Starting phenix.real_space_refine (version: dev) on Mon Feb 27 22:12:32 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nvn_12607/02_2023/7nvn_12607_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nvn_12607/02_2023/7nvn_12607.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nvn_12607/02_2023/7nvn_12607.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nvn_12607/02_2023/7nvn_12607.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nvn_12607/02_2023/7nvn_12607_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nvn_12607/02_2023/7nvn_12607_updated.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.007 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 Process input model Symmetric amino acids flipped Residue "A GLU 2": "OE1" <-> "OE2" Residue "A ARG 11": "NH1" <-> "NH2" Residue "A GLU 66": "OE1" <-> "OE2" Residue "A GLU 77": "OE1" <-> "OE2" Residue "A ARG 145": "NH1" <-> "NH2" Residue "A ARG 185": "NH1" <-> "NH2" Residue "A ARG 189": "NH1" <-> "NH2" Residue "A ARG 203": "NH1" <-> "NH2" Residue "A ARG 228": "NH1" <-> "NH2" Residue "A ARG 264": "NH1" <-> "NH2" Residue "A ARG 314": "NH1" <-> "NH2" Residue "A GLU 337": "OE1" <-> "OE2" Residue "A GLU 349": "OE1" <-> "OE2" Residue "A GLU 354": "OE1" <-> "OE2" Residue "A ARG 355": "NH1" <-> "NH2" Residue "A ARG 370": "NH1" <-> "NH2" Residue "A ARG 443": "NH1" <-> "NH2" Residue "A GLU 479": "OE1" <-> "OE2" Residue "A ARG 480": "NH1" <-> "NH2" Residue "A ARG 496": "NH1" <-> "NH2" Residue "B ARG 20": "NH1" <-> "NH2" Residue "B GLU 139": "OE1" <-> "OE2" Residue "B ARG 255": "NH1" <-> "NH2" Residue "B ARG 257": "NH1" <-> "NH2" Residue "B GLU 280": "OE1" <-> "OE2" Residue "B ARG 281": "NH1" <-> "NH2" Residue "B GLU 356": "OE1" <-> "OE2" Residue "B ARG 388": "NH1" <-> "NH2" Residue "B ARG 405": "NH1" <-> "NH2" Residue "B ARG 427": "NH1" <-> "NH2" Residue "B GLU 437": "OE1" <-> "OE2" Residue "B ARG 444": "NH1" <-> "NH2" Residue "B ARG 481": "NH1" <-> "NH2" Residue "D ARG 27": "NH1" <-> "NH2" Residue "D ARG 49": "NH1" <-> "NH2" Residue "D ARG 89": "NH1" <-> "NH2" Residue "D GLU 93": "OE1" <-> "OE2" Residue "D GLU 142": "OE1" <-> "OE2" Residue "D ARG 153": "NH1" <-> "NH2" Residue "D ARG 206": "NH1" <-> "NH2" Residue "D GLU 225": "OE1" <-> "OE2" Residue "D GLU 242": "OE1" <-> "OE2" Residue "D ARG 274": "NH1" <-> "NH2" Residue "D ARG 277": "NH1" <-> "NH2" Residue "D ARG 280": "NH1" <-> "NH2" Residue "D ARG 306": "NH1" <-> "NH2" Residue "D GLU 329": "OE1" <-> "OE2" Residue "D GLU 360": "OE1" <-> "OE2" Residue "D GLU 429": "OE1" <-> "OE2" Residue "D GLU 431": "OE1" <-> "OE2" Residue "D ARG 452": "NH1" <-> "NH2" Residue "D ARG 483": "NH1" <-> "NH2" Residue "D GLU 505": "OE1" <-> "OE2" Residue "D ARG 527": "NH1" <-> "NH2" Residue "E ARG 24": "NH1" <-> "NH2" Residue "E ARG 49": "NH1" <-> "NH2" Residue "E GLU 121": "OE1" <-> "OE2" Residue "E ARG 126": "NH1" <-> "NH2" Residue "E ARG 132": "NH1" <-> "NH2" Residue "E GLU 138": "OE1" <-> "OE2" Residue "E ARG 142": "NH1" <-> "NH2" Residue "E GLU 146": "OE1" <-> "OE2" Residue "E ARG 183": "NH1" <-> "NH2" Residue "E ARG 202": "NH1" <-> "NH2" Residue "E ARG 218": "NH1" <-> "NH2" Residue "E GLU 220": "OE1" <-> "OE2" Residue "E GLU 256": "OE1" <-> "OE2" Residue "E GLU 287": "OE1" <-> "OE2" Residue "E GLU 294": "OE1" <-> "OE2" Residue "E ARG 381": "NH1" <-> "NH2" Residue "E ARG 410": "NH1" <-> "NH2" Residue "E ARG 414": "NH1" <-> "NH2" Residue "E ARG 417": "NH1" <-> "NH2" Residue "E GLU 436": "OE1" <-> "OE2" Residue "E GLU 476": "OE1" <-> "OE2" Residue "E ARG 478": "NH1" <-> "NH2" Residue "E ARG 480": "NH1" <-> "NH2" Residue "E GLU 538": "OE1" <-> "OE2" Residue "G ARG 85": "NH1" <-> "NH2" Residue "G GLU 110": "OE1" <-> "OE2" Residue "G ARG 127": "NH1" <-> "NH2" Residue "G ARG 167": "NH1" <-> "NH2" Residue "G ARG 190": "NH1" <-> "NH2" Residue "G GLU 192": "OE1" <-> "OE2" Residue "G ARG 216": "NH1" <-> "NH2" Residue "G ARG 228": "NH1" <-> "NH2" Residue "G ARG 230": "NH1" <-> "NH2" Residue "G ARG 260": "NH1" <-> "NH2" Residue "G GLU 280": "OE1" <-> "OE2" Residue "G GLU 293": "OE1" <-> "OE2" Residue "G ARG 306": "NH1" <-> "NH2" Residue "G ARG 313": "NH1" <-> "NH2" Residue "G ARG 316": "NH1" <-> "NH2" Residue "G ARG 330": "NH1" <-> "NH2" Residue "G GLU 337": "OE1" <-> "OE2" Residue "G ARG 339": "NH1" <-> "NH2" Residue "G GLU 358": "OE1" <-> "OE2" Residue "G ARG 438": "NH1" <-> "NH2" Residue "G GLU 445": "OE1" <-> "OE2" Residue "G GLU 492": "OE1" <-> "OE2" Residue "G GLU 497": "OE1" <-> "OE2" Residue "H GLU 34": "OE1" <-> "OE2" Residue "H ARG 37": "NH1" <-> "NH2" Residue "H ARG 43": "NH1" <-> "NH2" Residue "H ARG 53": "NH1" <-> "NH2" Residue "H GLU 114": "OE1" <-> "OE2" Residue "H ARG 123": "NH1" <-> "NH2" Residue "H GLU 243": "OE1" <-> "OE2" Residue "H GLU 249": "OE1" <-> "OE2" Residue "H ARG 256": "NH1" <-> "NH2" Residue "H GLU 261": "OE1" <-> "OE2" Residue "H ARG 306": "NH1" <-> "NH2" Residue "H GLU 316": "OE1" <-> "OE2" Residue "H ARG 344": "NH1" <-> "NH2" Residue "H GLU 379": "OE1" <-> "OE2" Residue "H GLU 386": "OE1" <-> "OE2" Residue "H ARG 397": "NH1" <-> "NH2" Residue "H ARG 425": "NH1" <-> "NH2" Residue "H GLU 443": "OE1" <-> "OE2" Residue "H ARG 467": "NH1" <-> "NH2" Residue "H ARG 499": "NH1" <-> "NH2" Residue "H ARG 524": "NH1" <-> "NH2" Residue "N ARG 38": "NH1" <-> "NH2" Residue "N ARG 45": "NH1" <-> "NH2" Residue "N GLU 46": "OE1" <-> "OE2" Residue "N ARG 53": "NH1" <-> "NH2" Residue "N ARG 103": "NH1" <-> "NH2" Residue "Q GLU 17": "OE1" <-> "OE2" Residue "Q ARG 31": "NH1" <-> "NH2" Residue "Q GLU 38": "OE1" <-> "OE2" Residue "Q ARG 44": "NH1" <-> "NH2" Residue "Q GLU 75": "OE1" <-> "OE2" Residue "Q GLU 77": "OE1" <-> "OE2" Residue "Q GLU 113": "OE1" <-> "OE2" Residue "Q GLU 117": "OE1" <-> "OE2" Residue "Q ARG 120": "NH1" <-> "NH2" Residue "Q GLU 133": "OE1" <-> "OE2" Residue "Q ARG 137": "NH1" <-> "NH2" Residue "Q ARG 155": "NH1" <-> "NH2" Residue "Q ARG 165": "NH1" <-> "NH2" Residue "Q GLU 226": "OE1" <-> "OE2" Residue "Q GLU 252": "OE1" <-> "OE2" Residue "Q GLU 263": "OE1" <-> "OE2" Residue "Q GLU 273": "OE1" <-> "OE2" Residue "Q ARG 314": "NH1" <-> "NH2" Residue "Q ARG 322": "NH1" <-> "NH2" Residue "Q GLU 342": "OE1" <-> "OE2" Residue "Q GLU 354": "OE1" <-> "OE2" Residue "Q ARG 404": "NH1" <-> "NH2" Residue "Q ARG 407": "NH1" <-> "NH2" Residue "Q GLU 473": "OE1" <-> "OE2" Residue "Q GLU 483": "OE1" <-> "OE2" Residue "Q GLU 485": "OE1" <-> "OE2" Residue "Q ARG 520": "NH1" <-> "NH2" Residue "Z ARG 28": "NH1" <-> "NH2" Residue "Z ARG 35": "NH1" <-> "NH2" Residue "Z GLU 66": "OE1" <-> "OE2" Residue "Z GLU 112": "OE1" <-> "OE2" Residue "Z GLU 121": "OE1" <-> "OE2" Residue "Z GLU 135": "OE1" <-> "OE2" Residue "Z GLU 136": "OE1" <-> "OE2" Residue "Z ARG 141": "NH1" <-> "NH2" Residue "Z ARG 145": "NH1" <-> "NH2" Residue "Z ARG 157": "NH1" <-> "NH2" Residue "Z GLU 192": "OE1" <-> "OE2" Residue "Z GLU 195": "OE1" <-> "OE2" Residue "Z GLU 201": "OE1" <-> "OE2" Residue "Z ARG 208": "NH1" <-> "NH2" Residue "Z GLU 226": "OE1" <-> "OE2" Residue "Z GLU 257": "OE1" <-> "OE2" Residue "Z ARG 270": "NH1" <-> "NH2" Residue "Z GLU 276": "OE1" <-> "OE2" Residue "Z ARG 279": "NH1" <-> "NH2" Residue "Z ARG 318": "NH1" <-> "NH2" Residue "Z ARG 323": "NH1" <-> "NH2" Residue "Z GLU 358": "OE1" <-> "OE2" Residue "Z ARG 370": "NH1" <-> "NH2" Residue "Z GLU 415": "OE1" <-> "OE2" Residue "Z GLU 420": "OE1" <-> "OE2" Residue "Z ARG 432": "NH1" <-> "NH2" Residue "Z GLU 469": "OE1" <-> "OE2" Residue "Z GLU 485": "OE1" <-> "OE2" Residue "a ARG 11": "NH1" <-> "NH2" Residue "a GLU 15": "OE1" <-> "OE2" Residue "a GLU 77": "OE1" <-> "OE2" Residue "a GLU 106": "OE1" <-> "OE2" Residue "a ARG 145": "NH1" <-> "NH2" Residue "a ARG 185": "NH1" <-> "NH2" Residue "a ARG 189": "NH1" <-> "NH2" Residue "a ARG 203": "NH1" <-> "NH2" Residue "a ARG 228": "NH1" <-> "NH2" Residue "a ARG 264": "NH1" <-> "NH2" Residue "a ARG 314": "NH1" <-> "NH2" Residue "a GLU 341": "OE1" <-> "OE2" Residue "a GLU 349": "OE1" <-> "OE2" Residue "a ARG 355": "NH1" <-> "NH2" Residue "a ARG 370": "NH1" <-> "NH2" Residue "a ARG 443": "NH1" <-> "NH2" Residue "a ARG 480": "NH1" <-> "NH2" Residue "a ARG 496": "NH1" <-> "NH2" Residue "a GLU 505": "OE1" <-> "OE2" Residue "a GLU 536": "OE1" <-> "OE2" Residue "b ARG 20": "NH1" <-> "NH2" Residue "b GLU 197": "OE1" <-> "OE2" Residue "b ARG 255": "NH1" <-> "NH2" Residue "b ARG 257": "NH1" <-> "NH2" Residue "b GLU 280": "OE1" <-> "OE2" Residue "b ARG 281": "NH1" <-> "NH2" Residue "b GLU 387": "OE1" <-> "OE2" Residue "b ARG 388": "NH1" <-> "NH2" Residue "b ARG 405": "NH1" <-> "NH2" Residue "b ARG 427": "NH1" <-> "NH2" Residue "b GLU 437": "OE1" <-> "OE2" Residue "b ARG 444": "NH1" <-> "NH2" Residue "b GLU 471": "OE1" <-> "OE2" Residue "b ARG 481": "NH1" <-> "NH2" Residue "d ARG 27": "NH1" <-> "NH2" Residue "d ARG 49": "NH1" <-> "NH2" Residue "d ARG 89": "NH1" <-> "NH2" Residue "d GLU 93": "OE1" <-> "OE2" Residue "d GLU 142": "OE1" <-> "OE2" Residue "d ARG 153": "NH1" <-> "NH2" Residue "d ARG 206": "NH1" <-> "NH2" Residue "d ARG 274": "NH1" <-> "NH2" Residue "d ARG 277": "NH1" <-> "NH2" Residue "d ARG 280": "NH1" <-> "NH2" Residue "d ARG 306": "NH1" <-> "NH2" Residue "d GLU 329": "OE1" <-> "OE2" Residue "d GLU 363": "OE1" <-> "OE2" Residue "d GLU 429": "OE1" <-> "OE2" Residue "d GLU 431": "OE1" <-> "OE2" Residue "d GLU 447": "OE1" <-> "OE2" Residue "d ARG 452": "NH1" <-> "NH2" Residue "d GLU 467": "OE1" <-> "OE2" Residue "d ARG 483": "NH1" <-> "NH2" Residue "d ARG 527": "NH1" <-> "NH2" Residue "d ARG 539": "NH1" <-> "NH2" Residue "e ARG 24": "NH1" <-> "NH2" Residue "e GLU 32": "OE1" <-> "OE2" Residue "e ARG 49": "NH1" <-> "NH2" Residue "e GLU 121": "OE1" <-> "OE2" Residue "e ARG 126": "NH1" <-> "NH2" Residue "e ARG 132": "NH1" <-> "NH2" Residue "e GLU 138": "OE1" <-> "OE2" Residue "e ARG 142": "NH1" <-> "NH2" Residue "e GLU 146": "OE1" <-> "OE2" Residue "e GLU 163": "OE1" <-> "OE2" Residue "e ARG 183": "NH1" <-> "NH2" Residue "e ARG 202": "NH1" <-> "NH2" Residue "e ARG 218": "NH1" <-> "NH2" Residue "e GLU 256": "OE1" <-> "OE2" Residue "e GLU 287": "OE1" <-> "OE2" Residue "e GLU 294": "OE1" <-> "OE2" Residue "e ARG 381": "NH1" <-> "NH2" Residue "e ARG 410": "NH1" <-> "NH2" Residue "e ARG 414": "NH1" <-> "NH2" Residue "e ARG 417": "NH1" <-> "NH2" Residue "e GLU 436": "OE1" <-> "OE2" Residue "e GLU 464": "OE1" <-> "OE2" Residue "e GLU 476": "OE1" <-> "OE2" Residue "e ARG 478": "NH1" <-> "NH2" Residue "e ARG 480": "NH1" <-> "NH2" Residue "g ARG 85": "NH1" <-> "NH2" Residue "g ARG 127": "NH1" <-> "NH2" Residue "g ARG 167": "NH1" <-> "NH2" Residue "g ARG 190": "NH1" <-> "NH2" Residue "g ARG 216": "NH1" <-> "NH2" Residue "g ARG 228": "NH1" <-> "NH2" Residue "g ARG 230": "NH1" <-> "NH2" Residue "g ARG 260": "NH1" <-> "NH2" Residue "g GLU 293": "OE1" <-> "OE2" Residue "g ARG 306": "NH1" <-> "NH2" Residue "g ARG 313": "NH1" <-> "NH2" Residue "g ARG 316": "NH1" <-> "NH2" Residue "g ARG 330": "NH1" <-> "NH2" Residue "g ARG 339": "NH1" <-> "NH2" Residue "g GLU 358": "OE1" <-> "OE2" Residue "g ARG 438": "NH1" <-> "NH2" Residue "g GLU 445": "OE1" <-> "OE2" Residue "g GLU 473": "OE1" <-> "OE2" Residue "g GLU 497": "OE1" <-> "OE2" Residue "h ARG 37": "NH1" <-> "NH2" Residue "h ARG 43": "NH1" <-> "NH2" Residue "h ARG 53": "NH1" <-> "NH2" Residue "h GLU 114": "OE1" <-> "OE2" Residue "h ARG 123": "NH1" <-> "NH2" Residue "h GLU 243": "OE1" <-> "OE2" Residue "h ARG 256": "NH1" <-> "NH2" Residue "h GLU 279": "OE1" <-> "OE2" Residue "h ARG 306": "NH1" <-> "NH2" Residue "h GLU 317": "OE1" <-> "OE2" Residue "h ARG 344": "NH1" <-> "NH2" Residue "h GLU 386": "OE1" <-> "OE2" Residue "h ARG 397": "NH1" <-> "NH2" Residue "h ARG 425": "NH1" <-> "NH2" Residue "h GLU 443": "OE1" <-> "OE2" Residue "h ARG 467": "NH1" <-> "NH2" Residue "h GLU 489": "OE1" <-> "OE2" Residue "h ARG 499": "NH1" <-> "NH2" Residue "h ARG 524": "NH1" <-> "NH2" Residue "n GLU 6": "OE1" <-> "OE2" Residue "n ARG 38": "NH1" <-> "NH2" Residue "n ARG 45": "NH1" <-> "NH2" Residue "n GLU 46": "OE1" <-> "OE2" Residue "n ARG 53": "NH1" <-> "NH2" Residue "n ARG 103": "NH1" <-> "NH2" Residue "q GLU 26": "OE1" <-> "OE2" Residue "q ARG 31": "NH1" <-> "NH2" Residue "q ARG 44": "NH1" <-> "NH2" Residue "q GLU 61": "OE1" <-> "OE2" Residue "q GLU 77": "OE1" <-> "OE2" Residue "q GLU 94": "OE1" <-> "OE2" Residue "q GLU 117": "OE1" <-> "OE2" Residue "q ARG 120": "NH1" <-> "NH2" Residue "q GLU 133": "OE1" <-> "OE2" Residue "q ARG 137": "NH1" <-> "NH2" Residue "q ARG 155": "NH1" <-> "NH2" Residue "q ARG 165": "NH1" <-> "NH2" Residue "q PHE 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q GLU 263": "OE1" <-> "OE2" Residue "q ARG 314": "NH1" <-> "NH2" Residue "q ARG 322": "NH1" <-> "NH2" Residue "q GLU 368": "OE1" <-> "OE2" Residue "q ARG 404": "NH1" <-> "NH2" Residue "q ARG 407": "NH1" <-> "NH2" Residue "q GLU 443": "OE1" <-> "OE2" Residue "q GLU 473": "OE1" <-> "OE2" Residue "q GLU 494": "OE1" <-> "OE2" Residue "q ARG 520": "NH1" <-> "NH2" Residue "z ARG 28": "NH1" <-> "NH2" Residue "z ARG 35": "NH1" <-> "NH2" Residue "z GLU 112": "OE1" <-> "OE2" Residue "z GLU 136": "OE1" <-> "OE2" Residue "z ARG 141": "NH1" <-> "NH2" Residue "z ARG 145": "NH1" <-> "NH2" Residue "z ARG 157": "NH1" <-> "NH2" Residue "z ARG 208": "NH1" <-> "NH2" Residue "z GLU 226": "OE1" <-> "OE2" Residue "z GLU 240": "OE1" <-> "OE2" Residue "z ARG 270": "NH1" <-> "NH2" Residue "z GLU 276": "OE1" <-> "OE2" Residue "z ARG 279": "NH1" <-> "NH2" Residue "z ARG 318": "NH1" <-> "NH2" Residue "z ARG 323": "NH1" <-> "NH2" Residue "z GLU 357": "OE1" <-> "OE2" Residue "z GLU 358": "OE1" <-> "OE2" Residue "z ARG 370": "NH1" <-> "NH2" Residue "z GLU 420": "OE1" <-> "OE2" Residue "z ARG 432": "NH1" <-> "NH2" Residue "z GLU 472": "OE1" <-> "OE2" Residue "z GLU 485": "OE1" <-> "OE2" Residue "z GLU 491": "OE1" <-> "OE2" Residue "T ARG 2": "NH1" <-> "NH2" Residue "T GLU 53": "OE1" <-> "OE2" Residue "T GLU 108": "OE1" <-> "OE2" Residue "T GLU 123": "OE1" <-> "OE2" Residue "T GLU 158": "OE1" <-> "OE2" Residue "T ARG 162": "NH1" <-> "NH2" Residue "T GLU 205": "OE1" <-> "OE2" Residue "T GLU 405": "OE1" <-> "OE2" Residue "T GLU 412": "OE1" <-> "OE2" Residue "T GLU 421": "OE1" <-> "OE2" Time to flip residues: 0.17s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 69139 Number of models: 1 Model: "" Number of chains: 51 Chain: "A" Number of atoms: 4063 Number of conformers: 1 Conformer: "" Number of residues, atoms: 535, 4063 Classifications: {'peptide': 535} Link IDs: {'PTRANS': 14, 'TRANS': 520} Chain: "B" Number of atoms: 3952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 526, 3952 Classifications: {'peptide': 526} Link IDs: {'PTRANS': 10, 'TRANS': 515} Chain: "D" Number of atoms: 3919 Number of conformers: 1 Conformer: "" Number of residues, atoms: 519, 3919 Classifications: {'peptide': 519} Link IDs: {'PTRANS': 14, 'TRANS': 504} Chain: "E" Number of atoms: 4142 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 537, 4134 Classifications: {'peptide': 537} Link IDs: {'PTRANS': 18, 'TRANS': 518} Conformer: "B" Number of residues, atoms: 537, 4134 Classifications: {'peptide': 537} Link IDs: {'PTRANS': 18, 'TRANS': 518} bond proxies already assigned to first conformer: 4174 Chain: "G" Number of atoms: 4064 Number of conformers: 1 Conformer: "" Number of residues, atoms: 523, 4064 Classifications: {'peptide': 523} Link IDs: {'PTRANS': 16, 'TRANS': 506} Chain: "H" Number of atoms: 4026 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 4026 Classifications: {'peptide': 524} Link IDs: {'PTRANS': 16, 'TRANS': 507} Chain: "N" Number of atoms: 859 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 859 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 1, 'TRANS': 107} Chain breaks: 2 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "Q" Number of atoms: 4033 Number of conformers: 1 Conformer: "" Number of residues, atoms: 530, 4033 Classifications: {'peptide': 530} Link IDs: {'PTRANS': 15, 'TRANS': 514} Chain: "Z" Number of atoms: 4051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 529, 4051 Classifications: {'peptide': 529} Link IDs: {'PTRANS': 14, 'TRANS': 514} Chain: "a" Number of atoms: 4071 Number of conformers: 1 Conformer: "" Number of residues, atoms: 536, 4071 Classifications: {'peptide': 536} Link IDs: {'PTRANS': 14, 'TRANS': 521} Chain: "b" Number of atoms: 3960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 3960 Classifications: {'peptide': 527} Link IDs: {'PTRANS': 10, 'TRANS': 516} Chain: "d" Number of atoms: 3919 Number of conformers: 1 Conformer: "" Number of residues, atoms: 519, 3919 Classifications: {'peptide': 519} Link IDs: {'PTRANS': 14, 'TRANS': 504} Chain: "e" Number of atoms: 4148 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 538, 4140 Classifications: {'peptide': 538} Link IDs: {'PTRANS': 18, 'TRANS': 519} Conformer: "B" Number of residues, atoms: 538, 4140 Classifications: {'peptide': 538} Link IDs: {'PTRANS': 18, 'TRANS': 519} bond proxies already assigned to first conformer: 4180 Chain: "g" Number of atoms: 4064 Number of conformers: 1 Conformer: "" Number of residues, atoms: 523, 4064 Classifications: {'peptide': 523} Link IDs: {'PTRANS': 16, 'TRANS': 506} Chain: "h" Number of atoms: 4026 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 4026 Classifications: {'peptide': 524} Link IDs: {'PTRANS': 16, 'TRANS': 507} Chain: "n" Number of atoms: 854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 854 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 1, 'TRANS': 107} Chain breaks: 2 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "q" Number of atoms: 4029 Number of conformers: 1 Conformer: "" Number of residues, atoms: 529, 4029 Classifications: {'peptide': 529} Link IDs: {'PTRANS': 15, 'TRANS': 513} Chain: "z" Number of atoms: 4028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 526, 4028 Classifications: {'peptide': 526} Link IDs: {'PTRANS': 14, 'TRANS': 511} Chain: "T" Number of atoms: 2400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2400 Classifications: {'peptide': 307} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 12, 'TRANS': 294} Chain breaks: 3 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "H" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "Q" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "Z" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "a" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "b" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "d" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "e" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "g" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "h" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "q" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "z" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "Q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "Z" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "a" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "b" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "d" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "e" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "g" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "h" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "z" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 30.93, per 1000 atoms: 0.45 Number of scatterers: 69139 At special positions: 0 Unit cell: (186.56, 171.72, 187.62, 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) S 424 16.00 P 32 15.00 Al 16 13.00 Mg 16 11.99 F 48 9.00 O 13376 8.00 N 12027 7.00 C 43200 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 95 " distance=2.03 Simple disulfide: pdb=" SG CYS n 22 " - pdb=" SG CYS n 95 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Atom "HETATM68982 O3A ADP e 601 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 23.04 Conformation dependent library (CDL) restraints added in 8.9 seconds 17840 Ramachandran restraints generated. 8920 Oldfield, 0 Emsley, 8920 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 16700 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 324 helices and 112 sheets defined 50.1% alpha, 11.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.32 Creating SS restraints... Processing helix chain 'A' and resid 15 through 35 removed outlier: 3.586A pdb=" N VAL A 32 " --> pdb=" O ILE A 28 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N SER A 34 " --> pdb=" O ASN A 30 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N SER A 35 " --> pdb=" O ILE A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 64 Processing helix chain 'A' and resid 70 through 85 removed outlier: 3.979A pdb=" N LEU A 75 " --> pdb=" O ALA A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 109 removed outlier: 3.881A pdb=" N VAL A 94 " --> pdb=" O THR A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 135 Processing helix chain 'A' and resid 140 through 143 No H-bonds generated for 'chain 'A' and resid 140 through 143' Processing helix chain 'A' and resid 145 through 156 Processing helix chain 'A' and resid 163 through 179 removed outlier: 3.821A pdb=" N ASP A 166 " --> pdb=" O ILE A 163 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N ALA A 169 " --> pdb=" O ASP A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 207 No H-bonds generated for 'chain 'A' and resid 205 through 207' Processing helix chain 'A' and resid 257 through 281 removed outlier: 4.501A pdb=" N ASP A 261 " --> pdb=" O GLU A 258 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N ILE A 270 " --> pdb=" O GLU A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 303 removed outlier: 3.593A pdb=" N TYR A 299 " --> pdb=" O MET A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 323 Processing helix chain 'A' and resid 342 through 344 No H-bonds generated for 'chain 'A' and resid 342 through 344' Processing helix chain 'A' and resid 382 through 404 Processing helix chain 'A' and resid 414 through 429 removed outlier: 4.705A pdb=" N THR A 428 " --> pdb=" O GLU A 424 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N SER A 429 " --> pdb=" O ASN A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 456 removed outlier: 3.751A pdb=" N LEU A 446 " --> pdb=" O ALA A 442 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N VAL A 447 " --> pdb=" O ARG A 443 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N ILE A 448 " --> pdb=" O SER A 444 " (cutoff:3.500A) Proline residue: A 449 - end of helix Processing helix chain 'A' and resid 460 through 476 Processing helix chain 'A' and resid 478 through 485 removed outlier: 3.958A pdb=" N LYS A 481 " --> pdb=" O PRO A 478 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N ASN A 482 " --> pdb=" O GLU A 479 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TRP A 485 " --> pdb=" O ASN A 482 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 501 No H-bonds generated for 'chain 'A' and resid 498 through 501' Processing helix chain 'A' and resid 507 through 525 Processing helix chain 'B' and resid 21 through 39 Processing helix chain 'B' and resid 67 through 72 Processing helix chain 'B' and resid 79 through 94 Processing helix chain 'B' and resid 99 through 118 removed outlier: 3.964A pdb=" N THR B 103 " --> pdb=" O THR B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 144 Processing helix chain 'B' and resid 152 through 168 Processing helix chain 'B' and resid 171 through 190 removed outlier: 3.806A pdb=" N HIS B 174 " --> pdb=" O LEU B 171 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LYS B 176 " --> pdb=" O THR B 173 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N ASP B 177 " --> pdb=" O HIS B 174 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N THR B 180 " --> pdb=" O ASP B 177 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ARG B 189 " --> pdb=" O ALA B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 196 through 198 No H-bonds generated for 'chain 'B' and resid 196 through 198' Processing helix chain 'B' and resid 209 through 211 No H-bonds generated for 'chain 'B' and resid 209 through 211' Processing helix chain 'B' and resid 261 through 285 removed outlier: 3.855A pdb=" N HIS B 285 " --> pdb=" O ARG B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 307 Processing helix chain 'B' and resid 317 through 327 Processing helix chain 'B' and resid 338 through 340 No H-bonds generated for 'chain 'B' and resid 338 through 340' Processing helix chain 'B' and resid 380 through 402 Processing helix chain 'B' and resid 412 through 427 Processing helix chain 'B' and resid 431 through 454 removed outlier: 3.608A pdb=" N SER B 438 " --> pdb=" O VAL B 434 " (cutoff:3.500A) Proline residue: B 447 - end of helix removed outlier: 3.665A pdb=" N ALA B 454 " --> pdb=" O ILE B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 458 through 471 Processing helix chain 'B' and resid 488 through 491 No H-bonds generated for 'chain 'B' and resid 488 through 491' Processing helix chain 'B' and resid 497 through 515 Processing helix chain 'D' and resid 29 through 51 removed outlier: 4.829A pdb=" N THR D 50 " --> pdb=" O ASP D 46 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N SER D 51 " --> pdb=" O ALA D 47 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 80 Processing helix chain 'D' and resid 86 through 101 Processing helix chain 'D' and resid 106 through 126 removed outlier: 4.003A pdb=" N VAL D 110 " --> pdb=" O THR D 106 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N LYS D 122 " --> pdb=" O ASP D 118 " (cutoff:3.500A) Processing helix chain 'D' and resid 130 through 151 Processing helix chain 'D' and resid 160 through 172 Processing helix chain 'D' and resid 180 through 193 Proline residue: D 185 - end of helix removed outlier: 3.779A pdb=" N VAL D 191 " --> pdb=" O SER D 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 205 through 207 No H-bonds generated for 'chain 'D' and resid 205 through 207' Processing helix chain 'D' and resid 218 through 220 No H-bonds generated for 'chain 'D' and resid 218 through 220' Processing helix chain 'D' and resid 269 through 293 removed outlier: 3.938A pdb=" N ASP D 273 " --> pdb=" O TYR D 269 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N THR D 293 " --> pdb=" O GLN D 289 " (cutoff:3.500A) Processing helix chain 'D' and resid 311 through 319 Processing helix chain 'D' and resid 333 through 340 Processing helix chain 'D' and resid 348 through 350 No H-bonds generated for 'chain 'D' and resid 348 through 350' Processing helix chain 'D' and resid 353 through 355 No H-bonds generated for 'chain 'D' and resid 353 through 355' Processing helix chain 'D' and resid 395 through 417 Processing helix chain 'D' and resid 427 through 442 Processing helix chain 'D' and resid 447 through 469 removed outlier: 4.059A pdb=" N VAL D 460 " --> pdb=" O ASP D 456 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N ILE D 461 " --> pdb=" O ALA D 457 " (cutoff:3.500A) Proline residue: D 462 - end of helix Processing helix chain 'D' and resid 473 through 486 Processing helix chain 'D' and resid 503 through 506 No H-bonds generated for 'chain 'D' and resid 503 through 506' Processing helix chain 'D' and resid 512 through 530 Processing helix chain 'E' and resid 31 through 51 removed outlier: 4.480A pdb=" N THR E 50 " --> pdb=" O ASN E 46 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N SER E 51 " --> pdb=" O THR E 47 " (cutoff:3.500A) Processing helix chain 'E' and resid 74 through 80 Processing helix chain 'E' and resid 86 through 101 Processing helix chain 'E' and resid 108 through 125 removed outlier: 3.724A pdb=" N GLN E 122 " --> pdb=" O GLU E 118 " (cutoff:3.500A) Processing helix chain 'E' and resid 130 through 151 Processing helix chain 'E' and resid 163 through 175 removed outlier: 4.695A pdb=" N SER E 175 " --> pdb=" O THR E 171 " (cutoff:3.500A) Processing helix chain 'E' and resid 177 through 195 removed outlier: 3.815A pdb=" N SER E 180 " --> pdb=" O VAL E 177 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N ARG E 183 " --> pdb=" O SER E 180 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ASN E 191 " --> pdb=" O ILE E 188 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU E 194 " --> pdb=" O ASN E 191 " (cutoff:3.500A) Processing helix chain 'E' and resid 206 through 208 No H-bonds generated for 'chain 'E' and resid 206 through 208' Processing helix chain 'E' and resid 219 through 221 No H-bonds generated for 'chain 'E' and resid 219 through 221' Processing helix chain 'E' and resid 271 through 294 Processing helix chain 'E' and resid 308 through 316 Processing helix chain 'E' and resid 327 through 337 Processing helix chain 'E' and resid 345 through 347 No H-bonds generated for 'chain 'E' and resid 345 through 347' Processing helix chain 'E' and resid 392 through 414 Processing helix chain 'E' and resid 424 through 439 Processing helix chain 'E' and resid 443 through 465 removed outlier: 3.656A pdb=" N TYR E 446 " --> pdb=" O LEU E 443 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLU E 456 " --> pdb=" O ASP E 453 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ILE E 458 " --> pdb=" O LEU E 455 " (cutoff:3.500A) Proline residue: E 459 - end of helix Processing helix chain 'E' and resid 470 through 483 Processing helix chain 'E' and resid 501 through 504 No H-bonds generated for 'chain 'E' and resid 501 through 504' Processing helix chain 'E' and resid 510 through 528 Processing helix chain 'G' and resid 20 through 40 removed outlier: 3.783A pdb=" N ILE G 37 " --> pdb=" O ILE G 33 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N THR G 39 " --> pdb=" O ASP G 35 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N CYS G 40 " --> pdb=" O ILE G 36 " (cutoff:3.500A) Processing helix chain 'G' and resid 63 through 69 Processing helix chain 'G' and resid 75 through 90 Processing helix chain 'G' and resid 97 through 114 removed outlier: 3.795A pdb=" N HIS G 111 " --> pdb=" O SER G 107 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N PHE G 112 " --> pdb=" O VAL G 108 " (cutoff:3.500A) Processing helix chain 'G' and resid 119 through 140 Processing helix chain 'G' and resid 149 through 160 Processing helix chain 'G' and resid 164 through 183 removed outlier: 3.620A pdb=" N ARG G 167 " --> pdb=" O ALA G 164 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N SER G 170 " --> pdb=" O ARG G 167 " (cutoff:3.500A) Processing helix chain 'G' and resid 209 through 211 No H-bonds generated for 'chain 'G' and resid 209 through 211' Processing helix chain 'G' and resid 262 through 285 removed outlier: 4.535A pdb=" N LEU G 285 " --> pdb=" O ASP G 281 " (cutoff:3.500A) Processing helix chain 'G' and resid 298 through 306 Processing helix chain 'G' and resid 317 through 327 Processing helix chain 'G' and resid 335 through 337 No H-bonds generated for 'chain 'G' and resid 335 through 337' Processing helix chain 'G' and resid 340 through 342 No H-bonds generated for 'chain 'G' and resid 340 through 342' Processing helix chain 'G' and resid 381 through 403 Processing helix chain 'G' and resid 413 through 428 removed outlier: 3.789A pdb=" N LYS G 427 " --> pdb=" O THR G 423 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N ALA G 428 " --> pdb=" O GLU G 424 " (cutoff:3.500A) Processing helix chain 'G' and resid 433 through 455 removed outlier: 4.119A pdb=" N GLU G 445 " --> pdb=" O ALA G 441 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N VAL G 446 " --> pdb=" O GLN G 442 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N ILE G 447 " --> pdb=" O ALA G 443 " (cutoff:3.500A) Proline residue: G 448 - end of helix Processing helix chain 'G' and resid 459 through 471 removed outlier: 3.503A pdb=" N THR G 471 " --> pdb=" O ARG G 467 " (cutoff:3.500A) Processing helix chain 'G' and resid 490 through 493 No H-bonds generated for 'chain 'G' and resid 490 through 493' Processing helix chain 'G' and resid 499 through 518 Processing helix chain 'H' and resid 19 through 39 removed outlier: 3.792A pdb=" N VAL H 36 " --> pdb=" O ILE H 32 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N THR H 38 " --> pdb=" O GLU H 34 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N THR H 39 " --> pdb=" O ALA H 35 " (cutoff:3.500A) Processing helix chain 'H' and resid 62 through 68 Processing helix chain 'H' and resid 77 through 89 Processing helix chain 'H' and resid 94 through 113 removed outlier: 3.600A pdb=" N THR H 98 " --> pdb=" O THR H 94 " (cutoff:3.500A) Proline residue: H 110 - end of helix Processing helix chain 'H' and resid 118 through 139 Processing helix chain 'H' and resid 148 through 163 Processing helix chain 'H' and resid 169 through 185 removed outlier: 6.124A pdb=" N ALA H 173 " --> pdb=" O GLN H 170 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N PHE H 175 " --> pdb=" O LYS H 172 " (cutoff:3.500A) Processing helix chain 'H' and resid 192 through 194 No H-bonds generated for 'chain 'H' and resid 192 through 194' Processing helix chain 'H' and resid 260 through 283 Processing helix chain 'H' and resid 297 through 305 Processing helix chain 'H' and resid 316 through 326 Processing helix chain 'H' and resid 379 through 401 Processing helix chain 'H' and resid 411 through 426 removed outlier: 3.912A pdb=" N THR H 426 " --> pdb=" O ASP H 422 " (cutoff:3.500A) Processing helix chain 'H' and resid 430 through 453 removed outlier: 3.617A pdb=" N LEU H 434 " --> pdb=" O LYS H 430 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLU H 443 " --> pdb=" O ALA H 439 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N ILE H 444 " --> pdb=" O LYS H 440 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N ILE H 445 " --> pdb=" O ALA H 441 " (cutoff:3.500A) Proline residue: H 446 - end of helix Processing helix chain 'H' and resid 457 through 469 Processing helix chain 'H' and resid 487 through 490 No H-bonds generated for 'chain 'H' and resid 487 through 490' Processing helix chain 'H' and resid 496 through 515 Processing helix chain 'N' and resid 87 through 89 No H-bonds generated for 'chain 'N' and resid 87 through 89' Processing helix chain 'Q' and resid 11 through 14 No H-bonds generated for 'chain 'Q' and resid 11 through 14' Processing helix chain 'Q' and resid 24 through 27 No H-bonds generated for 'chain 'Q' and resid 24 through 27' Processing helix chain 'Q' and resid 29 through 46 removed outlier: 4.511A pdb=" N THR Q 45 " --> pdb=" O GLN Q 41 " (cutoff:3.500A) removed outlier: 5.760A pdb=" N ALA Q 46 " --> pdb=" O THR Q 42 " (cutoff:3.500A) Processing helix chain 'Q' and resid 69 through 75 Processing helix chain 'Q' and resid 81 through 96 Processing helix chain 'Q' and resid 101 through 121 Processing helix chain 'Q' and resid 125 through 146 Proline residue: Q 144 - end of helix Processing helix chain 'Q' and resid 158 through 170 removed outlier: 4.559A pdb=" N THR Q 166 " --> pdb=" O SER Q 162 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N SER Q 167 " --> pdb=" O LEU Q 163 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N SER Q 170 " --> pdb=" O THR Q 166 " (cutoff:3.500A) Processing helix chain 'Q' and resid 177 through 189 Processing helix chain 'Q' and resid 199 through 201 No H-bonds generated for 'chain 'Q' and resid 199 through 201' Processing helix chain 'Q' and resid 212 through 214 No H-bonds generated for 'chain 'Q' and resid 212 through 214' Processing helix chain 'Q' and resid 262 through 285 removed outlier: 4.888A pdb=" N SER Q 269 " --> pdb=" O LEU Q 265 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N LYS Q 270 " --> pdb=" O MET Q 266 " (cutoff:3.500A) Processing helix chain 'Q' and resid 299 through 307 Processing helix chain 'Q' and resid 318 through 328 Processing helix chain 'Q' and resid 382 through 404 Processing helix chain 'Q' and resid 414 through 429 removed outlier: 3.610A pdb=" N THR Q 429 " --> pdb=" O SER Q 425 " (cutoff:3.500A) Processing helix chain 'Q' and resid 434 through 456 removed outlier: 3.742A pdb=" N PHE Q 445 " --> pdb=" O PHE Q 441 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N GLU Q 446 " --> pdb=" O ALA Q 442 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ALA Q 447 " --> pdb=" O GLU Q 443 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N ILE Q 448 " --> pdb=" O ALA Q 444 " (cutoff:3.500A) Proline residue: Q 449 - end of helix Processing helix chain 'Q' and resid 460 through 473 Processing helix chain 'Q' and resid 492 through 495 No H-bonds generated for 'chain 'Q' and resid 492 through 495' Processing helix chain 'Q' and resid 501 through 520 Processing helix chain 'Z' and resid 3 through 7 removed outlier: 3.752A pdb=" N LEU Z 7 " --> pdb=" O ALA Z 3 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 3 through 7' Processing helix chain 'Z' and resid 16 through 37 removed outlier: 4.964A pdb=" N THR Z 36 " --> pdb=" O ASP Z 32 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N ASN Z 37 " --> pdb=" O VAL Z 33 " (cutoff:3.500A) Processing helix chain 'Z' and resid 60 through 66 Processing helix chain 'Z' and resid 72 through 88 Processing helix chain 'Z' and resid 92 through 110 removed outlier: 3.811A pdb=" N TYR Z 109 " --> pdb=" O GLN Z 105 " (cutoff:3.500A) Processing helix chain 'Z' and resid 116 through 137 Processing helix chain 'Z' and resid 145 through 159 removed outlier: 4.068A pdb=" N THR Z 158 " --> pdb=" O THR Z 154 " (cutoff:3.500A) Processing helix chain 'Z' and resid 162 through 178 removed outlier: 4.028A pdb=" N GLU Z 170 " --> pdb=" O ASP Z 166 " (cutoff:3.500A) Processing helix chain 'Z' and resid 188 through 190 No H-bonds generated for 'chain 'Z' and resid 188 through 190' Processing helix chain 'Z' and resid 201 through 203 No H-bonds generated for 'chain 'Z' and resid 201 through 203' Processing helix chain 'Z' and resid 253 through 262 Processing helix chain 'Z' and resid 265 through 281 removed outlier: 3.747A pdb=" N ARG Z 270 " --> pdb=" O PHE Z 266 " (cutoff:3.500A) Processing helix chain 'Z' and resid 299 through 308 removed outlier: 3.644A pdb=" N GLU Z 308 " --> pdb=" O ALA Z 304 " (cutoff:3.500A) Processing helix chain 'Z' and resid 318 through 327 removed outlier: 4.144A pdb=" N GLU Z 322 " --> pdb=" O ARG Z 318 " (cutoff:3.500A) Processing helix chain 'Z' and resid 341 through 343 No H-bonds generated for 'chain 'Z' and resid 341 through 343' Processing helix chain 'Z' and resid 381 through 403 Processing helix chain 'Z' and resid 413 through 428 Proline residue: Z 427 - end of helix Processing helix chain 'Z' and resid 432 through 455 removed outlier: 3.655A pdb=" N LEU Z 445 " --> pdb=" O ASP Z 442 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ILE Z 447 " --> pdb=" O LEU Z 444 " (cutoff:3.500A) Proline residue: Z 448 - end of helix Processing helix chain 'Z' and resid 459 through 473 Processing helix chain 'Z' and resid 489 through 492 No H-bonds generated for 'chain 'Z' and resid 489 through 492' Processing helix chain 'Z' and resid 498 through 517 Processing helix chain 'a' and resid 15 through 35 removed outlier: 3.622A pdb=" N VAL a 32 " --> pdb=" O ILE a 28 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N SER a 34 " --> pdb=" O ASN a 30 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N SER a 35 " --> pdb=" O ILE a 31 " (cutoff:3.500A) Processing helix chain 'a' and resid 58 through 64 Processing helix chain 'a' and resid 70 through 85 removed outlier: 3.959A pdb=" N LEU a 75 " --> pdb=" O ALA a 71 " (cutoff:3.500A) Processing helix chain 'a' and resid 90 through 109 removed outlier: 3.964A pdb=" N VAL a 94 " --> pdb=" O THR a 90 " (cutoff:3.500A) Processing helix chain 'a' and resid 114 through 135 Processing helix chain 'a' and resid 140 through 143 No H-bonds generated for 'chain 'a' and resid 140 through 143' Processing helix chain 'a' and resid 145 through 156 Processing helix chain 'a' and resid 163 through 179 removed outlier: 3.802A pdb=" N ASP a 166 " --> pdb=" O ILE a 163 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N ALA a 169 " --> pdb=" O ASP a 166 " (cutoff:3.500A) Processing helix chain 'a' and resid 205 through 207 No H-bonds generated for 'chain 'a' and resid 205 through 207' Processing helix chain 'a' and resid 257 through 281 removed outlier: 4.527A pdb=" N ASP a 261 " --> pdb=" O GLU a 258 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N ILE a 270 " --> pdb=" O GLU a 267 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ALA a 280 " --> pdb=" O LYS a 277 " (cutoff:3.500A) Processing helix chain 'a' and resid 294 through 303 removed outlier: 3.588A pdb=" N TYR a 299 " --> pdb=" O MET a 295 " (cutoff:3.500A) Processing helix chain 'a' and resid 313 through 323 Processing helix chain 'a' and resid 342 through 344 No H-bonds generated for 'chain 'a' and resid 342 through 344' Processing helix chain 'a' and resid 382 through 404 Processing helix chain 'a' and resid 414 through 429 removed outlier: 4.597A pdb=" N THR a 428 " --> pdb=" O GLU a 424 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N SER a 429 " --> pdb=" O ASN a 425 " (cutoff:3.500A) Processing helix chain 'a' and resid 433 through 456 removed outlier: 3.689A pdb=" N LEU a 446 " --> pdb=" O ALA a 442 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N VAL a 447 " --> pdb=" O ARG a 443 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N ILE a 448 " --> pdb=" O SER a 444 " (cutoff:3.500A) Proline residue: a 449 - end of helix Processing helix chain 'a' and resid 460 through 476 Processing helix chain 'a' and resid 478 through 485 removed outlier: 3.947A pdb=" N LYS a 481 " --> pdb=" O PRO a 478 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N ASN a 482 " --> pdb=" O GLU a 479 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N TRP a 485 " --> pdb=" O ASN a 482 " (cutoff:3.500A) Processing helix chain 'a' and resid 498 through 501 No H-bonds generated for 'chain 'a' and resid 498 through 501' Processing helix chain 'a' and resid 507 through 525 Processing helix chain 'b' and resid 21 through 39 Processing helix chain 'b' and resid 67 through 72 Processing helix chain 'b' and resid 79 through 94 Processing helix chain 'b' and resid 99 through 118 removed outlier: 3.931A pdb=" N THR b 103 " --> pdb=" O THR b 99 " (cutoff:3.500A) Processing helix chain 'b' and resid 125 through 144 Processing helix chain 'b' and resid 152 through 168 Processing helix chain 'b' and resid 171 through 190 removed outlier: 3.655A pdb=" N HIS b 174 " --> pdb=" O LEU b 171 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LYS b 176 " --> pdb=" O THR b 173 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N ASP b 177 " --> pdb=" O HIS b 174 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N THR b 180 " --> pdb=" O ASP b 177 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ARG b 189 " --> pdb=" O ALA b 186 " (cutoff:3.500A) Processing helix chain 'b' and resid 196 through 198 No H-bonds generated for 'chain 'b' and resid 196 through 198' Processing helix chain 'b' and resid 209 through 211 No H-bonds generated for 'chain 'b' and resid 209 through 211' Processing helix chain 'b' and resid 261 through 285 removed outlier: 3.907A pdb=" N HIS b 285 " --> pdb=" O ARG b 281 " (cutoff:3.500A) Processing helix chain 'b' and resid 298 through 307 Processing helix chain 'b' and resid 317 through 327 Processing helix chain 'b' and resid 380 through 402 Processing helix chain 'b' and resid 412 through 427 Processing helix chain 'b' and resid 431 through 454 removed outlier: 3.555A pdb=" N SER b 438 " --> pdb=" O VAL b 434 " (cutoff:3.500A) Proline residue: b 447 - end of helix removed outlier: 3.731A pdb=" N ALA b 454 " --> pdb=" O ILE b 450 " (cutoff:3.500A) Processing helix chain 'b' and resid 458 through 471 Processing helix chain 'b' and resid 488 through 491 No H-bonds generated for 'chain 'b' and resid 488 through 491' Processing helix chain 'b' and resid 497 through 515 Processing helix chain 'd' and resid 29 through 51 removed outlier: 4.804A pdb=" N THR d 50 " --> pdb=" O ASP d 46 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N SER d 51 " --> pdb=" O ALA d 47 " (cutoff:3.500A) Processing helix chain 'd' and resid 74 through 80 Processing helix chain 'd' and resid 86 through 101 Processing helix chain 'd' and resid 108 through 126 removed outlier: 4.000A pdb=" N LYS d 122 " --> pdb=" O ASP d 118 " (cutoff:3.500A) Processing helix chain 'd' and resid 130 through 151 Processing helix chain 'd' and resid 160 through 171 Processing helix chain 'd' and resid 180 through 193 Proline residue: d 185 - end of helix removed outlier: 3.974A pdb=" N VAL d 191 " --> pdb=" O SER d 187 " (cutoff:3.500A) Processing helix chain 'd' and resid 205 through 207 No H-bonds generated for 'chain 'd' and resid 205 through 207' Processing helix chain 'd' and resid 218 through 220 No H-bonds generated for 'chain 'd' and resid 218 through 220' Processing helix chain 'd' and resid 269 through 293 removed outlier: 4.042A pdb=" N ASP d 273 " --> pdb=" O TYR d 269 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N THR d 293 " --> pdb=" O GLN d 289 " (cutoff:3.500A) Processing helix chain 'd' and resid 311 through 319 Processing helix chain 'd' and resid 333 through 340 Processing helix chain 'd' and resid 348 through 350 No H-bonds generated for 'chain 'd' and resid 348 through 350' Processing helix chain 'd' and resid 353 through 355 No H-bonds generated for 'chain 'd' and resid 353 through 355' Processing helix chain 'd' and resid 395 through 417 Processing helix chain 'd' and resid 427 through 442 Processing helix chain 'd' and resid 447 through 469 removed outlier: 4.130A pdb=" N VAL d 460 " --> pdb=" O ASP d 456 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N ILE d 461 " --> pdb=" O ALA d 457 " (cutoff:3.500A) Proline residue: d 462 - end of helix Processing helix chain 'd' and resid 473 through 486 Processing helix chain 'd' and resid 503 through 506 No H-bonds generated for 'chain 'd' and resid 503 through 506' Processing helix chain 'd' and resid 512 through 530 Processing helix chain 'e' and resid 31 through 51 removed outlier: 4.440A pdb=" N THR e 50 " --> pdb=" O ASN e 46 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N SER e 51 " --> pdb=" O THR e 47 " (cutoff:3.500A) Processing helix chain 'e' and resid 74 through 80 Processing helix chain 'e' and resid 86 through 101 Processing helix chain 'e' and resid 108 through 126 removed outlier: 3.765A pdb=" N GLN e 122 " --> pdb=" O GLU e 118 " (cutoff:3.500A) Processing helix chain 'e' and resid 130 through 151 Processing helix chain 'e' and resid 163 through 175 removed outlier: 4.607A pdb=" N SER e 175 " --> pdb=" O THR e 171 " (cutoff:3.500A) Processing helix chain 'e' and resid 177 through 195 removed outlier: 3.781A pdb=" N SER e 180 " --> pdb=" O VAL e 177 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N ARG e 183 " --> pdb=" O SER e 180 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ASN e 191 " --> pdb=" O ILE e 188 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU e 194 " --> pdb=" O ASN e 191 " (cutoff:3.500A) Processing helix chain 'e' and resid 206 through 208 No H-bonds generated for 'chain 'e' and resid 206 through 208' Processing helix chain 'e' and resid 219 through 221 No H-bonds generated for 'chain 'e' and resid 219 through 221' Processing helix chain 'e' and resid 271 through 294 Processing helix chain 'e' and resid 308 through 316 Processing helix chain 'e' and resid 327 through 337 Processing helix chain 'e' and resid 345 through 347 No H-bonds generated for 'chain 'e' and resid 345 through 347' Processing helix chain 'e' and resid 392 through 414 Processing helix chain 'e' and resid 424 through 439 Processing helix chain 'e' and resid 443 through 465 removed outlier: 3.638A pdb=" N TYR e 446 " --> pdb=" O LEU e 443 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLU e 456 " --> pdb=" O ASP e 453 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE e 458 " --> pdb=" O LEU e 455 " (cutoff:3.500A) Proline residue: e 459 - end of helix Processing helix chain 'e' and resid 470 through 483 Processing helix chain 'e' and resid 501 through 504 No H-bonds generated for 'chain 'e' and resid 501 through 504' Processing helix chain 'e' and resid 510 through 528 Processing helix chain 'g' and resid 20 through 40 removed outlier: 3.792A pdb=" N ILE g 37 " --> pdb=" O ILE g 33 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N THR g 39 " --> pdb=" O ASP g 35 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N CYS g 40 " --> pdb=" O ILE g 36 " (cutoff:3.500A) Processing helix chain 'g' and resid 63 through 69 Processing helix chain 'g' and resid 75 through 90 Processing helix chain 'g' and resid 97 through 114 removed outlier: 3.832A pdb=" N HIS g 111 " --> pdb=" O SER g 107 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N PHE g 112 " --> pdb=" O VAL g 108 " (cutoff:3.500A) Processing helix chain 'g' and resid 119 through 140 Processing helix chain 'g' and resid 149 through 160 Processing helix chain 'g' and resid 164 through 183 removed outlier: 3.688A pdb=" N ARG g 167 " --> pdb=" O ALA g 164 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N SER g 170 " --> pdb=" O ARG g 167 " (cutoff:3.500A) Processing helix chain 'g' and resid 209 through 211 No H-bonds generated for 'chain 'g' and resid 209 through 211' Processing helix chain 'g' and resid 262 through 285 removed outlier: 4.396A pdb=" N LEU g 285 " --> pdb=" O ASP g 281 " (cutoff:3.500A) Processing helix chain 'g' and resid 298 through 306 Processing helix chain 'g' and resid 317 through 327 Processing helix chain 'g' and resid 335 through 337 No H-bonds generated for 'chain 'g' and resid 335 through 337' Processing helix chain 'g' and resid 340 through 342 No H-bonds generated for 'chain 'g' and resid 340 through 342' Processing helix chain 'g' and resid 381 through 403 Processing helix chain 'g' and resid 413 through 428 removed outlier: 3.597A pdb=" N LYS g 427 " --> pdb=" O THR g 423 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N ALA g 428 " --> pdb=" O GLU g 424 " (cutoff:3.500A) Processing helix chain 'g' and resid 434 through 455 removed outlier: 4.106A pdb=" N GLU g 445 " --> pdb=" O ALA g 441 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N VAL g 446 " --> pdb=" O GLN g 442 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N ILE g 447 " --> pdb=" O ALA g 443 " (cutoff:3.500A) Proline residue: g 448 - end of helix Processing helix chain 'g' and resid 459 through 471 removed outlier: 3.565A pdb=" N THR g 471 " --> pdb=" O ARG g 467 " (cutoff:3.500A) Processing helix chain 'g' and resid 490 through 493 No H-bonds generated for 'chain 'g' and resid 490 through 493' Processing helix chain 'g' and resid 499 through 518 Processing helix chain 'h' and resid 19 through 39 removed outlier: 3.801A pdb=" N VAL h 36 " --> pdb=" O ILE h 32 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N THR h 38 " --> pdb=" O GLU h 34 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N THR h 39 " --> pdb=" O ALA h 35 " (cutoff:3.500A) Processing helix chain 'h' and resid 62 through 68 Processing helix chain 'h' and resid 76 through 89 removed outlier: 3.611A pdb=" N VAL h 80 " --> pdb=" O ALA h 76 " (cutoff:3.500A) Processing helix chain 'h' and resid 94 through 113 removed outlier: 3.660A pdb=" N THR h 98 " --> pdb=" O THR h 94 " (cutoff:3.500A) Proline residue: h 110 - end of helix Processing helix chain 'h' and resid 118 through 139 Processing helix chain 'h' and resid 148 through 163 Processing helix chain 'h' and resid 169 through 184 removed outlier: 6.139A pdb=" N ALA h 173 " --> pdb=" O GLN h 170 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N PHE h 175 " --> pdb=" O LYS h 172 " (cutoff:3.500A) Processing helix chain 'h' and resid 192 through 194 No H-bonds generated for 'chain 'h' and resid 192 through 194' Processing helix chain 'h' and resid 260 through 283 Processing helix chain 'h' and resid 297 through 305 Processing helix chain 'h' and resid 316 through 326 Processing helix chain 'h' and resid 379 through 401 Processing helix chain 'h' and resid 411 through 426 removed outlier: 3.933A pdb=" N THR h 426 " --> pdb=" O ASP h 422 " (cutoff:3.500A) Processing helix chain 'h' and resid 430 through 453 removed outlier: 3.676A pdb=" N GLU h 443 " --> pdb=" O ALA h 439 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N ILE h 444 " --> pdb=" O LYS h 440 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N ILE h 445 " --> pdb=" O ALA h 441 " (cutoff:3.500A) Proline residue: h 446 - end of helix Processing helix chain 'h' and resid 457 through 469 Processing helix chain 'h' and resid 487 through 490 No H-bonds generated for 'chain 'h' and resid 487 through 490' Processing helix chain 'h' and resid 496 through 515 Processing helix chain 'n' and resid 87 through 89 No H-bonds generated for 'chain 'n' and resid 87 through 89' Processing helix chain 'q' and resid 11 through 14 No H-bonds generated for 'chain 'q' and resid 11 through 14' Processing helix chain 'q' and resid 24 through 27 No H-bonds generated for 'chain 'q' and resid 24 through 27' Processing helix chain 'q' and resid 29 through 46 removed outlier: 4.536A pdb=" N THR q 45 " --> pdb=" O GLN q 41 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N ALA q 46 " --> pdb=" O THR q 42 " (cutoff:3.500A) Processing helix chain 'q' and resid 69 through 75 Processing helix chain 'q' and resid 81 through 96 Processing helix chain 'q' and resid 101 through 121 Processing helix chain 'q' and resid 125 through 146 Proline residue: q 144 - end of helix Processing helix chain 'q' and resid 158 through 170 removed outlier: 4.613A pdb=" N THR q 166 " --> pdb=" O SER q 162 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N SER q 167 " --> pdb=" O LEU q 163 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N SER q 170 " --> pdb=" O THR q 166 " (cutoff:3.500A) Processing helix chain 'q' and resid 177 through 189 Processing helix chain 'q' and resid 199 through 201 No H-bonds generated for 'chain 'q' and resid 199 through 201' Processing helix chain 'q' and resid 212 through 214 No H-bonds generated for 'chain 'q' and resid 212 through 214' Processing helix chain 'q' and resid 262 through 285 removed outlier: 4.802A pdb=" N SER q 269 " --> pdb=" O LEU q 265 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N LYS q 270 " --> pdb=" O MET q 266 " (cutoff:3.500A) Processing helix chain 'q' and resid 299 through 307 Processing helix chain 'q' and resid 318 through 328 Processing helix chain 'q' and resid 382 through 404 Processing helix chain 'q' and resid 414 through 429 removed outlier: 3.622A pdb=" N THR q 429 " --> pdb=" O SER q 425 " (cutoff:3.500A) Processing helix chain 'q' and resid 434 through 456 removed outlier: 3.753A pdb=" N PHE q 445 " --> pdb=" O PHE q 441 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N GLU q 446 " --> pdb=" O ALA q 442 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ALA q 447 " --> pdb=" O GLU q 443 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N ILE q 448 " --> pdb=" O ALA q 444 " (cutoff:3.500A) Proline residue: q 449 - end of helix Processing helix chain 'q' and resid 460 through 473 Processing helix chain 'q' and resid 492 through 495 No H-bonds generated for 'chain 'q' and resid 492 through 495' Processing helix chain 'q' and resid 501 through 520 Processing helix chain 'z' and resid 3 through 7 removed outlier: 3.853A pdb=" N LEU z 7 " --> pdb=" O ALA z 3 " (cutoff:3.500A) No H-bonds generated for 'chain 'z' and resid 3 through 7' Processing helix chain 'z' and resid 16 through 37 removed outlier: 4.906A pdb=" N THR z 36 " --> pdb=" O ASP z 32 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N ASN z 37 " --> pdb=" O VAL z 33 " (cutoff:3.500A) Processing helix chain 'z' and resid 60 through 66 Processing helix chain 'z' and resid 72 through 88 Processing helix chain 'z' and resid 92 through 110 removed outlier: 3.827A pdb=" N TYR z 109 " --> pdb=" O GLN z 105 " (cutoff:3.500A) Processing helix chain 'z' and resid 116 through 137 Processing helix chain 'z' and resid 145 through 159 removed outlier: 4.084A pdb=" N THR z 158 " --> pdb=" O THR z 154 " (cutoff:3.500A) Processing helix chain 'z' and resid 162 through 178 removed outlier: 4.161A pdb=" N GLU z 170 " --> pdb=" O ASP z 166 " (cutoff:3.500A) Processing helix chain 'z' and resid 188 through 190 No H-bonds generated for 'chain 'z' and resid 188 through 190' Processing helix chain 'z' and resid 201 through 203 No H-bonds generated for 'chain 'z' and resid 201 through 203' Processing helix chain 'z' and resid 253 through 262 Processing helix chain 'z' and resid 265 through 281 removed outlier: 3.753A pdb=" N ARG z 270 " --> pdb=" O PHE z 266 " (cutoff:3.500A) Processing helix chain 'z' and resid 299 through 308 removed outlier: 3.628A pdb=" N GLU z 308 " --> pdb=" O ALA z 304 " (cutoff:3.500A) Processing helix chain 'z' and resid 318 through 327 removed outlier: 4.276A pdb=" N GLU z 322 " --> pdb=" O ARG z 318 " (cutoff:3.500A) Processing helix chain 'z' and resid 341 through 343 No H-bonds generated for 'chain 'z' and resid 341 through 343' Processing helix chain 'z' and resid 381 through 403 Processing helix chain 'z' and resid 413 through 428 Proline residue: z 427 - end of helix Processing helix chain 'z' and resid 432 through 455 removed outlier: 3.551A pdb=" N LEU z 445 " --> pdb=" O ASP z 442 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ILE z 447 " --> pdb=" O LEU z 444 " (cutoff:3.500A) Proline residue: z 448 - end of helix Processing helix chain 'z' and resid 459 through 473 Processing helix chain 'z' and resid 489 through 492 No H-bonds generated for 'chain 'z' and resid 489 through 492' Processing helix chain 'z' and resid 498 through 517 Processing helix chain 'T' and resid 10 through 26 removed outlier: 3.718A pdb=" N ALA T 18 " --> pdb=" O ASN T 14 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N LYS T 19 " --> pdb=" O GLN T 15 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER T 25 " --> pdb=" O TRP T 21 " (cutoff:3.500A) Processing helix chain 'T' and resid 42 through 45 No H-bonds generated for 'chain 'T' and resid 42 through 45' Processing helix chain 'T' and resid 70 through 78 Processing helix chain 'T' and resid 101 through 105 Processing helix chain 'T' and resid 111 through 124 removed outlier: 4.540A pdb=" N LEU T 117 " --> pdb=" O ASP T 114 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ASP T 118 " --> pdb=" O SER T 115 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N ARG T 121 " --> pdb=" O ASP T 118 " (cutoff:3.500A) Processing helix chain 'T' and resid 142 through 158 removed outlier: 4.814A pdb=" N GLY T 146 " --> pdb=" O GLY T 142 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE T 152 " --> pdb=" O GLY T 148 " (cutoff:3.500A) Processing helix chain 'T' and resid 181 through 195 removed outlier: 3.656A pdb=" N GLN T 191 " --> pdb=" O LEU T 187 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N GLU T 194 " --> pdb=" O HIS T 190 " (cutoff:3.500A) Processing helix chain 'T' and resid 204 through 215 Processing helix chain 'T' and resid 223 through 228 Processing helix chain 'T' and resid 230 through 236 Processing helix chain 'T' and resid 372 through 391 removed outlier: 3.579A pdb=" N PHE T 385 " --> pdb=" O SER T 382 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ARG T 390 " --> pdb=" O ALA T 387 " (cutoff:3.500A) Processing helix chain 'T' and resid 396 through 401 Processing helix chain 'T' and resid 405 through 423 removed outlier: 4.019A pdb=" N THR T 409 " --> pdb=" O GLU T 405 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 9 through 13 Processing sheet with id= B, first strand: chain 'A' and resid 43 through 46 Processing sheet with id= C, first strand: chain 'A' and resid 180 through 182 Processing sheet with id= D, first strand: chain 'A' and resid 196 through 199 Processing sheet with id= E, first strand: chain 'A' and resid 213 through 216 Processing sheet with id= F, first strand: chain 'A' and resid 346 through 348 removed outlier: 6.773A pdb=" N VAL A 285 " --> pdb=" O ALA A 235 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N LEU A 237 " --> pdb=" O VAL A 285 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N LEU A 287 " --> pdb=" O LEU A 237 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N MET A 306 " --> pdb=" O ILE A 286 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N THR A 288 " --> pdb=" O MET A 306 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N VAL A 308 " --> pdb=" O THR A 288 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 408 through 410 Processing sheet with id= H, first strand: chain 'A' and resid 486 through 489 removed outlier: 3.509A pdb=" N LYS A 494 " --> pdb=" O ASP A 489 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 17 through 19 Processing sheet with id= J, first strand: chain 'B' and resid 199 through 205 removed outlier: 6.171A pdb=" N CYS B 371 " --> pdb=" O HIS B 200 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N ILE B 202 " --> pdb=" O CYS B 371 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N ILE B 373 " --> pdb=" O ILE B 202 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N LYS B 204 " --> pdb=" O ILE B 373 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N LEU B 375 " --> pdb=" O LYS B 204 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain 'B' and resid 218 through 220 Processing sheet with id= L, first strand: chain 'B' and resid 344 through 346 removed outlier: 6.740A pdb=" N CYS B 289 " --> pdb=" O LEU B 238 " (cutoff:3.500A) removed outlier: 7.856A pdb=" N ALA B 240 " --> pdb=" O CYS B 289 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ILE B 291 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N MET B 310 " --> pdb=" O PHE B 290 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N ASN B 292 " --> pdb=" O MET B 310 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ILE B 312 " --> pdb=" O ASN B 292 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'B' and resid 406 through 408 Processing sheet with id= N, first strand: chain 'B' and resid 476 through 479 Processing sheet with id= O, first strand: chain 'D' and resid 59 through 62 Processing sheet with id= P, first strand: chain 'D' and resid 208 through 212 removed outlier: 6.852A pdb=" N VAL D 386 " --> pdb=" O LYS D 209 " (cutoff:3.500A) removed outlier: 8.286A pdb=" N VAL D 211 " --> pdb=" O VAL D 386 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ILE D 388 " --> pdb=" O VAL D 211 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'D' and resid 227 through 229 Processing sheet with id= R, first strand: chain 'D' and resid 357 through 359 removed outlier: 6.807A pdb=" N VAL D 297 " --> pdb=" O GLY D 247 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N ILE D 249 " --> pdb=" O VAL D 297 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N LEU D 299 " --> pdb=" O ILE D 249 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N MET D 323 " --> pdb=" O LEU D 298 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N ILE D 300 " --> pdb=" O MET D 323 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N ILE D 325 " --> pdb=" O ILE D 300 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'D' and resid 421 through 423 Processing sheet with id= T, first strand: chain 'D' and resid 491 through 494 Processing sheet with id= U, first strand: chain 'E' and resid 26 through 29 removed outlier: 3.611A pdb=" N LYS E 535 " --> pdb=" O SER E 26 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'E' and resid 59 through 62 Processing sheet with id= W, first strand: chain 'E' and resid 209 through 215 removed outlier: 6.803A pdb=" N VAL E 383 " --> pdb=" O LYS E 210 " (cutoff:3.500A) removed outlier: 7.758A pdb=" N GLU E 212 " --> pdb=" O VAL E 383 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N ILE E 385 " --> pdb=" O GLU E 212 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N LYS E 214 " --> pdb=" O ILE E 385 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N ILE E 387 " --> pdb=" O LYS E 214 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'E' and resid 228 through 230 Processing sheet with id= Y, first strand: chain 'E' and resid 354 through 356 removed outlier: 7.073A pdb=" N LEU E 299 " --> pdb=" O ALA E 249 " (cutoff:3.500A) removed outlier: 8.123A pdb=" N LEU E 251 " --> pdb=" O LEU E 299 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N ILE E 301 " --> pdb=" O LEU E 251 " (cutoff:3.500A) removed outlier: 8.023A pdb=" N CYS E 302 " --> pdb=" O PRO E 320 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N VAL E 322 " --> pdb=" O CYS E 302 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'E' and resid 418 through 420 Processing sheet with id= AA, first strand: chain 'G' and resid 48 through 51 Processing sheet with id= AB, first strand: chain 'G' and resid 184 through 187 Processing sheet with id= AC, first strand: chain 'G' and resid 199 through 205 removed outlier: 6.674A pdb=" N CYS G 372 " --> pdb=" O ARG G 200 " (cutoff:3.500A) removed outlier: 7.755A pdb=" N GLU G 202 " --> pdb=" O CYS G 372 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N ILE G 374 " --> pdb=" O GLU G 202 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N ILE G 204 " --> pdb=" O ILE G 374 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N LEU G 376 " --> pdb=" O ILE G 204 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N THR G 373 " --> pdb=" O LEU G 215 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'G' and resid 238 through 241 removed outlier: 6.680A pdb=" N VAL G 289 " --> pdb=" O VAL G 239 " (cutoff:3.500A) removed outlier: 8.239A pdb=" N LEU G 241 " --> pdb=" O VAL G 289 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ILE G 291 " --> pdb=" O LEU G 241 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N THR G 310 " --> pdb=" O VAL G 290 " (cutoff:3.500A) removed outlier: 8.044A pdb=" N THR G 292 " --> pdb=" O THR G 310 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N ILE G 312 " --> pdb=" O THR G 292 " (cutoff:3.500A) No H-bonds generated for sheet with id= AD Processing sheet with id= AE, first strand: chain 'G' and resid 351 through 355 Processing sheet with id= AF, first strand: chain 'G' and resid 407 through 409 Processing sheet with id= AG, first strand: chain 'G' and resid 478 through 480 Processing sheet with id= AH, first strand: chain 'H' and resid 14 through 17 Processing sheet with id= AI, first strand: chain 'H' and resid 47 through 50 Processing sheet with id= AJ, first strand: chain 'H' and resid 195 through 201 removed outlier: 6.639A pdb=" N CYS H 370 " --> pdb=" O GLY H 196 " (cutoff:3.500A) removed outlier: 7.937A pdb=" N LYS H 198 " --> pdb=" O CYS H 370 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N PHE H 372 " --> pdb=" O LYS H 198 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N VAL H 200 " --> pdb=" O PHE H 372 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N LEU H 374 " --> pdb=" O VAL H 200 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'H' and resid 213 through 217 Processing sheet with id= AL, first strand: chain 'H' and resid 237 through 240 removed outlier: 6.706A pdb=" N VAL H 288 " --> pdb=" O ALA H 238 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N LEU H 240 " --> pdb=" O VAL H 288 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N LEU H 290 " --> pdb=" O LEU H 240 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N PHE H 309 " --> pdb=" O VAL H 289 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N SER H 291 " --> pdb=" O PHE H 309 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ALA H 311 " --> pdb=" O SER H 291 " (cutoff:3.500A) No H-bonds generated for sheet with id= AL Processing sheet with id= AM, first strand: chain 'H' and resid 405 through 407 Processing sheet with id= AN, first strand: chain 'H' and resid 475 through 478 Processing sheet with id= AO, first strand: chain 'N' and resid 2 through 7 Processing sheet with id= AP, first strand: chain 'N' and resid 57 through 59 removed outlier: 3.569A pdb=" N SER N 50 " --> pdb=" O ASP N 58 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N SER N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N MET N 34 " --> pdb=" O SER N 50 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N THR N 52 " --> pdb=" O ASN N 32 " (cutoff:3.500A) removed outlier: 8.153A pdb=" N ASN N 32 " --> pdb=" O THR N 52 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N ASN N 98 " --> pdb=" O ASN N 32 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N MET N 34 " --> pdb=" O LYS N 96 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N LYS N 96 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N TRP N 36 " --> pdb=" O TYR N 94 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N TYR N 94 " --> pdb=" O TRP N 36 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N ARG N 38 " --> pdb=" O VAL N 92 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N VAL N 92 " --> pdb=" O ARG N 38 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'Q' and resid 20 through 23 Processing sheet with id= AR, first strand: chain 'Q' and resid 54 through 57 Processing sheet with id= AS, first strand: chain 'Q' and resid 202 through 208 removed outlier: 6.536A pdb=" N SER Q 373 " --> pdb=" O ARG Q 203 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N CYS Q 205 " --> pdb=" O SER Q 373 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N ILE Q 375 " --> pdb=" O CYS Q 205 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N ILE Q 207 " --> pdb=" O ILE Q 375 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N LEU Q 377 " --> pdb=" O ILE Q 207 " (cutoff:3.500A) Processing sheet with id= AT, first strand: chain 'Q' and resid 220 through 223 Processing sheet with id= AU, first strand: chain 'Q' and resid 240 through 242 removed outlier: 6.139A pdb=" N MET Q 311 " --> pdb=" O VAL Q 291 " (cutoff:3.500A) removed outlier: 7.543A pdb=" N THR Q 293 " --> pdb=" O MET Q 311 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N VAL Q 313 " --> pdb=" O THR Q 293 " (cutoff:3.500A) Processing sheet with id= AV, first strand: chain 'Q' and resid 408 through 410 Processing sheet with id= AW, first strand: chain 'Q' and resid 478 through 480 Processing sheet with id= AX, first strand: chain 'Z' and resid 12 through 15 Processing sheet with id= AY, first strand: chain 'Z' and resid 45 through 48 Processing sheet with id= AZ, first strand: chain 'Z' and resid 191 through 196 removed outlier: 6.618A pdb=" N VAL Z 372 " --> pdb=" O GLU Z 192 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N MET Z 194 " --> pdb=" O VAL Z 372 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N LEU Z 374 " --> pdb=" O MET Z 194 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N MET Z 196 " --> pdb=" O LEU Z 374 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N ILE Z 376 " --> pdb=" O MET Z 196 " (cutoff:3.500A) Processing sheet with id= BA, first strand: chain 'Z' and resid 210 through 212 Processing sheet with id= BB, first strand: chain 'Z' and resid 345 through 347 removed outlier: 6.707A pdb=" N GLY Z 288 " --> pdb=" O TYR Z 229 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N LEU Z 231 " --> pdb=" O GLY Z 288 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N VAL Z 290 " --> pdb=" O LEU Z 231 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N CYS Z 233 " --> pdb=" O VAL Z 290 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N ILE Z 292 " --> pdb=" O CYS Z 233 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N VAL Z 311 " --> pdb=" O VAL Z 291 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N ASN Z 293 " --> pdb=" O VAL Z 311 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N LEU Z 313 " --> pdb=" O ASN Z 293 " (cutoff:3.500A) Processing sheet with id= BC, first strand: chain 'Z' and resid 477 through 479 Processing sheet with id= BD, first strand: chain 'a' and resid 9 through 13 Processing sheet with id= BE, first strand: chain 'a' and resid 43 through 46 Processing sheet with id= BF, first strand: chain 'a' and resid 180 through 182 Processing sheet with id= BG, first strand: chain 'a' and resid 196 through 199 Processing sheet with id= BH, first strand: chain 'a' and resid 213 through 216 Processing sheet with id= BI, first strand: chain 'a' and resid 346 through 348 removed outlier: 6.789A pdb=" N VAL a 285 " --> pdb=" O ALA a 235 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N LEU a 237 " --> pdb=" O VAL a 285 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N LEU a 287 " --> pdb=" O LEU a 237 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N MET a 306 " --> pdb=" O ILE a 286 " (cutoff:3.500A) removed outlier: 7.718A pdb=" N THR a 288 " --> pdb=" O MET a 306 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N VAL a 308 " --> pdb=" O THR a 288 " (cutoff:3.500A) Processing sheet with id= BJ, first strand: chain 'a' and resid 408 through 410 Processing sheet with id= BK, first strand: chain 'a' and resid 486 through 489 Processing sheet with id= BL, first strand: chain 'b' and resid 17 through 19 Processing sheet with id= BM, first strand: chain 'b' and resid 199 through 205 removed outlier: 6.165A pdb=" N CYS b 371 " --> pdb=" O HIS b 200 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N ILE b 202 " --> pdb=" O CYS b 371 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N ILE b 373 " --> pdb=" O ILE b 202 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N LYS b 204 " --> pdb=" O ILE b 373 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N LEU b 375 " --> pdb=" O LYS b 204 " (cutoff:3.500A) No H-bonds generated for sheet with id= BM Processing sheet with id= BN, first strand: chain 'b' and resid 218 through 220 Processing sheet with id= BO, first strand: chain 'b' and resid 344 through 346 removed outlier: 6.835A pdb=" N CYS b 289 " --> pdb=" O LEU b 238 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N ALA b 240 " --> pdb=" O CYS b 289 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ILE b 291 " --> pdb=" O ALA b 240 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N MET b 310 " --> pdb=" O PHE b 290 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N ASN b 292 " --> pdb=" O MET b 310 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ILE b 312 " --> pdb=" O ASN b 292 " (cutoff:3.500A) Processing sheet with id= BP, first strand: chain 'b' and resid 406 through 408 Processing sheet with id= BQ, first strand: chain 'b' and resid 476 through 479 Processing sheet with id= BR, first strand: chain 'd' and resid 59 through 62 Processing sheet with id= BS, first strand: chain 'd' and resid 208 through 212 removed outlier: 6.728A pdb=" N VAL d 386 " --> pdb=" O LYS d 209 " (cutoff:3.500A) removed outlier: 8.189A pdb=" N VAL d 211 " --> pdb=" O VAL d 386 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ILE d 388 " --> pdb=" O VAL d 211 " (cutoff:3.500A) Processing sheet with id= BT, first strand: chain 'd' and resid 227 through 229 Processing sheet with id= BU, first strand: chain 'd' and resid 357 through 359 removed outlier: 6.985A pdb=" N VAL d 297 " --> pdb=" O GLY d 247 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N ILE d 249 " --> pdb=" O VAL d 297 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N LEU d 299 " --> pdb=" O ILE d 249 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N MET d 323 " --> pdb=" O LEU d 298 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N ILE d 300 " --> pdb=" O MET d 323 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N ILE d 325 " --> pdb=" O ILE d 300 " (cutoff:3.500A) Processing sheet with id= BV, first strand: chain 'd' and resid 421 through 423 Processing sheet with id= BW, first strand: chain 'd' and resid 491 through 494 Processing sheet with id= BX, first strand: chain 'e' and resid 25 through 29 removed outlier: 3.552A pdb=" N LYS e 535 " --> pdb=" O SER e 26 " (cutoff:3.500A) Processing sheet with id= BY, first strand: chain 'e' and resid 59 through 62 Processing sheet with id= BZ, first strand: chain 'e' and resid 209 through 215 removed outlier: 6.824A pdb=" N VAL e 383 " --> pdb=" O LYS e 210 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N GLU e 212 " --> pdb=" O VAL e 383 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N ILE e 385 " --> pdb=" O GLU e 212 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N LYS e 214 " --> pdb=" O ILE e 385 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N ILE e 387 " --> pdb=" O LYS e 214 " (cutoff:3.500A) Processing sheet with id= CA, first strand: chain 'e' and resid 228 through 230 Processing sheet with id= CB, first strand: chain 'e' and resid 354 through 356 removed outlier: 6.810A pdb=" N LEU e 299 " --> pdb=" O ALA e 249 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N LEU e 251 " --> pdb=" O LEU e 299 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N ILE e 301 " --> pdb=" O LEU e 251 " (cutoff:3.500A) removed outlier: 8.112A pdb=" N CYS e 302 " --> pdb=" O PRO e 320 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N VAL e 322 " --> pdb=" O CYS e 302 " (cutoff:3.500A) Processing sheet with id= CC, first strand: chain 'e' and resid 418 through 420 Processing sheet with id= CD, first strand: chain 'g' and resid 48 through 51 Processing sheet with id= CE, first strand: chain 'g' and resid 184 through 187 Processing sheet with id= CF, first strand: chain 'g' and resid 199 through 205 removed outlier: 6.728A pdb=" N CYS g 372 " --> pdb=" O ARG g 200 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N GLU g 202 " --> pdb=" O CYS g 372 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N ILE g 374 " --> pdb=" O GLU g 202 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N ILE g 204 " --> pdb=" O ILE g 374 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N LEU g 376 " --> pdb=" O ILE g 204 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N THR g 373 " --> pdb=" O LEU g 215 " (cutoff:3.500A) Processing sheet with id= CG, first strand: chain 'g' and resid 219 through 221 Processing sheet with id= CH, first strand: chain 'g' and resid 238 through 241 removed outlier: 6.657A pdb=" N VAL g 289 " --> pdb=" O VAL g 239 " (cutoff:3.500A) removed outlier: 8.255A pdb=" N LEU g 241 " --> pdb=" O VAL g 289 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N ILE g 291 " --> pdb=" O LEU g 241 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N THR g 310 " --> pdb=" O VAL g 290 " (cutoff:3.500A) removed outlier: 8.132A pdb=" N THR g 292 " --> pdb=" O THR g 310 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N ILE g 312 " --> pdb=" O THR g 292 " (cutoff:3.500A) No H-bonds generated for sheet with id= CH Processing sheet with id= CI, first strand: chain 'g' and resid 407 through 409 Processing sheet with id= CJ, first strand: chain 'g' and resid 478 through 480 Processing sheet with id= CK, first strand: chain 'h' and resid 14 through 17 Processing sheet with id= CL, first strand: chain 'h' and resid 47 through 50 Processing sheet with id= CM, first strand: chain 'h' and resid 195 through 201 removed outlier: 6.786A pdb=" N CYS h 370 " --> pdb=" O GLY h 196 " (cutoff:3.500A) removed outlier: 8.104A pdb=" N LYS h 198 " --> pdb=" O CYS h 370 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N PHE h 372 " --> pdb=" O LYS h 198 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N VAL h 200 " --> pdb=" O PHE h 372 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N LEU h 374 " --> pdb=" O VAL h 200 " (cutoff:3.500A) Processing sheet with id= CN, first strand: chain 'h' and resid 213 through 217 Processing sheet with id= CO, first strand: chain 'h' and resid 237 through 240 removed outlier: 6.726A pdb=" N VAL h 288 " --> pdb=" O ALA h 238 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N LEU h 240 " --> pdb=" O VAL h 288 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N LEU h 290 " --> pdb=" O LEU h 240 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N PHE h 309 " --> pdb=" O VAL h 289 " (cutoff:3.500A) removed outlier: 8.065A pdb=" N SER h 291 " --> pdb=" O PHE h 309 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ALA h 311 " --> pdb=" O SER h 291 " (cutoff:3.500A) No H-bonds generated for sheet with id= CO Processing sheet with id= CP, first strand: chain 'h' and resid 405 through 407 Processing sheet with id= CQ, first strand: chain 'h' and resid 475 through 478 Processing sheet with id= CR, first strand: chain 'n' and resid 2 through 6 Processing sheet with id= CS, first strand: chain 'n' and resid 93 through 97 removed outlier: 6.401A pdb=" N ARG n 38 " --> pdb=" O LEU n 47 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N LEU n 47 " --> pdb=" O ARG n 38 " (cutoff:3.500A) Processing sheet with id= CT, first strand: chain 'q' and resid 20 through 23 Processing sheet with id= CU, first strand: chain 'q' and resid 54 through 57 Processing sheet with id= CV, first strand: chain 'q' and resid 202 through 208 removed outlier: 6.487A pdb=" N SER q 373 " --> pdb=" O ARG q 203 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N CYS q 205 " --> pdb=" O SER q 373 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N ILE q 375 " --> pdb=" O CYS q 205 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N ILE q 207 " --> pdb=" O ILE q 375 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N LEU q 377 " --> pdb=" O ILE q 207 " (cutoff:3.500A) Processing sheet with id= CW, first strand: chain 'q' and resid 220 through 223 Processing sheet with id= CX, first strand: chain 'q' and resid 240 through 242 removed outlier: 6.107A pdb=" N MET q 311 " --> pdb=" O VAL q 291 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N THR q 293 " --> pdb=" O MET q 311 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N VAL q 313 " --> pdb=" O THR q 293 " (cutoff:3.500A) Processing sheet with id= CY, first strand: chain 'q' and resid 498 through 500 removed outlier: 3.515A pdb=" N CYS q 149 " --> pdb=" O LEU q 408 " (cutoff:3.500A) removed outlier: 8.306A pdb=" N VAL q 147 " --> pdb=" O PRO q 410 " (cutoff:3.500A) Processing sheet with id= CZ, first strand: chain 'q' and resid 478 through 480 Processing sheet with id= DA, first strand: chain 'z' and resid 12 through 15 Processing sheet with id= DB, first strand: chain 'z' and resid 45 through 48 Processing sheet with id= DC, first strand: chain 'z' and resid 191 through 196 removed outlier: 6.557A pdb=" N VAL z 372 " --> pdb=" O GLU z 192 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N MET z 194 " --> pdb=" O VAL z 372 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N LEU z 374 " --> pdb=" O MET z 194 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N MET z 196 " --> pdb=" O LEU z 374 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N ILE z 376 " --> pdb=" O MET z 196 " (cutoff:3.500A) Processing sheet with id= DD, first strand: chain 'z' and resid 210 through 212 Processing sheet with id= DE, first strand: chain 'z' and resid 345 through 347 removed outlier: 6.750A pdb=" N GLY z 288 " --> pdb=" O TYR z 229 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N LEU z 231 " --> pdb=" O GLY z 288 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N VAL z 290 " --> pdb=" O LEU z 231 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N CYS z 233 " --> pdb=" O VAL z 290 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N ILE z 292 " --> pdb=" O CYS z 233 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N VAL z 311 " --> pdb=" O VAL z 291 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N ASN z 293 " --> pdb=" O VAL z 311 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N LEU z 313 " --> pdb=" O ASN z 293 " (cutoff:3.500A) Processing sheet with id= DF, first strand: chain 'z' and resid 477 through 479 Processing sheet with id= DG, first strand: chain 'T' and resid 90 through 92 removed outlier: 8.091A pdb=" N VAL T 91 " --> pdb=" O ALA T 63 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N LEU T 65 " --> pdb=" O VAL T 91 " (cutoff:3.500A) removed outlier: 8.289A pdb=" N ILE T 64 " --> pdb=" O ILE T 4 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N HIS T 6 " --> pdb=" O ILE T 64 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N VAL T 66 " --> pdb=" O HIS T 6 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N GLN T 8 " --> pdb=" O VAL T 66 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N VAL T 5 " --> pdb=" O GLN T 131 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N PHE T 133 " --> pdb=" O VAL T 5 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N ILE T 7 " --> pdb=" O PHE T 133 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N LEU T 135 " --> pdb=" O ILE T 7 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N ALA T 9 " --> pdb=" O LEU T 135 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N HIS T 137 " --> pdb=" O ALA T 9 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N ILE T 163 " --> pdb=" O PHE T 133 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N LEU T 135 " --> pdb=" O ILE T 163 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ASN T 165 " --> pdb=" O LEU T 135 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N HIS T 137 " --> pdb=" O ASN T 165 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N PHE T 167 " --> pdb=" O HIS T 137 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N GLU T 198 " --> pdb=" O THR T 166 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N SER T 168 " --> pdb=" O GLU T 198 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N TYR T 200 " --> pdb=" O SER T 168 " (cutoff:3.500A) Processing sheet with id= DH, first strand: chain 'T' and resid 51 through 53 removed outlier: 3.505A pdb=" N VAL T 60 " --> pdb=" O ASN T 52 " (cutoff:3.500A) 3518 hydrogen bonds defined for protein. 9465 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 30.45 Time building geometry restraints manager: 25.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 23031 1.34 - 1.46: 10371 1.46 - 1.58: 35752 1.58 - 1.70: 96 1.70 - 1.82: 703 Bond restraints: 69953 Sorted by residual: bond pdb=" N ARG Z 15 " pdb=" CA ARG Z 15 " ideal model delta sigma weight residual 1.454 1.488 -0.034 1.18e-02 7.18e+03 8.36e+00 bond pdb=" N ILE q 207 " pdb=" CA ILE q 207 " ideal model delta sigma weight residual 1.458 1.492 -0.033 1.17e-02 7.31e+03 8.12e+00 bond pdb=" N ILE T 210 " pdb=" CA ILE T 210 " ideal model delta sigma weight residual 1.461 1.493 -0.032 1.19e-02 7.06e+03 7.37e+00 bond pdb=" N ARG z 15 " pdb=" CA ARG z 15 " ideal model delta sigma weight residual 1.454 1.486 -0.032 1.19e-02 7.06e+03 7.06e+00 bond pdb=" N ARG N 99 " pdb=" CA ARG N 99 " ideal model delta sigma weight residual 1.455 1.486 -0.032 1.25e-02 6.40e+03 6.50e+00 ... (remaining 69948 not shown) Histogram of bond angle deviations from ideal: 97.86 - 105.60: 1176 105.60 - 113.33: 40723 113.33 - 121.07: 34516 121.07 - 128.80: 17737 128.80 - 136.53: 318 Bond angle restraints: 94470 Sorted by residual: angle pdb=" C ASN n 100 " pdb=" N TRP n 101 " pdb=" CA TRP n 101 " ideal model delta sigma weight residual 122.38 115.04 7.34 1.81e+00 3.05e-01 1.64e+01 angle pdb=" CA GLY E 537 " pdb=" C GLY E 537 " pdb=" O GLY E 537 " ideal model delta sigma weight residual 121.58 117.97 3.61 9.00e-01 1.23e+00 1.61e+01 angle pdb=" C CYS A 357 " pdb=" N ASP A 358 " pdb=" CA ASP A 358 " ideal model delta sigma weight residual 122.49 117.02 5.47 1.55e+00 4.16e-01 1.24e+01 angle pdb=" C ASN N 98 " pdb=" N ARG N 99 " pdb=" CA ARG N 99 " ideal model delta sigma weight residual 123.05 116.89 6.16 1.79e+00 3.12e-01 1.18e+01 angle pdb=" C ARG n 99 " pdb=" N ASN n 100 " pdb=" CA ASN n 100 " ideal model delta sigma weight residual 121.54 127.95 -6.41 1.91e+00 2.74e-01 1.13e+01 ... (remaining 94465 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.93: 42313 34.93 - 69.86: 737 69.86 - 104.79: 76 104.79 - 139.72: 13 139.72 - 174.65: 10 Dihedral angle restraints: 43149 sinusoidal: 17344 harmonic: 25805 Sorted by residual: dihedral pdb=" O2A ADP D 601 " pdb=" O3A ADP D 601 " pdb=" PA ADP D 601 " pdb=" PB ADP D 601 " ideal model delta sinusoidal sigma weight residual 300.00 125.35 174.65 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" O2A ADP B 601 " pdb=" O3A ADP B 601 " pdb=" PA ADP B 601 " pdb=" PB ADP B 601 " ideal model delta sinusoidal sigma weight residual -60.00 111.44 -171.44 1 2.00e+01 2.50e-03 4.77e+01 dihedral pdb=" O2A ADP d 601 " pdb=" O3A ADP d 601 " pdb=" PA ADP d 601 " pdb=" PB ADP d 601 " ideal model delta sinusoidal sigma weight residual 300.00 130.41 169.60 1 2.00e+01 2.50e-03 4.76e+01 ... (remaining 43146 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 8024 0.039 - 0.078: 2211 0.078 - 0.116: 753 0.116 - 0.155: 212 0.155 - 0.194: 6 Chirality restraints: 11206 Sorted by residual: chirality pdb=" CA ILE q 207 " pdb=" N ILE q 207 " pdb=" C ILE q 207 " pdb=" CB ILE q 207 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.19 2.00e-01 2.50e+01 9.41e-01 chirality pdb=" CA LYS E 535 " pdb=" N LYS E 535 " pdb=" C LYS E 535 " pdb=" CB LYS E 535 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 8.48e-01 chirality pdb=" CA ILE T 210 " pdb=" N ILE T 210 " pdb=" C ILE T 210 " pdb=" CB ILE T 210 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.17 2.00e-01 2.50e+01 7.65e-01 ... (remaining 11203 not shown) Planarity restraints: 12067 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU T 150 " -0.022 2.00e-02 2.50e+03 4.43e-02 1.96e+01 pdb=" C LEU T 150 " 0.077 2.00e-02 2.50e+03 pdb=" O LEU T 150 " -0.029 2.00e-02 2.50e+03 pdb=" N LEU T 151 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE q 207 " -0.016 2.00e-02 2.50e+03 3.27e-02 1.07e+01 pdb=" C ILE q 207 " 0.057 2.00e-02 2.50e+03 pdb=" O ILE q 207 " -0.021 2.00e-02 2.50e+03 pdb=" N LEU q 208 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL T 116 " -0.016 2.00e-02 2.50e+03 3.27e-02 1.07e+01 pdb=" C VAL T 116 " 0.057 2.00e-02 2.50e+03 pdb=" O VAL T 116 " -0.021 2.00e-02 2.50e+03 pdb=" N LEU T 117 " -0.019 2.00e-02 2.50e+03 ... (remaining 12064 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 609 2.51 - 3.11: 52773 3.11 - 3.70: 108940 3.70 - 4.30: 164814 4.30 - 4.90: 273914 Nonbonded interactions: 601050 Sorted by model distance: nonbonded pdb=" O ASP T 161 " pdb=" OD1 ASP T 161 " model vdw 1.909 3.040 nonbonded pdb=" O2A ADP q 601 " pdb="MG MG q 602 " model vdw 1.928 2.170 nonbonded pdb=" OD1 ASP q 99 " pdb="MG MG q 602 " model vdw 1.929 2.170 nonbonded pdb="MG MG e 602 " pdb=" F2 AF3 e 603 " model vdw 1.940 2.120 nonbonded pdb=" O1A ADP B 601 " pdb="MG MG B 602 " model vdw 1.959 2.170 ... (remaining 601045 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'a' and (resid 2 through 536 or resid 601 through 603)) } ncs_group { reference = chain 'B' selection = (chain 'b' and (resid 2 through 527 or resid 601 through 603)) } ncs_group { reference = chain 'D' selection = chain 'd' } ncs_group { reference = (chain 'E' and (resid 2 through 8 or resid 10 through 538 or resid 601 through 6 \ 03)) selection = (chain 'e' and (resid 2 through 8 or resid 10 through 538 or resid 601 through 6 \ 03)) } ncs_group { reference = chain 'G' selection = chain 'g' } ncs_group { reference = chain 'H' selection = chain 'h' } ncs_group { reference = (chain 'N' and (resid 1 through 12 or resid 17 through 115)) selection = (chain 'n' and (resid 1 through 12 or resid 17 through 115)) } ncs_group { reference = (chain 'Q' and (resid 2 through 530 or resid 601 through 603)) selection = chain 'q' } ncs_group { reference = (chain 'Z' and (resid 2 through 527 or resid 601 through 603)) selection = chain 'z' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians Al 16 5.89 5 P 32 5.49 5 Mg 16 5.21 5 S 424 5.16 5 C 43200 2.51 5 N 12027 2.21 5 O 13376 1.98 5 F 48 1.80 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.050 Extract box with map and model: 17.290 Check model and map are aligned: 0.760 Process input model: 148.790 Find NCS groups from input model: 6.510 Set up NCS constraints: 0.610 Set refine NCS operators: 0.000 Set scattering table: 0.490 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:11.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 189.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 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 : 0.004 0.047 69953 Z= 0.241 Angle : 0.621 8.265 94470 Z= 0.345 Chirality : 0.043 0.194 11206 Planarity : 0.004 0.059 12067 Dihedral : 14.513 174.650 26443 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.20 % Favored : 96.68 % Rotamer Outliers : 1.66 % 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: -2.07 (0.08), residues: 8920 helix: -0.63 (0.07), residues: 4650 sheet: -1.42 (0.13), residues: 1238 loop : -2.37 (0.09), residues: 3032 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17840 Ramachandran restraints generated. 8920 Oldfield, 0 Emsley, 8920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17840 Ramachandran restraints generated. 8920 Oldfield, 0 Emsley, 8920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1610 residues out of total 7485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 1487 time to evaluate : 6.143 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 123 outliers final: 52 residues processed: 1588 average time/residue: 1.6792 time to fit residues: 3421.5083 Evaluate side-chains 1008 residues out of total 7485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 956 time to evaluate : 6.180 Switching outliers to nearest non-outliers outliers start: 52 outliers final: 48 residues processed: 6 average time/residue: 0.5492 time to fit residues: 14.5294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 885 random chunks: chunk 747 optimal weight: 8.9990 chunk 670 optimal weight: 3.9990 chunk 372 optimal weight: 7.9990 chunk 229 optimal weight: 7.9990 chunk 452 optimal weight: 10.0000 chunk 358 optimal weight: 6.9990 chunk 693 optimal weight: 5.9990 chunk 268 optimal weight: 0.6980 chunk 421 optimal weight: 2.9990 chunk 516 optimal weight: 3.9990 chunk 803 optimal weight: 9.9990 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN A 103 ASN A 251 GLN A 276 GLN A 425 ASN A 475 GLN B 122 HIS B 157 GLN B 227 ASN B 228 GLN B 288 ASN B 298 ASN B 381 GLN D 25 GLN ** D 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 138 GLN D 262 ASN D 271 GLN D 347 HIS D 350 GLN D 482 ASN E 55 ASN E 86 GLN E 122 GLN E 139 GLN E 278 GLN ** E 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 435 GLN E 465 ASN ** E 495 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 503 GLN ** E 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 12 GLN ** G 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 116 GLN G 174 ASN G 269 GLN ** G 420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 504 GLN H 60 ASN ** H 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 402 ASN H 470 GLN H 522 ASN N 3 GLN N 13 GLN N 81 GLN N 114 GLN Q 172 GLN ** Q 365 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 461 ASN ** Z 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 161 HIS ** Z 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 438 GLN Z 460 GLN a 103 ASN a 113 HIS ** a 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 251 GLN a 276 GLN a 435 GLN a 475 GLN a 492 ASN a 500 GLN b 122 HIS b 195 ASN b 228 GLN b 234 ASN b 294 GLN b 302 GLN b 381 GLN ** b 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 464 GLN b 502 GLN d 138 GLN d 271 GLN d 301 GLN ** d 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 366 ASN d 406 HIS e 55 ASN e 86 GLN e 122 GLN e 139 GLN e 278 GLN e 298 ASN e 360 GLN e 435 GLN e 465 ASN e 495 HIS e 503 GLN ** e 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 71 GLN g 111 HIS g 116 GLN g 188 ASN ** g 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 269 GLN g 301 GLN g 396 GLN ** g 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 504 GLN ** h 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 30 GLN h 107 GLN h 119 GLN h 130 GLN h 209 GLN h 234 ASN h 272 ASN h 470 GLN q 4 HIS q 34 GLN q 41 GLN q 172 GLN q 365 HIS ** z 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** z 161 HIS ** z 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** z 294 GLN ** z 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** z 368 ASN z 380 ASN z 425 HIS z 460 GLN z 475 GLN ** T 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 37 HIS T 184 ASN ** T 396 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 109 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.1692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.055 69953 Z= 0.384 Angle : 0.668 9.168 94470 Z= 0.336 Chirality : 0.045 0.187 11206 Planarity : 0.005 0.048 12067 Dihedral : 8.534 178.954 9713 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.03 % Favored : 96.91 % Rotamer Outliers : 4.17 % 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: -0.48 (0.08), residues: 8920 helix: 0.62 (0.07), residues: 4601 sheet: -0.83 (0.14), residues: 1207 loop : -1.43 (0.10), residues: 3112 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17840 Ramachandran restraints generated. 8920 Oldfield, 0 Emsley, 8920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17840 Ramachandran restraints generated. 8920 Oldfield, 0 Emsley, 8920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1264 residues out of total 7485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 311 poor density : 953 time to evaluate : 7.285 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 311 outliers final: 137 residues processed: 1169 average time/residue: 1.5339 time to fit residues: 2376.2703 Evaluate side-chains 989 residues out of total 7485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 852 time to evaluate : 6.148 Switching outliers to nearest non-outliers outliers start: 137 outliers final: 112 residues processed: 27 average time/residue: 0.9118 time to fit residues: 46.0223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 885 random chunks: chunk 446 optimal weight: 9.9990 chunk 249 optimal weight: 0.9990 chunk 668 optimal weight: 0.9980 chunk 547 optimal weight: 0.8980 chunk 221 optimal weight: 0.8980 chunk 805 optimal weight: 0.9990 chunk 869 optimal weight: 20.0000 chunk 717 optimal weight: 0.9980 chunk 798 optimal weight: 0.9990 chunk 274 optimal weight: 4.9990 chunk 645 optimal weight: 0.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 164 ASN ** A 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 502 GLN D 25 GLN D 32 GLN ** E 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 495 HIS ** E 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 522 GLN ** G 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 226 HIS G 472 GLN H 21 GLN H 60 ASN ** H 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 365 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 95 ASN Z 161 HIS Z 294 GLN a 251 GLN a 492 ASN b 122 HIS b 195 ASN ** d 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 366 ASN e 360 GLN ** e 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 64 ASN g 111 HIS ** g 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 30 GLN h 107 GLN h 119 GLN h 130 GLN h 234 ASN h 241 ASN h 470 GLN n 83 ASN z 31 GLN ** z 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 6 HIS T 37 HIS ** T 396 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.1909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 69953 Z= 0.175 Angle : 0.555 12.450 94470 Z= 0.276 Chirality : 0.041 0.179 11206 Planarity : 0.004 0.044 12067 Dihedral : 7.982 175.577 9713 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.77 % Favored : 97.17 % Rotamer Outliers : 3.80 % 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: 0.20 (0.09), residues: 8920 helix: 1.18 (0.08), residues: 4582 sheet: -0.59 (0.14), residues: 1197 loop : -1.07 (0.11), residues: 3141 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17840 Ramachandran restraints generated. 8920 Oldfield, 0 Emsley, 8920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17840 Ramachandran restraints generated. 8920 Oldfield, 0 Emsley, 8920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1253 residues out of total 7485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 283 poor density : 970 time to evaluate : 6.289 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 283 outliers final: 143 residues processed: 1172 average time/residue: 1.4909 time to fit residues: 2329.2019 Evaluate side-chains 998 residues out of total 7485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 855 time to evaluate : 6.194 Switching outliers to nearest non-outliers outliers start: 143 outliers final: 119 residues processed: 26 average time/residue: 0.9477 time to fit residues: 45.7610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 885 random chunks: chunk 795 optimal weight: 8.9990 chunk 605 optimal weight: 3.9990 chunk 417 optimal weight: 3.9990 chunk 89 optimal weight: 6.9990 chunk 384 optimal weight: 3.9990 chunk 540 optimal weight: 5.9990 chunk 808 optimal weight: 5.9990 chunk 855 optimal weight: 8.9990 chunk 422 optimal weight: 2.9990 chunk 765 optimal weight: 4.9990 chunk 230 optimal weight: 2.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 227 ASN D 25 GLN E 122 GLN ** E 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 522 GLN ** G 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 17 GLN ** H 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 60 ASN ** H 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 365 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 95 ASN a 492 ASN b 195 ASN ** b 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 318 ASN d 366 ASN e 290 GLN e 291 GLN ** e 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 235 ASN ** g 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 107 GLN h 119 GLN h 130 GLN h 234 ASN q 475 ASN ** z 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 37 HIS ** T 396 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.2215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.056 69953 Z= 0.397 Angle : 0.655 8.906 94470 Z= 0.325 Chirality : 0.045 0.185 11206 Planarity : 0.004 0.042 12067 Dihedral : 8.107 177.374 9713 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.55 % Favored : 96.40 % Rotamer Outliers : 4.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.09), residues: 8920 helix: 0.93 (0.07), residues: 4589 sheet: -0.56 (0.14), residues: 1235 loop : -0.97 (0.11), residues: 3096 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17840 Ramachandran restraints generated. 8920 Oldfield, 0 Emsley, 8920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17840 Ramachandran restraints generated. 8920 Oldfield, 0 Emsley, 8920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1185 residues out of total 7485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 328 poor density : 857 time to evaluate : 6.407 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 328 outliers final: 180 residues processed: 1090 average time/residue: 1.5488 time to fit residues: 2263.8238 Evaluate side-chains 1012 residues out of total 7485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 180 poor density : 832 time to evaluate : 6.217 Switching outliers to nearest non-outliers outliers start: 180 outliers final: 138 residues processed: 42 average time/residue: 1.1557 time to fit residues: 78.8012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 885 random chunks: chunk 712 optimal weight: 3.9990 chunk 485 optimal weight: 0.7980 chunk 12 optimal weight: 5.9990 chunk 636 optimal weight: 4.9990 chunk 352 optimal weight: 8.9990 chunk 729 optimal weight: 7.9990 chunk 591 optimal weight: 0.9980 chunk 1 optimal weight: 7.9990 chunk 436 optimal weight: 6.9990 chunk 767 optimal weight: 5.9990 chunk 215 optimal weight: 5.9990 overall best weight: 3.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 32 GLN ** E 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 522 GLN ** G 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 17 GLN ** H 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 60 ASN ** H 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 272 ASN ** Q 365 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 161 HIS Z 214 HIS a 492 ASN b 195 ASN b 464 GLN ** d 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 226 HIS ** g 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 119 GLN h 130 GLN h 470 GLN q 359 GLN ** z 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 37 HIS T 52 ASN ** T 396 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.2391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.049 69953 Z= 0.359 Angle : 0.631 8.990 94470 Z= 0.314 Chirality : 0.045 0.252 11206 Planarity : 0.004 0.046 12067 Dihedral : 7.988 178.008 9713 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.41 % Favored : 96.55 % Rotamer Outliers : 4.43 % 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: 0.06 (0.09), residues: 8920 helix: 0.89 (0.07), residues: 4571 sheet: -0.52 (0.14), residues: 1229 loop : -0.88 (0.11), residues: 3120 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17840 Ramachandran restraints generated. 8920 Oldfield, 0 Emsley, 8920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17840 Ramachandran restraints generated. 8920 Oldfield, 0 Emsley, 8920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1196 residues out of total 7485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 331 poor density : 865 time to evaluate : 6.351 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 331 outliers final: 183 residues processed: 1117 average time/residue: 1.5323 time to fit residues: 2275.7424 Evaluate side-chains 1013 residues out of total 7485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 183 poor density : 830 time to evaluate : 6.215 Switching outliers to nearest non-outliers outliers start: 183 outliers final: 155 residues processed: 29 average time/residue: 0.9225 time to fit residues: 49.9045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 885 random chunks: chunk 287 optimal weight: 0.8980 chunk 770 optimal weight: 7.9990 chunk 169 optimal weight: 6.9990 chunk 502 optimal weight: 3.9990 chunk 211 optimal weight: 4.9990 chunk 856 optimal weight: 8.9990 chunk 710 optimal weight: 0.7980 chunk 396 optimal weight: 3.9990 chunk 71 optimal weight: 8.9990 chunk 283 optimal weight: 0.0370 chunk 449 optimal weight: 1.9990 overall best weight: 1.5462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN ** B 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 472 ASN E 122 GLN ** E 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 17 GLN ** H 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 60 ASN ** H 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 365 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 161 HIS a 164 ASN a 492 ASN b 195 ASN ** b 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 235 ASN ** g 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 119 GLN h 130 GLN ** z 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 37 HIS T 52 ASN ** T 396 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.2464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 69953 Z= 0.212 Angle : 0.572 12.899 94470 Z= 0.283 Chirality : 0.042 0.202 11206 Planarity : 0.004 0.056 12067 Dihedral : 7.578 172.751 9713 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.29 % Favored : 96.68 % Rotamer Outliers : 3.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.09), residues: 8920 helix: 1.16 (0.08), residues: 4571 sheet: -0.42 (0.15), residues: 1199 loop : -0.81 (0.11), residues: 3150 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17840 Ramachandran restraints generated. 8920 Oldfield, 0 Emsley, 8920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17840 Ramachandran restraints generated. 8920 Oldfield, 0 Emsley, 8920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1176 residues out of total 7485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 281 poor density : 895 time to evaluate : 6.393 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 281 outliers final: 174 residues processed: 1112 average time/residue: 1.4805 time to fit residues: 2212.7394 Evaluate side-chains 1000 residues out of total 7485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 174 poor density : 826 time to evaluate : 6.152 Switching outliers to nearest non-outliers outliers start: 174 outliers final: 159 residues processed: 16 average time/residue: 0.9876 time to fit residues: 32.1852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 885 random chunks: chunk 825 optimal weight: 10.0000 chunk 96 optimal weight: 0.9980 chunk 487 optimal weight: 6.9990 chunk 625 optimal weight: 0.9990 chunk 484 optimal weight: 4.9990 chunk 720 optimal weight: 0.4980 chunk 478 optimal weight: 0.7980 chunk 852 optimal weight: 3.9990 chunk 533 optimal weight: 10.0000 chunk 520 optimal weight: 1.9990 chunk 393 optimal weight: 6.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 288 ASN D 472 ASN ** E 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 522 GLN ** G 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 71 GLN G 276 GLN H 17 GLN ** H 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 60 ASN ** H 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 365 HIS ** Z 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 95 ASN Z 161 HIS a 164 ASN a 492 ASN b 195 ASN d 235 ASN e 72 ASN e 503 GLN e 515 GLN g 235 ASN ** g 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 107 GLN h 119 GLN h 130 GLN h 234 ASN h 241 ASN ** h 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 37 HIS T 52 ASN ** T 396 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.2533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 69953 Z= 0.176 Angle : 0.557 16.939 94470 Z= 0.274 Chirality : 0.041 0.192 11206 Planarity : 0.004 0.050 12067 Dihedral : 7.236 163.876 9713 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.09 % Favored : 96.88 % Rotamer Outliers : 3.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.09), residues: 8920 helix: 1.32 (0.08), residues: 4578 sheet: -0.29 (0.15), residues: 1170 loop : -0.69 (0.11), residues: 3172 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17840 Ramachandran restraints generated. 8920 Oldfield, 0 Emsley, 8920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17840 Ramachandran restraints generated. 8920 Oldfield, 0 Emsley, 8920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1159 residues out of total 7485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 262 poor density : 897 time to evaluate : 6.265 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 262 outliers final: 174 residues processed: 1116 average time/residue: 1.5130 time to fit residues: 2265.4838 Evaluate side-chains 1017 residues out of total 7485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 174 poor density : 843 time to evaluate : 6.197 Switching outliers to nearest non-outliers outliers start: 174 outliers final: 157 residues processed: 18 average time/residue: 1.1104 time to fit residues: 37.5404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 885 random chunks: chunk 527 optimal weight: 1.9990 chunk 340 optimal weight: 0.8980 chunk 509 optimal weight: 0.9980 chunk 256 optimal weight: 1.9990 chunk 167 optimal weight: 1.9990 chunk 165 optimal weight: 7.9990 chunk 542 optimal weight: 7.9990 chunk 581 optimal weight: 0.9990 chunk 421 optimal weight: 3.9990 chunk 79 optimal weight: 0.9980 chunk 670 optimal weight: 3.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 288 ASN D 472 ASN E 122 GLN ** E 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 17 GLN ** H 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 60 ASN ** H 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 331 GLN N 83 ASN ** Z 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 164 ASN a 492 ASN b 195 ASN e 503 GLN ** e 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 221 ASN g 235 ASN ** g 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 107 GLN h 119 GLN h 130 GLN h 234 ASN ** h 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 37 HIS T 52 ASN ** T 396 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.2618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 69953 Z= 0.183 Angle : 0.557 13.698 94470 Z= 0.274 Chirality : 0.041 0.246 11206 Planarity : 0.003 0.051 12067 Dihedral : 7.088 160.999 9713 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.17 % Favored : 96.80 % Rotamer Outliers : 3.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.09), residues: 8920 helix: 1.38 (0.08), residues: 4568 sheet: -0.30 (0.15), residues: 1220 loop : -0.60 (0.11), residues: 3132 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17840 Ramachandran restraints generated. 8920 Oldfield, 0 Emsley, 8920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17840 Ramachandran restraints generated. 8920 Oldfield, 0 Emsley, 8920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1127 residues out of total 7485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 248 poor density : 879 time to evaluate : 6.250 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 248 outliers final: 173 residues processed: 1081 average time/residue: 1.5162 time to fit residues: 2202.1034 Evaluate side-chains 1013 residues out of total 7485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 173 poor density : 840 time to evaluate : 6.455 Switching outliers to nearest non-outliers outliers start: 173 outliers final: 160 residues processed: 13 average time/residue: 0.9602 time to fit residues: 28.0897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 885 random chunks: chunk 775 optimal weight: 5.9990 chunk 817 optimal weight: 9.9990 chunk 745 optimal weight: 20.0000 chunk 794 optimal weight: 1.9990 chunk 816 optimal weight: 5.9990 chunk 478 optimal weight: 5.9990 chunk 346 optimal weight: 0.0970 chunk 624 optimal weight: 0.9990 chunk 243 optimal weight: 0.8980 chunk 718 optimal weight: 0.6980 chunk 751 optimal weight: 0.0170 overall best weight: 0.5418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 288 ASN D 472 ASN ** E 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 174 ASN H 17 GLN ** H 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 60 ASN ** H 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 386 GLN a 164 ASN a 492 ASN b 195 ASN d 318 ASN e 72 ASN ** e 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 111 HIS g 157 ASN ** g 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 119 GLN h 130 GLN h 234 ASN h 241 ASN ** h 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 37 HIS T 52 ASN ** T 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 191 GLN T 396 HIS Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.2724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.036 69953 Z= 0.144 Angle : 0.545 14.241 94470 Z= 0.266 Chirality : 0.041 0.271 11206 Planarity : 0.003 0.042 12067 Dihedral : 6.823 154.863 9713 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.84 % Favored : 97.14 % Rotamer Outliers : 2.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.09), residues: 8920 helix: 1.53 (0.08), residues: 4564 sheet: -0.21 (0.15), residues: 1207 loop : -0.52 (0.11), residues: 3149 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17840 Ramachandran restraints generated. 8920 Oldfield, 0 Emsley, 8920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17840 Ramachandran restraints generated. 8920 Oldfield, 0 Emsley, 8920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1134 residues out of total 7485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 211 poor density : 923 time to evaluate : 6.463 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 211 outliers final: 161 residues processed: 1107 average time/residue: 1.5549 time to fit residues: 2312.1374 Evaluate side-chains 1007 residues out of total 7485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 161 poor density : 846 time to evaluate : 6.268 Switching outliers to nearest non-outliers outliers start: 161 outliers final: 150 residues processed: 13 average time/residue: 0.8855 time to fit residues: 27.7959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 885 random chunks: chunk 792 optimal weight: 6.9990 chunk 521 optimal weight: 3.9990 chunk 840 optimal weight: 7.9990 chunk 513 optimal weight: 5.9990 chunk 398 optimal weight: 5.9990 chunk 584 optimal weight: 0.0060 chunk 881 optimal weight: 0.9990 chunk 811 optimal weight: 7.9990 chunk 702 optimal weight: 0.7980 chunk 72 optimal weight: 0.0020 chunk 542 optimal weight: 6.9990 overall best weight: 1.1608 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 288 ASN D 350 GLN D 472 ASN ** E 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 17 GLN ** H 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 60 ASN ** H 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 272 ASN ** Z 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 492 ASN b 195 ASN ** e 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 235 ASN ** g 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 107 GLN h 119 GLN h 130 GLN h 431 GLN ** h 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** z 368 ASN T 37 HIS T 52 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.2759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 69953 Z= 0.181 Angle : 0.556 11.261 94470 Z= 0.272 Chirality : 0.041 0.286 11206 Planarity : 0.003 0.042 12067 Dihedral : 6.752 153.863 9713 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.02 % Favored : 96.97 % Rotamer Outliers : 2.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.09), residues: 8920 helix: 1.51 (0.08), residues: 4570 sheet: -0.17 (0.15), residues: 1222 loop : -0.48 (0.11), residues: 3128 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17840 Ramachandran restraints generated. 8920 Oldfield, 0 Emsley, 8920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17840 Ramachandran restraints generated. 8920 Oldfield, 0 Emsley, 8920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1053 residues out of total 7485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 187 poor density : 866 time to evaluate : 6.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 187 outliers final: 153 residues processed: 1033 average time/residue: 1.5558 time to fit residues: 2167.6194 Evaluate side-chains 993 residues out of total 7485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 153 poor density : 840 time to evaluate : 6.186 Switching outliers to nearest non-outliers outliers start: 153 outliers final: 150 residues processed: 3 average time/residue: 1.5058 time to fit residues: 14.5546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 885 random chunks: chunk 430 optimal weight: 3.9990 chunk 557 optimal weight: 9.9990 chunk 747 optimal weight: 30.0000 chunk 215 optimal weight: 0.9990 chunk 647 optimal weight: 0.9990 chunk 103 optimal weight: 0.8980 chunk 195 optimal weight: 1.9990 chunk 703 optimal weight: 10.0000 chunk 294 optimal weight: 4.9990 chunk 722 optimal weight: 0.7980 chunk 89 optimal weight: 3.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 288 ASN D 472 ASN ** E 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 17 GLN ** H 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 60 ASN ** H 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 492 ASN b 195 ASN e 72 ASN ** e 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 111 HIS ** g 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 119 GLN h 130 GLN h 241 ASN ** h 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** z 368 ASN T 6 HIS T 52 ASN ** T 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.132937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.116449 restraints weight = 98946.610| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 1.58 r_work: 0.3179 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3058 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3480 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3480 r_free = 0.3480 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3480 r_free = 0.3480 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3480 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.2796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 69953 Z= 0.179 Angle : 0.558 11.210 94470 Z= 0.273 Chirality : 0.041 0.280 11206 Planarity : 0.003 0.044 12067 Dihedral : 6.639 151.873 9713 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.05 % Favored : 96.94 % Rotamer Outliers : 2.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.09), residues: 8920 helix: 1.51 (0.08), residues: 4578 sheet: -0.09 (0.15), residues: 1179 loop : -0.47 (0.11), residues: 3163 =============================================================================== Job complete usr+sys time: 30160.56 seconds wall clock time: 522 minutes 26.64 seconds (31346.64 seconds total)