cutoff:3.500A) Processing helix chain 'F' and resid 26 through 46 removed outlier: 4.335A pdb=" N LYS F 30 " --> pdb=" O SER F 26 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N LYS F 46 " --> pdb=" O THR F 42 " (cutoff:3.500A) Processing helix chain 'F' and resid 53 through 70 removed outlier: 3.717A pdb=" N ARG F 57 " --> pdb=" O GLU F 53 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N CYS F 58 " --> pdb=" O GLU F 54 " (cutoff:3.500A) removed outlier: 8.013A pdb=" N HIS F 59 " --> pdb=" O VAL F 55 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N ILE F 60 " --> pdb=" O ALA F 56 " (cutoff:3.500A) removed outlier: 5.886A pdb=" N CYS F 61 " --> pdb=" O ARG F 57 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N ALA F 62 " --> pdb=" O CYS F 58 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N MET F 69 " --> pdb=" O ALA F 65 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N ASN F 70 " --> pdb=" O SER F 66 " (cutoff:3.500A) Processing helix chain 'F' and resid 88 through 102 removed outlier: 3.746A pdb=" N LYS F 92 " --> pdb=" O PRO F 88 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N HIS F 93 " --> pdb=" O LYS F 89 " (cutoff:3.500A) Processing helix chain 'F' and resid 271 through 276 removed outlier: 4.291A pdb=" N LYS F 275 " --> pdb=" O SER F 271 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N LYS F 276 " --> pdb=" O LEU F 272 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 271 through 276' Processing helix chain 'F' and resid 281 through 291 removed outlier: 3.705A pdb=" N ILE F 285 " --> pdb=" O THR F 281 " (cutoff:3.500A) Processing helix chain 'F' and resid 295 through 309 removed outlier: 3.886A pdb=" N ALA F 299 " --> pdb=" O PRO F 295 " (cutoff:3.500A) Processing helix chain 'F' and resid 315 through 333 removed outlier: 4.016A pdb=" N LEU F 319 " --> pdb=" O CYS F 315 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ILE F 330 " --> pdb=" O ASN F 326 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ASN F 333 " --> pdb=" O PHE F 329 " (cutoff:3.500A) Processing helix chain 'F' and resid 334 through 339 Processing helix chain 'F' and resid 340 through 355 removed outlier: 4.782A pdb=" N HIS F 344 " --> pdb=" O PRO F 340 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N PHE F 345 " --> pdb=" O ARG F 341 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VAL F 347 " --> pdb=" O ASP F 343 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N MET F 354 " --> pdb=" O MET F 350 " (cutoff:3.500A) Processing helix chain 'F' and resid 359 through 374 removed outlier: 3.874A pdb=" N VAL F 369 " --> pdb=" O CYS F 365 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ILE F 374 " --> pdb=" O LYS F 370 " (cutoff:3.500A) Processing helix chain 'F' and resid 376 through 387 Processing helix chain 'F' and resid 393 through 403 removed outlier: 4.852A pdb=" N PHE F 399 " --> pdb=" O ASP F 395 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N GLY F 403 " --> pdb=" O PHE F 399 " (cutoff:3.500A) Processing helix chain 'F' and resid 414 through 429 removed outlier: 3.699A pdb=" N TYR F 418 " --> pdb=" O THR F 414 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N LYS F 423 " --> pdb=" O ASN F 419 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N ARG F 424 " --> pdb=" O ILE F 420 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ILE F 425 " --> pdb=" O TRP F 421 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N MET F 427 " --> pdb=" O LYS F 423 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N ASP F 428 " --> pdb=" O ARG F 424 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N LEU F 429 " --> pdb=" O ILE F 425 " (cutoff:3.500A) Processing helix chain '2' and resid 203 through 217 Processing helix chain '2' and resid 225 through 238 removed outlier: 4.204A pdb=" N ALA 2 229 " --> pdb=" O SER 2 225 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ARG 2 230 " --> pdb=" O VAL 2 226 " (cutoff:3.500A) Processing helix chain '2' and resid 245 through 253 removed outlier: 4.124A pdb=" N LEU 2 249 " --> pdb=" O ASN 2 245 " (cutoff:3.500A) Processing helix chain '2' and resid 254 through 264 removed outlier: 4.102A pdb=" N CYS 2 263 " --> pdb=" O PHE 2 259 " (cutoff:3.500A) Proline residue: 2 264 - end of helix Processing helix chain '2' and resid 265 through 283 removed outlier: 5.458A pdb=" N LYS 2 269 " --> pdb=" O GLU 2 265 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N ILE 2 270 " --> pdb=" O GLU 2 266 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N PHE 2 271 " --> pdb=" O MET 2 267 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N LEU 2 273 " --> pdb=" O LYS 2 269 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N HIS 2 282 " --> pdb=" O ALA 2 278 " (cutoff:3.500A) Processing helix chain '2' and resid 285 through 291 removed outlier: 3.508A pdb=" N ILE 2 289 " --> pdb=" O ASP 2 285 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N SER 2 291 " --> pdb=" O ALA 2 287 " (cutoff:3.500A) Processing helix chain '2' and resid 477 through 491 removed outlier: 3.535A pdb=" N PHE 2 484 " --> pdb=" O GLU 2 480 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ASP 2 490 " --> pdb=" O LYS 2 486 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N ARG 2 491 " --> pdb=" O ILE 2 487 " (cutoff:3.500A) Processing helix chain '2' and resid 493 through 501 Processing helix chain '2' and resid 508 through 521 removed outlier: 4.251A pdb=" N LYS 2 512 " --> pdb=" O HIS 2 508 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N PHE 2 520 " --> pdb=" O ALA 2 516 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N GLY 2 521 " --> pdb=" O CYS 2 517 " (cutoff:3.500A) Processing helix chain '2' and resid 550 through 560 removed outlier: 4.804A pdb=" N LYS 2 554 " --> pdb=" O SER 2 550 " (cutoff:3.500A) Processing helix chain '2' and resid 594 through 600 removed outlier: 3.564A pdb=" N LEU 2 598 " --> pdb=" O GLY 2 594 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA 2 599 " --> pdb=" O ALA 2 595 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ASP 2 600 " --> pdb=" O LEU 2 596 " (cutoff:3.500A) No H-bonds generated for 'chain '2' and resid 594 through 600' Processing helix chain '2' and resid 613 through 626 removed outlier: 3.593A pdb=" N ARG 2 617 " --> pdb=" O ASN 2 613 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ILE 2 620 " --> pdb=" O ASP 2 616 " (cutoff:3.500A) Processing helix chain '2' and resid 662 through 667 Processing helix chain '2' and resid 670 through 675 removed outlier: 3.792A pdb=" N LEU 2 674 " --> pdb=" O THR 2 670 " (cutoff:3.500A) Processing helix chain '2' and resid 688 through 704 removed outlier: 3.848A pdb=" N ASP 2 692 " --> pdb=" O ASP 2 688 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N THR 2 697 " --> pdb=" O GLU 2 693 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N HIS 2 703 " --> pdb=" O VAL 2 699 " (cutoff:3.500A) Processing helix chain '2' and resid 759 through 773 removed outlier: 4.360A pdb=" N THR 2 772 " --> pdb=" O HIS 2 768 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LYS 2 773 " --> pdb=" O TYR 2 769 " (cutoff:3.500A) Processing helix chain '2' and resid 782 through 801 removed outlier: 4.797A pdb=" N VAL 2 786 " --> pdb=" O ASP 2 782 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N SER 2 787 " --> pdb=" O MET 2 783 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N ILE 2 798 " --> pdb=" O ARG 2 794 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N THR 2 800 " --> pdb=" O GLU 2 796 " (cutoff:3.500A) Processing helix chain '2' and resid 806 through 825 removed outlier: 3.800A pdb=" N LEU 2 810 " --> pdb=" O THR 2 806 " (cutoff:3.500A) Processing helix chain '2' and resid 830 through 849 removed outlier: 3.911A pdb=" N LEU 2 834 " --> pdb=" O SER 2 830 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ASP 2 835 " --> pdb=" O SER 2 831 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N ARG 2 836 " --> pdb=" O TYR 2 832 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ASP 2 847 " --> pdb=" O ASP 2 843 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALA 2 848 " --> pdb=" O SER 2 844 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N GLN 2 849 " --> pdb=" O PHE 2 845 " (cutoff:3.500A) Processing helix chain '2' and resid 851 through 860 removed outlier: 4.907A pdb=" N ARG 2 855 " --> pdb=" O VAL 2 851 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N GLN 2 856 " --> pdb=" O SER 2 852 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N ARG 2 858 " --> pdb=" O ARG 2 854 " (cutoff:3.500A) Processing helix chain '3' and resid 19 through 36 removed outlier: 4.546A pdb=" N ARG 3 24 " --> pdb=" O VAL 3 20 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N PHE 3 31 " --> pdb=" O ARG 3 27 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N THR 3 36 " --> pdb=" O LEU 3 32 " (cutoff:3.500A) Processing helix chain '3' and resid 37 through 58 Processing helix chain '3' and resid 99 through 107 removed outlier: 3.918A pdb=" N LEU 3 103 " --> pdb=" O SER 3 99 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N PHE 3 106 " --> pdb=" O ASP 3 102 " (cutoff:3.500A) Processing helix chain '3' and resid 108 through 117 Processing helix chain '3' and resid 118 through 136 Proline residue: 3 123 - end of helix Processing helix chain '3' and resid 244 through 249 removed outlier: 8.567A pdb=" N THR 3 249 " --> pdb=" O TYR 3 245 " (cutoff:3.500A) Processing helix chain '3' and resid 343 through 356 removed outlier: 3.844A pdb=" N LYS 3 355 " --> pdb=" O ASN 3 351 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N LYS 3 356 " --> pdb=" O LYS 3 352 " (cutoff:3.500A) Processing helix chain '3' and resid 358 through 369 removed outlier: 5.182A 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 removed outlier: 3.548A pdb=" N ALA 3 380 " --> pdb=" O HIS 3 376 " (cutoff:3.500A) Processing helix chain '3' and resid 415 through 426 removed outlier: 3.809A pdb=" N ARG 3 420 " --> pdb=" O SER 3 416 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ASN 3 424 " --> pdb=" O ARG 3 420 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N THR 3 425 " --> pdb=" O PHE 3 421 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ALA 3 426 " --> pdb=" O VAL 3 422 " (cutoff:3.500A) Processing helix chain '3' and resid 461 through 466 removed outlier: 3.688A pdb=" N ALA 3 465 " --> pdb=" O ALA 3 461 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N ASP 3 466 " --> pdb=" O MET 3 462 " (cutoff:3.500A) No H-bonds generated for 'chain '3' and resid 461 through 466' Processing helix chain '3' and resid 474 through 479 removed outlier: 3.998A pdb=" N MET 3 478 " --> pdb=" O GLU 3 474 " (cutoff:3.500A) removed outlier: 5.749A pdb=" N THR 3 479 " --> pdb=" O PHE 3 475 " (cutoff:3.500A) No H-bonds generated for 'chain '3' and resid 474 through 479' Processing helix chain '3' and resid 480 through 490 removed outlier: 4.231A pdb=" N ALA 3 485 " --> pdb=" O VAL 3 481 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N HIS 3 487 " --> pdb=" O ARG 3 483 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N GLU 3 488 " --> pdb=" O VAL 3 484 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N VAL 3 489 " --> pdb=" O ALA 3 485 " (cutoff:3.500A) Processing helix chain '3' and resid 528 through 534 removed outlier: 4.930A pdb=" N ASN 3 532 " --> pdb=" O ASP 3 528 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N ILE 3 533 " --> pdb=" O PRO 3 529 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ALA 3 534 " --> pdb=" O HIS 3 530 " (cutoff:3.500A) No H-bonds generated for 'chain '3' and resid 528 through 534' Processing helix chain '3' and resid 536 through 544 removed outlier: 5.718A pdb=" N ASP 3 544 " --> pdb=" O LEU 3 540 " (cutoff:3.500A) Processing helix chain '3' and resid 554 through 570 removed outlier: 5.210A pdb=" N ASP 3 558 " --> pdb=" O ASN 3 554 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N SER 3 560 " --> pdb=" O ILE 3 556 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N ILE 3 561 " --> pdb=" O ARG 3 557 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLU 3 563 " --> pdb=" O ARG 3 559 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N ARG 3 570 " --> pdb=" O LEU 3 566 " (cutoff:3.500A) Processing helix chain '3' and resid 653 through 666 removed outlier: 4.549A pdb=" N ARG 3 657 " --> pdb=" O ILE 3 653 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N LYS 3 658 " --> pdb=" O PRO 3 654 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N TYR 3 662 " --> pdb=" O LYS 3 658 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ALA 3 663 " --> pdb=" O TYR 3 659 " (cutoff:3.500A) Processing helix chain '3' and resid 673 through 694 removed outlier: 3.511A pdb=" N ASN 3 677 " --> pdb=" O GLN 3 673 " (cutoff:3.500A) removed outlier: 5.228A pdb=" N VAL 3 678 " --> pdb=" O GLU 3 674 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ASP 3 685 " --> pdb=" O LYS 3 681 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASN 3 688 " --> pdb=" O THR 3 684 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N ASN 3 691 " --> pdb=" O ARG 3 687 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N THR 3 692 " --> pdb=" O ASN 3 688 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LYS 3 693 " --> pdb=" O ASP 3 689 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N LYS 3 694 " --> pdb=" O ASP 3 690 " (cutoff:3.500A) Processing helix chain '3' and resid 698 through 717 removed outlier: 3.684A pdb=" N LEU 3 702 " --> pdb=" O THR 3 698 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N LEU 3 705 " --> pdb=" O THR 3 701 " (cutoff:3.500A) Processing helix chain '3' and resid 722 through 737 removed outlier: 4.052A pdb=" N LEU 3 733 " --> pdb=" O ALA 3 729 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N ARG 3 734 " --> pdb=" O ALA 3 730 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N PHE 3 735 " --> pdb=" O ASN 3 731 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ALA 3 736 " --> pdb=" O LEU 3 732 " (cutoff:3.500A) Processing helix chain '4' and resid 186 through 201 removed outlier: 3.566A pdb=" N CYS 4 190 " --> pdb=" O SER 4 186 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N PHE 4 201 " --> pdb=" O PHE 4 197 " (cutoff:3.500A) Processing helix chain '4' and resid 203 through 209 removed outlier: 3.805A pdb=" N LYS 4 207 " --> pdb=" O TYR 4 203 " (cutoff:3.500A) Processing helix chain '4' and resid 226 through 234 removed outlier: 3.962A pdb=" N LEU 4 230 " --> pdb=" O TYR 4 226 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N ARG 4 234 " --> pdb=" O LEU 4 230 " (cutoff:3.500A) Processing helix chain '4' and resid 244 through 252 removed outlier: 5.142A pdb=" N LEU 4 248 " --> pdb=" O ASP 4 244 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N LYS 4 252 " --> pdb=" O LEU 4 248 " (cutoff:3.500A) Processing helix chain '4' and resid 254 through 265 removed outlier: 4.155A pdb=" N HIS 4 259 " --> pdb=" O GLU 4 255 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLN 4 260 " --> pdb=" O ASP 4 256 " (cutoff:3.500A) Proline residue: 4 265 - end of helix Processing helix chain '4' and resid 266 through 288 removed outlier: 4.033A pdb=" N GLN 4 274 " --> pdb=" O SER 4 270 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LYS 4 277 " --> pdb=" O ASP 4 273 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VAL 4 285 " --> pdb=" O VAL 4 281 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N ASP 4 286 " --> pdb=" O SER 4 282 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N ASN 4 287 " --> pdb=" O LEU 4 283 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N ASN 4 288 " --> pdb=" O ILE 4 284 " (cutoff:3.500A) Processing helix chain '4' and resid 292 through 299 removed outlier: 4.080A pdb=" N ILE 4 296 " --> pdb=" O ASP 4 292 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N GLU 4 297 " --> pdb=" O LEU 4 293 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N THR 4 298 " --> pdb=" O ASP 4 294 " (cutoff:3.500A) Processing helix chain '4' and resid 385 through 390 removed outlier: 4.147A pdb=" N CYS 4 389 " --> pdb=" O ILE 4 385 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N SER 4 390 " --> pdb=" O HIS 4 386 " (cutoff:3.500A) No H-bonds generated for 'chain '4' and resid 385 through 390' Processing helix chain '4' and resid 477 through 482 removed outlier: 4.063A pdb=" N ILE 4 481 " --> pdb=" O ASP 4 477 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N GLU 4 482 " --> pdb=" O THR 4 478 " (cutoff:3.500A) No H-bonds generated for 'chain '4' and resid 477 through 482' Processing helix chain '4' and resid 483 through 492 Processing helix chain '4' and resid 502 through 515 removed outlier: 3.579A pdb=" N ALA 4 514 " --> pdb=" O ARG 4 510 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ARG 4 515 " --> pdb=" O GLU 4 511 " (cutoff:3.500A) Processing helix chain '4' and resid 517 through 528 removed outlier: 4.743A pdb=" N ALA 4 523 " --> pdb=" O TYR 4 519 " (cutoff:3.500A) removed outlier: 4.246A 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 Processing helix chain '4' and resid 573 through 586 Proline residue: 4 586 - end of helix Processing helix chain '4' and resid 597 through 602 Processing helix chain '4' and resid 619 through 625 removed outlier: 3.993A pdb=" N SER 4 624 " --> pdb=" O ALA 4 620 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N ASP 4 625 " --> pdb=" O LEU 4 621 " (cutoff:3.500A) Processing helix chain '4' and resid 638 through 651 removed outlier: 4.255A pdb=" N VAL 4 644 " --> pdb=" O SER 4 640 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N LEU 4 645 " --> pdb=" O THR 4 641 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N HIS 4 646 " --> pdb=" O ARG 4 642 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N GLU 4 647 " --> pdb=" O SER 4 643 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N VAL 4 648 " --> pdb=" O VAL 4 644 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N GLU 4 650 " --> pdb=" O HIS 4 646 " (cutoff:3.500A) Processing helix chain '4' and resid 687 through 692 removed outlier: 4.484A pdb=" N ILE 4 692 " --> pdb=" O VAL 4 688 " (cutoff:3.500A) Processing helix chain '4' and resid 695 through 702 removed outlier: 3.789A pdb=" N LEU 4 699 " --> pdb=" O PRO 4 695 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N PHE 4 702 " --> pdb=" O LEU 4 698 " (cutoff:3.500A) Processing helix chain '4' and resid 714 through 731 removed outlier: 6.565A pdb=" N ARG 4 718 " --> pdb=" O GLU 4 714 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N GLU 4 719 " --> pdb=" O LYS 4 715 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N LEU 4 720 " --> pdb=" O ASN 4 716 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N LEU 4 727 " --> pdb=" O HIS 4 723 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N TYR 4 728 " --> pdb=" O LEU 4 724 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLU 4 730 " --> pdb=" O ASN 4 726 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N ASP 4 731 " --> pdb=" O LEU 4 727 " (cutoff:3.500A) Processing helix chain '4' and resid 733 through 738 removed outlier: 5.014A pdb=" N SER 4 737 " --> pdb=" O PRO 4 733 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N GLN 4 738 " --> pdb=" O GLU 4 734 " (cutoff:3.500A) No H-bonds generated for 'chain '4' and resid 733 through 738' Processing helix chain '4' and resid 743 through 757 removed outlier: 3.858A pdb=" N LEU 4 747 " --> pdb=" O PRO 4 743 " (cutoff:3.500A) Processing helix chain '4' and resid 763 through 779 removed outlier: 4.453A pdb=" N LYS 4 767 " --> pdb=" O THR 4 763 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N THR 4 768 " --> pdb=" O GLU 4 764 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N GLU 4 769 " --> pdb=" O ALA 4 765 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ARG 4 772 " --> pdb=" O THR 4 768 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N LYS 4 779 " --> pdb=" O VAL 4 775 " (cutoff:3.500A) Processing helix chain '4' and resid 794 through 813 removed outlier: 4.515A pdb=" N LEU 4 798 " --> pdb=" O THR 4 794 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLU 4 799 " --> pdb=" O THR 4 795 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ALA 4 807 " --> pdb=" O ARG 4 803 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N LYS 4 812 " --> pdb=" O HIS 4 808 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N LEU 4 813 " --> pdb=" O ALA 4 809 " (cutoff:3.500A) Processing helix chain '4' and resid 818 through 834 removed outlier: 4.007A pdb=" N VAL 4 822 " --> pdb=" O GLU 4 818 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLN 4 823 " --> pdb=" O LEU 4 819 " (cutoff:3.500A) Processing helix chain '5' and resid 23 through 37 removed outlier: 4.298A pdb=" N ILE 5 27 " --> pdb=" O ASP 5 23 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N PHE 5 34 " --> pdb=" O SER 5 30 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE 5 35 " --> pdb=" O PHE 5 31 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N LEU 5 36 " --> pdb=" O LYS 5 32 " (cutoff:3.500A) Processing helix chain '5' and resid 44 through 57 removed outlier: 5.213A pdb=" N ASP 5 48 " --> pdb=" O PHE 5 44 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU 5 55 " --> pdb=" O ARG 5 51 " (cutoff:3.500A) Processing helix chain '5' and resid 64 through 72 removed outlier: 4.703A pdb=" N LEU 5 68 " --> pdb=" O ASN 5 64 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ILE 5 69 " --> pdb=" O MET 5 65 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N GLY 5 70 " --> pdb=" O GLU 5 66 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N TYR 5 71 " --> pdb=" O HIS 5 67 " (cutoff:3.500A) Processing helix chain '5' and resid 73 through 82 removed outlier: 4.455A pdb=" N LYS 5 77 " --> pdb=" O GLU 5 73 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N LYS 5 78 " --> pdb=" O ASP 5 74 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ASP 5 81 " --> pdb=" O LYS 5 77 " (cutoff:3.500A) Processing helix chain '5' and resid 83 through 109 Proline residue: 5 88 - end of helix Processing helix chain '5' and resid 147 through 152 removed outlier: 3.678A pdb=" N LEU 5 151 " --> pdb=" O PRO 5 147 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N ASP 5 152 " --> pdb=" O LEU 5 148 " (cutoff:3.500A) No H-bonds generated for 'chain '5' and resid 147 through 152' Processing helix chain '5' and resid 350 through 364 removed outlier: 4.365A pdb=" N GLU 5 354 " --> pdb=" O THR 5 350 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N GLU 5 355 " --> pdb=" O GLU 5 351 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N GLU 5 356 " --> pdb=" O GLU 5 352 " (cutoff:3.500A) Proline residue: 5 364 - end of helix Processing helix chain '5' and resid 365 through 376 removed outlier: 5.337A 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 removed outlier: 3.734A pdb=" N ALA 5 387 " --> pdb=" O ASP 5 383 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ILE 5 388 " --> pdb=" O ILE 5 384 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N VAL 5 389 " --> pdb=" O LYS 5 385 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N CYS 5 390 " --> pdb=" O LYS 5 386 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N MET 5 393 " --> pdb=" O VAL 5 389 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N GLY 5 394 " --> pdb=" O CYS 5 390 " (cutoff:3.500A) Processing helix chain '5' and resid 421 through 434 removed outlier: 3.627A pdb=" N LEU 5 425 " --> pdb=" O ALA 5 421 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N LEU 5 426 " --> pdb=" O LYS 5 422 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N GLU 5 430 " --> pdb=" O LEU 5 426 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N LYS 5 431 " --> pdb=" O LYS 5 427 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL 5 432 " --> pdb=" O PHE 5 428 " (cutoff:3.500A) Proline residue: 5 434 - end of helix Processing helix chain '5' and resid 467 through 473 removed outlier: 4.307A pdb=" N ALA 5 472 " --> pdb=" O ALA 5 468 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N ASP 5 473 " --> pdb=" O MET 5 469 " (cutoff:3.500A) Processing helix chain '5' and resid 486 through 499 removed outlier: 4.199A pdb=" N ALA 5 492 " --> pdb=" O GLU 5 488 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ILE 5 493 " --> pdb=" O ASP 5 489 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N GLU 5 498 " --> pdb=" O HIS 5 494 " (cutoff:3.500A) Processing helix chain '5' and resid 530 through 535 removed outlier: 3.999A pdb=" N SER 5 535 " --> pdb=" O ASP 5 531 " (cutoff:3.500A) Processing helix chain '5' and resid 542 through 549 removed outlier: 4.334A pdb=" N ILE 5 546 " --> pdb=" O PHE 5 542 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N LEU 5 547 " --> pdb=" O GLN 5 543 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N SER 5 548 " --> pdb=" O THR 5 544 " (cutoff:3.500A) Processing helix chain '5' and resid 561 through 578 removed outlier: 3.613A pdb=" N ASP 5 565 " --> pdb=" O ASN 5 561 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N ILE 5 566 " --> pdb=" O GLU 5 562 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N ASN 5 574 " --> pdb=" O ASN 5 570 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N ILE 5 575 " --> pdb=" O HIS 5 571 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N HIS 5 576 " --> pdb=" O VAL 5 572 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N THR 5 577 " --> pdb=" O ILE 5 573 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N GLY 5 578 " --> pdb=" O ASN 5 574 " (cutoff:3.500A) Processing helix chain '5' and resid 579 through 592 removed outlier: 3.518A pdb=" N ASN 5 585 " --> pdb=" O ASN 5 581 " (cutoff:3.500A) Processing helix chain '5' and resid 595 through 609 removed outlier: 3.657A pdb=" N MET 5 599 " --> pdb=" O SER 5 595 " (cutoff:3.500A) Processing helix chain '5' and resid 615 through 638 removed outlier: 3.563A pdb=" N ALA 5 619 " --> pdb=" O SER 5 615 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N GLU 5 620 " --> pdb=" O PRO 5 616 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N LYS 5 621 " --> pdb=" O GLN 5 617 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N LEU 5 622 " --> pdb=" O ALA 5 618 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N SER 5 623 " --> pdb=" O ALA 5 619 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ASN 5 625 " --> pdb=" O LYS 5 621 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ILE 5 635 " --> pdb=" O LYS 5 631 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN 5 636 " --> pdb=" O GLN 5 632 " (cutoff:3.500A) Processing helix chain '5' and resid 649 through 667 removed outlier: 3.676A pdb=" N LEU 5 653 " --> pdb=" O THR 5 649 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ILE 5 656 " --> pdb=" O GLN 5 652 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ILE 5 657 " --> pdb=" O LEU 5 653 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ARG 5 658 " --> pdb=" O GLU 5 654 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N GLU 5 661 " --> pdb=" O ILE 5 657 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N GLU 5 667 " --> pdb=" O LEU 5 663 " (cutoff:3.500A) Processing helix chain '5' and resid 674 through 693 removed outlier: 4.591A pdb=" N GLU 5 679 " --> pdb=" O ARG 5 675 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N ALA 5 686 " --> pdb=" O ARG 5 682 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N SER 5 687 " --> pdb=" O LEU 5 683 " (cutoff:3.500A) Processing helix chain '6' and resid 104 through 123 removed outlier: 4.606A pdb=" N GLU 6 109 " --> pdb=" O ASP 6 105 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LYS 6 110 " --> pdb=" O VAL 6 106 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N PHE 6 122 " --> pdb=" O PHE 6 118 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N SER 6 123 " --> pdb=" O LEU 6 119 " (cutoff:3.500A) Processing helix chain '6' and resid 135 through 147 removed outlier: 4.199A pdb=" N TYR 6 146 " --> pdb=" O PHE 6 142 " (cutoff:3.500A) Processing helix chain '6' and resid 154 through 161 removed outlier: 3.693A pdb=" N LEU 6 158 " --> pdb=" O ASP 6 154 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N ARG 6 161 " --> pdb=" O HIS 6 157 " (cutoff:3.500A) Processing helix chain '6' and resid 164 through 174 removed outlier: 3.611A pdb=" N ALA 6 169 " --> pdb=" O ALA 6 165 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N GLU 6 172 " --> pdb=" O MET 6 168 " (cutoff:3.500A) Processing helix chain '6' and resid 175 through 193 Proline residue: 6 179 - end of helix Processing helix chain '6' and resid 510 through 522 removed outlier: 4.873A pdb=" N ASN 6 514 " --> pdb=" O SER 6 510 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N LYS 6 521 " --> pdb=" O LYS 6 517 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N ASP 6 522 " --> pdb=" O GLU 6 518 " (cutoff:3.500A) Processing helix chain '6' and resid 524 through 535 removed outlier: 3.890A pdb=" N ILE 6 533 " --> pdb=" O LEU 6 529 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N ALA 6 534 " --> pdb=" O VAL 6 530 " (cutoff:3.500A) Proline residue: 6 535 - end of helix Processing helix chain '6' and resid 540 through 553 removed outlier: 3.610A pdb=" N LYS 6 544 " --> pdb=" O HIS 6 540 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N MET 6 551 " --> pdb=" O ILE 6 547 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N LEU 6 552 " --> pdb=" O LEU 6 548 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N GLY 6 553 " --> pdb=" O LEU 6 549 " (cutoff:3.500A) Processing helix chain '6' and resid 580 through 592 removed outlier: 3.836A pdb=" N PHE 6 584 " --> pdb=" O SER 6 580 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU 6 585 " --> pdb=" O LYS 6 581 " (cutoff:3.500A) Processing helix chain '6' and resid 604 through 610 removed outlier: 4.530A pdb=" N ALA 6 610 " --> pdb=" O ALA 6 606 " (cutoff:3.500A) Processing helix chain '6' and resid 626 through 631 removed outlier: 4.737A pdb=" N ALA 6 631 " --> pdb=" O ALA 6 627 " (cutoff:3.500A) Processing helix chain '6' and resid 645 through 659 removed outlier: 4.156A pdb=" N GLN 6 649 " --> pdb=" O ASP 6 645 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N GLN 6 658 " --> pdb=" O GLU 6 654 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N GLN 6 659 " --> pdb=" O ALA 6 655 " (cutoff:3.500A) Processing helix chain '6' and resid 694 through 700 removed outlier: 3.941A pdb=" N ASN 6 698 " --> pdb=" O SER 6 694 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ASN 6 700 " --> pdb=" O ARG 6 696 " (cutoff:3.500A) Processing helix chain '6' and resid 702 through 708 removed outlier: 3.803A pdb=" N ARG 6 708 " --> pdb=" O PRO 6 704 " (cutoff:3.500A) Processing helix chain '6' and resid 720 through 736 removed outlier: 3.680A pdb=" N GLU 6 726 " --> pdb=" O LYS 6 722 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N HIS 6 735 " --> pdb=" O ILE 6 731 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N MET 6 736 " --> pdb=" O VAL 6 732 " (cutoff:3.500A) Processing helix chain '6' and resid 747 through 759 removed outlier: 3.716A pdb=" N ARG 6 753 " --> pdb=" O GLU 6 749 " (cutoff:3.500A) Processing helix chain '6' and resid 766 through 787 removed outlier: 3.557A pdb=" N GLU 6 775 " --> pdb=" O SER 6 771 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ASP 6 784 " --> pdb=" O LEU 6 780 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N GLN 6 786 " --> pdb=" O LYS 6 782 " (cutoff:3.500A) Processing helix chain '6' and resid 796 through 815 removed outlier: 4.487A pdb=" N LEU 6 800 " --> pdb=" O THR 6 796 " (cutoff:3.500A) Processing helix chain '6' and resid 820 through 835 removed outlier: 3.625A pdb=" N ILE 6 824 " --> pdb=" O THR 6 820 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLU 6 826 " --> pdb=" O SER 6 822 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ALA 6 827 " --> pdb=" O PHE 6 823 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N ILE 6 835 " --> pdb=" O LEU 6 831 " (cutoff:3.500A) Processing helix chain '7' and resid 1 through 6 removed outlier: 4.884A pdb=" N LEU 7 5 " --> pdb=" O MET 7 1 " (cutoff:3.500A) Proline residue: 7 6 - end of helix No H-bonds generated for 'chain '7' and resid 1 through 6' Processing helix chain '7' and resid 13 through 28 removed outlier: 3.597A pdb=" N ASN 7 19 " --> pdb=" O ASN 7 15 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N VAL 7 26 " --> pdb=" O THR 7 22 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N PHE 7 28 " --> pdb=" O PHE 7 24 " (cutoff:3.500A) Processing helix chain '7' and resid 61 through 73 Processing helix chain '7' and resid 81 through 96 removed outlier: 4.323A pdb=" N ILE 7 85 " --> pdb=" O ASP 7 81 " (cutoff:3.500A) Processing helix chain '7' and resid 101 through 110 removed outlier: 5.026A pdb=" N ALA 7 105 " --> pdb=" O ASP 7 101 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N GLN 7 108 " --> pdb=" O SER 7 104 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N ASN 7 109 " --> pdb=" O ALA 7 105 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ALA 7 110 " --> pdb=" O ILE 7 106 " (cutoff:3.500A) Processing helix chain '7' and resid 111 through 125 removed outlier: 4.764A pdb=" N GLU 7 115 " --> pdb=" O ASN 7 111 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LEU 7 116 " --> pdb=" O HIS 7 112 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ARG 7 119 " --> pdb=" O GLU 7 115 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ASN 7 124 " --> pdb=" O ALA 7 120 " (cutoff:3.500A) Processing helix chain '7' and resid 137 through 147 removed outlier: 4.223A pdb=" N VAL 7 141 " --> pdb=" O ASP 7 137 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ILE 7 142 " --> pdb=" O VAL 7 138 " (cutoff:3.500A) Processing helix chain '7' and resid 208 through 216 removed outlier: 3.645A pdb=" N ALA 7 212 " --> pdb=" O SER 7 208 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ARG 7 214 " --> pdb=" O ASN 7 210 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N TYR 7 215 " --> pdb=" O CYS 7 211 " (cutoff:3.500A) Processing helix chain '7' and resid 286 through 293 removed outlier: 4.014A pdb=" N GLN 7 291 " --> pdb=" O GLU 7 287 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ASN 7 292 " --> pdb=" O GLU 7 288 " (cutoff:3.500A) removed outlier: 5.097A pdb=" N GLN 7 293 " --> pdb=" O CYS 7 289 " (cutoff:3.500A) Processing helix chain '7' and resid 318 through 323 removed outlier: 3.633A pdb=" N VAL 7 322 " --> pdb=" O LEU 7 318 " (cutoff:3.500A) Proline residue: 7 323 - end of helix No H-bonds generated for 'chain '7' and resid 318 through 323' Processing helix chain '7' and resid 394 through 408 removed outlier: 3.840A pdb=" N GLU 7 398 " --> pdb=" O THR 7 394 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N GLU 7 399 " --> pdb=" O SER 7 395 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N SER 7 407 " --> pdb=" O GLU 7 403 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N GLY 7 408 " --> pdb=" O LEU 7 404 " (cutoff:3.500A) Processing helix chain '7' and resid 409 through 420 removed outlier: 6.322A 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 Processing helix chain '7' and resid 466 through 477 removed outlier: 4.409A pdb=" N LEU 7 470 " --> pdb=" O LYS 7 466 " (cutoff:3.500A) Processing helix chain '7' and resid 511 through 517 removed outlier: 3.577A pdb=" N LEU 7 515 " --> pdb=" O GLY 7 511 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ALA 7 516 " --> pdb=" O ALA 7 512 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N ASP 7 517 " --> pdb=" O LEU 7 513 " (cutoff:3.500A) No H-bonds generated for 'chain '7' and resid 511 through 517' Processing helix chain '7' and resid 525 through 530 removed outlier: 3.851A pdb=" N MET 7 529 " --> pdb=" O GLU 7 525 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N ASP 7 530 " --> pdb=" O PHE 7 526 " (cutoff:3.500A) No H-bonds generated for 'chain '7' and resid 525 through 530' Processing helix chain '7' and resid 531 through 543 removed outlier: 3.696A pdb=" N GLU 7 539 " --> pdb=" O THR 7 535 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N GLU 7 542 " --> pdb=" O HIS 7 538 " (cutoff:3.500A) Processing helix chain '7' and resid 579 through 584 Processing helix chain '7' and resid 587 through 595 removed outlier: 5.427A pdb=" N ARG 7 593 " --> pdb=" O ALA 7 589 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N PHE 7 594 " --> pdb=" O LEU 7 590 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N ASP 7 595 " --> pdb=" O LEU 7 591 " (cutoff:3.500A) Processing helix chain '7' and resid 605 through 623 removed outlier: 3.858A pdb=" N ASP 7 609 " --> pdb=" O SER 7 605 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N GLU 7 610 " --> pdb=" O ARG 7 606 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LYS 7 611 " --> pdb=" O ASP 7 607 " (cutoff:3.500A) Processing helix chain '7' and resid 634 through 648 removed outlier: 3.544A pdb=" N THR 7 647 " --> pdb=" O ALA 7 643 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N LYS 7 648 " --> pdb=" O TYR 7 644 " (cutoff:3.500A) Processing helix chain '7' and resid 653 through 674 removed outlier: 3.529A pdb=" N ASN 7 657 " --> pdb=" O SER 7 653 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N TYR 7 659 " --> pdb=" O ALA 7 655 " (cutoff:3.500A) Processing helix chain '7' and resid 685 through 704 Processing helix chain '7' and resid 709 through 729 removed outlier: 4.550A pdb=" N VAL 7 713 " --> pdb=" O ASP 7 709 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N GLU 7 714 " --> pdb=" O ILE 7 710 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N GLU 7 715 " --> pdb=" O ASP 7 711 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N LYS 7 724 " --> pdb=" O VAL 7 720 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N GLU 7 725 " --> pdb=" O ARG 7 721 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N SER 7 726 " --> pdb=" O VAL 7 722 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N LEU 7 727 " --> pdb=" O SER 7 723 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N TYR 7 728 " --> pdb=" O LYS 7 724 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N GLN 7 729 " --> pdb=" O GLU 7 725 " (cutoff:3.500A) Processing helix chain '7' and resid 337 through 343 removed outlier: 3.591A pdb=" N VAL 7 340 " --> pdb=" O GLY 7 337 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ARG 7 341 " --> pdb=" O THR 7 338 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N LEU 7 343 " --> pdb=" O VAL 7 340 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain 'A' and resid 508 through 511 removed outlier: 3.622A pdb=" N LEU A 509 " --> pdb=" O THR A 560 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU A 564 " --> pdb=" O VAL A 511 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N ILE A 561 " --> pdb=" O LYS A 592 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N LEU A 593 " --> pdb=" O SER A 471 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N THR A 473 " --> pdb=" O LEU A 593 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL A 595 " --> pdb=" O THR A 473 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA A 597 " --> pdb=" O ILE A 475 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N THR A 620 " --> pdb=" O THR A 474 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'A' and resid 655 through 659 removed outlier: 5.066A pdb=" N ASN A 656 " --> pdb=" O ASP A 651 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ASP A 651 " --> pdb=" O ASN A 656 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N SER A 646 " --> pdb=" O LEU A 682 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N THR A 652 " --> pdb=" O ASP A 676 " (cutoff:3.500A) removed outlier: 9.282A pdb=" N ASP A 676 " --> pdb=" O THR A 652 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N GLY A 769 " --> pdb=" O LYS A 679 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N VAL A 773 " --> pdb=" O ARG A 683 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'A' and resid 878 through 881 removed outlier: 7.427A pdb=" N ILE A 878 " --> pdb=" O ASN A 895 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'B' and resid 313 through 317 Processing sheet with id= 5, first strand: chain 'B' and resid 359 through 364 removed outlier: 3.534A pdb=" N LEU B 361 " --> pdb=" O ILE B 421 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL B 423 " --> pdb=" O LEU B 361 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'C' and resid 102 through 106 removed outlier: 3.734A pdb=" N ASN C 103 " --> pdb=" O ILE C 234 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LYS C 233 " --> pdb=" O LEU C 199 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N PHE C 205 " --> pdb=" O ILE C 237 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N VAL C 127 " --> pdb=" O ALA C 200 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N VAL C 202 " --> pdb=" O VAL C 127 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'C' and resid 533 through 536 removed outlier: 7.202A pdb=" N MET C 533 " --> pdb=" O LYS C 610 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'D' and resid 126 through 132 removed outlier: 3.514A pdb=" N VAL D 213 " --> pdb=" O ILE D 128 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ASP D 217 " --> pdb=" O LEU D 132 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N CYS D 250 " --> pdb=" O PHE D 216 " (cutoff:3.500A) removed outlier: 5.467A pdb=" N ARG D 271 " --> pdb=" O SER D 97 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ILE D 99 " --> pdb=" O ARG D 271 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N MET D 275 " --> pdb=" O VAL D 101 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'D' and resid 468 through 471 removed outlier: 8.225A pdb=" N PHE D 468 " --> pdb=" O GLN D 507 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'E' and resid 59 through 62 removed outlier: 3.669A pdb=" N ILE E 131 " --> pdb=" O VAL E 60 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ASP E 133 " --> pdb=" O LEU E 62 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N THR E 169 " --> pdb=" O LEU E 132 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N PHE E 189 " --> pdb=" O GLN E 36 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N TYR E 38 " --> pdb=" O PHE E 189 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'E' and resid 432 through 435 removed outlier: 5.636A pdb=" N LEU E 432 " --> pdb=" O ASN E 453 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ASN E 453 " --> pdb=" O LEU E 432 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain '2' and resid 240 through 244 Processing sheet with id= 13, first strand: chain '2' and resid 318 through 322 removed outlier: 4.234A pdb=" N VAL 2 426 " --> pdb=" O VAL 2 320 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLY 2 322 " --> pdb=" O VAL 2 424 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain '2' and resid 330 through 334 Processing sheet with id= 15, first strand: chain '2' and resid 345 through 350 removed outlier: 5.572A pdb=" N LYS 2 338 " --> pdb=" O ASN 2 376 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ARG 2 374 " --> pdb=" O ASN 2 340 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain '2' and resid 523 through 527 removed outlier: 3.661A pdb=" N VAL 2 523 " --> pdb=" O GLY 2 535 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLY 2 535 " --> pdb=" O VAL 2 523 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL 2 527 " --> pdb=" O HIS 2 531 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N HIS 2 531 " --> pdb=" O VAL 2 527 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain '2' and resid 602 through 607 removed outlier: 3.659A pdb=" N ALA 2 649 " --> pdb=" O ILE 2 606 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N ILE 2 537 " --> pdb=" O CYS 2 644 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ILE 2 646 " --> pdb=" O ILE 2 537 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N ALA 2 648 " --> pdb=" O VAL 2 539 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N LEU 2 541 " --> pdb=" O ALA 2 648 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ALA 2 650 " --> pdb=" O LEU 2 541 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N GLY 2 543 " --> pdb=" O ALA 2 650 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N ILE 2 679 " --> pdb=" O ASN 2 538 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL 2 683 " --> pdb=" O LEU 2 542 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N ASP 2 544 " --> pdb=" O VAL 2 683 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain '2' and resid 627 through 632 removed outlier: 4.973A pdb=" N GLN 2 627 " --> pdb=" O ALA 2 642 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N ILE 2 629 " --> pdb=" O LEU 2 640 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU 2 640 " --> pdb=" O ILE 2 629 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N THR 2 638 " --> pdb=" O ILE 2 631 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain '3' and resid 94 through 98 removed outlier: 3.703A pdb=" N ILE 3 96 " --> pdb=" O LYS 3 154 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain '3' and resid 180 through 184 removed outlier: 3.819A pdb=" N VAL 3 182 " --> pdb=" O VAL 3 294 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain '3' and resid 193 through 196 removed outlier: 3.976A pdb=" N ARG 3 193 " --> pdb=" O HIS 3 253 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N HIS 3 253 " --> pdb=" O ARG 3 193 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N GLN 3 254 " --> pdb=" O LEU 3 278 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain '3' and resid 198 through 204 removed outlier: 3.599A pdb=" N ARG 3 212 " --> pdb=" O SER 3 199 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain '3' and resid 428 through 432 removed outlier: 4.260A pdb=" N VAL 3 469 " --> pdb=" O LEU 3 428 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ILE 3 430 " --> pdb=" O VAL 3 469 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N ASP 3 473 " --> pdb=" O THR 3 432 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N SER 3 511 " --> pdb=" O GLY 3 468 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA 3 515 " --> pdb=" O ILE 3 472 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL 3 512 " --> pdb=" O ILE 3 403 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N MET 3 407 " --> pdb=" O ALA 3 514 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N GLY 3 409 " --> pdb=" O ALA 3 516 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU 3 545 " --> pdb=" O ASN 3 404 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N VAL 3 408 " --> pdb=" O PHE 3 547 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain '3' and resid 493 through 498 removed outlier: 5.305A pdb=" N GLN 3 493 " --> pdb=" O ALA 3 508 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE 3 497 " --> pdb=" O THR 3 504 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N THR 3 504 " --> pdb=" O ILE 3 497 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain '4' and resid 240 through 243 Processing sheet with id= 26, first strand: chain '4' and resid 323 through 329 removed outlier: 3.976A pdb=" N LYS 4 324 " --> pdb=" O PHE 4 439 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N PHE 4 439 " --> pdb=" O LYS 4 324 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N THR 4 436 " --> pdb=" O VAL 4 464 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N VAL 4 464 " --> pdb=" O THR 4 436 " (cutoff:3.500A) removed outlier: 9.679A pdb=" N THR 4 459 " --> pdb=" O SER 4 414 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N SER 4 416 " --> pdb=" O THR 4 459 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N VAL 4 461 " --> pdb=" O SER 4 416 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N TYR 4 420 " --> pdb=" O VAL 4 463 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU 4 417 " --> pdb=" O ILE 4 397 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N ILE 4 397 " --> pdb=" O LEU 4 417 " (cutoff:3.500A) removed outlier: 7.336A pdb=" N ASP 4 393 " --> pdb=" O ASP 4 421 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain '4' and resid 344 through 349 removed outlier: 3.600A pdb=" N CYS 4 349 " --> pdb=" O HIS 4 354 " (cutoff:3.500A) removed outlier: 5.676A pdb=" N HIS 4 354 " --> pdb=" O CYS 4 349 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain '4' and resid 548 through 552 removed outlier: 5.941A pdb=" N THR 4 548 " --> pdb=" O GLY 4 560 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N GLY 4 556 " --> pdb=" O PHE 4 552 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N SER 4 669 " --> pdb=" O GLY 4 560 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ILE 4 562 " --> pdb=" O SER 4 669 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N ILE 4 671 " --> pdb=" O ILE 4 562 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE 4 631 " --> pdb=" O LEU 4 672 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N SER 4 674 " --> pdb=" O ILE 4 631 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL 4 589 " --> pdb=" O VAL 4 628 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain '4' and resid 603 through 608 removed outlier: 3.839A pdb=" N TYR 4 604 " --> pdb=" O GLU 4 617 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N GLN 4 613 " --> pdb=" O ASP 4 608 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain '4' and resid 652 through 655 removed outlier: 5.332A pdb=" N GLN 4 652 " --> pdb=" O ALA 4 667 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE 4 654 " --> pdb=" O LEU 4 665 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain '4' and resid 563 through 569 removed outlier: 3.721A pdb=" N LEU 4 704 " --> pdb=" O ASN 4 563 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain '5' and resid 59 through 63 removed outlier: 4.134A pdb=" N LEU 5 61 " --> pdb=" O GLN 5 136 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N ILE 5 138 " --> pdb=" O LEU 5 61 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain '5' and resid 172 through 177 removed outlier: 6.490A pdb=" N ASP 5 252 " --> pdb=" O ARG 5 280 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ARG 5 280 " --> pdb=" O ASP 5 252 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N GLN 5 254 " --> pdb=" O CYS 5 278 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N CYS 5 278 " --> pdb=" O GLN 5 254 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain '5' and resid 187 through 193 removed outlier: 4.111A pdb=" N HIS 5 188 " --> pdb=" O CYS 5 183 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N CYS 5 183 " --> pdb=" O HIS 5 188 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ILE 5 181 " --> pdb=" O THR 5 190 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N SER 5 180 " --> pdb=" O ILE 5 244 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain '5' and resid 292 through 295 Processing sheet with id= 36, first strand: chain '5' and resid 298 through 302 Processing sheet with id= 37, first strand: chain '5' and resid 411 through 416 removed outlier: 3.824A pdb=" N MET 5 552 " --> pdb=" O ASN 5 411 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N PHE 5 554 " --> pdb=" O LEU 5 413 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU 5 415 " --> pdb=" O PHE 5 554 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain '5' and resid 436 through 440 removed outlier: 3.582A pdb=" N ASP 5 480 " --> pdb=" O THR 5 439 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain '5' and resid 451 through 456 removed outlier: 7.428A pdb=" N SER 5 452 " --> pdb=" O GLU 5 465 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N GLU 5 465 " --> pdb=" O SER 5 452 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N GLN 5 454 " --> pdb=" O TYR 5 463 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N GLU 5 461 " --> pdb=" O ASP 5 456 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain '5' and resid 500 through 504 removed outlier: 7.743A pdb=" N GLN 5 500 " --> pdb=" O SER 5 515 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ILE 5 504 " --> pdb=" O THR 5 511 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain '6' and resid 149 through 153 Processing sheet with id= 42, first strand: chain '6' and resid 289 through 292 removed outlier: 3.963A pdb=" N ARG 6 394 " --> pdb=" O ILE 6 462 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain '6' and resid 296 through 300 removed outlier: 7.171A pdb=" N ARG 6 350 " --> pdb=" O SER 6 308 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N ALA 6 316 " --> pdb=" O CYS 6 311 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain '6' and resid 401 through 406 removed outlier: 4.395A pdb=" N ILE 6 402 " --> pdb=" O SER 6 453 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N SER 6 453 " --> pdb=" O ILE 6 402 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL 6 404 " --> pdb=" O LYS 6 451 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N THR 6 449 " --> pdb=" O ASP 6 406 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain '6' and resid 570 through 575 removed outlier: 3.871A pdb=" N LEU 6 711 " --> pdb=" O ASN 6 570 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N CYS 6 572 " --> pdb=" O LEU 6 711 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain '6' and resid 594 through 598 removed outlier: 3.949A pdb=" N ILE 6 635 " --> pdb=" O ARG 6 594 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N VAL 6 596 " --> pdb=" O ILE 6 635 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N THR 6 598 " --> pdb=" O CYS 6 637 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N CYS 6 636 " --> pdb=" O SER 6 677 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N LEU 6 679 " --> pdb=" O CYS 6 636 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain '6' and resid 308 through 311 removed outlier: 4.796A pdb=" N SER 6 308 " --> pdb=" O ASN 6 347 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ASN 6 347 " --> pdb=" O SER 6 308 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N THR 6 310 " --> pdb=" O THR 6 345 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain '6' and resid 355 through 362 removed outlier: 5.829A pdb=" N ASP 6 355 " --> pdb=" O GLY 6 383 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLY 6 383 " --> pdb=" O ASP 6 355 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N GLN 6 357 " --> pdb=" O LEU 6 381 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N VAL 6 379 " --> pdb=" O VAL 6 359 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain '7' and resid 76 through 80 removed outlier: 4.199A pdb=" N ILE 7 80 " --> pdb=" O TYR 7 203 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain '7' and resid 239 through 242 removed outlier: 4.007A pdb=" N ARG 7 382 " --> pdb=" O ASP 7 350 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N THR 7 352 " --> pdb=" O PHE 7 380 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N PHE 7 380 " --> pdb=" O THR 7 352 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain '7' and resid 251 through 256 removed outlier: 4.158A pdb=" N LYS 7 252 " --> pdb=" O PHE 7 310 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N GLU 7 256 " --> pdb=" O LYS 7 306 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N LYS 7 306 " --> pdb=" O GLU 7 256 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE 7 315 " --> pdb=" O LEU 7 331 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N LEU 7 331 " --> pdb=" O ILE 7 315 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU 7 376 " --> pdb=" O ASN 7 332 " (cutoff:3.500A) removed outlier: 5.382A pdb=" N ASN 7 336 " --> pdb=" O ALA 7 378 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain '7' and resid 266 through 272 removed outlier: 4.639A pdb=" N TYR 7 267 " --> pdb=" O CYS 7 262 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N GLN 7 271 " --> pdb=" O ILE 7 258 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N ALA 7 259 " --> pdb=" O SER 7 301 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N GLN 7 297 " --> pdb=" O ASP 7 263 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain '7' and resid 440 through 444 removed outlier: 4.160A pdb=" N VAL 7 440 " --> pdb=" O GLY 7 452 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N MET 7 448 " --> pdb=" O VAL 7 444 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain '7' and resid 479 through 483 removed outlier: 3.547A pdb=" N VAL 7 481 " --> pdb=" O ILE 7 520 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N THR 7 483 " --> pdb=" O CYS 7 522 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ASP 7 524 " --> pdb=" O THR 7 483 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N SER 7 562 " --> pdb=" O GLY 7 519 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N LEU 7 564 " --> pdb=" O CYS 7 521 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N ILE 7 454 " --> pdb=" O THR 7 561 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ILE 7 563 " --> pdb=" O ILE 7 454 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA 7 565 " --> pdb=" O VAL 7 456 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N LEU 7 458 " --> pdb=" O ALA 7 565 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ILE 7 596 " --> pdb=" O ASN 7 455 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N CYS 7 457 " --> pdb=" O ILE 7 596 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain '7' and resid 495 through 499 removed outlier: 4.829A pdb=" N GLU 7 509 " --> pdb=" O ALA 7 496 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain '7' and resid 544 through 549 removed outlier: 7.910A pdb=" N GLN 7 544 " --> pdb=" O ALA 7 559 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE 7 548 " --> pdb=" O THR 7 555 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N THR 7 555 " --> pdb=" O ILE 7 548 " (cutoff:3.500A) 1935 hydrogen bonds defined for protein. 5766 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 194 hydrogen bonds 388 hydrogen bond angles 0 basepair planarities 83 basepair parallelities 152 stacking parallelities Total time for adding SS restraints: 40.79 Time building geometry restraints manager: 76.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.79 - 1.00: 51896 1.00 - 1.21: 86 1.21 - 1.41: 22376 1.41 - 1.62: 31789 1.62 - 1.83: 382 Bond restraints: 106529 Sorted by residual: bond pdb=" O3' DA X 84 " pdb=" P DT X 85 " ideal model delta sigma weight residual 1.607 1.456 0.151 1.50e-02 4.44e+03 1.01e+02 bond pdb=" C2' DC Y 35 " pdb=" H2' DC Y 35 " ideal model delta sigma weight residual 0.970 0.795 0.175 2.00e-02 2.50e+03 7.68e+01 bond pdb=" C4 ATP E2001 " pdb=" C5 ATP E2001 " ideal model delta sigma weight residual 1.388 1.467 -0.079 1.00e-02 1.00e+04 6.19e+01 bond pdb=" C4 ATP D2001 " pdb=" C5 ATP D2001 " ideal model delta sigma weight residual 1.388 1.465 -0.077 1.00e-02 1.00e+04 5.89e+01 bond pdb=" C4 ATP A2001 " pdb=" C5 ATP A2001 " ideal model delta sigma weight residual 1.388 1.464 -0.076 1.00e-02 1.00e+04 5.70e+01 ... (remaining 106524 not shown) Histogram of bond angle deviations from ideal: 86.24 - 96.48: 9 96.48 - 106.72: 6581 106.72 - 116.96: 134922 116.96 - 127.20: 50486 127.20 - 137.44: 804 Bond angle restraints: 192802 Sorted by residual: angle pdb=" PB ATP D2001 " pdb=" O3B ATP D2001 " pdb=" PG ATP D2001 " ideal model delta sigma weight residual 139.87 116.42 23.45 1.00e+00 1.00e+00 5.50e+02 angle pdb=" PA ATP E2001 " pdb=" O3A ATP E2001 " pdb=" PB ATP E2001 " ideal model delta sigma weight residual 136.83 114.33 22.50 1.00e+00 1.00e+00 5.06e+02 angle pdb=" PA ATP D2001 " pdb=" O3A ATP D2001 " pdb=" PB ATP D2001 " ideal model delta sigma weight residual 136.83 114.65 22.18 1.00e+00 1.00e+00 4.92e+02 angle pdb=" PB ATP A2001 " pdb=" O3B ATP A2001 " pdb=" PG ATP A2001 " ideal model delta sigma weight residual 139.87 118.94 20.93 1.00e+00 1.00e+00 4.38e+02 angle pdb=" C3' DC Y 35 " pdb=" C2' DC Y 35 " pdb=" H2' DC Y 35 " ideal model delta sigma weight residual 109.00 137.44 -28.44 1.50e+00 4.44e-01 3.59e+02 ... (remaining 192797 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.46: 44561 24.46 - 48.92: 3804 48.92 - 73.38: 902 73.38 - 97.84: 51 97.84 - 122.30: 2 Dihedral angle restraints: 49320 sinusoidal: 28303 harmonic: 21017 Sorted by residual: dihedral pdb=" CA GLU 6 133 " pdb=" C GLU 6 133 " pdb=" N LYS 6 134 " pdb=" CA LYS 6 134 " ideal model delta harmonic sigma weight residual -180.00 -150.19 -29.81 0 5.00e+00 4.00e-02 3.56e+01 dihedral pdb=" CA ILE 2 255 " pdb=" C ILE 2 255 " pdb=" N LEU 2 256 " pdb=" CA LEU 2 256 " ideal model delta harmonic sigma weight residual 180.00 150.26 29.74 0 5.00e+00 4.00e-02 3.54e+01 dihedral pdb=" CA PRO 3 93 " pdb=" C PRO 3 93 " pdb=" N HIS 3 94 " pdb=" CA HIS 3 94 " ideal model delta harmonic sigma weight residual 180.00 150.52 29.48 0 5.00e+00 4.00e-02 3.48e+01 ... (remaining 49317 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.105: 7624 0.105 - 0.211: 868 0.211 - 0.316: 52 0.316 - 0.422: 4 0.422 - 0.527: 2 Chirality restraints: 8550 Sorted by residual: chirality pdb=" CA ARG F 57 " pdb=" N ARG F 57 " pdb=" C ARG F 57 " pdb=" CB ARG F 57 " both_signs ideal model delta sigma weight residual False 2.51 1.98 0.53 2.00e-01 2.50e+01 6.95e+00 chirality pdb=" CB THR 3 432 " pdb=" CA THR 3 432 " pdb=" OG1 THR 3 432 " pdb=" CG2 THR 3 432 " both_signs ideal model delta sigma weight residual False 2.55 2.04 0.51 2.00e-01 2.50e+01 6.44e+00 chirality pdb=" CB ILE F 346 " pdb=" CA ILE F 346 " pdb=" CG1 ILE F 346 " pdb=" CG2 ILE F 346 " both_signs ideal model delta sigma weight residual False 2.64 2.25 0.39 2.00e-01 2.50e+01 3.81e+00 ... (remaining 8547 not shown) Planarity restraints: 14902 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 214 " -0.082 2.00e-02 2.50e+03 4.88e-01 3.57e+03 pdb=" CG ASN C 214 " 0.007 2.00e-02 2.50e+03 pdb=" OD1 ASN C 214 " 0.081 2.00e-02 2.50e+03 pdb=" ND2 ASN C 214 " -0.000 2.00e-02 2.50e+03 pdb="HD21 ASN C 214 " -0.844 2.00e-02 2.50e+03 pdb="HD22 ASN C 214 " 0.838 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 212 " 0.260 2.00e-02 2.50e+03 2.73e-01 1.12e+03 pdb=" CG ASN C 212 " -0.020 2.00e-02 2.50e+03 pdb=" OD1 ASN C 212 " -0.249 2.00e-02 2.50e+03 pdb=" ND2 ASN C 212 " -0.002 2.00e-02 2.50e+03 pdb="HD21 ASN C 212 " 0.404 2.00e-02 2.50e+03 pdb="HD22 ASN C 212 " -0.393 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN 4 377 " -0.157 2.00e-02 2.50e+03 1.56e-01 3.67e+02 pdb=" CG ASN 4 377 " 0.012 2.00e-02 2.50e+03 pdb=" OD1 ASN 4 377 " 0.150 2.00e-02 2.50e+03 pdb=" ND2 ASN 4 377 " 0.001 2.00e-02 2.50e+03 pdb="HD21 ASN 4 377 " -0.226 2.00e-02 2.50e+03 pdb="HD22 ASN 4 377 " 0.220 2.00e-02 2.50e+03 ... (remaining 14899 not shown) Histogram of nonbonded interaction distances: 1.25 - 1.92: 884 1.92 - 2.59: 123429 2.59 - 3.26: 318645 3.26 - 3.93: 386294 3.93 - 4.60: 602135 Nonbonded interactions: 1431387 Sorted by model distance: nonbonded pdb=" O ALA 4 392 " pdb=" HG SER 6 281 " model vdw 1.253 1.850 nonbonded pdb=" HH TYR 7 203 " pdb=" O ASN 7 336 " model vdw 1.267 1.850 nonbonded pdb=" O MET 3 306 " pdb=" HG SER 5 206 " model vdw 1.285 1.850 nonbonded pdb=" OE1 GLN 7 543 " pdb=" HG1 THR 7 545 " model vdw 1.329 1.850 nonbonded pdb=" O MET D 326 " pdb=" HG1 THR D 330 " model vdw 1.353 1.850 ... (remaining 1431382 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 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: 4.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 1.150 Extract box with map and model: 12.330 Check model and map are aligned: 1.240 Set scattering table: 0.770 Process input model: 356.050 Find NCS groups from input model: 2.540 Set up NCS constraints: 0.240 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 380.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6658 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.151 54551 Z= 0.742 Angle : 1.276 23.450 74525 Z= 0.737 Chirality : 0.067 0.527 8550 Planarity : 0.008 0.100 8873 Dihedral : 18.432 122.299 21132 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.10 % Allowed : 10.40 % Favored : 89.50 % Rotamer: Outliers : 0.54 % Allowed : 6.28 % Favored : 93.18 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.03 (0.08), residues: 6088 helix: -3.22 (0.07), residues: 2463 sheet: -3.54 (0.14), residues: 759 loop : -3.34 (0.10), residues: 2866 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.004 TRP 6 344 HIS 0.027 0.003 HIS F 59 PHE 0.048 0.004 PHE 7 363 TYR 0.047 0.004 TYR C 439 ARG 0.031 0.002 ARG 5 630 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12176 Ramachandran restraints generated. 6088 Oldfield, 0 Emsley, 6088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12176 Ramachandran restraints generated. 6088 Oldfield, 0 Emsley, 6088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 486 is missing expected H atoms. Skipping. Residue THR 109 is missing expected H atoms. Skipping. Residue THR 44 is missing expected H atoms. Skipping. Evaluate side-chains 783 residues out of total 5543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 753 time to evaluate : 6.650 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: B 263 MET cc_start: 0.5164 (ptp) cc_final: 0.4688 (pmm) REVERT: C 236 LEU cc_start: 0.7755 (mt) cc_final: 0.6974 (pt) REVERT: C 306 MET cc_start: 0.6011 (ttp) cc_final: 0.4797 (tmm) REVERT: C 342 ASN cc_start: 0.7972 (OUTLIER) cc_final: 0.6900 (m110) REVERT: C 585 MET cc_start: 0.6808 (ttt) cc_final: 0.6544 (ttt) REVERT: D 385 ASP cc_start: 0.7342 (p0) cc_final: 0.6699 (m-30) REVERT: D 522 MET cc_start: 0.6997 (ptp) cc_final: 0.4100 (mmm) REVERT: D 526 TRP cc_start: 0.5059 (m100) cc_final: 0.4664 (m100) REVERT: E 170 MET cc_start: 0.6487 (OUTLIER) cc_final: 0.6045 (mmt) REVERT: E 450 TRP cc_start: 0.6643 (m100) cc_final: 0.6040 (m100) REVERT: F 48 MET cc_start: 0.2204 (ttt) cc_final: 0.1267 (mmt) REVERT: F 360 ASP cc_start: 0.6504 (m-30) cc_final: 0.5967 (p0) REVERT: F 402 LEU cc_start: 0.6283 (OUTLIER) cc_final: 0.5803 (mp) REVERT: F 424 ARG cc_start: 0.8078 (ttt180) cc_final: 0.6710 (tmt170) REVERT: F 427 MET cc_start: 0.5614 (mpp) cc_final: 0.5083 (mpp) REVERT: 2 622 GLU cc_start: 0.7748 (tp30) cc_final: 0.7490 (mm-30) REVERT: 3 382 LEU cc_start: 0.8019 (tt) cc_final: 0.7620 (tt) REVERT: 3 415 LYS cc_start: 0.8081 (mppt) cc_final: 0.7706 (pttp) REVERT: 3 474 GLU cc_start: 0.8453 (mt-10) cc_final: 0.8222 (mt-10) REVERT: 3 723 LYS cc_start: 0.8415 (tttt) cc_final: 0.8189 (tttt) REVERT: 4 302 LYS cc_start: 0.5938 (tptt) cc_final: 0.5544 (tptt) REVERT: 5 65 MET cc_start: 0.7613 (mtm) cc_final: 0.7278 (ppp) REVERT: 5 105 SER cc_start: 0.7899 (m) cc_final: 0.7645 (p) REVERT: 5 159 ILE cc_start: 0.7097 (mt) cc_final: 0.6797 (pt) REVERT: 5 393 MET cc_start: 0.8310 (mtp) cc_final: 0.7681 (mmp) REVERT: 5 527 TYR cc_start: 0.6048 (m-80) cc_final: 0.5684 (m-80) REVERT: 6 779 GLU cc_start: 0.8104 (tt0) cc_final: 0.7788 (tp30) REVERT: 6 801 GLU cc_start: 0.7944 (pt0) cc_final: 0.7743 (tt0) REVERT: 7 61 PRO cc_start: 0.7410 (Cg_exo) cc_final: 0.7199 (Cg_endo) REVERT: 7 520 ILE cc_start: 0.5560 (mm) cc_final: 0.5206 (tt) outliers start: 30 outliers final: 10 residues processed: 773 average time/residue: 1.6064 time to fit residues: 1954.9376 Evaluate side-chains 476 residues out of total 5543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 463 time to evaluate : 6.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 628 random chunks: chunk 530 optimal weight: 2.9990 chunk 475 optimal weight: 1.9990 chunk 264 optimal weight: 0.9980 chunk 162 optimal weight: 0.9980 chunk 321 optimal weight: 3.9990 chunk 254 optimal weight: 0.8980 chunk 492 optimal weight: 1.9990 chunk 190 optimal weight: 5.9990 chunk 299 optimal weight: 6.9990 chunk 366 optimal weight: 2.9990 chunk 570 optimal weight: 2.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 789 HIS A 820 GLN ** B 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 438 GLN C 241 ASN C 246 ASN ** C 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 370 ASN D 489 ASN ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 67 GLN F 407 GLN 2 621 HIS ** 2 666 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 55 ASN 3 308 GLN 4 563 ASN 4 797 GLN 5 494 HIS 5 636 ASN 7 615 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6655 moved from start: 0.2382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 54551 Z= 0.223 Angle : 0.691 7.702 74525 Z= 0.375 Chirality : 0.043 0.200 8550 Planarity : 0.005 0.076 8873 Dihedral : 17.713 124.285 8854 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.44 % Favored : 91.52 % Rotamer: Outliers : 0.04 % Allowed : 4.19 % Favored : 95.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.81 (0.09), residues: 6088 helix: -1.93 (0.09), residues: 2485 sheet: -3.01 (0.15), residues: 768 loop : -2.91 (0.11), residues: 2835 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 266 HIS 0.014 0.001 HIS 5 576 PHE 0.022 0.002 PHE C 408 TYR 0.024 0.002 TYR B 473 ARG 0.012 0.001 ARG D 396 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12176 Ramachandran restraints generated. 6088 Oldfield, 0 Emsley, 6088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12176 Ramachandran restraints generated. 6088 Oldfield, 0 Emsley, 6088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 486 is missing expected H atoms. Skipping. Residue THR 109 is missing expected H atoms. Skipping. Residue THR 44 is missing expected H atoms. Skipping. Evaluate side-chains 588 residues out of total 5543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 586 time to evaluate : 6.514 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: A 602 MET cc_start: 0.6130 (tpp) cc_final: 0.5920 (tpp) REVERT: B 263 MET cc_start: 0.5663 (ptp) cc_final: 0.5263 (pmm) REVERT: C 306 MET cc_start: 0.6376 (ttp) cc_final: 0.5239 (tmm) REVERT: C 585 MET cc_start: 0.7020 (ttt) cc_final: 0.6657 (ttt) REVERT: D 385 ASP cc_start: 0.7086 (p0) cc_final: 0.6293 (m-30) REVERT: E 98 ASP cc_start: 0.8806 (m-30) cc_final: 0.8470 (t0) REVERT: E 450 TRP cc_start: 0.7046 (m100) cc_final: 0.6692 (m100) REVERT: F 48 MET cc_start: 0.1963 (ttt) cc_final: 0.1360 (mmt) REVERT: F 424 ARG cc_start: 0.8153 (ttt180) cc_final: 0.6864 (tmt170) REVERT: 2 452 GLU cc_start: 0.7865 (mt-10) cc_final: 0.7595 (mm-30) REVERT: 2 456 ILE cc_start: 0.6181 (tt) cc_final: 0.5978 (mp) REVERT: 2 612 MET cc_start: 0.7075 (mtm) cc_final: 0.6847 (mtm) REVERT: 3 44 SER cc_start: 0.8669 (m) cc_final: 0.8263 (p) REVERT: 3 264 MET cc_start: 0.7619 (mpp) cc_final: 0.7359 (mpp) REVERT: 4 302 LYS cc_start: 0.5781 (tptt) cc_final: 0.5515 (tptt) REVERT: 4 610 ASP cc_start: 0.8053 (m-30) cc_final: 0.7239 (m-30) REVERT: 5 65 MET cc_start: 0.8255 (mtm) cc_final: 0.7944 (ppp) REVERT: 5 105 SER cc_start: 0.7944 (m) cc_final: 0.7663 (p) REVERT: 5 159 ILE cc_start: 0.7539 (mt) cc_final: 0.6984 (pt) REVERT: 5 393 MET cc_start: 0.8404 (mtp) cc_final: 0.7530 (mpp) REVERT: 5 433 SER cc_start: 0.7735 (m) cc_final: 0.7410 (m) REVERT: 5 478 CYS cc_start: 0.8160 (m) cc_final: 0.7946 (m) REVERT: 5 684 PHE cc_start: 0.7548 (t80) cc_final: 0.6863 (t80) REVERT: 7 66 MET cc_start: 0.8388 (mtp) cc_final: 0.8136 (mtp) REVERT: 7 448 MET cc_start: 0.4917 (tpp) cc_final: 0.4703 (tpp) outliers start: 2 outliers final: 0 residues processed: 588 average time/residue: 1.3871 time to fit residues: 1316.9194 Evaluate side-chains 445 residues out of total 5543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 445 time to evaluate : 6.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 628 random chunks: chunk 316 optimal weight: 0.7980 chunk 176 optimal weight: 2.9990 chunk 474 optimal weight: 4.9990 chunk 388 optimal weight: 0.8980 chunk 157 optimal weight: 0.8980 chunk 571 optimal weight: 2.9990 chunk 617 optimal weight: 7.9990 chunk 508 optimal weight: 3.9990 chunk 566 optimal weight: 10.0000 chunk 194 optimal weight: 7.9990 chunk 458 optimal weight: 2.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 303 GLN C 241 ASN C 246 ASN ** C 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 93 HIS 2 313 ASN 2 439 ASN ** 3 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 574 ASN ** 5 576 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 652 GLN 6 149 ASN ** 6 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 653 HIS 7 264 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6700 moved from start: 0.3152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 54551 Z= 0.220 Angle : 0.637 8.118 74525 Z= 0.348 Chirality : 0.041 0.230 8550 Planarity : 0.004 0.065 8873 Dihedral : 17.219 121.218 8854 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.79 % Favored : 91.21 % Rotamer: Outliers : 0.02 % Allowed : 3.18 % Favored : 96.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.18 (0.10), residues: 6088 helix: -1.24 (0.09), residues: 2492 sheet: -2.57 (0.17), residues: 743 loop : -2.78 (0.11), residues: 2853 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP F 421 HIS 0.008 0.001 HIS 4 735 PHE 0.025 0.002 PHE C 408 TYR 0.054 0.002 TYR B 473 ARG 0.019 0.001 ARG C 545 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12176 Ramachandran restraints generated. 6088 Oldfield, 0 Emsley, 6088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12176 Ramachandran restraints generated. 6088 Oldfield, 0 Emsley, 6088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 486 is missing expected H atoms. Skipping. Residue THR 109 is missing expected H atoms. Skipping. Residue THR 44 is missing expected H atoms. Skipping. Evaluate side-chains 556 residues out of total 5543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 555 time to evaluate : 6.606 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: B 263 MET cc_start: 0.5901 (ptp) cc_final: 0.5495 (pmm) REVERT: C 306 MET cc_start: 0.6774 (ttp) cc_final: 0.4949 (tmm) REVERT: C 320 MET cc_start: 0.7598 (ptm) cc_final: 0.7288 (ptm) REVERT: C 585 MET cc_start: 0.7012 (ttt) cc_final: 0.6619 (ttt) REVERT: D 385 ASP cc_start: 0.7380 (p0) cc_final: 0.7156 (p0) REVERT: D 526 TRP cc_start: 0.4971 (m100) cc_final: 0.4629 (m100) REVERT: E 109 VAL cc_start: 0.9162 (t) cc_final: 0.8904 (p) REVERT: E 450 TRP cc_start: 0.7124 (m100) cc_final: 0.6711 (m100) REVERT: F 48 MET cc_start: 0.2096 (ttt) cc_final: 0.0996 (mmt) REVERT: F 421 TRP cc_start: 0.6542 (t60) cc_final: 0.6314 (t60) REVERT: F 424 ARG cc_start: 0.8250 (ttt180) cc_final: 0.6843 (tmt170) REVERT: F 427 MET cc_start: 0.6367 (mpp) cc_final: 0.6152 (mmt) REVERT: 2 456 ILE cc_start: 0.6539 (tt) cc_final: 0.6122 (mp) REVERT: 2 612 MET cc_start: 0.7309 (mtm) cc_final: 0.7087 (mtm) REVERT: 2 688 ASP cc_start: 0.8422 (p0) cc_final: 0.8053 (p0) REVERT: 3 44 SER cc_start: 0.8694 (m) cc_final: 0.8285 (p) REVERT: 3 723 LYS cc_start: 0.8598 (tttt) cc_final: 0.8358 (tttt) REVERT: 4 302 LYS cc_start: 0.6135 (tptt) cc_final: 0.5871 (tptt) REVERT: 5 65 MET cc_start: 0.8294 (mtm) cc_final: 0.7879 (tmm) REVERT: 5 105 SER cc_start: 0.7947 (m) cc_final: 0.7646 (p) REVERT: 5 278 CYS cc_start: 0.6487 (p) cc_final: 0.6267 (p) REVERT: 5 393 MET cc_start: 0.8484 (mtp) cc_final: 0.7745 (mmp) REVERT: 5 478 CYS cc_start: 0.8217 (m) cc_final: 0.7982 (m) REVERT: 5 684 PHE cc_start: 0.7539 (t80) cc_final: 0.6891 (t80) outliers start: 1 outliers final: 0 residues processed: 556 average time/residue: 1.3642 time to fit residues: 1236.2499 Evaluate side-chains 438 residues out of total 5543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 438 time to evaluate : 6.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 628 random chunks: chunk 564 optimal weight: 4.9990 chunk 429 optimal weight: 2.9990 chunk 296 optimal weight: 10.0000 chunk 63 optimal weight: 8.9990 chunk 272 optimal weight: 4.9990 chunk 383 optimal weight: 0.8980 chunk 573 optimal weight: 4.9990 chunk 607 optimal weight: 20.0000 chunk 299 optimal weight: 9.9990 chunk 543 optimal weight: 10.0000 chunk 163 optimal weight: 3.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 297 GLN ** B 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 246 ASN C 264 HIS ** C 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 418 ASN ** D 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 422 GLN 3 29 GLN 3 51 ASN ** 4 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 759 HIS ** 5 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 411 ASN ** 5 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 586 GLN 6 149 ASN ** 6 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6855 moved from start: 0.3911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 54551 Z= 0.328 Angle : 0.712 7.841 74525 Z= 0.393 Chirality : 0.044 0.187 8550 Planarity : 0.005 0.078 8873 Dihedral : 17.219 120.297 8854 Min Nonbonded Distance : 1.821 Molprobity Statistics. All-atom Clashscore : 16.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.33 % Favored : 88.67 % Rotamer: Outliers : 0.02 % Allowed : 3.91 % Favored : 96.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.28 (0.10), residues: 6088 helix: -1.24 (0.09), residues: 2520 sheet: -2.65 (0.17), residues: 769 loop : -2.92 (0.11), residues: 2799 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP F 421 HIS 0.009 0.002 HIS 5 576 PHE 0.029 0.002 PHE F 98 TYR 0.042 0.002 TYR B 473 ARG 0.007 0.001 ARG 2 310 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12176 Ramachandran restraints generated. 6088 Oldfield, 0 Emsley, 6088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12176 Ramachandran restraints generated. 6088 Oldfield, 0 Emsley, 6088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 486 is missing expected H atoms. Skipping. Residue THR 109 is missing expected H atoms. Skipping. Residue THR 44 is missing expected H atoms. Skipping. Evaluate side-chains 506 residues out of total 5543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 505 time to evaluate : 6.536 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: B 237 SER cc_start: 0.8952 (p) cc_final: 0.8707 (p) REVERT: B 263 MET cc_start: 0.6399 (ptp) cc_final: 0.5976 (pmm) REVERT: C 306 MET cc_start: 0.6546 (ttp) cc_final: 0.5057 (tmm) REVERT: C 585 MET cc_start: 0.8082 (ttt) cc_final: 0.7326 (ttt) REVERT: D 385 ASP cc_start: 0.7302 (p0) cc_final: 0.7086 (p0) REVERT: E 109 VAL cc_start: 0.9257 (t) cc_final: 0.8999 (p) REVERT: E 450 TRP cc_start: 0.7193 (m100) cc_final: 0.6852 (m100) REVERT: F 48 MET cc_start: 0.2530 (ttt) cc_final: 0.1219 (mmt) REVERT: F 95 MET cc_start: 0.9017 (tmm) cc_final: 0.8723 (ttt) REVERT: F 389 PHE cc_start: 0.8322 (m-80) cc_final: 0.8053 (m-80) REVERT: F 418 TYR cc_start: 0.8111 (t80) cc_final: 0.7467 (t80) REVERT: 2 612 MET cc_start: 0.7421 (mtm) cc_final: 0.7095 (mtm) REVERT: 2 688 ASP cc_start: 0.8340 (p0) cc_final: 0.8069 (p0) REVERT: 3 264 MET cc_start: 0.7574 (mpp) cc_final: 0.7362 (mpp) REVERT: 3 723 LYS cc_start: 0.8665 (tttt) cc_final: 0.8381 (tttt) REVERT: 4 302 LYS cc_start: 0.6202 (tptt) cc_final: 0.5955 (tptt) REVERT: 4 414 SER cc_start: 0.7930 (m) cc_final: 0.7583 (t) REVERT: 4 536 VAL cc_start: 0.8375 (t) cc_final: 0.7875 (t) REVERT: 4 706 TYR cc_start: 0.8154 (m-80) cc_final: 0.7072 (m-80) REVERT: 5 65 MET cc_start: 0.8220 (mtm) cc_final: 0.7747 (tmm) REVERT: 5 105 SER cc_start: 0.8166 (m) cc_final: 0.7860 (p) REVERT: 5 338 GLU cc_start: 0.6997 (tt0) cc_final: 0.6240 (tm-30) REVERT: 5 393 MET cc_start: 0.8685 (mtp) cc_final: 0.8162 (mmp) REVERT: 5 406 LEU cc_start: 0.9110 (tt) cc_final: 0.8587 (mp) REVERT: 5 684 PHE cc_start: 0.7965 (t80) cc_final: 0.7160 (t80) REVERT: 6 263 PHE cc_start: 0.6430 (m-80) cc_final: 0.6141 (m-10) REVERT: 6 320 ASN cc_start: 0.7577 (p0) cc_final: 0.7348 (p0) outliers start: 1 outliers final: 1 residues processed: 506 average time/residue: 1.3189 time to fit residues: 1079.8021 Evaluate side-chains 413 residues out of total 5543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 412 time to evaluate : 6.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 628 random chunks: chunk 505 optimal weight: 2.9990 chunk 344 optimal weight: 3.9990 chunk 8 optimal weight: 8.9990 chunk 451 optimal weight: 6.9990 chunk 250 optimal weight: 0.8980 chunk 518 optimal weight: 4.9990 chunk 419 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 309 optimal weight: 3.9990 chunk 544 optimal weight: 7.9990 chunk 153 optimal weight: 1.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 303 GLN ** B 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 246 ASN ** C 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 492 GLN 3 569 HIS ** 4 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 576 HIS ** 6 750 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6808 moved from start: 0.4294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 54551 Z= 0.219 Angle : 0.619 9.120 74525 Z= 0.338 Chirality : 0.041 0.184 8550 Planarity : 0.004 0.070 8873 Dihedral : 17.032 121.558 8854 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 13.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.31 % Favored : 90.69 % Rotamer: Outliers : 0.04 % Allowed : 2.29 % Favored : 97.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.91 (0.10), residues: 6088 helix: -0.84 (0.10), residues: 2518 sheet: -2.47 (0.17), residues: 771 loop : -2.82 (0.11), residues: 2799 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP D 526 HIS 0.008 0.001 HIS 3 569 PHE 0.024 0.001 PHE C 408 TYR 0.035 0.001 TYR B 473 ARG 0.016 0.000 ARG 5 161 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12176 Ramachandran restraints generated. 6088 Oldfield, 0 Emsley, 6088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12176 Ramachandran restraints generated. 6088 Oldfield, 0 Emsley, 6088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 486 is missing expected H atoms. Skipping. Residue THR 109 is missing expected H atoms. Skipping. Residue THR 44 is missing expected H atoms. Skipping. Evaluate side-chains 516 residues out of total 5543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 514 time to evaluate : 6.537 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: B 237 SER cc_start: 0.8934 (p) cc_final: 0.8726 (p) REVERT: B 263 MET cc_start: 0.6203 (ptp) cc_final: 0.5788 (pmm) REVERT: C 103 ASN cc_start: 0.8657 (t0) cc_final: 0.8441 (t0) REVERT: C 306 MET cc_start: 0.6545 (ttp) cc_final: 0.5055 (tmm) REVERT: C 524 LEU cc_start: 0.9177 (mt) cc_final: 0.8867 (mt) REVERT: C 585 MET cc_start: 0.7915 (ttt) cc_final: 0.7135 (ttt) REVERT: C 609 GLU cc_start: 0.6824 (tt0) cc_final: 0.6544 (tm-30) REVERT: D 385 ASP cc_start: 0.7317 (p0) cc_final: 0.6090 (m-30) REVERT: E 109 VAL cc_start: 0.9241 (t) cc_final: 0.8981 (p) REVERT: E 450 TRP cc_start: 0.7212 (m100) cc_final: 0.6886 (m100) REVERT: F 48 MET cc_start: 0.2748 (ttt) cc_final: 0.1396 (mmt) REVERT: F 389 PHE cc_start: 0.8307 (m-80) cc_final: 0.8082 (m-80) REVERT: F 418 TYR cc_start: 0.8119 (t80) cc_final: 0.7479 (t80) REVERT: 2 407 GLU cc_start: 0.6725 (tt0) cc_final: 0.5890 (mp0) REVERT: 2 612 MET cc_start: 0.7415 (mtm) cc_final: 0.7062 (mtm) REVERT: 2 688 ASP cc_start: 0.8501 (p0) cc_final: 0.8192 (p0) REVERT: 3 44 SER cc_start: 0.8741 (m) cc_final: 0.8336 (p) REVERT: 3 723 LYS cc_start: 0.8676 (tttt) cc_final: 0.8407 (tttt) REVERT: 4 414 SER cc_start: 0.7999 (m) cc_final: 0.7599 (t) REVERT: 4 536 VAL cc_start: 0.8365 (t) cc_final: 0.7894 (t) REVERT: 4 706 TYR cc_start: 0.8196 (m-80) cc_final: 0.7132 (m-80) REVERT: 5 65 MET cc_start: 0.8119 (mtm) cc_final: 0.7725 (tmm) REVERT: 5 105 SER cc_start: 0.8113 (m) cc_final: 0.7795 (p) REVERT: 5 338 GLU cc_start: 0.6622 (tt0) cc_final: 0.6215 (tm-30) REVERT: 5 393 MET cc_start: 0.8658 (mtp) cc_final: 0.8111 (mmp) REVERT: 5 406 LEU cc_start: 0.9068 (tt) cc_final: 0.8555 (mp) REVERT: 5 469 MET cc_start: 0.8780 (mmt) cc_final: 0.8541 (mmm) REVERT: 5 478 CYS cc_start: 0.8313 (m) cc_final: 0.8038 (m) REVERT: 5 684 PHE cc_start: 0.7840 (t80) cc_final: 0.7063 (t80) REVERT: 6 320 ASN cc_start: 0.7840 (p0) cc_final: 0.7595 (p0) outliers start: 2 outliers final: 0 residues processed: 516 average time/residue: 1.3217 time to fit residues: 1110.9611 Evaluate side-chains 418 residues out of total 5543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 418 time to evaluate : 6.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 628 random chunks: chunk 204 optimal weight: 9.9990 chunk 546 optimal weight: 3.9990 chunk 119 optimal weight: 0.7980 chunk 356 optimal weight: 4.9990 chunk 149 optimal weight: 10.0000 chunk 607 optimal weight: 10.0000 chunk 504 optimal weight: 0.7980 chunk 281 optimal weight: 6.9990 chunk 50 optimal weight: 0.5980 chunk 200 optimal weight: 9.9990 chunk 318 optimal weight: 4.9990 overall best weight: 2.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 839 ASN ** B 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 246 ASN ** C 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 489 ASN ** 2 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 193 ASN ** 4 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 149 ASN ** 6 750 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6830 moved from start: 0.4657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 54551 Z= 0.231 Angle : 0.613 6.776 74525 Z= 0.337 Chirality : 0.041 0.185 8550 Planarity : 0.004 0.068 8873 Dihedral : 16.889 123.547 8854 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 13.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.64 % Favored : 89.36 % Rotamer: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.73 (0.10), residues: 6088 helix: -0.64 (0.10), residues: 2540 sheet: -2.44 (0.17), residues: 787 loop : -2.76 (0.11), residues: 2761 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 266 HIS 0.007 0.001 HIS A 416 PHE 0.031 0.001 PHE 6 709 TYR 0.043 0.002 TYR B 473 ARG 0.005 0.000 ARG C 145 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12176 Ramachandran restraints generated. 6088 Oldfield, 0 Emsley, 6088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12176 Ramachandran restraints generated. 6088 Oldfield, 0 Emsley, 6088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 486 is missing expected H atoms. Skipping. Residue THR 109 is missing expected H atoms. Skipping. Residue THR 44 is missing expected H atoms. Skipping. Evaluate side-chains 498 residues out of total 5543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 498 time to evaluate : 6.457 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: B 237 SER cc_start: 0.8907 (p) cc_final: 0.8643 (p) REVERT: B 263 MET cc_start: 0.6461 (ptp) cc_final: 0.6024 (pmm) REVERT: C 103 ASN cc_start: 0.8749 (t0) cc_final: 0.8546 (t0) REVERT: C 306 MET cc_start: 0.6658 (ttp) cc_final: 0.5176 (tmm) REVERT: C 524 LEU cc_start: 0.9208 (mt) cc_final: 0.8815 (mt) REVERT: C 585 MET cc_start: 0.8050 (ttt) cc_final: 0.7294 (ttt) REVERT: D 385 ASP cc_start: 0.7398 (p0) cc_final: 0.6180 (m-30) REVERT: E 109 VAL cc_start: 0.9256 (t) cc_final: 0.8998 (p) REVERT: F 48 MET cc_start: 0.2629 (ttt) cc_final: 0.1193 (mmt) REVERT: F 365 CYS cc_start: 0.6564 (m) cc_final: 0.6270 (m) REVERT: F 389 PHE cc_start: 0.8332 (m-80) cc_final: 0.8073 (m-80) REVERT: F 418 TYR cc_start: 0.8209 (t80) cc_final: 0.7579 (t80) REVERT: 3 264 MET cc_start: 0.7476 (mpp) cc_final: 0.7252 (mpp) REVERT: 3 723 LYS cc_start: 0.8719 (tttt) cc_final: 0.8498 (tttt) REVERT: 4 414 SER cc_start: 0.7800 (m) cc_final: 0.7455 (t) REVERT: 5 65 MET cc_start: 0.8187 (mtm) cc_final: 0.7737 (tmm) REVERT: 5 105 SER cc_start: 0.8168 (m) cc_final: 0.7878 (p) REVERT: 5 338 GLU cc_start: 0.6759 (tt0) cc_final: 0.6222 (tm-30) REVERT: 5 393 MET cc_start: 0.8779 (mtp) cc_final: 0.8220 (mmp) REVERT: 5 406 LEU cc_start: 0.9033 (tt) cc_final: 0.8610 (mp) REVERT: 5 478 CYS cc_start: 0.8259 (m) cc_final: 0.8037 (m) REVERT: 5 684 PHE cc_start: 0.7842 (t80) cc_final: 0.7078 (t80) REVERT: 6 303 GLU cc_start: 0.7124 (tp30) cc_final: 0.6679 (tp30) REVERT: 6 320 ASN cc_start: 0.7945 (p0) cc_final: 0.7661 (p0) outliers start: 0 outliers final: 0 residues processed: 498 average time/residue: 1.3148 time to fit residues: 1073.1807 Evaluate side-chains 414 residues out of total 5543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 414 time to evaluate : 6.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 628 random chunks: chunk 585 optimal weight: 3.9990 chunk 68 optimal weight: 0.6980 chunk 346 optimal weight: 3.9990 chunk 443 optimal weight: 3.9990 chunk 343 optimal weight: 5.9990 chunk 511 optimal weight: 2.9990 chunk 339 optimal weight: 4.9990 chunk 605 optimal weight: 8.9990 chunk 378 optimal weight: 1.9990 chunk 369 optimal weight: 6.9990 chunk 279 optimal weight: 3.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 246 ASN ** C 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 454 ASN 2 538 ASN ** 4 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 750 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6859 moved from start: 0.4969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 54551 Z= 0.258 Angle : 0.631 6.698 74525 Z= 0.347 Chirality : 0.042 0.194 8550 Planarity : 0.005 0.069 8873 Dihedral : 16.881 125.894 8854 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 15.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.10 % Favored : 88.90 % Rotamer: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.75 (0.10), residues: 6088 helix: -0.65 (0.10), residues: 2550 sheet: -2.42 (0.17), residues: 795 loop : -2.79 (0.11), residues: 2743 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 494 HIS 0.008 0.001 HIS 3 569 PHE 0.024 0.002 PHE D 485 TYR 0.054 0.002 TYR B 473 ARG 0.009 0.000 ARG 5 529 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12176 Ramachandran restraints generated. 6088 Oldfield, 0 Emsley, 6088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12176 Ramachandran restraints generated. 6088 Oldfield, 0 Emsley, 6088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 486 is missing expected H atoms. Skipping. Residue THR 109 is missing expected H atoms. Skipping. Residue THR 44 is missing expected H atoms. Skipping. Evaluate side-chains 480 residues out of total 5543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 480 time to evaluate : 6.504 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: B 237 SER cc_start: 0.8843 (p) cc_final: 0.8619 (p) REVERT: B 263 MET cc_start: 0.6455 (ptp) cc_final: 0.5944 (pmm) REVERT: C 141 MET cc_start: 0.1543 (mmp) cc_final: 0.1222 (mmp) REVERT: C 306 MET cc_start: 0.6745 (ttp) cc_final: 0.5255 (tmm) REVERT: C 326 MET cc_start: 0.9018 (mtm) cc_final: 0.8800 (mtp) REVERT: C 524 LEU cc_start: 0.9215 (mt) cc_final: 0.8827 (mt) REVERT: C 585 MET cc_start: 0.8080 (ttt) cc_final: 0.7342 (ttt) REVERT: D 385 ASP cc_start: 0.7480 (p0) cc_final: 0.7267 (p0) REVERT: E 109 VAL cc_start: 0.9214 (t) cc_final: 0.8981 (p) REVERT: F 48 MET cc_start: 0.2702 (ttt) cc_final: 0.1282 (mmt) REVERT: F 389 PHE cc_start: 0.8350 (m-80) cc_final: 0.8095 (m-80) REVERT: F 418 TYR cc_start: 0.8246 (t80) cc_final: 0.7628 (t80) REVERT: 2 612 MET cc_start: 0.7720 (mtm) cc_final: 0.7222 (mtm) REVERT: 3 723 LYS cc_start: 0.8797 (tttt) cc_final: 0.8501 (tttt) REVERT: 4 414 SER cc_start: 0.7902 (m) cc_final: 0.7515 (t) REVERT: 5 65 MET cc_start: 0.8205 (mtm) cc_final: 0.7757 (tmm) REVERT: 5 105 SER cc_start: 0.8230 (m) cc_final: 0.7949 (p) REVERT: 5 338 GLU cc_start: 0.6874 (tt0) cc_final: 0.6211 (tm-30) REVERT: 5 393 MET cc_start: 0.8789 (mtp) cc_final: 0.8045 (mmm) REVERT: 5 684 PHE cc_start: 0.7969 (t80) cc_final: 0.7271 (t80) REVERT: 7 721 ARG cc_start: 0.5821 (ptt-90) cc_final: 0.5615 (mmm160) outliers start: 0 outliers final: 0 residues processed: 480 average time/residue: 1.2727 time to fit residues: 1003.3112 Evaluate side-chains 397 residues out of total 5543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 397 time to evaluate : 6.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 628 random chunks: chunk 374 optimal weight: 5.9990 chunk 241 optimal weight: 4.9990 chunk 361 optimal weight: 5.9990 chunk 182 optimal weight: 6.9990 chunk 118 optimal weight: 1.9990 chunk 117 optimal weight: 0.8980 chunk 384 optimal weight: 0.1980 chunk 412 optimal weight: 0.2980 chunk 299 optimal weight: 4.9990 chunk 56 optimal weight: 4.9990 chunk 475 optimal weight: 10.0000 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 852 GLN ** B 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 241 ASN C 246 ASN ** C 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 366 ASN 3 365 GLN ** 4 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 632 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 652 GLN ** 6 750 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6820 moved from start: 0.5178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 54551 Z= 0.193 Angle : 0.585 7.442 74525 Z= 0.319 Chirality : 0.040 0.184 8550 Planarity : 0.004 0.091 8873 Dihedral : 16.743 131.299 8854 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 13.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.72 % Favored : 90.28 % Rotamer: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.44 (0.10), residues: 6088 helix: -0.37 (0.10), residues: 2553 sheet: -2.28 (0.17), residues: 771 loop : -2.65 (0.11), residues: 2764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 266 HIS 0.005 0.001 HIS A 416 PHE 0.029 0.001 PHE 3 345 TYR 0.040 0.001 TYR C 125 ARG 0.009 0.000 ARG F 337 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12176 Ramachandran restraints generated. 6088 Oldfield, 0 Emsley, 6088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12176 Ramachandran restraints generated. 6088 Oldfield, 0 Emsley, 6088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 486 is missing expected H atoms. Skipping. Residue THR 109 is missing expected H atoms. Skipping. Residue THR 44 is missing expected H atoms. Skipping. Evaluate side-chains 496 residues out of total 5543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 496 time to evaluate : 6.515 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: B 237 SER cc_start: 0.8838 (p) cc_final: 0.8599 (p) REVERT: C 141 MET cc_start: 0.1102 (mmp) cc_final: 0.0893 (mmp) REVERT: C 306 MET cc_start: 0.6610 (ttp) cc_final: 0.5184 (tmm) REVERT: C 326 MET cc_start: 0.9014 (mtm) cc_final: 0.8702 (mtp) REVERT: C 524 LEU cc_start: 0.9206 (mt) cc_final: 0.8988 (mt) REVERT: C 585 MET cc_start: 0.7988 (ttt) cc_final: 0.7275 (ttt) REVERT: D 385 ASP cc_start: 0.7414 (p0) cc_final: 0.6159 (m-30) REVERT: E 109 VAL cc_start: 0.9234 (t) cc_final: 0.9016 (p) REVERT: F 48 MET cc_start: 0.2695 (ttt) cc_final: 0.1267 (mmt) REVERT: F 389 PHE cc_start: 0.8330 (m-80) cc_final: 0.8101 (m-80) REVERT: F 393 ARG cc_start: 0.7324 (mpt90) cc_final: 0.6779 (mmm-85) REVERT: F 418 TYR cc_start: 0.8239 (t80) cc_final: 0.7658 (t80) REVERT: 2 341 CYS cc_start: 0.9113 (m) cc_final: 0.7873 (t) REVERT: 2 612 MET cc_start: 0.7701 (mtm) cc_final: 0.7208 (mtm) REVERT: 3 264 MET cc_start: 0.7439 (mpp) cc_final: 0.7234 (mpp) REVERT: 3 503 HIS cc_start: 0.7778 (p90) cc_final: 0.7526 (p90) REVERT: 3 723 LYS cc_start: 0.8813 (tttt) cc_final: 0.8524 (tttt) REVERT: 4 414 SER cc_start: 0.7832 (m) cc_final: 0.7453 (t) REVERT: 4 577 ILE cc_start: 0.7294 (mt) cc_final: 0.7054 (mt) REVERT: 4 755 LYS cc_start: 0.9190 (ttpt) cc_final: 0.8246 (tppt) REVERT: 5 65 MET cc_start: 0.8157 (mtm) cc_final: 0.7725 (tmm) REVERT: 5 105 SER cc_start: 0.8188 (m) cc_final: 0.7937 (p) REVERT: 5 270 MET cc_start: 0.8540 (mtt) cc_final: 0.7846 (mtt) REVERT: 5 338 GLU cc_start: 0.6723 (tt0) cc_final: 0.6075 (tm-30) REVERT: 5 393 MET cc_start: 0.8715 (mtp) cc_final: 0.7990 (mmm) REVERT: 5 478 CYS cc_start: 0.8505 (m) cc_final: 0.8228 (m) REVERT: 5 684 PHE cc_start: 0.7839 (t80) cc_final: 0.7013 (t80) REVERT: 6 303 GLU cc_start: 0.7270 (tp30) cc_final: 0.6844 (tp30) REVERT: 6 808 GLU cc_start: 0.6643 (tp30) cc_final: 0.6410 (tp30) REVERT: 7 707 MET cc_start: 0.7935 (tpp) cc_final: 0.7356 (tpp) outliers start: 0 outliers final: 0 residues processed: 496 average time/residue: 1.2781 time to fit residues: 1046.1799 Evaluate side-chains 412 residues out of total 5543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 412 time to evaluate : 6.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 628 random chunks: chunk 550 optimal weight: 5.9990 chunk 579 optimal weight: 0.9990 chunk 529 optimal weight: 1.9990 chunk 564 optimal weight: 0.7980 chunk 339 optimal weight: 2.9990 chunk 245 optimal weight: 8.9990 chunk 442 optimal weight: 5.9990 chunk 173 optimal weight: 6.9990 chunk 509 optimal weight: 0.8980 chunk 533 optimal weight: 3.9990 chunk 562 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 241 ASN ** C 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 240 HIS ** D 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 366 ASN ** 4 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 632 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 750 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6801 moved from start: 0.5361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 54551 Z= 0.177 Angle : 0.567 6.772 74525 Z= 0.309 Chirality : 0.040 0.182 8550 Planarity : 0.004 0.069 8873 Dihedral : 16.598 139.873 8854 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.90 % Favored : 91.10 % Rotamer: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.18 (0.11), residues: 6088 helix: -0.14 (0.10), residues: 2561 sheet: -2.14 (0.17), residues: 788 loop : -2.53 (0.11), residues: 2739 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 266 HIS 0.006 0.001 HIS A 416 PHE 0.018 0.001 PHE 6 761 TYR 0.031 0.001 TYR C 125 ARG 0.009 0.000 ARG 2 854 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12176 Ramachandran restraints generated. 6088 Oldfield, 0 Emsley, 6088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12176 Ramachandran restraints generated. 6088 Oldfield, 0 Emsley, 6088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 486 is missing expected H atoms. Skipping. Residue THR 109 is missing expected H atoms. Skipping. Residue THR 44 is missing expected H atoms. Skipping. Evaluate side-chains 494 residues out of total 5543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 494 time to evaluate : 6.326 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: B 237 SER cc_start: 0.8797 (p) cc_final: 0.8596 (p) REVERT: C 306 MET cc_start: 0.6615 (ttp) cc_final: 0.5237 (tmm) REVERT: C 524 LEU cc_start: 0.9217 (mt) cc_final: 0.9016 (mt) REVERT: C 585 MET cc_start: 0.7968 (ttt) cc_final: 0.7240 (ttt) REVERT: E 109 VAL cc_start: 0.9225 (t) cc_final: 0.9013 (p) REVERT: F 48 MET cc_start: 0.2624 (ttt) cc_final: 0.1029 (mmt) REVERT: F 389 PHE cc_start: 0.8318 (m-80) cc_final: 0.8063 (m-80) REVERT: F 418 TYR cc_start: 0.8192 (t80) cc_final: 0.7667 (t80) REVERT: 2 341 CYS cc_start: 0.9064 (m) cc_final: 0.7893 (t) REVERT: 2 612 MET cc_start: 0.7703 (mtm) cc_final: 0.7232 (mtm) REVERT: 2 692 ASP cc_start: 0.9121 (m-30) cc_final: 0.8750 (m-30) REVERT: 3 503 HIS cc_start: 0.7750 (p90) cc_final: 0.7516 (p90) REVERT: 3 723 LYS cc_start: 0.8825 (tttt) cc_final: 0.8571 (tttt) REVERT: 4 302 LYS cc_start: 0.6322 (tptt) cc_final: 0.6051 (tptp) REVERT: 4 414 SER cc_start: 0.7895 (m) cc_final: 0.7542 (t) REVERT: 4 577 ILE cc_start: 0.7261 (mt) cc_final: 0.7036 (mt) REVERT: 4 755 LYS cc_start: 0.9133 (ttpt) cc_final: 0.8252 (tppt) REVERT: 5 65 MET cc_start: 0.8061 (mtm) cc_final: 0.7712 (tmm) REVERT: 5 105 SER cc_start: 0.8208 (m) cc_final: 0.7952 (p) REVERT: 5 270 MET cc_start: 0.8489 (mtt) cc_final: 0.7757 (mtt) REVERT: 5 338 GLU cc_start: 0.6876 (tt0) cc_final: 0.6441 (tm-30) REVERT: 5 393 MET cc_start: 0.8685 (mtp) cc_final: 0.7956 (mmm) REVERT: 5 478 CYS cc_start: 0.8486 (m) cc_final: 0.8204 (m) REVERT: 5 538 ASP cc_start: 0.6922 (m-30) cc_final: 0.6602 (t70) REVERT: 5 684 PHE cc_start: 0.7773 (t80) cc_final: 0.6980 (t80) REVERT: 6 303 GLU cc_start: 0.7265 (tp30) cc_final: 0.6831 (tp30) REVERT: 7 506 MET cc_start: 0.6904 (mmt) cc_final: 0.6411 (mmm) outliers start: 0 outliers final: 0 residues processed: 494 average time/residue: 1.2350 time to fit residues: 1001.6574 Evaluate side-chains 411 residues out of total 5543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 411 time to evaluate : 6.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 628 random chunks: chunk 370 optimal weight: 0.9990 chunk 596 optimal weight: 8.9990 chunk 364 optimal weight: 1.9990 chunk 282 optimal weight: 5.9990 chunk 414 optimal weight: 0.7980 chunk 625 optimal weight: 10.0000 chunk 575 optimal weight: 2.9990 chunk 498 optimal weight: 0.5980 chunk 51 optimal weight: 0.8980 chunk 384 optimal weight: 0.3980 chunk 305 optimal weight: 4.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 320 ASN ** 4 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 632 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 570 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6759 moved from start: 0.5510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 54551 Z= 0.157 Angle : 0.550 6.602 74525 Z= 0.297 Chirality : 0.040 0.184 8550 Planarity : 0.004 0.075 8873 Dihedral : 16.457 146.702 8854 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.41 % Favored : 92.59 % Rotamer: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.88 (0.11), residues: 6088 helix: 0.11 (0.10), residues: 2570 sheet: -2.02 (0.17), residues: 802 loop : -2.36 (0.12), residues: 2716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 266 HIS 0.005 0.001 HIS A 416 PHE 0.020 0.001 PHE C 213 TYR 0.030 0.001 TYR B 473 ARG 0.014 0.000 ARG 7 666 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12176 Ramachandran restraints generated. 6088 Oldfield, 0 Emsley, 6088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12176 Ramachandran restraints generated. 6088 Oldfield, 0 Emsley, 6088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 486 is missing expected H atoms. Skipping. Residue THR 109 is missing expected H atoms. Skipping. Residue THR 44 is missing expected H atoms. Skipping. Evaluate side-chains 498 residues out of total 5543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 498 time to evaluate : 6.275 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: C 118 LEU cc_start: 0.5612 (tp) cc_final: 0.4580 (pt) REVERT: C 306 MET cc_start: 0.6577 (ttp) cc_final: 0.5229 (tmm) REVERT: C 585 MET cc_start: 0.7947 (ttt) cc_final: 0.7174 (ttt) REVERT: D 385 ASP cc_start: 0.7634 (p0) cc_final: 0.6425 (m-30) REVERT: E 109 VAL cc_start: 0.9215 (t) cc_final: 0.9013 (p) REVERT: E 450 TRP cc_start: 0.7022 (m100) cc_final: 0.6639 (m100) REVERT: F 48 MET cc_start: 0.2620 (ttt) cc_final: 0.1029 (mmt) REVERT: F 337 ARG cc_start: 0.8203 (mtm110) cc_final: 0.7916 (ttm-80) REVERT: F 389 PHE cc_start: 0.8162 (m-80) cc_final: 0.7930 (m-80) REVERT: F 418 TYR cc_start: 0.8221 (t80) cc_final: 0.7768 (t80) REVERT: 2 341 CYS cc_start: 0.8969 (m) cc_final: 0.7885 (t) REVERT: 2 612 MET cc_start: 0.7617 (mtm) cc_final: 0.7269 (mtm) REVERT: 3 264 MET cc_start: 0.7447 (mpp) cc_final: 0.7239 (mpp) REVERT: 3 723 LYS cc_start: 0.8819 (tttt) cc_final: 0.8422 (tttt) REVERT: 4 302 LYS cc_start: 0.6301 (tptt) cc_final: 0.6036 (tptp) REVERT: 4 414 SER cc_start: 0.7900 (m) cc_final: 0.7534 (t) REVERT: 4 755 LYS cc_start: 0.9130 (ttpt) cc_final: 0.8231 (tppt) REVERT: 5 65 MET cc_start: 0.7899 (mtm) cc_final: 0.7612 (tmm) REVERT: 5 105 SER cc_start: 0.8165 (m) cc_final: 0.7904 (p) REVERT: 5 270 MET cc_start: 0.8454 (mtt) cc_final: 0.7718 (mtt) REVERT: 5 338 GLU cc_start: 0.6858 (tt0) cc_final: 0.6201 (tm-30) REVERT: 5 393 MET cc_start: 0.8654 (mtp) cc_final: 0.7885 (mmm) REVERT: 5 478 CYS cc_start: 0.8489 (m) cc_final: 0.8184 (m) REVERT: 5 538 ASP cc_start: 0.6822 (m-30) cc_final: 0.6451 (t70) REVERT: 5 684 PHE cc_start: 0.7760 (t80) cc_final: 0.7127 (t80) REVERT: 6 808 GLU cc_start: 0.7708 (mm-30) cc_final: 0.7276 (tp30) REVERT: 7 506 MET cc_start: 0.6873 (mmt) cc_final: 0.6492 (mmm) outliers start: 0 outliers final: 0 residues processed: 498 average time/residue: 1.2247 time to fit residues: 1006.9696 Evaluate side-chains 412 residues out of total 5543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 412 time to evaluate : 6.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 628 random chunks: chunk 395 optimal weight: 6.9990 chunk 530 optimal weight: 0.6980 chunk 152 optimal weight: 9.9990 chunk 459 optimal weight: 4.9990 chunk 73 optimal weight: 5.9990 chunk 138 optimal weight: 7.9990 chunk 498 optimal weight: 4.9990 chunk 208 optimal weight: 2.9990 chunk 512 optimal weight: 10.0000 chunk 63 optimal weight: 9.9990 chunk 91 optimal weight: 3.9990 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 366 ASN ** 2 666 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 579 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 632 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 750 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.103573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.086650 restraints weight = 726011.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.088024 restraints weight = 438517.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.088490 restraints weight = 321977.921| |-----------------------------------------------------------------------------| r_work (final): 0.3848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7101 moved from start: 0.5774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 54551 Z= 0.318 Angle : 0.676 8.783 74525 Z= 0.373 Chirality : 0.043 0.173 8550 Planarity : 0.005 0.059 8873 Dihedral : 16.706 145.981 8854 Min Nonbonded Distance : 1.802 Molprobity Statistics. All-atom Clashscore : 18.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.93 % Favored : 88.07 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.50 (0.10), residues: 6088 helix: -0.45 (0.10), residues: 2578 sheet: -2.23 (0.17), residues: 778 loop : -2.69 (0.11), residues: 2732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 613 HIS 0.007 0.002 HIS C 65 PHE 0.032 0.002 PHE B 475 TYR 0.033 0.002 TYR B 473 ARG 0.008 0.001 ARG E 385 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 19998.81 seconds wall clock time: 349 minutes 3.18 seconds (20943.18 seconds total)