Starting phenix.real_space_refine on Fri Mar 15 14:21:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nvn_12607/03_2024/7nvn_12607_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nvn_12607/03_2024/7nvn_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_12607/03_2024/7nvn_12607.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nvn_12607/03_2024/7nvn_12607.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nvn_12607/03_2024/7nvn_12607_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nvn_12607/03_2024/7nvn_12607_updated.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.007 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 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. 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: 0.23s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 30.75, per 1000 atoms: 0.44 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: 20.89 Conformation dependent library (CDL) restraints added in 10.8 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: 10.65 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: 27.04 Time building geometry restraints manager: 22.99 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 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: 2.960 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: 15.760 Check model and map are aligned: 0.780 Set scattering table: 0.480 Process input model: 149.850 Find NCS groups from input model: 6.470 Set up NCS constraints: 0.660 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:8.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 185.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7376 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 % Allowed : 9.46 % Favored : 88.89 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP n 101 HIS 0.007 0.001 HIS Z 161 PHE 0.022 0.001 PHE N 29 TYR 0.017 0.001 TYR T 106 ARG 0.004 0.000 ARG e 27 *********************** 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 : 6.195 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 PHE cc_start: 0.7697 (t80) cc_final: 0.7331 (t80) REVERT: A 51 ASP cc_start: 0.6466 (t0) cc_final: 0.5978 (t70) REVERT: A 66 GLU cc_start: 0.7343 (tt0) cc_final: 0.7103 (mm-30) REVERT: A 146 ASP cc_start: 0.6201 (p0) cc_final: 0.5976 (p0) REVERT: A 193 ASN cc_start: 0.7406 (m110) cc_final: 0.7182 (m110) REVERT: A 230 VAL cc_start: 0.7401 (m) cc_final: 0.7167 (t) REVERT: A 233 LYS cc_start: 0.7708 (mmtm) cc_final: 0.7145 (mmtt) REVERT: A 261 ASP cc_start: 0.6987 (p0) cc_final: 0.6700 (t0) REVERT: A 277 LYS cc_start: 0.8186 (mttt) cc_final: 0.7874 (mttm) REVERT: A 321 LYS cc_start: 0.7917 (mtmt) cc_final: 0.7547 (tptp) REVERT: A 354 GLU cc_start: 0.6665 (mm-30) cc_final: 0.6459 (mm-30) REVERT: A 384 MET cc_start: 0.8098 (ttt) cc_final: 0.7815 (ttt) REVERT: A 430 MET cc_start: 0.6447 (mmm) cc_final: 0.5445 (mmm) REVERT: A 459 ASP cc_start: 0.8123 (t0) cc_final: 0.7872 (t0) REVERT: A 505 GLU cc_start: 0.7326 (mt-10) cc_final: 0.7059 (mt-10) REVERT: A 528 ASP cc_start: 0.7439 (p0) cc_final: 0.6873 (t0) REVERT: A 531 ILE cc_start: 0.8740 (mt) cc_final: 0.8538 (mp) REVERT: B 19 GLU cc_start: 0.7587 (mt-10) cc_final: 0.7354 (mt-10) REVERT: B 87 MET cc_start: 0.7838 (ttp) cc_final: 0.7445 (ptm) REVERT: B 160 MET cc_start: 0.8026 (mmm) cc_final: 0.7807 (mmm) REVERT: B 227 ASN cc_start: 0.7999 (t0) cc_final: 0.7324 (t0) REVERT: B 246 THR cc_start: 0.7280 (t) cc_final: 0.6872 (m) REVERT: B 248 LYS cc_start: 0.7974 (mtpt) cc_final: 0.7575 (mtmt) REVERT: B 278 LYS cc_start: 0.6820 (tppt) cc_final: 0.6592 (ttmt) REVERT: B 301 GLU cc_start: 0.7313 (tt0) cc_final: 0.7026 (mt-10) REVERT: B 402 LYS cc_start: 0.7646 (mtmm) cc_final: 0.7135 (mmtt) REVERT: B 414 GLU cc_start: 0.6597 (mp0) cc_final: 0.5894 (mp0) REVERT: B 445 MET cc_start: 0.7864 (tpp) cc_final: 0.7584 (tpp) REVERT: B 456 TYR cc_start: 0.8716 (m-80) cc_final: 0.8403 (m-10) REVERT: B 485 ILE cc_start: 0.7559 (pt) cc_final: 0.7323 (pp) REVERT: D 32 GLN cc_start: 0.7454 (mt0) cc_final: 0.7206 (mm110) REVERT: D 65 LYS cc_start: 0.8137 (mtmm) cc_final: 0.7919 (mtpt) REVERT: D 222 GLU cc_start: 0.7435 (tt0) cc_final: 0.6954 (mt-10) REVERT: D 224 VAL cc_start: 0.8090 (t) cc_final: 0.7827 (m) REVERT: D 257 LYS cc_start: 0.7699 (mmtm) cc_final: 0.7306 (tmmt) REVERT: D 274 ARG cc_start: 0.7179 (OUTLIER) cc_final: 0.6896 (ttm-80) REVERT: D 358 SER cc_start: 0.7794 (m) cc_final: 0.7508 (t) REVERT: D 368 ASN cc_start: 0.7127 (m110) cc_final: 0.6529 (m110) REVERT: D 375 LYS cc_start: 0.8563 (mtpt) cc_final: 0.8324 (ttmt) REVERT: D 384 LYS cc_start: 0.7761 (mptt) cc_final: 0.7029 (mppt) REVERT: D 458 MET cc_start: 0.7730 (mmm) cc_final: 0.7372 (mpp) REVERT: D 467 GLU cc_start: 0.7093 (tt0) cc_final: 0.6788 (mt-10) REVERT: D 496 ARG cc_start: 0.8038 (ttp80) cc_final: 0.7742 (tmm160) REVERT: E 93 GLU cc_start: 0.6811 (mm-30) cc_final: 0.6546 (mm-30) REVERT: E 121 GLU cc_start: 0.7303 (tt0) cc_final: 0.6833 (tt0) REVERT: E 125 ASP cc_start: 0.7896 (m-30) cc_final: 0.7647 (m-30) REVERT: E 263 LYS cc_start: 0.7829 (ttmt) cc_final: 0.7154 (tttt) REVERT: E 290 GLN cc_start: 0.7388 (tp-100) cc_final: 0.6985 (tm-30) REVERT: E 381 ARG cc_start: 0.7913 (ttp80) cc_final: 0.7580 (ttt-90) REVERT: E 439 LYS cc_start: 0.7929 (mtmm) cc_final: 0.7556 (mptt) REVERT: E 526 MET cc_start: 0.8435 (ttt) cc_final: 0.8132 (ttt) REVERT: G 9 VAL cc_start: 0.8319 (p) cc_final: 0.8005 (t) REVERT: G 15 LYS cc_start: 0.7630 (mmmt) cc_final: 0.6923 (mtmm) REVERT: G 17 GLU cc_start: 0.7148 (mp0) cc_final: 0.6585 (mp0) REVERT: G 18 SER cc_start: 0.8176 (p) cc_final: 0.7632 (m) REVERT: G 68 ARG cc_start: 0.8049 (ttp-170) cc_final: 0.7664 (ptp90) REVERT: G 82 GLU cc_start: 0.7675 (mm-30) cc_final: 0.7426 (mm-30) REVERT: G 110 GLU cc_start: 0.7587 (tt0) cc_final: 0.7161 (tp30) REVERT: G 192 GLU cc_start: 0.7463 (pt0) cc_final: 0.6676 (pp20) REVERT: G 208 ILE cc_start: 0.7549 (pt) cc_final: 0.7133 (pp) REVERT: G 247 TYR cc_start: 0.8973 (t80) cc_final: 0.8757 (t80) REVERT: G 248 LYS cc_start: 0.8134 (mtpt) cc_final: 0.7753 (mmpt) REVERT: G 260 ARG cc_start: 0.7166 (mtt90) cc_final: 0.6882 (mtm-85) REVERT: G 270 MET cc_start: 0.7397 (mtp) cc_final: 0.7043 (mtp) REVERT: G 276 GLN cc_start: 0.7415 (tt0) cc_final: 0.7101 (tm-30) REVERT: G 277 GLN cc_start: 0.7231 (tp-100) cc_final: 0.6701 (mp10) REVERT: G 306 ARG cc_start: 0.7636 (ttp-170) cc_final: 0.7388 (ttp80) REVERT: G 388 GLU cc_start: 0.7493 (tt0) cc_final: 0.7165 (tt0) REVERT: G 429 MET cc_start: 0.7348 (mtm) cc_final: 0.6936 (mtm) REVERT: G 508 THR cc_start: 0.8033 (m) cc_final: 0.7829 (m) REVERT: G 511 GLU cc_start: 0.7512 (mm-30) cc_final: 0.7035 (mp0) REVERT: H 5 PRO cc_start: 0.6767 (Cg_exo) cc_final: 0.6450 (Cg_endo) REVERT: H 119 GLN cc_start: 0.7766 (mm-40) cc_final: 0.7538 (mm-40) REVERT: H 160 MET cc_start: 0.7963 (mtp) cc_final: 0.7609 (mtp) REVERT: H 177 LYS cc_start: 0.7231 (ttmt) cc_final: 0.6781 (tmmt) REVERT: H 279 GLU cc_start: 0.7210 (tp30) cc_final: 0.6773 (mt-10) REVERT: H 317 GLU cc_start: 0.7521 (mp0) cc_final: 0.7256 (tt0) REVERT: H 344 ARG cc_start: 0.7239 (ttm110) cc_final: 0.6920 (mtt-85) REVERT: H 349 GLU cc_start: 0.7794 (tt0) cc_final: 0.7550 (tt0) REVERT: H 368 LYS cc_start: 0.7940 (mttt) cc_final: 0.7402 (mmtp) REVERT: H 379 GLU cc_start: 0.7063 (tp30) cc_final: 0.6851 (tm-30) REVERT: H 383 GLU cc_start: 0.7541 (mm-30) cc_final: 0.7333 (mm-30) REVERT: H 482 GLU cc_start: 0.7636 (mt-10) cc_final: 0.7384 (mt-10) REVERT: H 489 GLU cc_start: 0.7597 (mt-10) cc_final: 0.7308 (mp0) REVERT: H 497 MET cc_start: 0.7443 (tpp) cc_final: 0.6959 (tpt) REVERT: H 518 GLU cc_start: 0.8114 (tt0) cc_final: 0.7913 (tt0) REVERT: Q 31 ARG cc_start: 0.7352 (mmp-170) cc_final: 0.6679 (mmt90) REVERT: Q 77 GLU cc_start: 0.7161 (mm-30) cc_final: 0.6839 (mt-10) REVERT: Q 142 ILE cc_start: 0.7671 (mt) cc_final: 0.7460 (mt) REVERT: Q 193 ASP cc_start: 0.6842 (m-30) cc_final: 0.6402 (m-30) REVERT: Q 249 MET cc_start: 0.7469 (ptp) cc_final: 0.6746 (mmm) REVERT: Q 254 LYS cc_start: 0.8464 (tttm) cc_final: 0.7436 (ttpt) REVERT: Q 281 LYS cc_start: 0.7450 (ttmt) cc_final: 0.7209 (tptp) REVERT: Q 296 LYS cc_start: 0.7652 (pttm) cc_final: 0.7445 (pttt) REVERT: Q 316 ASN cc_start: 0.8038 (OUTLIER) cc_final: 0.7808 (p0) REVERT: Q 318 LYS cc_start: 0.8035 (pttm) cc_final: 0.7496 (ptmm) REVERT: Q 387 ASP cc_start: 0.7060 (t0) cc_final: 0.6837 (t0) REVERT: Q 481 ASP cc_start: 0.7303 (t0) cc_final: 0.7012 (t0) REVERT: Z 108 LEU cc_start: 0.8057 (tt) cc_final: 0.7777 (tp) REVERT: Z 163 GLU cc_start: 0.6600 (tp30) cc_final: 0.6279 (tp30) REVERT: Z 195 GLU cc_start: 0.7863 (pt0) cc_final: 0.7385 (pt0) REVERT: Z 223 LYS cc_start: 0.7573 (mptt) cc_final: 0.7299 (mmtt) REVERT: Z 241 LYS cc_start: 0.8533 (ttmt) cc_final: 0.7661 (pttp) REVERT: Z 264 ARG cc_start: 0.7260 (mtp85) cc_final: 0.6901 (mtp-110) REVERT: Z 265 LYS cc_start: 0.7333 (tptp) cc_final: 0.7104 (ttpp) REVERT: Z 272 LYS cc_start: 0.7330 (mmtp) cc_final: 0.6842 (mtpp) REVERT: Z 303 ASP cc_start: 0.7314 (t70) cc_final: 0.6847 (OUTLIER) REVERT: Z 307 LYS cc_start: 0.7832 (mmtp) cc_final: 0.7471 (mtpt) REVERT: Z 322 GLU cc_start: 0.7447 (tt0) cc_final: 0.7054 (tt0) REVERT: Z 352 GLU cc_start: 0.8023 (tt0) cc_final: 0.7806 (tt0) REVERT: Z 359 LYS cc_start: 0.7787 (mttt) cc_final: 0.7205 (mttp) REVERT: Z 381 LYS cc_start: 0.8325 (tptt) cc_final: 0.7989 (tppp) REVERT: Z 495 TRP cc_start: 0.8051 (m100) cc_final: 0.7503 (m100) REVERT: a 10 ASP cc_start: 0.7395 (m-30) cc_final: 0.7087 (p0) REVERT: a 181 TYR cc_start: 0.7775 (p90) cc_final: 0.7555 (p90) REVERT: a 265 GLN cc_start: 0.7288 (pt0) cc_final: 0.6984 (tp40) REVERT: a 321 LYS cc_start: 0.7841 (mmtm) cc_final: 0.7622 (tptp) REVERT: a 361 LEU cc_start: 0.8465 (OUTLIER) cc_final: 0.8223 (pt) REVERT: a 443 ARG cc_start: 0.7387 (ttp80) cc_final: 0.7107 (ttt90) REVERT: a 510 LYS cc_start: 0.7627 (mmtt) cc_final: 0.7410 (mptp) REVERT: b 6 LEU cc_start: 0.5020 (tp) cc_final: 0.4305 (tp) REVERT: b 17 ASP cc_start: 0.6873 (p0) cc_final: 0.6550 (p0) REVERT: b 89 ARG cc_start: 0.7858 (ttp80) cc_final: 0.7532 (tmm160) REVERT: b 93 ASP cc_start: 0.7415 (m-30) cc_final: 0.6700 (m-30) REVERT: b 114 GLU cc_start: 0.7909 (pt0) cc_final: 0.7419 (tt0) REVERT: b 173 THR cc_start: 0.8231 (t) cc_final: 0.8026 (t) REVERT: b 185 GLU cc_start: 0.7259 (mt-10) cc_final: 0.6837 (mm-30) REVERT: b 223 LYS cc_start: 0.8426 (mttm) cc_final: 0.8085 (mtpt) REVERT: b 248 LYS cc_start: 0.8016 (mtpt) cc_final: 0.7759 (mtmt) REVERT: b 254 SER cc_start: 0.8592 (p) cc_final: 0.8388 (p) REVERT: b 301 GLU cc_start: 0.7531 (tt0) cc_final: 0.7234 (tt0) REVERT: b 403 ASP cc_start: 0.8128 (t0) cc_final: 0.7921 (t0) REVERT: b 436 MET cc_start: 0.8048 (mtt) cc_final: 0.7843 (mtt) REVERT: b 445 MET cc_start: 0.8095 (tpp) cc_final: 0.7855 (tpp) REVERT: b 478 LEU cc_start: 0.8048 (mt) cc_final: 0.7744 (mm) REVERT: b 516 ARG cc_start: 0.7570 (mtp85) cc_final: 0.7366 (mtp180) REVERT: d 42 LYS cc_start: 0.7033 (tttp) cc_final: 0.6527 (tptt) REVERT: d 63 ASP cc_start: 0.7124 (m-30) cc_final: 0.6902 (m-30) REVERT: d 81 MET cc_start: 0.7919 (ptm) cc_final: 0.7661 (ptm) REVERT: d 90 MET cc_start: 0.8052 (mtm) cc_final: 0.7757 (mtp) REVERT: d 93 GLU cc_start: 0.7144 (mm-30) cc_final: 0.6731 (mm-30) REVERT: d 132 ILE cc_start: 0.8266 (mt) cc_final: 0.7966 (mp) REVERT: d 285 ASN cc_start: 0.7914 (t0) cc_final: 0.7471 (t0) REVERT: d 334 GLU cc_start: 0.7331 (tp30) cc_final: 0.6760 (pm20) REVERT: d 384 LYS cc_start: 0.7661 (mmtp) cc_final: 0.7099 (mmpt) REVERT: e 23 ASP cc_start: 0.7967 (m-30) cc_final: 0.7528 (m-30) REVERT: e 27 ARG cc_start: 0.7903 (ttp-170) cc_final: 0.7384 (ttt180) REVERT: e 29 MET cc_start: 0.7749 (mtp) cc_final: 0.7181 (mtp) REVERT: e 93 GLU cc_start: 0.7107 (mm-30) cc_final: 0.6709 (mt-10) REVERT: e 96 LYS cc_start: 0.7745 (tttm) cc_final: 0.6997 (ttmt) REVERT: e 121 GLU cc_start: 0.6945 (tt0) cc_final: 0.6599 (tt0) REVERT: e 126 ARG cc_start: 0.7329 (mtm180) cc_final: 0.6800 (mtp85) REVERT: e 150 LYS cc_start: 0.7708 (ttmt) cc_final: 0.7282 (ttpt) REVERT: e 187 GLU cc_start: 0.7118 (tt0) cc_final: 0.6670 (pt0) REVERT: e 449 ARG cc_start: 0.7448 (mtt180) cc_final: 0.7183 (mtt-85) REVERT: e 464 GLU cc_start: 0.7177 (tt0) cc_final: 0.6735 (tt0) REVERT: e 478 ARG cc_start: 0.7334 (ttp-170) cc_final: 0.7017 (ttm170) REVERT: e 502 LYS cc_start: 0.6811 (tttm) cc_final: 0.6465 (ttmm) REVERT: e 515 GLN cc_start: 0.7943 (tp40) cc_final: 0.7697 (tp40) REVERT: e 532 ASP cc_start: 0.8211 (t0) cc_final: 0.7800 (t0) REVERT: g 8 LEU cc_start: 0.7856 (mt) cc_final: 0.7353 (mm) REVERT: g 48 LYS cc_start: 0.8120 (mtmt) cc_final: 0.7838 (mttp) REVERT: g 80 MET cc_start: 0.8509 (mmm) cc_final: 0.8222 (mmm) REVERT: g 111 HIS cc_start: 0.6855 (t-90) cc_final: 0.6648 (t70) REVERT: g 167 ARG cc_start: 0.7396 (mtt-85) cc_final: 0.7061 (mtm-85) REVERT: g 186 GLU cc_start: 0.7046 (tt0) cc_final: 0.6501 (tt0) REVERT: g 191 LYS cc_start: 0.7814 (mtpt) cc_final: 0.7304 (mptt) REVERT: g 202 GLU cc_start: 0.6826 (mm-30) cc_final: 0.6452 (mm-30) REVERT: g 208 ILE cc_start: 0.7193 (pt) cc_final: 0.6260 (pp) REVERT: g 211 ASP cc_start: 0.7493 (p0) cc_final: 0.7199 (p0) REVERT: g 219 MET cc_start: 0.8505 (ttp) cc_final: 0.8224 (ttp) REVERT: g 277 GLN cc_start: 0.6941 (tp-100) cc_final: 0.6203 (pt0) REVERT: g 294 LYS cc_start: 0.8039 (mmtp) cc_final: 0.7694 (mmtp) REVERT: g 381 LYS cc_start: 0.7710 (tppt) cc_final: 0.7364 (mptt) REVERT: g 395 MET cc_start: 0.8247 (mtm) cc_final: 0.7996 (mtp) REVERT: g 396 GLN cc_start: 0.7778 (mm-40) cc_final: 0.7566 (mm-40) REVERT: g 476 GLU cc_start: 0.7423 (pm20) cc_final: 0.6940 (mm-30) REVERT: h 10 LYS cc_start: 0.7957 (ttmt) cc_final: 0.7521 (ttpt) REVERT: h 17 GLN cc_start: 0.8040 (tt0) cc_final: 0.7663 (tt0) REVERT: h 30 GLN cc_start: 0.7701 (mm-40) cc_final: 0.7372 (mm110) REVERT: h 51 ASP cc_start: 0.7405 (p0) cc_final: 0.6758 (p0) REVERT: h 84 LYS cc_start: 0.7579 (mttt) cc_final: 0.7354 (mttt) REVERT: h 119 GLN cc_start: 0.8034 (mm-40) cc_final: 0.7815 (mm110) REVERT: h 177 LYS cc_start: 0.7824 (tmtt) cc_final: 0.7623 (ttpp) REVERT: h 217 LYS cc_start: 0.8964 (ttpt) cc_final: 0.8686 (ttpt) REVERT: h 247 LYS cc_start: 0.8312 (pttp) cc_final: 0.7946 (ptpp) REVERT: h 254 GLU cc_start: 0.8056 (tm-30) cc_final: 0.7821 (tp30) REVERT: h 276 ASP cc_start: 0.7156 (t0) cc_final: 0.6869 (m-30) REVERT: h 320 LYS cc_start: 0.7493 (mmtt) cc_final: 0.7226 (mtpp) REVERT: h 340 ASP cc_start: 0.7736 (OUTLIER) cc_final: 0.7528 (p0) REVERT: h 344 ARG cc_start: 0.7235 (ttm110) cc_final: 0.6509 (mtm-85) REVERT: h 356 GLU cc_start: 0.7234 (mt-10) cc_final: 0.7000 (mt-10) REVERT: h 368 LYS cc_start: 0.7593 (mttt) cc_final: 0.7015 (mtpp) REVERT: h 383 GLU cc_start: 0.7359 (mm-30) cc_final: 0.7061 (mm-30) REVERT: h 440 LYS cc_start: 0.8211 (tptt) cc_final: 0.7842 (tppt) REVERT: h 518 GLU cc_start: 0.8009 (tt0) cc_final: 0.7796 (tt0) REVERT: q 17 GLU cc_start: 0.7502 (tt0) cc_final: 0.7297 (tm-30) REVERT: q 31 ARG cc_start: 0.7396 (mmp-170) cc_final: 0.6644 (mtt180) REVERT: q 61 GLU cc_start: 0.7191 (mt-10) cc_final: 0.6940 (mt-10) REVERT: q 66 THR cc_start: 0.7946 (t) cc_final: 0.7706 (t) REVERT: q 117 GLU cc_start: 0.7087 (tt0) cc_final: 0.6551 (mt-10) REVERT: q 212 ILE cc_start: 0.8367 (OUTLIER) cc_final: 0.8060 (mm) REVERT: q 249 MET cc_start: 0.7411 (ptp) cc_final: 0.7092 (ptp) REVERT: q 277 ASP cc_start: 0.8405 (t70) cc_final: 0.8048 (t0) REVERT: q 406 LYS cc_start: 0.7652 (ptmt) cc_final: 0.6817 (mmtm) REVERT: q 443 GLU cc_start: 0.7142 (tm-30) cc_final: 0.6407 (mp0) REVERT: q 483 GLU cc_start: 0.7207 (mp0) cc_final: 0.6784 (mm-30) REVERT: q 505 TYR cc_start: 0.8126 (t80) cc_final: 0.7769 (t80) REVERT: z 10 LYS cc_start: 0.7992 (mtmt) cc_final: 0.7431 (pmtt) REVERT: z 31 GLN cc_start: 0.7575 (tt0) cc_final: 0.7146 (tt0) REVERT: z 32 ASP cc_start: 0.7069 (t0) cc_final: 0.6850 (m-30) REVERT: z 66 GLU cc_start: 0.7609 (mm-30) cc_final: 0.7407 (mm-30) REVERT: z 98 ILE cc_start: 0.8070 (mt) cc_final: 0.7861 (mm) REVERT: z 181 LYS cc_start: 0.7052 (mttt) cc_final: 0.6062 (mmmt) REVERT: z 203 ASP cc_start: 0.8045 (m-30) cc_final: 0.7808 (m-30) REVERT: z 220 ASP cc_start: 0.7243 (m-30) cc_final: 0.6882 (t0) REVERT: z 272 LYS cc_start: 0.7996 (mmtp) cc_final: 0.7674 (mtpp) REVERT: z 307 LYS cc_start: 0.8017 (mmtp) cc_final: 0.6940 (ttpt) REVERT: z 359 LYS cc_start: 0.7790 (mttt) cc_final: 0.7073 (mtmm) REVERT: z 517 LEU cc_start: 0.8312 (mt) cc_final: 0.8029 (mm) REVERT: T 16 ILE cc_start: 0.8356 (mt) cc_final: 0.8120 (mm) REVERT: T 48 ASN cc_start: 0.6404 (t0) cc_final: 0.6053 (t0) REVERT: T 122 LYS cc_start: 0.8544 (mtmm) cc_final: 0.8237 (mtpp) REVERT: T 131 GLN cc_start: 0.8379 (tt0) cc_final: 0.8136 (tt0) REVERT: T 154 LYS cc_start: 0.8434 (mmtm) cc_final: 0.7830 (mtpt) REVERT: T 167 PHE cc_start: 0.8288 (m-80) cc_final: 0.7865 (m-80) REVERT: T 414 ASN cc_start: 0.7703 (m-40) cc_final: 0.7489 (m110) outliers start: 123 outliers final: 52 residues processed: 1588 average time/residue: 1.6354 time to fit residues: 3322.5895 Evaluate side-chains 1102 residues out of total 7485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 1046 time to evaluate : 6.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 166 ASP Chi-restraints excluded: chain A residue 284 ASN Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 134 THR Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 184 SER Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 273 ASP Chi-restraints excluded: chain D residue 274 ARG Chi-restraints excluded: chain D residue 536 VAL Chi-restraints excluded: chain E residue 367 THR Chi-restraints excluded: chain E residue 418 VAL Chi-restraints excluded: chain G residue 7 VAL Chi-restraints excluded: chain G residue 96 THR Chi-restraints excluded: chain G residue 332 VAL Chi-restraints excluded: chain G residue 440 VAL Chi-restraints excluded: chain H residue 251 ASP Chi-restraints excluded: chain H residue 341 VAL Chi-restraints excluded: chain H residue 400 ILE Chi-restraints excluded: chain N residue 83 ASN Chi-restraints excluded: chain Q residue 170 SER Chi-restraints excluded: chain Q residue 316 ASN Chi-restraints excluded: chain Z residue 4 VAL Chi-restraints excluded: chain Z residue 407 VAL Chi-restraints excluded: chain Z residue 408 VAL Chi-restraints excluded: chain Z residue 488 VAL Chi-restraints excluded: chain a residue 166 ASP Chi-restraints excluded: chain a residue 361 LEU Chi-restraints excluded: chain b residue 66 ASP Chi-restraints excluded: chain b residue 326 VAL Chi-restraints excluded: chain d residue 71 THR Chi-restraints excluded: chain d residue 168 THR Chi-restraints excluded: chain d residue 385 THR Chi-restraints excluded: chain d residue 430 ILE Chi-restraints excluded: chain e residue 145 ILE Chi-restraints excluded: chain e residue 228 VAL Chi-restraints excluded: chain e residue 418 VAL Chi-restraints excluded: chain e residue 507 ILE Chi-restraints excluded: chain g residue 96 THR Chi-restraints excluded: chain g residue 310 THR Chi-restraints excluded: chain g residue 440 VAL Chi-restraints excluded: chain h residue 32 ILE Chi-restraints excluded: chain h residue 211 VAL Chi-restraints excluded: chain h residue 340 ASP Chi-restraints excluded: chain h residue 473 THR Chi-restraints excluded: chain q residue 170 SER Chi-restraints excluded: chain q residue 212 ILE Chi-restraints excluded: chain q residue 234 VAL Chi-restraints excluded: chain z residue 488 VAL Chi-restraints excluded: chain T residue 143 THR 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: 0.6980 chunk 372 optimal weight: 7.9990 chunk 229 optimal weight: 6.9990 chunk 452 optimal weight: 9.9990 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: 0.4980 chunk 803 optimal weight: 10.0000 overall best weight: 2.1784 ------------------------------------------------------------------------------- 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 138 GLN 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 269 GLN G 277 GLN ** G 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 504 GLN ** H 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 53 ASN 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 ** 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 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 228 GLN b 234 ASN b 294 GLN b 302 GLN b 381 GLN b 464 GLN b 502 GLN d 138 GLN d 271 GLN ** d 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 366 ASN d 406 HIS d 472 ASN 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 116 GLN g 188 ASN g 269 GLN g 301 GLN ** g 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 504 GLN ** h 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 107 GLN h 130 GLN h 209 GLN h 234 ASN h 272 ASN h 470 GLN 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 T 37 HIS T 184 ASN T 190 HIS T 396 HIS Total number of N/Q/H flips: 108 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7424 moved from start: 0.1289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 69953 Z= 0.268 Angle : 0.599 7.892 94470 Z= 0.301 Chirality : 0.043 0.191 11206 Planarity : 0.004 0.046 12067 Dihedral : 8.641 178.878 9791 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.65 % Favored : 97.29 % Rotamer: Outliers : 3.06 % Allowed : 16.48 % Favored : 80.46 % 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: -0.31 (0.09), residues: 8920 helix: 0.83 (0.07), residues: 4585 sheet: -0.81 (0.14), residues: 1172 loop : -1.45 (0.10), residues: 3163 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP g 168 HIS 0.012 0.001 HIS G 420 PHE 0.025 0.002 PHE a 167 TYR 0.014 0.002 TYR e 420 ARG 0.007 0.000 ARG E 132 *********************** 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 1292 residues out of total 7485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 228 poor density : 1064 time to evaluate : 6.256 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 PHE cc_start: 0.7682 (t80) cc_final: 0.7262 (t80) REVERT: A 51 ASP cc_start: 0.6486 (t0) cc_final: 0.6002 (t70) REVERT: A 207 GLU cc_start: 0.7337 (mt-10) cc_final: 0.6849 (mt-10) REVERT: A 230 VAL cc_start: 0.7379 (OUTLIER) cc_final: 0.7052 (t) REVERT: A 261 ASP cc_start: 0.6758 (p0) cc_final: 0.6407 (t0) REVERT: A 277 LYS cc_start: 0.7635 (mttt) cc_final: 0.7368 (mttm) REVERT: A 321 LYS cc_start: 0.8003 (mtmt) cc_final: 0.7717 (tptp) REVERT: A 354 GLU cc_start: 0.6584 (mm-30) cc_final: 0.6209 (tp30) REVERT: A 384 MET cc_start: 0.8139 (ttt) cc_final: 0.7853 (ttt) REVERT: A 430 MET cc_start: 0.6219 (mmm) cc_final: 0.5289 (mmm) REVERT: A 433 ARG cc_start: 0.6951 (OUTLIER) cc_final: 0.6056 (mmm-85) REVERT: A 459 ASP cc_start: 0.8185 (t0) cc_final: 0.7944 (t0) REVERT: A 528 ASP cc_start: 0.7439 (p0) cc_final: 0.6782 (t0) REVERT: B 19 GLU cc_start: 0.7467 (mt-10) cc_final: 0.7265 (mt-10) REVERT: B 77 ASP cc_start: 0.7617 (OUTLIER) cc_final: 0.7306 (m-30) REVERT: B 87 MET cc_start: 0.7881 (ttp) cc_final: 0.7517 (ptm) REVERT: B 248 LYS cc_start: 0.7967 (mtpt) cc_final: 0.7599 (mtmt) REVERT: B 278 LYS cc_start: 0.6989 (tppt) cc_final: 0.6755 (tttt) REVERT: B 301 GLU cc_start: 0.7428 (tt0) cc_final: 0.7081 (tt0) REVERT: B 402 LYS cc_start: 0.7727 (mtmm) cc_final: 0.7140 (mmtt) REVERT: B 414 GLU cc_start: 0.6742 (mp0) cc_final: 0.6180 (mp0) REVERT: B 445 MET cc_start: 0.7714 (tpp) cc_final: 0.7414 (tpp) REVERT: B 456 TYR cc_start: 0.8708 (m-80) cc_final: 0.8362 (m-10) REVERT: D 32 GLN cc_start: 0.7546 (mt0) cc_final: 0.7290 (mm-40) REVERT: D 65 LYS cc_start: 0.8254 (mtmm) cc_final: 0.7977 (mtpt) REVERT: D 82 GLN cc_start: 0.8217 (OUTLIER) cc_final: 0.7634 (mm-40) REVERT: D 196 ASP cc_start: 0.7681 (t0) cc_final: 0.6659 (p0) REVERT: D 222 GLU cc_start: 0.7405 (tt0) cc_final: 0.6940 (mt-10) REVERT: D 257 LYS cc_start: 0.7716 (mmtm) cc_final: 0.7370 (ttpp) REVERT: D 274 ARG cc_start: 0.7161 (OUTLIER) cc_final: 0.6897 (ttm-80) REVERT: D 358 SER cc_start: 0.7812 (m) cc_final: 0.7521 (t) REVERT: D 368 ASN cc_start: 0.7065 (m110) cc_final: 0.6502 (m110) REVERT: D 375 LYS cc_start: 0.8485 (mtpt) cc_final: 0.8257 (ttmt) REVERT: D 384 LYS cc_start: 0.7676 (mptt) cc_final: 0.6956 (mppt) REVERT: D 458 MET cc_start: 0.7933 (mmm) cc_final: 0.7573 (mpp) REVERT: D 496 ARG cc_start: 0.8052 (ttp80) cc_final: 0.7754 (tmm160) REVERT: E 20 LYS cc_start: 0.8052 (tttp) cc_final: 0.7771 (ttpt) REVERT: E 21 ASP cc_start: 0.7327 (t0) cc_final: 0.7063 (t0) REVERT: E 93 GLU cc_start: 0.6898 (mm-30) cc_final: 0.6545 (mm-30) REVERT: E 121 GLU cc_start: 0.7283 (tt0) cc_final: 0.6731 (tt0) REVERT: E 125 ASP cc_start: 0.7990 (m-30) cc_final: 0.7702 (m-30) REVERT: E 198 ASP cc_start: 0.7879 (OUTLIER) cc_final: 0.7675 (t70) REVERT: E 263 LYS cc_start: 0.7809 (ttmt) cc_final: 0.7133 (tttt) REVERT: E 290 GLN cc_start: 0.7413 (tp-100) cc_final: 0.7070 (tm-30) REVERT: E 381 ARG cc_start: 0.7984 (ttp80) cc_final: 0.7604 (ttt-90) REVERT: E 439 LYS cc_start: 0.7905 (mtmm) cc_final: 0.7564 (mptt) REVERT: G 9 VAL cc_start: 0.8362 (p) cc_final: 0.7889 (t) REVERT: G 15 LYS cc_start: 0.7580 (mmmt) cc_final: 0.6915 (mtmm) REVERT: G 17 GLU cc_start: 0.7044 (mp0) cc_final: 0.6596 (mp0) REVERT: G 71 GLN cc_start: 0.8185 (OUTLIER) cc_final: 0.7882 (tt0) REVERT: G 81 ILE cc_start: 0.8525 (OUTLIER) cc_final: 0.8233 (mp) REVERT: G 82 GLU cc_start: 0.7725 (mm-30) cc_final: 0.7475 (mm-30) REVERT: G 110 GLU cc_start: 0.7586 (tt0) cc_final: 0.7170 (tp30) REVERT: G 192 GLU cc_start: 0.7502 (pt0) cc_final: 0.6714 (pp20) REVERT: G 208 ILE cc_start: 0.7858 (pt) cc_final: 0.7486 (pp) REVERT: G 248 LYS cc_start: 0.8242 (mtpt) cc_final: 0.7810 (mmpt) REVERT: G 255 ASP cc_start: 0.6615 (OUTLIER) cc_final: 0.6248 (t70) REVERT: G 260 ARG cc_start: 0.7121 (mtt90) cc_final: 0.6859 (mtm-85) REVERT: G 270 MET cc_start: 0.7502 (mtp) cc_final: 0.7079 (mtp) REVERT: G 276 GLN cc_start: 0.7514 (tt0) cc_final: 0.7224 (tm-30) REVERT: G 277 GLN cc_start: 0.7430 (tp40) cc_final: 0.6743 (mp10) REVERT: G 306 ARG cc_start: 0.7710 (ttp-170) cc_final: 0.7423 (ttp80) REVERT: G 367 LYS cc_start: 0.8330 (pttt) cc_final: 0.7926 (pptt) REVERT: G 429 MET cc_start: 0.7260 (mtm) cc_final: 0.6889 (mtm) REVERT: G 511 GLU cc_start: 0.7581 (mm-30) cc_final: 0.7119 (mp0) REVERT: H 151 GLN cc_start: 0.7443 (OUTLIER) cc_final: 0.7163 (tt0) REVERT: H 160 MET cc_start: 0.7914 (mtp) cc_final: 0.7526 (mtp) REVERT: H 279 GLU cc_start: 0.7254 (tp30) cc_final: 0.6874 (mt-10) REVERT: H 317 GLU cc_start: 0.7540 (mp0) cc_final: 0.7272 (tt0) REVERT: H 344 ARG cc_start: 0.7218 (ttm110) cc_final: 0.7009 (mtt-85) REVERT: H 349 GLU cc_start: 0.7880 (tt0) cc_final: 0.7656 (tt0) REVERT: H 368 LYS cc_start: 0.8021 (mttt) cc_final: 0.7481 (mmtp) REVERT: H 379 GLU cc_start: 0.7232 (tp30) cc_final: 0.6990 (tm-30) REVERT: H 383 GLU cc_start: 0.7627 (mm-30) cc_final: 0.7337 (mm-30) REVERT: H 440 LYS cc_start: 0.7686 (mmtp) cc_final: 0.7353 (tptp) REVERT: H 482 GLU cc_start: 0.7831 (mt-10) cc_final: 0.7551 (mt-10) REVERT: H 489 GLU cc_start: 0.7648 (mt-10) cc_final: 0.7438 (mp0) REVERT: H 497 MET cc_start: 0.7421 (tpp) cc_final: 0.6958 (tpt) REVERT: Q 31 ARG cc_start: 0.7383 (mmp-170) cc_final: 0.6708 (mmt90) REVERT: Q 77 GLU cc_start: 0.7151 (mm-30) cc_final: 0.6892 (mt-10) REVERT: Q 193 ASP cc_start: 0.6736 (m-30) cc_final: 0.6304 (m-30) REVERT: Q 212 ILE cc_start: 0.8352 (OUTLIER) cc_final: 0.8011 (mp) REVERT: Q 249 MET cc_start: 0.7514 (ptp) cc_final: 0.6869 (mmm) REVERT: Q 281 LYS cc_start: 0.7597 (ttmt) cc_final: 0.7345 (tptp) REVERT: Q 296 LYS cc_start: 0.7666 (pttm) cc_final: 0.7384 (pttt) REVERT: Q 318 LYS cc_start: 0.8243 (pttm) cc_final: 0.7649 (ptmm) REVERT: Q 354 GLU cc_start: 0.7634 (tm-30) cc_final: 0.7392 (tm-30) REVERT: Q 387 ASP cc_start: 0.7085 (t0) cc_final: 0.6814 (t0) REVERT: Q 406 LYS cc_start: 0.7683 (OUTLIER) cc_final: 0.7295 (mppt) REVERT: Q 436 TYR cc_start: 0.7030 (m-80) cc_final: 0.6819 (m-80) REVERT: Q 481 ASP cc_start: 0.7526 (t0) cc_final: 0.7209 (t0) REVERT: Z 44 MET cc_start: 0.8877 (mmm) cc_final: 0.8613 (mmt) REVERT: Z 108 LEU cc_start: 0.7999 (tt) cc_final: 0.7597 (tp) REVERT: Z 163 GLU cc_start: 0.6512 (tp30) cc_final: 0.6163 (tp30) REVERT: Z 195 GLU cc_start: 0.7876 (pt0) cc_final: 0.7372 (pt0) REVERT: Z 196 MET cc_start: 0.8705 (mtm) cc_final: 0.8501 (mtm) REVERT: Z 223 LYS cc_start: 0.7747 (mptt) cc_final: 0.7491 (mmtt) REVERT: Z 239 TYR cc_start: 0.8254 (t80) cc_final: 0.8008 (t80) REVERT: Z 241 LYS cc_start: 0.8529 (ttmt) cc_final: 0.7613 (pttp) REVERT: Z 264 ARG cc_start: 0.7321 (mtp85) cc_final: 0.6985 (mtp-110) REVERT: Z 272 LYS cc_start: 0.7407 (mmtp) cc_final: 0.6911 (mtpp) REVERT: Z 303 ASP cc_start: 0.7468 (t70) cc_final: 0.6844 (m-30) REVERT: Z 307 LYS cc_start: 0.7822 (mmtp) cc_final: 0.7418 (mtpt) REVERT: Z 322 GLU cc_start: 0.7449 (tt0) cc_final: 0.7122 (tt0) REVERT: Z 352 GLU cc_start: 0.8019 (tt0) cc_final: 0.7782 (tt0) REVERT: Z 359 LYS cc_start: 0.7709 (mttt) cc_final: 0.7184 (mttp) REVERT: Z 381 LYS cc_start: 0.8311 (tptt) cc_final: 0.7969 (tppp) REVERT: Z 487 MET cc_start: 0.7131 (OUTLIER) cc_final: 0.6418 (ppp) REVERT: Z 495 TRP cc_start: 0.8063 (m100) cc_final: 0.7501 (m100) REVERT: Z 496 ASP cc_start: 0.7505 (m-30) cc_final: 0.7218 (m-30) REVERT: a 212 SER cc_start: 0.7624 (p) cc_final: 0.7404 (t) REVERT: a 265 GLN cc_start: 0.7134 (pt0) cc_final: 0.6857 (tp40) REVERT: a 384 MET cc_start: 0.7848 (ttt) cc_final: 0.7533 (ttt) REVERT: a 443 ARG cc_start: 0.7532 (ttp80) cc_final: 0.7230 (ttt90) REVERT: b 6 LEU cc_start: 0.5026 (tp) cc_final: 0.4148 (tp) REVERT: b 17 ASP cc_start: 0.6579 (p0) cc_final: 0.6076 (p0) REVERT: b 57 ARG cc_start: 0.5221 (OUTLIER) cc_final: 0.3137 (ttt-90) REVERT: b 89 ARG cc_start: 0.7927 (ttp80) cc_final: 0.7617 (tmm160) REVERT: b 93 ASP cc_start: 0.7367 (m-30) cc_final: 0.6647 (m-30) REVERT: b 173 THR cc_start: 0.8461 (t) cc_final: 0.8242 (t) REVERT: b 223 LYS cc_start: 0.8457 (mttm) cc_final: 0.8141 (mtpt) REVERT: b 236 LYS cc_start: 0.7916 (OUTLIER) cc_final: 0.7313 (mtmm) REVERT: b 248 LYS cc_start: 0.7991 (mtpt) cc_final: 0.7783 (mtmt) REVERT: b 301 GLU cc_start: 0.7602 (tt0) cc_final: 0.7221 (tt0) REVERT: b 407 VAL cc_start: 0.7901 (t) cc_final: 0.7613 (m) REVERT: b 436 MET cc_start: 0.8153 (mtt) cc_final: 0.7925 (mtt) REVERT: b 445 MET cc_start: 0.8121 (tpp) cc_final: 0.7889 (tpp) REVERT: b 478 LEU cc_start: 0.8167 (mt) cc_final: 0.7894 (mt) REVERT: b 516 ARG cc_start: 0.7629 (mtp85) cc_final: 0.7413 (mtp180) REVERT: d 42 LYS cc_start: 0.7050 (tttp) cc_final: 0.6635 (tptt) REVERT: d 60 MET cc_start: 0.8414 (ttp) cc_final: 0.7860 (ttp) REVERT: d 63 ASP cc_start: 0.7180 (m-30) cc_final: 0.6924 (m-30) REVERT: d 81 MET cc_start: 0.8009 (ptm) cc_final: 0.7773 (ptm) REVERT: d 90 MET cc_start: 0.8084 (mtm) cc_final: 0.7773 (mtp) REVERT: d 93 GLU cc_start: 0.7146 (mm-30) cc_final: 0.6746 (mm-30) REVERT: d 132 ILE cc_start: 0.8346 (mt) cc_final: 0.8044 (mp) REVERT: d 285 ASN cc_start: 0.7944 (t0) cc_final: 0.7474 (t0) REVERT: d 305 LEU cc_start: 0.7896 (mt) cc_final: 0.7552 (pt) REVERT: d 334 GLU cc_start: 0.7345 (tp30) cc_final: 0.7097 (tp30) REVERT: d 384 LYS cc_start: 0.7459 (mmtp) cc_final: 0.6960 (mmpt) REVERT: d 443 LEU cc_start: 0.7953 (OUTLIER) cc_final: 0.7752 (tt) REVERT: e 23 ASP cc_start: 0.8028 (m-30) cc_final: 0.7735 (m-30) REVERT: e 27 ARG cc_start: 0.7992 (ttp-170) cc_final: 0.7496 (ttt180) REVERT: e 29 MET cc_start: 0.8011 (mtp) cc_final: 0.7380 (mtp) REVERT: e 93 GLU cc_start: 0.6989 (mm-30) cc_final: 0.6591 (mt-10) REVERT: e 96 LYS cc_start: 0.7782 (tttm) cc_final: 0.7072 (ttmt) REVERT: e 121 GLU cc_start: 0.6921 (tt0) cc_final: 0.6530 (tt0) REVERT: e 122 GLN cc_start: 0.7212 (OUTLIER) cc_final: 0.6713 (mp10) REVERT: e 126 ARG cc_start: 0.7230 (mtm180) cc_final: 0.6713 (mtp85) REVERT: e 150 LYS cc_start: 0.7686 (ttmt) cc_final: 0.7345 (ttpt) REVERT: e 187 GLU cc_start: 0.7033 (tt0) cc_final: 0.6580 (pt0) REVERT: e 239 MET cc_start: 0.8536 (mtt) cc_final: 0.8176 (mtt) REVERT: e 449 ARG cc_start: 0.6954 (mtt180) cc_final: 0.6721 (mtt-85) REVERT: e 464 GLU cc_start: 0.6737 (tt0) cc_final: 0.6275 (tm-30) REVERT: e 478 ARG cc_start: 0.7294 (ttp-170) cc_final: 0.7024 (ttm170) REVERT: e 502 LYS cc_start: 0.6927 (tttm) cc_final: 0.6541 (ttmm) REVERT: e 515 GLN cc_start: 0.7928 (tp40) cc_final: 0.7337 (tp40) REVERT: e 532 ASP cc_start: 0.8268 (t0) cc_final: 0.7952 (t0) REVERT: g 8 LEU cc_start: 0.7796 (mt) cc_final: 0.7228 (mm) REVERT: g 15 LYS cc_start: 0.7822 (OUTLIER) cc_final: 0.7094 (mmtp) REVERT: g 48 LYS cc_start: 0.8102 (mtmt) cc_final: 0.7840 (mttp) REVERT: g 110 GLU cc_start: 0.8264 (OUTLIER) cc_final: 0.7504 (tt0) REVERT: g 167 ARG cc_start: 0.7430 (mtt-85) cc_final: 0.7046 (mtm-85) REVERT: g 186 GLU cc_start: 0.7009 (tt0) cc_final: 0.6608 (tt0) REVERT: g 191 LYS cc_start: 0.7664 (mtpt) cc_final: 0.7364 (mptt) REVERT: g 192 GLU cc_start: 0.6946 (tt0) cc_final: 0.6022 (pp20) REVERT: g 202 GLU cc_start: 0.7016 (mm-30) cc_final: 0.6581 (mm-30) REVERT: g 208 ILE cc_start: 0.7258 (pt) cc_final: 0.6408 (pp) REVERT: g 211 ASP cc_start: 0.7717 (p0) cc_final: 0.7462 (p0) REVERT: g 274 TYR cc_start: 0.8017 (t80) cc_final: 0.7611 (t80) REVERT: g 277 GLN cc_start: 0.6966 (tp-100) cc_final: 0.6246 (pt0) REVERT: g 294 LYS cc_start: 0.8074 (mmtp) cc_final: 0.7660 (mmtp) REVERT: g 381 LYS cc_start: 0.7745 (tppt) cc_final: 0.7334 (mptt) REVERT: h 10 LYS cc_start: 0.8001 (ttmt) cc_final: 0.7516 (ttpt) REVERT: h 17 GLN cc_start: 0.8069 (tt0) cc_final: 0.7834 (tt0) REVERT: h 30 GLN cc_start: 0.7794 (mm-40) cc_final: 0.7389 (mm110) REVERT: h 46 ASP cc_start: 0.7592 (m-30) cc_final: 0.7250 (m-30) REVERT: h 51 ASP cc_start: 0.7467 (p0) cc_final: 0.7002 (p0) REVERT: h 119 GLN cc_start: 0.7977 (mm-40) cc_final: 0.7692 (mm110) REVERT: h 153 LYS cc_start: 0.7921 (mttm) cc_final: 0.7372 (mptt) REVERT: h 188 ASP cc_start: 0.7746 (t0) cc_final: 0.7521 (p0) REVERT: h 217 LYS cc_start: 0.8975 (ttpt) cc_final: 0.8590 (ttpt) REVERT: h 247 LYS cc_start: 0.8299 (pttp) cc_final: 0.7964 (ptpp) REVERT: h 254 GLU cc_start: 0.8106 (tm-30) cc_final: 0.7904 (tp30) REVERT: h 276 ASP cc_start: 0.7258 (t0) cc_final: 0.6938 (m-30) REVERT: h 320 LYS cc_start: 0.7658 (mmtt) cc_final: 0.7414 (mtmm) REVERT: h 344 ARG cc_start: 0.7302 (ttm110) cc_final: 0.6585 (mtm-85) REVERT: h 356 GLU cc_start: 0.7241 (mt-10) cc_final: 0.6824 (mt-10) REVERT: h 368 LYS cc_start: 0.7613 (mttt) cc_final: 0.6995 (mtpp) REVERT: h 379 GLU cc_start: 0.8065 (tm-30) cc_final: 0.7479 (tm-30) REVERT: h 383 GLU cc_start: 0.7365 (mm-30) cc_final: 0.7016 (mm-30) REVERT: h 440 LYS cc_start: 0.8190 (tptt) cc_final: 0.7814 (tppt) REVERT: h 524 ARG cc_start: 0.5511 (mmm-85) cc_final: 0.5265 (mmm-85) REVERT: n 83 ASN cc_start: 0.2461 (OUTLIER) cc_final: 0.1433 (m110) REVERT: q 3 LEU cc_start: 0.5353 (OUTLIER) cc_final: 0.4574 (tt) REVERT: q 17 GLU cc_start: 0.7475 (tt0) cc_final: 0.7250 (tm-30) REVERT: q 31 ARG cc_start: 0.7490 (mmp-170) cc_final: 0.6899 (mmt-90) REVERT: q 117 GLU cc_start: 0.7102 (tt0) cc_final: 0.6555 (mt-10) REVERT: q 212 ILE cc_start: 0.8205 (OUTLIER) cc_final: 0.7887 (mm) REVERT: q 238 LYS cc_start: 0.7283 (mmtp) cc_final: 0.6678 (mmtp) REVERT: q 277 ASP cc_start: 0.8480 (t70) cc_final: 0.8084 (t0) REVERT: q 357 ASP cc_start: 0.6135 (p0) cc_final: 0.5892 (p0) REVERT: q 406 LYS cc_start: 0.7647 (ptmt) cc_final: 0.6800 (mmtm) REVERT: q 443 GLU cc_start: 0.7065 (tm-30) cc_final: 0.6785 (mp0) REVERT: q 483 GLU cc_start: 0.7343 (mp0) cc_final: 0.6897 (mm-30) REVERT: q 505 TYR cc_start: 0.8126 (t80) cc_final: 0.7746 (t80) REVERT: z 10 LYS cc_start: 0.7993 (mtmt) cc_final: 0.7417 (pmtt) REVERT: z 15 ARG cc_start: 0.7536 (OUTLIER) cc_final: 0.6784 (mtm-85) REVERT: z 31 GLN cc_start: 0.7577 (tt0) cc_final: 0.7129 (tt0) REVERT: z 181 LYS cc_start: 0.7035 (mttt) cc_final: 0.6057 (mmmt) REVERT: z 195 GLU cc_start: 0.8332 (mt-10) cc_final: 0.8006 (mt-10) REVERT: z 201 GLU cc_start: 0.7478 (OUTLIER) cc_final: 0.7271 (pt0) REVERT: z 203 ASP cc_start: 0.8321 (m-30) cc_final: 0.7951 (m-30) REVERT: z 220 ASP cc_start: 0.7246 (m-30) cc_final: 0.6877 (t0) REVERT: z 272 LYS cc_start: 0.7978 (mmtp) cc_final: 0.7666 (mtpp) REVERT: z 307 LYS cc_start: 0.7888 (mmtp) cc_final: 0.6792 (ttpt) REVERT: z 359 LYS cc_start: 0.7803 (mttt) cc_final: 0.6922 (mtmm) REVERT: z 388 LYS cc_start: 0.7528 (OUTLIER) cc_final: 0.6891 (mttt) REVERT: z 517 LEU cc_start: 0.8420 (mt) cc_final: 0.8152 (mm) REVERT: T 49 VAL cc_start: 0.8741 (OUTLIER) cc_final: 0.8484 (t) REVERT: T 69 GLU cc_start: 0.7919 (OUTLIER) cc_final: 0.7658 (pt0) REVERT: T 94 GLN cc_start: 0.5761 (mp10) cc_final: 0.5460 (mt0) REVERT: T 131 GLN cc_start: 0.8447 (tt0) cc_final: 0.8216 (tt0) REVERT: T 154 LYS cc_start: 0.8555 (mmtm) cc_final: 0.7844 (mtpt) REVERT: T 167 PHE cc_start: 0.8379 (m-80) cc_final: 0.7796 (m-80) REVERT: T 403 MET cc_start: 0.7880 (mtp) cc_final: 0.7509 (mtp) REVERT: T 412 GLU cc_start: 0.6980 (tp30) cc_final: 0.6777 (tp30) outliers start: 228 outliers final: 102 residues processed: 1223 average time/residue: 1.5536 time to fit residues: 2465.9909 Evaluate side-chains 1097 residues out of total 7485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 968 time to evaluate : 6.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 SER Chi-restraints excluded: chain A residue 166 ASP Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 284 ASN Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 433 ARG Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain A residue 508 ILE Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 77 ASP Chi-restraints excluded: chain B residue 97 ASP Chi-restraints excluded: chain B residue 101 SER Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 416 LEU Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 79 LYS Chi-restraints excluded: chain D residue 82 GLN Chi-restraints excluded: chain D residue 136 SER Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 184 SER Chi-restraints excluded: chain D residue 273 ASP Chi-restraints excluded: chain D residue 274 ARG Chi-restraints excluded: chain D residue 355 MET Chi-restraints excluded: chain D residue 400 GLU Chi-restraints excluded: chain D residue 404 SER Chi-restraints excluded: chain D residue 447 GLU Chi-restraints excluded: chain D residue 536 VAL Chi-restraints excluded: chain E residue 198 ASP Chi-restraints excluded: chain E residue 245 ASP Chi-restraints excluded: chain E residue 418 VAL Chi-restraints excluded: chain E residue 522 GLN Chi-restraints excluded: chain G residue 7 VAL Chi-restraints excluded: chain G residue 71 GLN Chi-restraints excluded: chain G residue 81 ILE Chi-restraints excluded: chain G residue 83 ILE Chi-restraints excluded: chain G residue 96 THR Chi-restraints excluded: chain G residue 235 ASN Chi-restraints excluded: chain G residue 255 ASP Chi-restraints excluded: chain G residue 332 VAL Chi-restraints excluded: chain G residue 354 LYS Chi-restraints excluded: chain G residue 373 THR Chi-restraints excluded: chain G residue 440 VAL Chi-restraints excluded: chain G residue 463 LEU Chi-restraints excluded: chain G residue 524 SER Chi-restraints excluded: chain H residue 2 MET Chi-restraints excluded: chain H residue 151 GLN Chi-restraints excluded: chain H residue 251 ASP Chi-restraints excluded: chain H residue 276 ASP Chi-restraints excluded: chain H residue 362 THR Chi-restraints excluded: chain N residue 83 ASN Chi-restraints excluded: chain Q residue 105 LEU Chi-restraints excluded: chain Q residue 146 LEU Chi-restraints excluded: chain Q residue 212 ILE Chi-restraints excluded: chain Q residue 286 THR Chi-restraints excluded: chain Q residue 406 LYS Chi-restraints excluded: chain Z residue 32 ASP Chi-restraints excluded: chain Z residue 373 THR Chi-restraints excluded: chain Z residue 407 VAL Chi-restraints excluded: chain Z residue 408 VAL Chi-restraints excluded: chain Z residue 479 VAL Chi-restraints excluded: chain Z residue 487 MET Chi-restraints excluded: chain a residue 84 LYS Chi-restraints excluded: chain a residue 166 ASP Chi-restraints excluded: chain a residue 177 LEU Chi-restraints excluded: chain a residue 329 SER Chi-restraints excluded: chain a residue 391 SER Chi-restraints excluded: chain b residue 51 ILE Chi-restraints excluded: chain b residue 57 ARG Chi-restraints excluded: chain b residue 66 ASP Chi-restraints excluded: chain b residue 182 LEU Chi-restraints excluded: chain b residue 184 VAL Chi-restraints excluded: chain b residue 236 LYS Chi-restraints excluded: chain b residue 326 VAL Chi-restraints excluded: chain b residue 371 CYS Chi-restraints excluded: chain d residue 67 ASP Chi-restraints excluded: chain d residue 184 SER Chi-restraints excluded: chain d residue 203 VAL Chi-restraints excluded: chain d residue 368 ASN Chi-restraints excluded: chain d residue 385 THR Chi-restraints excluded: chain d residue 394 ASN Chi-restraints excluded: chain d residue 395 LYS Chi-restraints excluded: chain d residue 443 LEU Chi-restraints excluded: chain e residue 122 GLN Chi-restraints excluded: chain e residue 145 ILE Chi-restraints excluded: chain e residue 330 ILE Chi-restraints excluded: chain e residue 418 VAL Chi-restraints excluded: chain e residue 498 THR Chi-restraints excluded: chain e residue 507 ILE Chi-restraints excluded: chain g residue 15 LYS Chi-restraints excluded: chain g residue 39 THR Chi-restraints excluded: chain g residue 83 ILE Chi-restraints excluded: chain g residue 96 THR Chi-restraints excluded: chain g residue 110 GLU Chi-restraints excluded: chain g residue 161 THR Chi-restraints excluded: chain g residue 397 VAL Chi-restraints excluded: chain g residue 440 VAL Chi-restraints excluded: chain g residue 460 ILE Chi-restraints excluded: chain h residue 38 THR Chi-restraints excluded: chain h residue 85 SER Chi-restraints excluded: chain h residue 211 VAL Chi-restraints excluded: chain h residue 221 SER Chi-restraints excluded: chain h residue 405 VAL Chi-restraints excluded: chain h residue 427 ILE Chi-restraints excluded: chain n residue 12 VAL Chi-restraints excluded: chain n residue 83 ASN Chi-restraints excluded: chain q residue 3 LEU Chi-restraints excluded: chain q residue 43 THR Chi-restraints excluded: chain q residue 45 THR Chi-restraints excluded: chain q residue 150 SER Chi-restraints excluded: chain q residue 212 ILE Chi-restraints excluded: chain q residue 226 GLU Chi-restraints excluded: chain q residue 234 VAL Chi-restraints excluded: chain q residue 385 MET Chi-restraints excluded: chain q residue 480 LEU Chi-restraints excluded: chain z residue 4 VAL Chi-restraints excluded: chain z residue 15 ARG Chi-restraints excluded: chain z residue 32 ASP Chi-restraints excluded: chain z residue 149 ILE Chi-restraints excluded: chain z residue 179 ILE Chi-restraints excluded: chain z residue 201 GLU Chi-restraints excluded: chain z residue 388 LYS Chi-restraints excluded: chain z residue 526 MET Chi-restraints excluded: chain T residue 49 VAL Chi-restraints excluded: chain T residue 69 GLU Chi-restraints excluded: chain T residue 391 ARG Chi-restraints excluded: chain T residue 395 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 885 random chunks: chunk 446 optimal weight: 10.0000 chunk 249 optimal weight: 0.1980 chunk 668 optimal weight: 1.9990 chunk 547 optimal weight: 2.9990 chunk 221 optimal weight: 6.9990 chunk 805 optimal weight: 0.9980 chunk 869 optimal weight: 8.9990 chunk 717 optimal weight: 5.9990 chunk 798 optimal weight: 0.4980 chunk 274 optimal weight: 6.9990 chunk 645 optimal weight: 2.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN A 164 ASN ** A 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 25 GLN ** E 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 495 HIS ** 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 174 ASN G 226 HIS G 472 GLN H 21 GLN H 60 ASN ** H 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 53 ASN ** Q 365 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 161 HIS Z 294 GLN ** a 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 251 GLN a 492 ASN b 122 HIS b 195 ASN ** d 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 366 ASN d 472 ASN ** e 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 360 GLN ** e 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 64 ASN g 396 GLN ** g 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 107 GLN h 234 ASN h 241 ASN q 359 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 190 HIS T 414 ASN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7411 moved from start: 0.1613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 69953 Z= 0.193 Angle : 0.549 7.573 94470 Z= 0.274 Chirality : 0.042 0.182 11206 Planarity : 0.004 0.044 12067 Dihedral : 8.144 176.745 9759 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.86 % Favored : 97.08 % Rotamer: Outliers : 3.48 % Allowed : 17.20 % Favored : 79.32 % 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: 0.23 (0.09), residues: 8920 helix: 1.23 (0.08), residues: 4579 sheet: -0.64 (0.14), residues: 1213 loop : -1.06 (0.11), residues: 3128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP N 101 HIS 0.012 0.001 HIS G 111 PHE 0.021 0.001 PHE a 167 TYR 0.015 0.001 TYR Q 505 ARG 0.006 0.000 ARG E 132 *********************** 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 1302 residues out of total 7485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 259 poor density : 1043 time to evaluate : 6.348 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 PHE cc_start: 0.7656 (t80) cc_final: 0.7260 (t80) REVERT: A 51 ASP cc_start: 0.6466 (t0) cc_final: 0.5973 (t70) REVERT: A 63 LYS cc_start: 0.7822 (OUTLIER) cc_final: 0.7161 (mtmm) REVERT: A 156 MET cc_start: 0.8165 (mtp) cc_final: 0.7937 (mtp) REVERT: A 230 VAL cc_start: 0.7324 (OUTLIER) cc_final: 0.7028 (t) REVERT: A 261 ASP cc_start: 0.6802 (p0) cc_final: 0.6388 (t0) REVERT: A 277 LYS cc_start: 0.7684 (mttt) cc_final: 0.7378 (mttm) REVERT: A 321 LYS cc_start: 0.7874 (mtmt) cc_final: 0.7592 (tptt) REVERT: A 354 GLU cc_start: 0.6614 (mm-30) cc_final: 0.6207 (tp30) REVERT: A 358 ASP cc_start: 0.7731 (t0) cc_final: 0.7487 (t70) REVERT: A 384 MET cc_start: 0.8147 (ttt) cc_final: 0.7858 (ttt) REVERT: A 430 MET cc_start: 0.6158 (mmm) cc_final: 0.5294 (mmm) REVERT: A 459 ASP cc_start: 0.8207 (t0) cc_final: 0.7986 (t0) REVERT: B 87 MET cc_start: 0.7841 (ttp) cc_final: 0.7440 (ttp) REVERT: B 114 GLU cc_start: 0.7602 (OUTLIER) cc_final: 0.7332 (pt0) REVERT: B 248 LYS cc_start: 0.7943 (mtpt) cc_final: 0.7565 (mtmt) REVERT: B 301 GLU cc_start: 0.7390 (tt0) cc_final: 0.7049 (tt0) REVERT: B 402 LYS cc_start: 0.7556 (mtmm) cc_final: 0.6956 (mmtt) REVERT: B 414 GLU cc_start: 0.6637 (mp0) cc_final: 0.6070 (mp0) REVERT: B 445 MET cc_start: 0.7710 (tpp) cc_final: 0.7400 (tpp) REVERT: B 456 TYR cc_start: 0.8691 (m-80) cc_final: 0.8334 (m-80) REVERT: D 32 GLN cc_start: 0.7524 (mt0) cc_final: 0.7292 (mm-40) REVERT: D 65 LYS cc_start: 0.8268 (mtmm) cc_final: 0.7980 (mtpt) REVERT: D 82 GLN cc_start: 0.8114 (OUTLIER) cc_final: 0.7543 (mm-40) REVERT: D 196 ASP cc_start: 0.7671 (t0) cc_final: 0.6613 (p0) REVERT: D 222 GLU cc_start: 0.7370 (tt0) cc_final: 0.6814 (mt-10) REVERT: D 257 LYS cc_start: 0.7676 (mmtm) cc_final: 0.7159 (tmmt) REVERT: D 274 ARG cc_start: 0.7127 (OUTLIER) cc_final: 0.6921 (ttm-80) REVERT: D 358 SER cc_start: 0.7877 (m) cc_final: 0.7443 (t) REVERT: D 368 ASN cc_start: 0.6996 (m110) cc_final: 0.6491 (m110) REVERT: D 384 LYS cc_start: 0.7588 (mptt) cc_final: 0.7340 (mptm) REVERT: D 458 MET cc_start: 0.7948 (mmm) cc_final: 0.7649 (mpp) REVERT: D 467 GLU cc_start: 0.7400 (OUTLIER) cc_final: 0.7007 (mt-10) REVERT: D 496 ARG cc_start: 0.8049 (ttp80) cc_final: 0.7748 (tmm160) REVERT: E 20 LYS cc_start: 0.7987 (tttp) cc_final: 0.7744 (ttpt) REVERT: E 21 ASP cc_start: 0.7403 (t0) cc_final: 0.7154 (t0) REVERT: E 48 MET cc_start: 0.8327 (OUTLIER) cc_final: 0.8076 (mmm) REVERT: E 71 THR cc_start: 0.8549 (OUTLIER) cc_final: 0.8324 (t) REVERT: E 93 GLU cc_start: 0.6909 (mm-30) cc_final: 0.6524 (mm-30) REVERT: E 121 GLU cc_start: 0.7189 (tt0) cc_final: 0.6715 (tt0) REVERT: E 122 GLN cc_start: 0.7217 (mt0) cc_final: 0.6950 (mt0) REVERT: E 125 ASP cc_start: 0.7921 (m-30) cc_final: 0.7686 (m-30) REVERT: E 198 ASP cc_start: 0.7797 (OUTLIER) cc_final: 0.7579 (t70) REVERT: E 263 LYS cc_start: 0.7771 (ttmt) cc_final: 0.7115 (tttt) REVERT: E 290 GLN cc_start: 0.7334 (tp-100) cc_final: 0.6958 (tm-30) REVERT: E 361 GLU cc_start: 0.7591 (tt0) cc_final: 0.7341 (tt0) REVERT: E 381 ARG cc_start: 0.7993 (ttp80) cc_final: 0.7687 (ttt-90) REVERT: E 439 LYS cc_start: 0.7877 (mtmm) cc_final: 0.7574 (mptt) REVERT: E 502 LYS cc_start: 0.7682 (tttt) cc_final: 0.7172 (tmtm) REVERT: G 8 LEU cc_start: 0.6453 (OUTLIER) cc_final: 0.6044 (mm) REVERT: G 9 VAL cc_start: 0.8415 (p) cc_final: 0.8105 (m) REVERT: G 15 LYS cc_start: 0.7556 (mmmt) cc_final: 0.6846 (mtmm) REVERT: G 17 GLU cc_start: 0.7025 (mp0) cc_final: 0.6552 (mp0) REVERT: G 71 GLN cc_start: 0.8178 (OUTLIER) cc_final: 0.7887 (tt0) REVERT: G 82 GLU cc_start: 0.7778 (mm-30) cc_final: 0.7522 (mm-30) REVERT: G 110 GLU cc_start: 0.7680 (tt0) cc_final: 0.7221 (tp30) REVERT: G 192 GLU cc_start: 0.7373 (pt0) cc_final: 0.6722 (pp20) REVERT: G 248 LYS cc_start: 0.8257 (mtpt) cc_final: 0.7811 (mmpt) REVERT: G 270 MET cc_start: 0.7548 (mtp) cc_final: 0.7178 (mtp) REVERT: G 276 GLN cc_start: 0.7483 (tt0) cc_final: 0.7191 (tm-30) REVERT: G 277 GLN cc_start: 0.7478 (tp40) cc_final: 0.6775 (mp10) REVERT: G 306 ARG cc_start: 0.7696 (ttp-170) cc_final: 0.7453 (ttp80) REVERT: G 367 LYS cc_start: 0.8442 (pttt) cc_final: 0.8024 (pptt) REVERT: G 429 MET cc_start: 0.7230 (mtm) cc_final: 0.6870 (mtm) REVERT: G 511 GLU cc_start: 0.7574 (mm-30) cc_final: 0.7236 (mp0) REVERT: H 151 GLN cc_start: 0.7366 (OUTLIER) cc_final: 0.7124 (tt0) REVERT: H 160 MET cc_start: 0.7920 (mtp) cc_final: 0.7521 (mtp) REVERT: H 254 GLU cc_start: 0.7954 (OUTLIER) cc_final: 0.7528 (tt0) REVERT: H 279 GLU cc_start: 0.7198 (tp30) cc_final: 0.6831 (mt-10) REVERT: H 317 GLU cc_start: 0.7549 (mp0) cc_final: 0.7259 (tt0) REVERT: H 349 GLU cc_start: 0.7861 (tt0) cc_final: 0.7586 (tt0) REVERT: H 368 LYS cc_start: 0.8014 (mttt) cc_final: 0.7518 (mmtp) REVERT: H 379 GLU cc_start: 0.7189 (tp30) cc_final: 0.6950 (tm-30) REVERT: H 383 GLU cc_start: 0.7614 (mm-30) cc_final: 0.7329 (mm-30) REVERT: H 440 LYS cc_start: 0.7604 (mmtp) cc_final: 0.7348 (mtpt) REVERT: H 482 GLU cc_start: 0.7829 (mt-10) cc_final: 0.7547 (mt-10) REVERT: H 497 MET cc_start: 0.7442 (tpp) cc_final: 0.6986 (tpt) REVERT: Q 14 MET cc_start: 0.8641 (mtm) cc_final: 0.8384 (mtm) REVERT: Q 31 ARG cc_start: 0.7392 (mmp-170) cc_final: 0.6628 (mtt90) REVERT: Q 193 ASP cc_start: 0.6764 (m-30) cc_final: 0.6349 (m-30) REVERT: Q 200 ASP cc_start: 0.7968 (m-30) cc_final: 0.7730 (m-30) REVERT: Q 212 ILE cc_start: 0.8367 (OUTLIER) cc_final: 0.8009 (mp) REVERT: Q 249 MET cc_start: 0.7458 (ptp) cc_final: 0.7060 (mmm) REVERT: Q 281 LYS cc_start: 0.7613 (ttmt) cc_final: 0.7355 (tptp) REVERT: Q 286 THR cc_start: 0.8778 (OUTLIER) cc_final: 0.8356 (p) REVERT: Q 296 LYS cc_start: 0.7695 (pttm) cc_final: 0.7404 (pttt) REVERT: Q 318 LYS cc_start: 0.8124 (pttm) cc_final: 0.7472 (ptmm) REVERT: Q 322 ARG cc_start: 0.7344 (mtt90) cc_final: 0.7100 (mtp180) REVERT: Q 354 GLU cc_start: 0.7669 (tm-30) cc_final: 0.7348 (tm-30) REVERT: Q 387 ASP cc_start: 0.7121 (t0) cc_final: 0.6867 (t0) REVERT: Q 406 LYS cc_start: 0.7682 (OUTLIER) cc_final: 0.7476 (mppt) REVERT: Q 436 TYR cc_start: 0.6990 (m-80) cc_final: 0.6777 (m-80) REVERT: Q 481 ASP cc_start: 0.7503 (t0) cc_final: 0.7218 (t0) REVERT: Z 44 MET cc_start: 0.8952 (mmm) cc_final: 0.8675 (mmt) REVERT: Z 108 LEU cc_start: 0.7996 (tt) cc_final: 0.7584 (tp) REVERT: Z 163 GLU cc_start: 0.6470 (tp30) cc_final: 0.5904 (tp30) REVERT: Z 195 GLU cc_start: 0.7913 (pt0) cc_final: 0.7437 (pt0) REVERT: Z 223 LYS cc_start: 0.7773 (mptt) cc_final: 0.7507 (mmtt) REVERT: Z 239 TYR cc_start: 0.8178 (t80) cc_final: 0.7945 (t80) REVERT: Z 241 LYS cc_start: 0.8519 (ttmt) cc_final: 0.7638 (pttp) REVERT: Z 264 ARG cc_start: 0.7306 (mtp85) cc_final: 0.6940 (mtp-110) REVERT: Z 272 LYS cc_start: 0.7352 (mmtp) cc_final: 0.6885 (mtpp) REVERT: Z 303 ASP cc_start: 0.7429 (t70) cc_final: 0.6798 (m-30) REVERT: Z 307 LYS cc_start: 0.7767 (mmtp) cc_final: 0.7401 (mtpt) REVERT: Z 318 ARG cc_start: 0.7006 (mtt-85) cc_final: 0.6756 (mtm-85) REVERT: Z 322 GLU cc_start: 0.7474 (tt0) cc_final: 0.7119 (tt0) REVERT: Z 340 SER cc_start: 0.7180 (OUTLIER) cc_final: 0.6551 (p) REVERT: Z 381 LYS cc_start: 0.8281 (tptt) cc_final: 0.7988 (tppp) REVERT: Z 445 LEU cc_start: 0.8123 (mt) cc_final: 0.7828 (mm) REVERT: Z 487 MET cc_start: 0.7141 (OUTLIER) cc_final: 0.6434 (ppp) REVERT: Z 495 TRP cc_start: 0.8012 (m100) cc_final: 0.7440 (m100) REVERT: Z 496 ASP cc_start: 0.7426 (m-30) cc_final: 0.7131 (m-30) REVERT: a 23 MET cc_start: 0.5695 (OUTLIER) cc_final: 0.5348 (ttp) REVERT: a 212 SER cc_start: 0.7578 (p) cc_final: 0.7322 (t) REVERT: a 265 GLN cc_start: 0.7164 (pt0) cc_final: 0.6865 (tp40) REVERT: a 321 LYS cc_start: 0.8282 (OUTLIER) cc_final: 0.7900 (tmtt) REVERT: a 368 LYS cc_start: 0.7693 (ptmt) cc_final: 0.7052 (ptpt) REVERT: a 384 MET cc_start: 0.7907 (ttt) cc_final: 0.7600 (ttt) REVERT: a 388 MET cc_start: 0.8513 (mtp) cc_final: 0.8265 (mtp) REVERT: a 443 ARG cc_start: 0.7411 (ttp80) cc_final: 0.7097 (ttt90) REVERT: b 6 LEU cc_start: 0.4985 (tp) cc_final: 0.4333 (tp) REVERT: b 17 ASP cc_start: 0.6669 (p0) cc_final: 0.6174 (p0) REVERT: b 57 ARG cc_start: 0.5123 (OUTLIER) cc_final: 0.3098 (ttt-90) REVERT: b 89 ARG cc_start: 0.7895 (ttp80) cc_final: 0.7604 (tmm160) REVERT: b 93 ASP cc_start: 0.7293 (m-30) cc_final: 0.6645 (m-30) REVERT: b 173 THR cc_start: 0.8483 (t) cc_final: 0.8275 (t) REVERT: b 223 LYS cc_start: 0.8469 (mttm) cc_final: 0.8077 (mtpt) REVERT: b 236 LYS cc_start: 0.7795 (OUTLIER) cc_final: 0.7260 (mtmm) REVERT: b 301 GLU cc_start: 0.7579 (tt0) cc_final: 0.7152 (tt0) REVERT: b 316 ASP cc_start: 0.7064 (t0) cc_final: 0.6771 (m-30) REVERT: b 407 VAL cc_start: 0.8096 (t) cc_final: 0.7840 (m) REVERT: b 436 MET cc_start: 0.8236 (mtt) cc_final: 0.7977 (mtt) REVERT: b 445 MET cc_start: 0.8083 (tpp) cc_final: 0.7775 (tpp) REVERT: b 491 LEU cc_start: 0.6570 (mm) cc_final: 0.6342 (mm) REVERT: b 516 ARG cc_start: 0.7576 (mtp85) cc_final: 0.7315 (mtp180) REVERT: b 522 LYS cc_start: 0.7974 (mttt) cc_final: 0.7416 (mtmt) REVERT: d 42 LYS cc_start: 0.7077 (tttp) cc_final: 0.6496 (tptt) REVERT: d 46 ASP cc_start: 0.7859 (m-30) cc_final: 0.7541 (m-30) REVERT: d 60 MET cc_start: 0.8341 (ttp) cc_final: 0.7771 (ttp) REVERT: d 63 ASP cc_start: 0.7168 (m-30) cc_final: 0.6947 (m-30) REVERT: d 81 MET cc_start: 0.8061 (ptm) cc_final: 0.7857 (ptm) REVERT: d 90 MET cc_start: 0.8060 (mtm) cc_final: 0.7667 (mtp) REVERT: d 93 GLU cc_start: 0.7138 (mm-30) cc_final: 0.6730 (mm-30) REVERT: d 132 ILE cc_start: 0.8353 (mt) cc_final: 0.8060 (mp) REVERT: d 285 ASN cc_start: 0.7941 (t0) cc_final: 0.7474 (t0) REVERT: d 305 LEU cc_start: 0.7814 (mt) cc_final: 0.7542 (pt) REVERT: d 334 GLU cc_start: 0.7439 (tp30) cc_final: 0.7129 (tp30) REVERT: d 384 LYS cc_start: 0.7406 (mmtp) cc_final: 0.6977 (mmpt) REVERT: e 23 ASP cc_start: 0.8035 (m-30) cc_final: 0.7718 (m-30) REVERT: e 27 ARG cc_start: 0.7922 (ttp-170) cc_final: 0.7528 (ttt180) REVERT: e 29 MET cc_start: 0.7927 (mtp) cc_final: 0.7623 (mtp) REVERT: e 93 GLU cc_start: 0.7104 (mm-30) cc_final: 0.6658 (mt-10) REVERT: e 96 LYS cc_start: 0.7791 (tttm) cc_final: 0.7069 (ttmt) REVERT: e 126 ARG cc_start: 0.7175 (mtm180) cc_final: 0.6639 (mtp85) REVERT: e 150 LYS cc_start: 0.7686 (ttmt) cc_final: 0.7324 (ttpt) REVERT: e 449 ARG cc_start: 0.6936 (mtt180) cc_final: 0.6687 (mtt-85) REVERT: e 464 GLU cc_start: 0.6619 (tt0) cc_final: 0.6051 (tm-30) REVERT: e 478 ARG cc_start: 0.7315 (ttp-170) cc_final: 0.7053 (ttm170) REVERT: e 502 LYS cc_start: 0.6884 (tttm) cc_final: 0.6547 (ttmm) REVERT: e 515 GLN cc_start: 0.7898 (tp40) cc_final: 0.7289 (tp40) REVERT: e 532 ASP cc_start: 0.8237 (t0) cc_final: 0.7976 (t0) REVERT: g 8 LEU cc_start: 0.7701 (mt) cc_final: 0.7138 (mm) REVERT: g 110 GLU cc_start: 0.8178 (OUTLIER) cc_final: 0.7643 (tp30) REVERT: g 167 ARG cc_start: 0.7463 (mtt-85) cc_final: 0.7083 (mtm-85) REVERT: g 186 GLU cc_start: 0.7099 (tt0) cc_final: 0.6614 (tt0) REVERT: g 191 LYS cc_start: 0.7693 (mtpt) cc_final: 0.7341 (mptt) REVERT: g 192 GLU cc_start: 0.6938 (tt0) cc_final: 0.6135 (pp20) REVERT: g 202 GLU cc_start: 0.6986 (mm-30) cc_final: 0.6588 (mm-30) REVERT: g 208 ILE cc_start: 0.7284 (pt) cc_final: 0.6482 (pp) REVERT: g 211 ASP cc_start: 0.7679 (p0) cc_final: 0.7438 (p0) REVERT: g 274 TYR cc_start: 0.7981 (t80) cc_final: 0.7649 (t80) REVERT: g 277 GLN cc_start: 0.7001 (tp-100) cc_final: 0.6193 (pt0) REVERT: g 294 LYS cc_start: 0.8102 (mmtp) cc_final: 0.7700 (mmtp) REVERT: g 367 LYS cc_start: 0.8501 (OUTLIER) cc_final: 0.8025 (pptt) REVERT: g 381 LYS cc_start: 0.7878 (tppt) cc_final: 0.7418 (mptt) REVERT: g 383 ILE cc_start: 0.8314 (OUTLIER) cc_final: 0.8091 (mp) REVERT: g 476 GLU cc_start: 0.7032 (pm20) cc_final: 0.6694 (mm-30) REVERT: h 10 LYS cc_start: 0.8002 (ttmt) cc_final: 0.7495 (ttpt) REVERT: h 17 GLN cc_start: 0.7997 (tt0) cc_final: 0.7792 (tt0) REVERT: h 30 GLN cc_start: 0.7762 (mm-40) cc_final: 0.7448 (mm110) REVERT: h 51 ASP cc_start: 0.7598 (p0) cc_final: 0.7354 (p0) REVERT: h 119 GLN cc_start: 0.7972 (mm-40) cc_final: 0.7658 (mm110) REVERT: h 153 LYS cc_start: 0.7901 (mttm) cc_final: 0.7368 (mptt) REVERT: h 188 ASP cc_start: 0.7740 (t0) cc_final: 0.7502 (p0) REVERT: h 217 LYS cc_start: 0.8966 (ttpt) cc_final: 0.8691 (ttpt) REVERT: h 247 LYS cc_start: 0.8305 (pttp) cc_final: 0.7922 (ptpp) REVERT: h 254 GLU cc_start: 0.8084 (tm-30) cc_final: 0.7883 (tp30) REVERT: h 276 ASP cc_start: 0.7325 (t0) cc_final: 0.7001 (m-30) REVERT: h 320 LYS cc_start: 0.7655 (mmtt) cc_final: 0.7415 (mtmm) REVERT: h 344 ARG cc_start: 0.7289 (ttm110) cc_final: 0.6598 (mtm-85) REVERT: h 356 GLU cc_start: 0.7275 (mt-10) cc_final: 0.6909 (mt-10) REVERT: h 368 LYS cc_start: 0.7555 (mttt) cc_final: 0.6967 (mtpp) REVERT: h 379 GLU cc_start: 0.8062 (tm-30) cc_final: 0.7539 (tm-30) REVERT: h 440 LYS cc_start: 0.8202 (tptt) cc_final: 0.7830 (tppt) REVERT: h 524 ARG cc_start: 0.5476 (mmm-85) cc_final: 0.5192 (mmm-85) REVERT: n 83 ASN cc_start: 0.2446 (OUTLIER) cc_final: 0.1399 (m110) REVERT: q 3 LEU cc_start: 0.5368 (OUTLIER) cc_final: 0.4587 (tt) REVERT: q 17 GLU cc_start: 0.7460 (tt0) cc_final: 0.7234 (tm-30) REVERT: q 31 ARG cc_start: 0.7466 (mmp-170) cc_final: 0.6917 (mmt-90) REVERT: q 55 MET cc_start: 0.7754 (OUTLIER) cc_final: 0.7294 (mtt) REVERT: q 117 GLU cc_start: 0.7081 (tt0) cc_final: 0.6544 (mt-10) REVERT: q 212 ILE cc_start: 0.8108 (OUTLIER) cc_final: 0.7851 (mm) REVERT: q 238 LYS cc_start: 0.7236 (mmtp) cc_final: 0.6741 (mmtp) REVERT: q 277 ASP cc_start: 0.8443 (t70) cc_final: 0.8225 (t0) REVERT: q 312 LEU cc_start: 0.8575 (OUTLIER) cc_final: 0.8310 (mt) REVERT: q 406 LYS cc_start: 0.7532 (ptmt) cc_final: 0.6696 (mmtm) REVERT: q 483 GLU cc_start: 0.7299 (mp0) cc_final: 0.6923 (mm-30) REVERT: q 498 LEU cc_start: 0.8643 (OUTLIER) cc_final: 0.8295 (mt) REVERT: q 505 TYR cc_start: 0.8081 (t80) cc_final: 0.7675 (t80) REVERT: z 10 LYS cc_start: 0.7995 (mtmt) cc_final: 0.7311 (pmtt) REVERT: z 15 ARG cc_start: 0.7581 (OUTLIER) cc_final: 0.6742 (mtm-85) REVERT: z 32 ASP cc_start: 0.6869 (t0) cc_final: 0.6506 (m-30) REVERT: z 36 THR cc_start: 0.8564 (OUTLIER) cc_final: 0.8194 (p) REVERT: z 181 LYS cc_start: 0.6972 (mttt) cc_final: 0.6109 (mmmt) REVERT: z 195 GLU cc_start: 0.8366 (mt-10) cc_final: 0.7966 (mt-10) REVERT: z 201 GLU cc_start: 0.7480 (OUTLIER) cc_final: 0.7265 (pt0) REVERT: z 203 ASP cc_start: 0.8317 (m-30) cc_final: 0.7954 (m-30) REVERT: z 272 LYS cc_start: 0.7931 (mmtp) cc_final: 0.7651 (mtpp) REVERT: z 307 LYS cc_start: 0.7897 (mmtp) cc_final: 0.6829 (ttpt) REVERT: z 359 LYS cc_start: 0.7810 (mttt) cc_final: 0.6939 (mtmm) REVERT: z 388 LYS cc_start: 0.7480 (OUTLIER) cc_final: 0.6805 (mtpt) REVERT: T 49 VAL cc_start: 0.8609 (OUTLIER) cc_final: 0.8374 (t) REVERT: T 69 GLU cc_start: 0.7897 (OUTLIER) cc_final: 0.7635 (pt0) REVERT: T 94 GLN cc_start: 0.5726 (mp10) cc_final: 0.5415 (mt0) REVERT: T 167 PHE cc_start: 0.8302 (m-80) cc_final: 0.8087 (m-80) REVERT: T 233 MET cc_start: 0.7188 (tpt) cc_final: 0.6668 (tpt) REVERT: T 262 ARG cc_start: 0.7756 (ttm-80) cc_final: 0.7275 (tpp80) outliers start: 259 outliers final: 110 residues processed: 1221 average time/residue: 1.5243 time to fit residues: 2425.5641 Evaluate side-chains 1102 residues out of total 7485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 955 time to evaluate : 6.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 63 LYS Chi-restraints excluded: chain A residue 119 SER Chi-restraints excluded: chain A residue 166 ASP Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 284 ASN Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 97 ASP Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 114 GLU Chi-restraints excluded: chain B residue 134 THR Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 416 LEU Chi-restraints excluded: chain B residue 460 ASP Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 73 ASP Chi-restraints excluded: chain D residue 79 LYS Chi-restraints excluded: chain D residue 82 GLN Chi-restraints excluded: chain D residue 136 SER Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 184 SER Chi-restraints excluded: chain D residue 186 MET Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 273 ASP Chi-restraints excluded: chain D residue 274 ARG Chi-restraints excluded: chain D residue 355 MET Chi-restraints excluded: chain D residue 404 SER Chi-restraints excluded: chain D residue 447 GLU Chi-restraints excluded: chain D residue 467 GLU Chi-restraints excluded: chain D residue 536 VAL Chi-restraints excluded: chain E residue 48 MET Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 198 ASP Chi-restraints excluded: chain E residue 245 ASP Chi-restraints excluded: chain E residue 308 ASP Chi-restraints excluded: chain E residue 418 VAL Chi-restraints excluded: chain G residue 7 VAL Chi-restraints excluded: chain G residue 8 LEU Chi-restraints excluded: chain G residue 71 GLN Chi-restraints excluded: chain G residue 83 ILE Chi-restraints excluded: chain G residue 96 THR Chi-restraints excluded: chain G residue 332 VAL Chi-restraints excluded: chain G residue 373 THR Chi-restraints excluded: chain G residue 440 VAL Chi-restraints excluded: chain G residue 463 LEU Chi-restraints excluded: chain G residue 508 THR Chi-restraints excluded: chain G residue 524 SER Chi-restraints excluded: chain H residue 142 THR Chi-restraints excluded: chain H residue 151 GLN Chi-restraints excluded: chain H residue 254 GLU Chi-restraints excluded: chain H residue 341 VAL Chi-restraints excluded: chain H residue 427 ILE Chi-restraints excluded: chain N residue 83 ASN Chi-restraints excluded: chain Q residue 105 LEU Chi-restraints excluded: chain Q residue 146 LEU Chi-restraints excluded: chain Q residue 212 ILE Chi-restraints excluded: chain Q residue 286 THR Chi-restraints excluded: chain Q residue 366 GLU Chi-restraints excluded: chain Q residue 406 LYS Chi-restraints excluded: chain Q residue 486 VAL Chi-restraints excluded: chain Q residue 517 THR Chi-restraints excluded: chain Z residue 107 ASP Chi-restraints excluded: chain Z residue 340 SER Chi-restraints excluded: chain Z residue 373 THR Chi-restraints excluded: chain Z residue 407 VAL Chi-restraints excluded: chain Z residue 408 VAL Chi-restraints excluded: chain Z residue 479 VAL Chi-restraints excluded: chain Z residue 487 MET Chi-restraints excluded: chain a residue 1 MET Chi-restraints excluded: chain a residue 23 MET Chi-restraints excluded: chain a residue 84 LYS Chi-restraints excluded: chain a residue 166 ASP Chi-restraints excluded: chain a residue 321 LYS Chi-restraints excluded: chain a residue 367 THR Chi-restraints excluded: chain a residue 391 SER Chi-restraints excluded: chain a residue 508 ILE Chi-restraints excluded: chain b residue 57 ARG Chi-restraints excluded: chain b residue 66 ASP Chi-restraints excluded: chain b residue 182 LEU Chi-restraints excluded: chain b residue 236 LYS Chi-restraints excluded: chain b residue 334 THR Chi-restraints excluded: chain b residue 371 CYS Chi-restraints excluded: chain b residue 416 LEU Chi-restraints excluded: chain b residue 446 LEU Chi-restraints excluded: chain d residue 67 ASP Chi-restraints excluded: chain d residue 71 THR Chi-restraints excluded: chain d residue 115 SER Chi-restraints excluded: chain d residue 134 SER Chi-restraints excluded: chain d residue 157 LEU Chi-restraints excluded: chain d residue 168 THR Chi-restraints excluded: chain d residue 184 SER Chi-restraints excluded: chain d residue 203 VAL Chi-restraints excluded: chain d residue 385 THR Chi-restraints excluded: chain d residue 394 ASN Chi-restraints excluded: chain d residue 395 LYS Chi-restraints excluded: chain e residue 145 ILE Chi-restraints excluded: chain e residue 298 ASN Chi-restraints excluded: chain e residue 330 ILE Chi-restraints excluded: chain e residue 418 VAL Chi-restraints excluded: chain g residue 39 THR Chi-restraints excluded: chain g residue 59 MET Chi-restraints excluded: chain g residue 83 ILE Chi-restraints excluded: chain g residue 96 THR Chi-restraints excluded: chain g residue 110 GLU Chi-restraints excluded: chain g residue 161 THR Chi-restraints excluded: chain g residue 367 LYS Chi-restraints excluded: chain g residue 383 ILE Chi-restraints excluded: chain g residue 397 VAL Chi-restraints excluded: chain g residue 432 VAL Chi-restraints excluded: chain g residue 440 VAL Chi-restraints excluded: chain g residue 460 ILE Chi-restraints excluded: chain g residue 519 ILE Chi-restraints excluded: chain h residue 38 THR Chi-restraints excluded: chain h residue 85 SER Chi-restraints excluded: chain h residue 211 VAL Chi-restraints excluded: chain h residue 395 ILE Chi-restraints excluded: chain h residue 405 VAL Chi-restraints excluded: chain h residue 473 THR Chi-restraints excluded: chain n residue 12 VAL Chi-restraints excluded: chain n residue 83 ASN Chi-restraints excluded: chain q residue 3 LEU Chi-restraints excluded: chain q residue 45 THR Chi-restraints excluded: chain q residue 55 MET Chi-restraints excluded: chain q residue 150 SER Chi-restraints excluded: chain q residue 212 ILE Chi-restraints excluded: chain q residue 226 GLU Chi-restraints excluded: chain q residue 234 VAL Chi-restraints excluded: chain q residue 312 LEU Chi-restraints excluded: chain q residue 385 MET Chi-restraints excluded: chain q residue 480 LEU Chi-restraints excluded: chain q residue 498 LEU Chi-restraints excluded: chain z residue 4 VAL Chi-restraints excluded: chain z residue 15 ARG Chi-restraints excluded: chain z residue 36 THR Chi-restraints excluded: chain z residue 149 ILE Chi-restraints excluded: chain z residue 179 ILE Chi-restraints excluded: chain z residue 201 GLU Chi-restraints excluded: chain z residue 388 LYS Chi-restraints excluded: chain z residue 442 ASP Chi-restraints excluded: chain z residue 464 VAL Chi-restraints excluded: chain z residue 479 VAL Chi-restraints excluded: chain T residue 12 CYS Chi-restraints excluded: chain T residue 49 VAL Chi-restraints excluded: chain T residue 69 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 885 random chunks: chunk 795 optimal weight: 5.9990 chunk 605 optimal weight: 0.4980 chunk 417 optimal weight: 0.8980 chunk 89 optimal weight: 3.9990 chunk 384 optimal weight: 6.9990 chunk 540 optimal weight: 6.9990 chunk 808 optimal weight: 0.9990 chunk 855 optimal weight: 9.9990 chunk 422 optimal weight: 2.9990 chunk 765 optimal weight: 5.9990 chunk 230 optimal weight: 8.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 25 GLN ** E 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 495 HIS ** 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 235 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** ** Q 365 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 492 ASN b 195 ASN d 301 GLN d 318 ASN d 366 ASN e 122 GLN e 290 GLN e 291 GLN e 515 GLN ** g 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 107 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** ** z 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 6 HIS T 37 HIS Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7427 moved from start: 0.1866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 69953 Z= 0.233 Angle : 0.560 7.373 94470 Z= 0.278 Chirality : 0.042 0.176 11206 Planarity : 0.004 0.044 12067 Dihedral : 7.947 174.871 9753 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.13 % Favored : 96.83 % Rotamer: Outliers : 3.78 % Allowed : 17.68 % Favored : 78.53 % 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: 0.40 (0.09), residues: 8920 helix: 1.29 (0.08), residues: 4580 sheet: -0.49 (0.14), residues: 1212 loop : -0.87 (0.11), residues: 3128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP N 101 HIS 0.012 0.001 HIS G 111 PHE 0.020 0.001 PHE a 167 TYR 0.018 0.001 TYR g 303 ARG 0.006 0.000 ARG e 381 *********************** 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 1294 residues out of total 7485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 282 poor density : 1012 time to evaluate : 6.192 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 PHE cc_start: 0.7658 (t80) cc_final: 0.7264 (t80) REVERT: A 44 MET cc_start: 0.8653 (OUTLIER) cc_final: 0.8443 (mtp) REVERT: A 51 ASP cc_start: 0.6452 (t0) cc_final: 0.5975 (t70) REVERT: A 63 LYS cc_start: 0.7770 (OUTLIER) cc_final: 0.7375 (mtmm) REVERT: A 123 LEU cc_start: 0.8060 (OUTLIER) cc_final: 0.7627 (tp) REVERT: A 230 VAL cc_start: 0.7305 (OUTLIER) cc_final: 0.7002 (t) REVERT: A 261 ASP cc_start: 0.6813 (p0) cc_final: 0.6420 (t0) REVERT: A 277 LYS cc_start: 0.7784 (mttt) cc_final: 0.7453 (mttm) REVERT: A 321 LYS cc_start: 0.7854 (mtmt) cc_final: 0.7522 (tptp) REVERT: A 354 GLU cc_start: 0.6593 (mm-30) cc_final: 0.6102 (tp30) REVERT: A 358 ASP cc_start: 0.7946 (t0) cc_final: 0.7569 (t70) REVERT: A 384 MET cc_start: 0.8147 (ttt) cc_final: 0.7863 (ttt) REVERT: A 430 MET cc_start: 0.6153 (mmm) cc_final: 0.5173 (mmm) REVERT: A 459 ASP cc_start: 0.8263 (t0) cc_final: 0.7967 (t0) REVERT: B 87 MET cc_start: 0.7854 (ttp) cc_final: 0.7501 (ttp) REVERT: B 114 GLU cc_start: 0.7662 (OUTLIER) cc_final: 0.7401 (pt0) REVERT: B 132 GLU cc_start: 0.7390 (OUTLIER) cc_final: 0.7110 (mp0) REVERT: B 248 LYS cc_start: 0.7909 (mtpt) cc_final: 0.7561 (mtmt) REVERT: B 276 LYS cc_start: 0.7638 (ttpt) cc_final: 0.7202 (ttmm) REVERT: B 301 GLU cc_start: 0.7418 (tt0) cc_final: 0.7037 (tt0) REVERT: B 347 LYS cc_start: 0.8326 (mmtm) cc_final: 0.7609 (mppt) REVERT: B 402 LYS cc_start: 0.7601 (mtmm) cc_final: 0.6996 (mptp) REVERT: B 414 GLU cc_start: 0.6638 (mp0) cc_final: 0.6090 (mp0) REVERT: B 445 MET cc_start: 0.7759 (tpp) cc_final: 0.7418 (tpp) REVERT: B 456 TYR cc_start: 0.8713 (m-80) cc_final: 0.8384 (m-10) REVERT: D 32 GLN cc_start: 0.7537 (mt0) cc_final: 0.7298 (mm-40) REVERT: D 65 LYS cc_start: 0.8301 (mtmm) cc_final: 0.7995 (mtpt) REVERT: D 82 GLN cc_start: 0.8153 (OUTLIER) cc_final: 0.7598 (mm-40) REVERT: D 196 ASP cc_start: 0.7609 (t0) cc_final: 0.6541 (p0) REVERT: D 222 GLU cc_start: 0.7396 (tt0) cc_final: 0.6818 (mt-10) REVERT: D 257 LYS cc_start: 0.7717 (mmtm) cc_final: 0.7315 (ttpp) REVERT: D 358 SER cc_start: 0.7919 (m) cc_final: 0.7477 (t) REVERT: D 368 ASN cc_start: 0.7036 (m110) cc_final: 0.6470 (m110) REVERT: D 384 LYS cc_start: 0.7562 (mptt) cc_final: 0.7330 (mptm) REVERT: D 458 MET cc_start: 0.8001 (mmm) cc_final: 0.7720 (mpp) REVERT: D 467 GLU cc_start: 0.7314 (OUTLIER) cc_final: 0.6926 (mt-10) REVERT: D 496 ARG cc_start: 0.8055 (ttp80) cc_final: 0.7732 (tmm160) REVERT: E 20 LYS cc_start: 0.7982 (tttp) cc_final: 0.7739 (ttpt) REVERT: E 21 ASP cc_start: 0.7444 (t0) cc_final: 0.7211 (t0) REVERT: E 48 MET cc_start: 0.8354 (OUTLIER) cc_final: 0.8049 (mmm) REVERT: E 93 GLU cc_start: 0.6851 (mm-30) cc_final: 0.6468 (mm-30) REVERT: E 121 GLU cc_start: 0.7052 (tt0) cc_final: 0.6605 (tt0) REVERT: E 125 ASP cc_start: 0.7870 (m-30) cc_final: 0.7606 (m-30) REVERT: E 188 ILE cc_start: 0.8405 (OUTLIER) cc_final: 0.8038 (mt) REVERT: E 198 ASP cc_start: 0.7729 (OUTLIER) cc_final: 0.7494 (t70) REVERT: E 263 LYS cc_start: 0.7830 (ttmt) cc_final: 0.7081 (tttt) REVERT: E 290 GLN cc_start: 0.7362 (tp-100) cc_final: 0.6953 (tm-30) REVERT: E 361 GLU cc_start: 0.7629 (tt0) cc_final: 0.7409 (tt0) REVERT: E 381 ARG cc_start: 0.7986 (ttp80) cc_final: 0.7750 (ttt-90) REVERT: E 439 LYS cc_start: 0.7834 (mtmm) cc_final: 0.7583 (mptt) REVERT: E 502 LYS cc_start: 0.7592 (tttt) cc_final: 0.7163 (tmtm) REVERT: G 8 LEU cc_start: 0.6454 (OUTLIER) cc_final: 0.6064 (mm) REVERT: G 9 VAL cc_start: 0.8395 (p) cc_final: 0.8125 (m) REVERT: G 15 LYS cc_start: 0.7531 (mmmt) cc_final: 0.6807 (mtmm) REVERT: G 17 GLU cc_start: 0.6972 (mp0) cc_final: 0.6481 (mp0) REVERT: G 54 MET cc_start: 0.8106 (OUTLIER) cc_final: 0.7758 (mtp) REVERT: G 69 GLU cc_start: 0.7599 (mm-30) cc_final: 0.7352 (mm-30) REVERT: G 71 GLN cc_start: 0.8220 (OUTLIER) cc_final: 0.7931 (tt0) REVERT: G 81 ILE cc_start: 0.8495 (OUTLIER) cc_final: 0.8220 (mp) REVERT: G 82 GLU cc_start: 0.7703 (mm-30) cc_final: 0.7417 (mm-30) REVERT: G 110 GLU cc_start: 0.7689 (tt0) cc_final: 0.7227 (tp30) REVERT: G 166 SER cc_start: 0.7488 (p) cc_final: 0.7245 (m) REVERT: G 192 GLU cc_start: 0.7419 (pt0) cc_final: 0.6747 (pp20) REVERT: G 210 GLU cc_start: 0.7802 (OUTLIER) cc_final: 0.7547 (mp0) REVERT: G 234 LYS cc_start: 0.7265 (tptp) cc_final: 0.6842 (tptt) REVERT: G 248 LYS cc_start: 0.8331 (mtpt) cc_final: 0.7890 (mmpt) REVERT: G 255 ASP cc_start: 0.6754 (OUTLIER) cc_final: 0.6416 (t0) REVERT: G 270 MET cc_start: 0.7561 (mtp) cc_final: 0.7180 (mtp) REVERT: G 276 GLN cc_start: 0.7514 (tt0) cc_final: 0.7219 (tm-30) REVERT: G 277 GLN cc_start: 0.7501 (tp40) cc_final: 0.6735 (mp10) REVERT: G 429 MET cc_start: 0.7242 (mtm) cc_final: 0.6976 (mtm) REVERT: G 477 THR cc_start: 0.8533 (OUTLIER) cc_final: 0.8225 (t) REVERT: G 511 GLU cc_start: 0.7566 (mm-30) cc_final: 0.7248 (mp0) REVERT: H 151 GLN cc_start: 0.7473 (OUTLIER) cc_final: 0.7151 (tt0) REVERT: H 279 GLU cc_start: 0.7267 (tp30) cc_final: 0.6895 (mt-10) REVERT: H 317 GLU cc_start: 0.7562 (mp0) cc_final: 0.7268 (tt0) REVERT: H 349 GLU cc_start: 0.7878 (tt0) cc_final: 0.7609 (tt0) REVERT: H 368 LYS cc_start: 0.8130 (mttt) cc_final: 0.7568 (mmtp) REVERT: H 379 GLU cc_start: 0.7179 (tp30) cc_final: 0.6906 (tm-30) REVERT: H 383 GLU cc_start: 0.7703 (mm-30) cc_final: 0.7407 (mm-30) REVERT: H 440 LYS cc_start: 0.7663 (mmtp) cc_final: 0.7391 (mtpt) REVERT: H 482 GLU cc_start: 0.7897 (mt-10) cc_final: 0.7595 (mt-10) REVERT: H 497 MET cc_start: 0.7415 (tpp) cc_final: 0.6954 (tpt) REVERT: Q 14 MET cc_start: 0.8672 (mtm) cc_final: 0.8452 (mtm) REVERT: Q 31 ARG cc_start: 0.7384 (mmp-170) cc_final: 0.6635 (mtt180) REVERT: Q 193 ASP cc_start: 0.6749 (m-30) cc_final: 0.6348 (m-30) REVERT: Q 200 ASP cc_start: 0.7953 (m-30) cc_final: 0.7717 (m-30) REVERT: Q 249 MET cc_start: 0.7452 (ptp) cc_final: 0.7065 (mmm) REVERT: Q 281 LYS cc_start: 0.7569 (ttmt) cc_final: 0.7295 (tptp) REVERT: Q 296 LYS cc_start: 0.7751 (pttm) cc_final: 0.7420 (pttt) REVERT: Q 318 LYS cc_start: 0.8102 (pttm) cc_final: 0.7592 (ptmm) REVERT: Q 354 GLU cc_start: 0.7729 (tm-30) cc_final: 0.7486 (tm-30) REVERT: Q 387 ASP cc_start: 0.7130 (t0) cc_final: 0.6912 (t0) REVERT: Q 436 TYR cc_start: 0.7059 (m-80) cc_final: 0.6809 (m-80) REVERT: Q 481 ASP cc_start: 0.7584 (t0) cc_final: 0.7338 (t0) REVERT: Z 17 GLN cc_start: 0.6839 (OUTLIER) cc_final: 0.6084 (pp30) REVERT: Z 44 MET cc_start: 0.9020 (mmm) cc_final: 0.8716 (mmt) REVERT: Z 108 LEU cc_start: 0.8006 (tt) cc_final: 0.7610 (tp) REVERT: Z 163 GLU cc_start: 0.6798 (tp30) cc_final: 0.6306 (tp30) REVERT: Z 195 GLU cc_start: 0.7941 (pt0) cc_final: 0.7513 (pt0) REVERT: Z 223 LYS cc_start: 0.7807 (mptt) cc_final: 0.7537 (mmtt) REVERT: Z 239 TYR cc_start: 0.8172 (t80) cc_final: 0.7901 (t80) REVERT: Z 241 LYS cc_start: 0.8546 (ttmt) cc_final: 0.7612 (pttp) REVERT: Z 264 ARG cc_start: 0.7301 (mtp85) cc_final: 0.6901 (mtp-110) REVERT: Z 272 LYS cc_start: 0.7417 (mmtp) cc_final: 0.6939 (mtpp) REVERT: Z 303 ASP cc_start: 0.7449 (t70) cc_final: 0.6801 (m-30) REVERT: Z 307 LYS cc_start: 0.7799 (mmtp) cc_final: 0.7405 (mtpt) REVERT: Z 322 GLU cc_start: 0.7464 (tt0) cc_final: 0.7104 (tt0) REVERT: Z 340 SER cc_start: 0.7139 (OUTLIER) cc_final: 0.6716 (p) REVERT: Z 381 LYS cc_start: 0.8305 (tptt) cc_final: 0.8013 (tppp) REVERT: Z 445 LEU cc_start: 0.8073 (mt) cc_final: 0.7736 (mm) REVERT: Z 487 MET cc_start: 0.7098 (OUTLIER) cc_final: 0.6392 (ppp) REVERT: Z 495 TRP cc_start: 0.8009 (m100) cc_final: 0.7473 (m100) REVERT: Z 496 ASP cc_start: 0.7495 (m-30) cc_final: 0.7217 (m-30) REVERT: a 23 MET cc_start: 0.5787 (OUTLIER) cc_final: 0.5470 (ttp) REVERT: a 212 SER cc_start: 0.7525 (p) cc_final: 0.7298 (t) REVERT: a 265 GLN cc_start: 0.7196 (pt0) cc_final: 0.6843 (tp40) REVERT: a 368 LYS cc_start: 0.7836 (ptmt) cc_final: 0.7154 (ptpt) REVERT: a 384 MET cc_start: 0.8014 (ttt) cc_final: 0.7670 (ttt) REVERT: b 6 LEU cc_start: 0.4960 (tp) cc_final: 0.4249 (tp) REVERT: b 89 ARG cc_start: 0.7956 (ttp80) cc_final: 0.7641 (tmm160) REVERT: b 93 ASP cc_start: 0.7328 (m-30) cc_final: 0.6578 (m-30) REVERT: b 223 LYS cc_start: 0.8425 (mttm) cc_final: 0.8044 (mtpt) REVERT: b 236 LYS cc_start: 0.7807 (OUTLIER) cc_final: 0.7273 (mtmm) REVERT: b 301 GLU cc_start: 0.7585 (tt0) cc_final: 0.7088 (tt0) REVERT: b 316 ASP cc_start: 0.7110 (t0) cc_final: 0.6785 (m-30) REVERT: b 387 GLU cc_start: 0.7307 (OUTLIER) cc_final: 0.7073 (tt0) REVERT: b 407 VAL cc_start: 0.8114 (t) cc_final: 0.7895 (m) REVERT: b 445 MET cc_start: 0.8048 (tpp) cc_final: 0.7761 (tpp) REVERT: b 516 ARG cc_start: 0.7575 (mtp85) cc_final: 0.7251 (mtp180) REVERT: b 522 LYS cc_start: 0.7983 (mttt) cc_final: 0.7339 (mtmt) REVERT: d 42 LYS cc_start: 0.7092 (tttp) cc_final: 0.6424 (tptt) REVERT: d 46 ASP cc_start: 0.7909 (m-30) cc_final: 0.7558 (m-30) REVERT: d 60 MET cc_start: 0.8349 (ttp) cc_final: 0.7825 (ttp) REVERT: d 63 ASP cc_start: 0.7181 (m-30) cc_final: 0.6961 (m-30) REVERT: d 81 MET cc_start: 0.8110 (ptm) cc_final: 0.7891 (ptm) REVERT: d 93 GLU cc_start: 0.7136 (mm-30) cc_final: 0.6727 (mm-30) REVERT: d 132 ILE cc_start: 0.8354 (mt) cc_final: 0.8079 (mp) REVERT: d 304 ILE cc_start: 0.8100 (OUTLIER) cc_final: 0.7550 (mt) REVERT: d 334 GLU cc_start: 0.7474 (tp30) cc_final: 0.7161 (tp30) REVERT: d 384 LYS cc_start: 0.7322 (mmtp) cc_final: 0.6891 (mmpt) REVERT: e 23 ASP cc_start: 0.8087 (m-30) cc_final: 0.7786 (m-30) REVERT: e 27 ARG cc_start: 0.8014 (ttp-170) cc_final: 0.7601 (ttt180) REVERT: e 29 MET cc_start: 0.8012 (mtp) cc_final: 0.7710 (mtp) REVERT: e 93 GLU cc_start: 0.7048 (mm-30) cc_final: 0.6647 (mt-10) REVERT: e 96 LYS cc_start: 0.7677 (tttm) cc_final: 0.6974 (ttmt) REVERT: e 121 GLU cc_start: 0.6941 (tt0) cc_final: 0.6660 (tt0) REVERT: e 126 ARG cc_start: 0.7298 (mtm180) cc_final: 0.6740 (mtp85) REVERT: e 146 GLU cc_start: 0.7000 (mt-10) cc_final: 0.6719 (mt-10) REVERT: e 150 LYS cc_start: 0.7696 (ttmt) cc_final: 0.7339 (ttpt) REVERT: e 464 GLU cc_start: 0.6584 (tt0) cc_final: 0.5975 (mm-30) REVERT: e 478 ARG cc_start: 0.7337 (ttp-170) cc_final: 0.7076 (ttm170) REVERT: e 502 LYS cc_start: 0.6983 (tttm) cc_final: 0.6628 (ttmp) REVERT: e 515 GLN cc_start: 0.7878 (tp-100) cc_final: 0.7377 (tp40) REVERT: e 532 ASP cc_start: 0.8272 (t0) cc_final: 0.8027 (t0) REVERT: g 110 GLU cc_start: 0.8271 (OUTLIER) cc_final: 0.7386 (tt0) REVERT: g 167 ARG cc_start: 0.7519 (mtt-85) cc_final: 0.7177 (mtm-85) REVERT: g 186 GLU cc_start: 0.7069 (tt0) cc_final: 0.6517 (tt0) REVERT: g 191 LYS cc_start: 0.7714 (mtpt) cc_final: 0.7232 (mptt) REVERT: g 192 GLU cc_start: 0.6959 (tt0) cc_final: 0.6128 (pp20) REVERT: g 202 GLU cc_start: 0.6891 (mm-30) cc_final: 0.6526 (mm-30) REVERT: g 274 TYR cc_start: 0.7978 (t80) cc_final: 0.7649 (t80) REVERT: g 277 GLN cc_start: 0.7021 (tp-100) cc_final: 0.6232 (pt0) REVERT: g 294 LYS cc_start: 0.8126 (mmtp) cc_final: 0.7710 (mmtp) REVERT: g 367 LYS cc_start: 0.8476 (OUTLIER) cc_final: 0.8024 (pptt) REVERT: g 381 LYS cc_start: 0.7896 (tppt) cc_final: 0.7429 (mptt) REVERT: g 383 ILE cc_start: 0.8327 (OUTLIER) cc_final: 0.8105 (mp) REVERT: g 476 GLU cc_start: 0.7059 (pm20) cc_final: 0.6674 (mm-30) REVERT: g 519 ILE cc_start: 0.8012 (mt) cc_final: 0.7760 (mp) REVERT: h 10 LYS cc_start: 0.8074 (ttmt) cc_final: 0.7486 (ttpt) REVERT: h 17 GLN cc_start: 0.8061 (tt0) cc_final: 0.7850 (tt0) REVERT: h 119 GLN cc_start: 0.8013 (mm-40) cc_final: 0.7676 (mm110) REVERT: h 153 LYS cc_start: 0.7910 (mttm) cc_final: 0.7384 (mptt) REVERT: h 188 ASP cc_start: 0.7812 (t0) cc_final: 0.7537 (p0) REVERT: h 217 LYS cc_start: 0.8984 (ttpt) cc_final: 0.8743 (ttpt) REVERT: h 247 LYS cc_start: 0.8350 (pttp) cc_final: 0.7960 (ptpp) REVERT: h 254 GLU cc_start: 0.8061 (tm-30) cc_final: 0.7826 (tp30) REVERT: h 276 ASP cc_start: 0.7348 (t0) cc_final: 0.7059 (m-30) REVERT: h 320 LYS cc_start: 0.7658 (mmtt) cc_final: 0.7399 (mtpp) REVERT: h 344 ARG cc_start: 0.7407 (ttm110) cc_final: 0.6719 (mtm-85) REVERT: h 356 GLU cc_start: 0.7308 (mt-10) cc_final: 0.6760 (mt-10) REVERT: h 368 LYS cc_start: 0.7604 (mttt) cc_final: 0.6938 (mtpp) REVERT: h 379 GLU cc_start: 0.8110 (tm-30) cc_final: 0.7543 (tm-30) REVERT: h 383 GLU cc_start: 0.7491 (mm-30) cc_final: 0.7112 (mm-30) REVERT: h 440 LYS cc_start: 0.8206 (tptt) cc_final: 0.7807 (tppt) REVERT: h 524 ARG cc_start: 0.5735 (mmm-85) cc_final: 0.5452 (mmm-85) REVERT: n 83 ASN cc_start: 0.2394 (OUTLIER) cc_final: 0.1312 (m110) REVERT: q 3 LEU cc_start: 0.5362 (OUTLIER) cc_final: 0.4605 (tt) REVERT: q 17 GLU cc_start: 0.7479 (tt0) cc_final: 0.7196 (tm-30) REVERT: q 31 ARG cc_start: 0.7490 (mmp-170) cc_final: 0.6930 (mmt-90) REVERT: q 55 MET cc_start: 0.7756 (OUTLIER) cc_final: 0.7338 (mtt) REVERT: q 117 GLU cc_start: 0.7084 (tt0) cc_final: 0.6537 (mt-10) REVERT: q 155 ARG cc_start: 0.8197 (mmt-90) cc_final: 0.7954 (mmt90) REVERT: q 212 ILE cc_start: 0.8118 (OUTLIER) cc_final: 0.7829 (mm) REVERT: q 238 LYS cc_start: 0.7236 (mmtp) cc_final: 0.6695 (mmtp) REVERT: q 277 ASP cc_start: 0.8462 (t70) cc_final: 0.8245 (t0) REVERT: q 312 LEU cc_start: 0.8558 (OUTLIER) cc_final: 0.8305 (mt) REVERT: q 406 LYS cc_start: 0.7613 (ptmt) cc_final: 0.6738 (mmtm) REVERT: q 483 GLU cc_start: 0.7316 (mp0) cc_final: 0.6951 (mm-30) REVERT: q 498 LEU cc_start: 0.8767 (OUTLIER) cc_final: 0.8292 (mt) REVERT: q 505 TYR cc_start: 0.8106 (t80) cc_final: 0.7672 (t80) REVERT: z 10 LYS cc_start: 0.8056 (mtmt) cc_final: 0.7376 (pmtt) REVERT: z 15 ARG cc_start: 0.7594 (OUTLIER) cc_final: 0.6652 (mtm-85) REVERT: z 32 ASP cc_start: 0.6886 (t0) cc_final: 0.6543 (m-30) REVERT: z 36 THR cc_start: 0.8654 (OUTLIER) cc_final: 0.8284 (p) REVERT: z 181 LYS cc_start: 0.6992 (mttt) cc_final: 0.6091 (mmmt) REVERT: z 195 GLU cc_start: 0.8478 (mt-10) cc_final: 0.8157 (mt-10) REVERT: z 201 GLU cc_start: 0.7516 (OUTLIER) cc_final: 0.7303 (pt0) REVERT: z 203 ASP cc_start: 0.8275 (m-30) cc_final: 0.7911 (m-30) REVERT: z 272 LYS cc_start: 0.7884 (mmtp) cc_final: 0.7626 (mtpp) REVERT: z 307 LYS cc_start: 0.7899 (mmtp) cc_final: 0.6872 (ttpt) REVERT: z 359 LYS cc_start: 0.7849 (mttt) cc_final: 0.6964 (mtmm) REVERT: z 388 LYS cc_start: 0.7454 (OUTLIER) cc_final: 0.6821 (mtpt) REVERT: z 430 LYS cc_start: 0.8345 (tppt) cc_final: 0.7737 (mmmt) REVERT: z 487 MET cc_start: 0.7068 (OUTLIER) cc_final: 0.5718 (ppp) REVERT: z 492 VAL cc_start: 0.8142 (p) cc_final: 0.7438 (p) REVERT: T 48 ASN cc_start: 0.6191 (OUTLIER) cc_final: 0.5921 (t0) REVERT: T 49 VAL cc_start: 0.8598 (OUTLIER) cc_final: 0.8376 (t) REVERT: T 69 GLU cc_start: 0.7965 (OUTLIER) cc_final: 0.7672 (pt0) REVERT: T 94 GLN cc_start: 0.5759 (mp10) cc_final: 0.5483 (mt0) REVERT: T 167 PHE cc_start: 0.8320 (m-80) cc_final: 0.8086 (m-80) REVERT: T 200 TYR cc_start: 0.7750 (m-80) cc_final: 0.7424 (m-80) REVERT: T 233 MET cc_start: 0.7156 (tpt) cc_final: 0.6662 (tpt) REVERT: T 412 GLU cc_start: 0.6982 (tp30) cc_final: 0.6689 (tp30) outliers start: 282 outliers final: 142 residues processed: 1216 average time/residue: 1.5386 time to fit residues: 2445.1941 Evaluate side-chains 1128 residues out of total 7485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 185 poor density : 943 time to evaluate : 6.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 44 MET Chi-restraints excluded: chain A residue 63 LYS Chi-restraints excluded: chain A residue 119 SER Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 166 ASP Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 284 ASN Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 97 ASP Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 114 GLU Chi-restraints excluded: chain B residue 132 GLU Chi-restraints excluded: chain B residue 134 THR Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 413 SER Chi-restraints excluded: chain B residue 416 LEU Chi-restraints excluded: chain B residue 437 GLU Chi-restraints excluded: chain B residue 460 ASP Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 73 ASP Chi-restraints excluded: chain D residue 79 LYS Chi-restraints excluded: chain D residue 82 GLN Chi-restraints excluded: chain D residue 136 SER Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 184 SER Chi-restraints excluded: chain D residue 186 MET Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 273 ASP Chi-restraints excluded: chain D residue 404 SER Chi-restraints excluded: chain D residue 430 ILE Chi-restraints excluded: chain D residue 446 MET Chi-restraints excluded: chain D residue 467 GLU Chi-restraints excluded: chain E residue 48 MET Chi-restraints excluded: chain E residue 188 ILE Chi-restraints excluded: chain E residue 198 ASP Chi-restraints excluded: chain E residue 269 THR Chi-restraints excluded: chain E residue 308 ASP Chi-restraints excluded: chain E residue 418 VAL Chi-restraints excluded: chain G residue 7 VAL Chi-restraints excluded: chain G residue 8 LEU Chi-restraints excluded: chain G residue 54 MET Chi-restraints excluded: chain G residue 71 GLN Chi-restraints excluded: chain G residue 81 ILE Chi-restraints excluded: chain G residue 83 ILE Chi-restraints excluded: chain G residue 96 THR Chi-restraints excluded: chain G residue 210 GLU Chi-restraints excluded: chain G residue 255 ASP Chi-restraints excluded: chain G residue 265 THR Chi-restraints excluded: chain G residue 332 VAL Chi-restraints excluded: chain G residue 373 THR Chi-restraints excluded: chain G residue 440 VAL Chi-restraints excluded: chain G residue 463 LEU Chi-restraints excluded: chain G residue 477 THR Chi-restraints excluded: chain G residue 508 THR Chi-restraints excluded: chain H residue 120 ILE Chi-restraints excluded: chain H residue 142 THR Chi-restraints excluded: chain H residue 151 GLN Chi-restraints excluded: chain H residue 251 ASP Chi-restraints excluded: chain H residue 362 THR Chi-restraints excluded: chain H residue 405 VAL Chi-restraints excluded: chain H residue 427 ILE Chi-restraints excluded: chain N residue 83 ASN Chi-restraints excluded: chain Q residue 105 LEU Chi-restraints excluded: chain Q residue 146 LEU Chi-restraints excluded: chain Q residue 212 ILE Chi-restraints excluded: chain Q residue 366 GLU Chi-restraints excluded: chain Q residue 480 LEU Chi-restraints excluded: chain Q residue 486 VAL Chi-restraints excluded: chain Q residue 517 THR Chi-restraints excluded: chain Z residue 17 GLN Chi-restraints excluded: chain Z residue 32 ASP Chi-restraints excluded: chain Z residue 107 ASP Chi-restraints excluded: chain Z residue 340 SER Chi-restraints excluded: chain Z residue 373 THR Chi-restraints excluded: chain Z residue 407 VAL Chi-restraints excluded: chain Z residue 408 VAL Chi-restraints excluded: chain Z residue 430 LYS Chi-restraints excluded: chain Z residue 479 VAL Chi-restraints excluded: chain Z residue 487 MET Chi-restraints excluded: chain Z residue 488 VAL Chi-restraints excluded: chain a residue 1 MET Chi-restraints excluded: chain a residue 23 MET Chi-restraints excluded: chain a residue 166 ASP Chi-restraints excluded: chain a residue 329 SER Chi-restraints excluded: chain a residue 367 THR Chi-restraints excluded: chain a residue 391 SER Chi-restraints excluded: chain b residue 51 ILE Chi-restraints excluded: chain b residue 66 ASP Chi-restraints excluded: chain b residue 153 VAL Chi-restraints excluded: chain b residue 182 LEU Chi-restraints excluded: chain b residue 236 LYS Chi-restraints excluded: chain b residue 371 CYS Chi-restraints excluded: chain b residue 387 GLU Chi-restraints excluded: chain b residue 416 LEU Chi-restraints excluded: chain d residue 67 ASP Chi-restraints excluded: chain d residue 71 THR Chi-restraints excluded: chain d residue 115 SER Chi-restraints excluded: chain d residue 134 SER Chi-restraints excluded: chain d residue 136 SER Chi-restraints excluded: chain d residue 157 LEU Chi-restraints excluded: chain d residue 158 SER Chi-restraints excluded: chain d residue 168 THR Chi-restraints excluded: chain d residue 184 SER Chi-restraints excluded: chain d residue 203 VAL Chi-restraints excluded: chain d residue 239 THR Chi-restraints excluded: chain d residue 304 ILE Chi-restraints excluded: chain d residue 385 THR Chi-restraints excluded: chain d residue 394 ASN Chi-restraints excluded: chain d residue 395 LYS Chi-restraints excluded: chain d residue 404 SER Chi-restraints excluded: chain d residue 430 ILE Chi-restraints excluded: chain d residue 536 VAL Chi-restraints excluded: chain e residue 145 ILE Chi-restraints excluded: chain e residue 298 ASN Chi-restraints excluded: chain e residue 308 ASP Chi-restraints excluded: chain e residue 330 ILE Chi-restraints excluded: chain e residue 418 VAL Chi-restraints excluded: chain e residue 498 THR Chi-restraints excluded: chain g residue 17 GLU Chi-restraints excluded: chain g residue 39 THR Chi-restraints excluded: chain g residue 59 MET Chi-restraints excluded: chain g residue 83 ILE Chi-restraints excluded: chain g residue 96 THR Chi-restraints excluded: chain g residue 110 GLU Chi-restraints excluded: chain g residue 161 THR Chi-restraints excluded: chain g residue 310 THR Chi-restraints excluded: chain g residue 367 LYS Chi-restraints excluded: chain g residue 383 ILE Chi-restraints excluded: chain g residue 397 VAL Chi-restraints excluded: chain g residue 432 VAL Chi-restraints excluded: chain g residue 440 VAL Chi-restraints excluded: chain g residue 460 ILE Chi-restraints excluded: chain g residue 471 THR Chi-restraints excluded: chain g residue 486 THR Chi-restraints excluded: chain h residue 38 THR Chi-restraints excluded: chain h residue 85 SER Chi-restraints excluded: chain h residue 211 VAL Chi-restraints excluded: chain h residue 395 ILE Chi-restraints excluded: chain h residue 405 VAL Chi-restraints excluded: chain h residue 427 ILE Chi-restraints excluded: chain h residue 473 THR Chi-restraints excluded: chain n residue 12 VAL Chi-restraints excluded: chain n residue 83 ASN Chi-restraints excluded: chain q residue 3 LEU Chi-restraints excluded: chain q residue 43 THR Chi-restraints excluded: chain q residue 45 THR Chi-restraints excluded: chain q residue 55 MET Chi-restraints excluded: chain q residue 150 SER Chi-restraints excluded: chain q residue 200 ASP Chi-restraints excluded: chain q residue 212 ILE Chi-restraints excluded: chain q residue 226 GLU Chi-restraints excluded: chain q residue 312 LEU Chi-restraints excluded: chain q residue 322 ARG Chi-restraints excluded: chain q residue 385 MET Chi-restraints excluded: chain q residue 480 LEU Chi-restraints excluded: chain q residue 498 LEU Chi-restraints excluded: chain z residue 4 VAL Chi-restraints excluded: chain z residue 15 ARG Chi-restraints excluded: chain z residue 36 THR Chi-restraints excluded: chain z residue 88 THR Chi-restraints excluded: chain z residue 149 ILE Chi-restraints excluded: chain z residue 179 ILE Chi-restraints excluded: chain z residue 201 GLU Chi-restraints excluded: chain z residue 388 LYS Chi-restraints excluded: chain z residue 442 ASP Chi-restraints excluded: chain z residue 464 VAL Chi-restraints excluded: chain z residue 479 VAL Chi-restraints excluded: chain z residue 487 MET Chi-restraints excluded: chain z residue 488 VAL Chi-restraints excluded: chain T residue 12 CYS Chi-restraints excluded: chain T residue 48 ASN Chi-restraints excluded: chain T residue 49 VAL Chi-restraints excluded: chain T residue 69 GLU Chi-restraints excluded: chain T residue 84 ILE Chi-restraints excluded: chain T residue 143 THR Chi-restraints excluded: chain T residue 232 THR Chi-restraints excluded: chain T residue 395 LEU 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: 8.9990 chunk 12 optimal weight: 6.9990 chunk 636 optimal weight: 0.9980 chunk 352 optimal weight: 9.9990 chunk 729 optimal weight: 7.9990 chunk 591 optimal weight: 1.9990 chunk 1 optimal weight: 8.9990 chunk 436 optimal weight: 8.9990 chunk 767 optimal weight: 3.9990 chunk 215 optimal weight: 6.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 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 235 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** ** Q 365 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 214 HIS ** a 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 492 ASN b 195 ASN d 318 ASN e 122 GLN e 360 GLN ** 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 30 GLN h 107 GLN h 130 GLN h 234 ASN h 241 ASN ** 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 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 37 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7469 moved from start: 0.2098 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= 0.386 Angle : 0.641 17.773 94470 Z= 0.318 Chirality : 0.045 0.254 11206 Planarity : 0.004 0.050 12067 Dihedral : 8.082 176.175 9747 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.62 % Favored : 96.33 % Rotamer: Outliers : 4.23 % Allowed : 18.35 % Favored : 77.42 % 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: 0.19 (0.09), residues: 8920 helix: 1.02 (0.07), residues: 4586 sheet: -0.49 (0.14), residues: 1255 loop : -0.85 (0.11), residues: 3079 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP N 101 HIS 0.011 0.001 HIS G 111 PHE 0.033 0.002 PHE a 167 TYR 0.021 0.002 TYR g 303 ARG 0.009 0.001 ARG A 370 *********************** 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 1261 residues out of total 7485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 315 poor density : 946 time to evaluate : 6.149 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 PHE cc_start: 0.7651 (t80) cc_final: 0.7218 (t80) REVERT: A 51 ASP cc_start: 0.6303 (t0) cc_final: 0.5813 (t70) REVERT: A 123 LEU cc_start: 0.8183 (OUTLIER) cc_final: 0.7748 (tp) REVERT: A 230 VAL cc_start: 0.7199 (OUTLIER) cc_final: 0.6888 (t) REVERT: A 321 LYS cc_start: 0.7877 (mtmt) cc_final: 0.7563 (tptt) REVERT: A 354 GLU cc_start: 0.6546 (mm-30) cc_final: 0.5871 (tp30) REVERT: A 384 MET cc_start: 0.8145 (ttt) cc_final: 0.7863 (ttt) REVERT: A 389 GLU cc_start: 0.7063 (tt0) cc_final: 0.6849 (tt0) REVERT: A 430 MET cc_start: 0.6030 (mmm) cc_final: 0.5360 (mmm) REVERT: A 459 ASP cc_start: 0.8301 (t0) cc_final: 0.7983 (t0) REVERT: B 87 MET cc_start: 0.7833 (ttp) cc_final: 0.7587 (ttp) REVERT: B 132 GLU cc_start: 0.7509 (OUTLIER) cc_final: 0.7162 (mp0) REVERT: B 248 LYS cc_start: 0.8016 (mtpt) cc_final: 0.7662 (mtmt) REVERT: B 276 LYS cc_start: 0.7692 (ttpt) cc_final: 0.7258 (ttmm) REVERT: B 301 GLU cc_start: 0.7581 (tt0) cc_final: 0.7146 (tt0) REVERT: B 347 LYS cc_start: 0.8358 (mmtm) cc_final: 0.7606 (mppt) REVERT: B 402 LYS cc_start: 0.7603 (mtmm) cc_final: 0.6986 (mptp) REVERT: B 405 ARG cc_start: 0.7635 (OUTLIER) cc_final: 0.7314 (mtt180) REVERT: B 414 GLU cc_start: 0.6681 (mp0) cc_final: 0.6167 (mp0) REVERT: B 445 MET cc_start: 0.7942 (tpp) cc_final: 0.7460 (tpp) REVERT: B 456 TYR cc_start: 0.8737 (m-80) cc_final: 0.8401 (m-10) REVERT: D 32 GLN cc_start: 0.7589 (mt0) cc_final: 0.7349 (mm-40) REVERT: D 65 LYS cc_start: 0.8321 (mtmm) cc_final: 0.8024 (mtpt) REVERT: D 82 GLN cc_start: 0.8277 (OUTLIER) cc_final: 0.7677 (mm-40) REVERT: D 222 GLU cc_start: 0.7451 (tt0) cc_final: 0.6778 (mt-10) REVERT: D 257 LYS cc_start: 0.7754 (mmtm) cc_final: 0.7335 (ttpp) REVERT: D 326 LYS cc_start: 0.8565 (pttt) cc_final: 0.8316 (ptmt) REVERT: D 384 LYS cc_start: 0.7698 (mptt) cc_final: 0.6962 (mppt) REVERT: D 400 GLU cc_start: 0.7240 (OUTLIER) cc_final: 0.6797 (mm-30) REVERT: D 446 MET cc_start: 0.7411 (OUTLIER) cc_final: 0.7045 (ttp) REVERT: D 458 MET cc_start: 0.8267 (mmm) cc_final: 0.7965 (mpp) REVERT: D 459 GLU cc_start: 0.6605 (mt-10) cc_final: 0.6309 (tp30) REVERT: D 496 ARG cc_start: 0.8015 (ttp80) cc_final: 0.7706 (tmm160) REVERT: D 506 GLU cc_start: 0.7374 (mm-30) cc_final: 0.7170 (mm-30) REVERT: E 20 LYS cc_start: 0.7981 (tttp) cc_final: 0.7710 (ttpt) REVERT: E 21 ASP cc_start: 0.7566 (t0) cc_final: 0.7362 (t0) REVERT: E 93 GLU cc_start: 0.6852 (mm-30) cc_final: 0.6466 (mm-30) REVERT: E 121 GLU cc_start: 0.7176 (tt0) cc_final: 0.6744 (tt0) REVERT: E 125 ASP cc_start: 0.7946 (m-30) cc_final: 0.7664 (m-30) REVERT: E 188 ILE cc_start: 0.8450 (OUTLIER) cc_final: 0.8083 (mt) REVERT: E 198 ASP cc_start: 0.7653 (OUTLIER) cc_final: 0.7403 (t70) REVERT: E 263 LYS cc_start: 0.7809 (ttmt) cc_final: 0.7097 (tttt) REVERT: E 290 GLN cc_start: 0.7358 (tp-100) cc_final: 0.6968 (tm-30) REVERT: E 439 LYS cc_start: 0.7736 (mtmm) cc_final: 0.7464 (mptt) REVERT: E 446 TYR cc_start: 0.8096 (m-80) cc_final: 0.7582 (m-80) REVERT: E 502 LYS cc_start: 0.7444 (tttt) cc_final: 0.7110 (tttm) REVERT: G 8 LEU cc_start: 0.6244 (OUTLIER) cc_final: 0.5906 (mm) REVERT: G 9 VAL cc_start: 0.8309 (p) cc_final: 0.8086 (m) REVERT: G 15 LYS cc_start: 0.7378 (mmmt) cc_final: 0.6677 (mtmm) REVERT: G 17 GLU cc_start: 0.6932 (mp0) cc_final: 0.6443 (mp0) REVERT: G 69 GLU cc_start: 0.7624 (mm-30) cc_final: 0.7352 (mm-30) REVERT: G 71 GLN cc_start: 0.8376 (OUTLIER) cc_final: 0.8033 (tt0) REVERT: G 81 ILE cc_start: 0.8566 (OUTLIER) cc_final: 0.8273 (mp) REVERT: G 82 GLU cc_start: 0.7728 (mm-30) cc_final: 0.7428 (mm-30) REVERT: G 96 THR cc_start: 0.8514 (OUTLIER) cc_final: 0.8305 (t) REVERT: G 110 GLU cc_start: 0.7680 (tt0) cc_final: 0.7248 (tp30) REVERT: G 166 SER cc_start: 0.7368 (p) cc_final: 0.7131 (m) REVERT: G 210 GLU cc_start: 0.7838 (OUTLIER) cc_final: 0.7608 (mp0) REVERT: G 234 LYS cc_start: 0.7206 (tptp) cc_final: 0.6431 (tppt) REVERT: G 248 LYS cc_start: 0.8410 (mtpt) cc_final: 0.7708 (mmpt) REVERT: G 255 ASP cc_start: 0.6920 (OUTLIER) cc_final: 0.6698 (m-30) REVERT: G 270 MET cc_start: 0.7573 (mtp) cc_final: 0.7357 (mtp) REVERT: G 276 GLN cc_start: 0.7569 (tt0) cc_final: 0.7278 (tm-30) REVERT: G 277 GLN cc_start: 0.7527 (tp40) cc_final: 0.6804 (mp10) REVERT: G 429 MET cc_start: 0.7291 (mtm) cc_final: 0.6955 (mtm) REVERT: G 477 THR cc_start: 0.8499 (OUTLIER) cc_final: 0.8020 (t) REVERT: G 511 GLU cc_start: 0.7560 (mm-30) cc_final: 0.7254 (mp0) REVERT: H 151 GLN cc_start: 0.7544 (OUTLIER) cc_final: 0.7203 (tt0) REVERT: H 279 GLU cc_start: 0.7254 (tp30) cc_final: 0.6866 (mt-10) REVERT: H 317 GLU cc_start: 0.7466 (mp0) cc_final: 0.7257 (tt0) REVERT: H 344 ARG cc_start: 0.7722 (OUTLIER) cc_final: 0.7118 (mtp-110) REVERT: H 356 GLU cc_start: 0.7562 (OUTLIER) cc_final: 0.7355 (mt-10) REVERT: H 368 LYS cc_start: 0.8117 (mttt) cc_final: 0.7599 (mmtm) REVERT: H 383 GLU cc_start: 0.7782 (mm-30) cc_final: 0.7406 (mm-30) REVERT: H 440 LYS cc_start: 0.7587 (mmtp) cc_final: 0.7287 (mtpt) REVERT: H 482 GLU cc_start: 0.7969 (mt-10) cc_final: 0.7719 (mt-10) REVERT: H 497 MET cc_start: 0.7370 (tpp) cc_final: 0.7138 (tpp) REVERT: Q 31 ARG cc_start: 0.7355 (mmp-170) cc_final: 0.6615 (mtt180) REVERT: Q 193 ASP cc_start: 0.6859 (m-30) cc_final: 0.6479 (m-30) REVERT: Q 249 MET cc_start: 0.7413 (ptp) cc_final: 0.7087 (mmm) REVERT: Q 281 LYS cc_start: 0.7702 (ttmt) cc_final: 0.7402 (tptp) REVERT: Q 286 THR cc_start: 0.8734 (OUTLIER) cc_final: 0.8369 (p) REVERT: Q 296 LYS cc_start: 0.7856 (pttm) cc_final: 0.7431 (pttt) REVERT: Q 318 LYS cc_start: 0.8159 (pttm) cc_final: 0.7564 (ptmm) REVERT: Q 322 ARG cc_start: 0.7366 (mtt90) cc_final: 0.7113 (mtp180) REVERT: Q 354 GLU cc_start: 0.7782 (tm-30) cc_final: 0.7526 (tm-30) REVERT: Q 481 ASP cc_start: 0.7658 (t0) cc_final: 0.7445 (t0) REVERT: Z 17 GLN cc_start: 0.7023 (OUTLIER) cc_final: 0.6141 (pp30) REVERT: Z 44 MET cc_start: 0.9134 (mmm) cc_final: 0.8797 (mmt) REVERT: Z 108 LEU cc_start: 0.7980 (tt) cc_final: 0.7608 (tp) REVERT: Z 163 GLU cc_start: 0.6882 (tp30) cc_final: 0.6204 (tp30) REVERT: Z 195 GLU cc_start: 0.7973 (pt0) cc_final: 0.7379 (pt0) REVERT: Z 223 LYS cc_start: 0.7822 (mptt) cc_final: 0.7557 (mmtt) REVERT: Z 241 LYS cc_start: 0.8581 (ttmt) cc_final: 0.7698 (pttp) REVERT: Z 264 ARG cc_start: 0.7401 (mtp85) cc_final: 0.6992 (mtp-110) REVERT: Z 272 LYS cc_start: 0.7397 (mmtp) cc_final: 0.6890 (mtpp) REVERT: Z 303 ASP cc_start: 0.7357 (t70) cc_final: 0.6620 (m-30) REVERT: Z 307 LYS cc_start: 0.7807 (mmtp) cc_final: 0.7474 (mtpt) REVERT: Z 322 GLU cc_start: 0.7469 (tt0) cc_final: 0.7093 (tt0) REVERT: Z 340 SER cc_start: 0.7432 (OUTLIER) cc_final: 0.7107 (p) REVERT: Z 445 LEU cc_start: 0.8209 (mt) cc_final: 0.7995 (mm) REVERT: Z 495 TRP cc_start: 0.8044 (m100) cc_final: 0.7492 (m100) REVERT: Z 496 ASP cc_start: 0.7588 (m-30) cc_final: 0.7320 (m-30) REVERT: a 23 MET cc_start: 0.5816 (OUTLIER) cc_final: 0.5464 (ttp) REVERT: a 265 GLN cc_start: 0.7227 (pt0) cc_final: 0.6834 (tp40) REVERT: a 361 LEU cc_start: 0.8681 (OUTLIER) cc_final: 0.8344 (pt) REVERT: a 384 MET cc_start: 0.8052 (ttt) cc_final: 0.7733 (ttt) REVERT: b 89 ARG cc_start: 0.8019 (ttp80) cc_final: 0.7805 (tmm160) REVERT: b 93 ASP cc_start: 0.7252 (m-30) cc_final: 0.6492 (m-30) REVERT: b 223 LYS cc_start: 0.8416 (mttm) cc_final: 0.8018 (mtpt) REVERT: b 236 LYS cc_start: 0.7978 (OUTLIER) cc_final: 0.7571 (mtmm) REVERT: b 316 ASP cc_start: 0.7334 (t0) cc_final: 0.6953 (m-30) REVERT: b 387 GLU cc_start: 0.7375 (OUTLIER) cc_final: 0.7144 (tt0) REVERT: b 407 VAL cc_start: 0.8031 (t) cc_final: 0.7804 (m) REVERT: b 445 MET cc_start: 0.8048 (tpp) cc_final: 0.7753 (tpp) REVERT: b 452 ASP cc_start: 0.7614 (m-30) cc_final: 0.7304 (m-30) REVERT: b 516 ARG cc_start: 0.7599 (mtp85) cc_final: 0.7294 (mtp180) REVERT: b 522 LYS cc_start: 0.8015 (mttt) cc_final: 0.7140 (mppt) REVERT: d 42 LYS cc_start: 0.7190 (tttp) cc_final: 0.6381 (tptt) REVERT: d 46 ASP cc_start: 0.7893 (m-30) cc_final: 0.7482 (m-30) REVERT: d 60 MET cc_start: 0.8440 (ttp) cc_final: 0.8001 (ttp) REVERT: d 63 ASP cc_start: 0.7190 (m-30) cc_final: 0.6971 (m-30) REVERT: d 93 GLU cc_start: 0.7123 (mm-30) cc_final: 0.6698 (mm-30) REVERT: d 132 ILE cc_start: 0.8262 (mt) cc_final: 0.7995 (mp) REVERT: d 334 GLU cc_start: 0.7528 (tp30) cc_final: 0.7182 (tp30) REVERT: d 384 LYS cc_start: 0.7491 (mmtp) cc_final: 0.7027 (mmpt) REVERT: e 27 ARG cc_start: 0.8062 (ttp-170) cc_final: 0.7474 (ttt180) REVERT: e 29 MET cc_start: 0.8099 (mtp) cc_final: 0.7454 (mtp) REVERT: e 93 GLU cc_start: 0.7142 (mm-30) cc_final: 0.6711 (mt-10) REVERT: e 96 LYS cc_start: 0.7744 (tttm) cc_final: 0.7068 (ttmt) REVERT: e 121 GLU cc_start: 0.6970 (tt0) cc_final: 0.6607 (tt0) REVERT: e 122 GLN cc_start: 0.7224 (OUTLIER) cc_final: 0.6724 (mp10) REVERT: e 126 ARG cc_start: 0.7374 (mtm180) cc_final: 0.6753 (mtp85) REVERT: e 146 GLU cc_start: 0.6951 (mt-10) cc_final: 0.6682 (mt-10) REVERT: e 150 LYS cc_start: 0.7620 (ttmt) cc_final: 0.7235 (ttpt) REVERT: e 464 GLU cc_start: 0.6713 (tt0) cc_final: 0.6351 (tm-30) REVERT: e 474 MET cc_start: 0.7972 (OUTLIER) cc_final: 0.5842 (tmm) REVERT: e 478 ARG cc_start: 0.7328 (ttp-170) cc_final: 0.6994 (ttm170) REVERT: e 502 LYS cc_start: 0.7091 (tttm) cc_final: 0.6753 (ttmp) REVERT: e 515 GLN cc_start: 0.7826 (tp-100) cc_final: 0.7292 (tp40) REVERT: e 532 ASP cc_start: 0.8395 (t0) cc_final: 0.8096 (t0) REVERT: g 110 GLU cc_start: 0.8285 (OUTLIER) cc_final: 0.7531 (tt0) REVERT: g 153 LEU cc_start: 0.7720 (OUTLIER) cc_final: 0.7510 (mp) REVERT: g 186 GLU cc_start: 0.6993 (tt0) cc_final: 0.6572 (tt0) REVERT: g 191 LYS cc_start: 0.7674 (mtpt) cc_final: 0.7192 (mptt) REVERT: g 192 GLU cc_start: 0.6869 (tt0) cc_final: 0.6139 (pp20) REVERT: g 202 GLU cc_start: 0.6975 (mm-30) cc_final: 0.6585 (mm-30) REVERT: g 274 TYR cc_start: 0.8010 (t80) cc_final: 0.7680 (t80) REVERT: g 277 GLN cc_start: 0.7054 (tp-100) cc_final: 0.6271 (pt0) REVERT: g 294 LYS cc_start: 0.8137 (mmtp) cc_final: 0.7738 (mmtp) REVERT: g 367 LYS cc_start: 0.8468 (OUTLIER) cc_final: 0.8140 (pptt) REVERT: g 381 LYS cc_start: 0.7887 (tppt) cc_final: 0.7437 (mptt) REVERT: g 415 GLU cc_start: 0.7265 (OUTLIER) cc_final: 0.6993 (mm-30) REVERT: h 10 LYS cc_start: 0.8113 (ttmt) cc_final: 0.7451 (ttpt) REVERT: h 17 GLN cc_start: 0.8108 (tt0) cc_final: 0.7884 (tt0) REVERT: h 119 GLN cc_start: 0.7979 (mm-40) cc_final: 0.7579 (mm110) REVERT: h 153 LYS cc_start: 0.7921 (mttm) cc_final: 0.7400 (mptt) REVERT: h 217 LYS cc_start: 0.9021 (ttpt) cc_final: 0.8619 (ttpt) REVERT: h 247 LYS cc_start: 0.8392 (pttp) cc_final: 0.8061 (ptpp) REVERT: h 254 GLU cc_start: 0.8066 (OUTLIER) cc_final: 0.7830 (tp30) REVERT: h 276 ASP cc_start: 0.7360 (t0) cc_final: 0.7042 (m-30) REVERT: h 320 LYS cc_start: 0.7706 (mmtt) cc_final: 0.7437 (mtpp) REVERT: h 344 ARG cc_start: 0.7375 (ttm110) cc_final: 0.6570 (mtm-85) REVERT: h 356 GLU cc_start: 0.7416 (OUTLIER) cc_final: 0.6983 (mt-10) REVERT: h 368 LYS cc_start: 0.7819 (mttt) cc_final: 0.7189 (mtpp) REVERT: h 379 GLU cc_start: 0.8155 (tm-30) cc_final: 0.7569 (tm-30) REVERT: h 383 GLU cc_start: 0.7529 (mm-30) cc_final: 0.7151 (mm-30) REVERT: h 440 LYS cc_start: 0.8234 (tptt) cc_final: 0.7846 (tppt) REVERT: n 83 ASN cc_start: 0.2251 (OUTLIER) cc_final: 0.1145 (m110) REVERT: q 3 LEU cc_start: 0.5440 (OUTLIER) cc_final: 0.4614 (tt) REVERT: q 17 GLU cc_start: 0.7484 (tt0) cc_final: 0.7212 (tm-30) REVERT: q 31 ARG cc_start: 0.7589 (mmp-170) cc_final: 0.6925 (mmt-90) REVERT: q 55 MET cc_start: 0.7847 (OUTLIER) cc_final: 0.7388 (mtt) REVERT: q 117 GLU cc_start: 0.7163 (tt0) cc_final: 0.6610 (mt-10) REVERT: q 130 GLU cc_start: 0.6678 (OUTLIER) cc_final: 0.6394 (mp0) REVERT: q 212 ILE cc_start: 0.8006 (OUTLIER) cc_final: 0.7672 (mm) REVERT: q 238 LYS cc_start: 0.7401 (mmtp) cc_final: 0.7002 (mmtp) REVERT: q 277 ASP cc_start: 0.8591 (t70) cc_final: 0.8179 (t0) REVERT: q 312 LEU cc_start: 0.8566 (OUTLIER) cc_final: 0.7976 (tt) REVERT: q 319 TRP cc_start: 0.7174 (m100) cc_final: 0.6308 (m100) REVERT: q 406 LYS cc_start: 0.7747 (ptmt) cc_final: 0.6838 (mmtm) REVERT: q 483 GLU cc_start: 0.7293 (mp0) cc_final: 0.6898 (mm-30) REVERT: q 498 LEU cc_start: 0.8910 (OUTLIER) cc_final: 0.8573 (mt) REVERT: q 505 TYR cc_start: 0.8161 (t80) cc_final: 0.7690 (t80) REVERT: z 5 LYS cc_start: 0.8064 (OUTLIER) cc_final: 0.7743 (mmtt) REVERT: z 10 LYS cc_start: 0.8036 (mtmt) cc_final: 0.7364 (pmtt) REVERT: z 15 ARG cc_start: 0.7682 (OUTLIER) cc_final: 0.6648 (mtm-85) REVERT: z 32 ASP cc_start: 0.7026 (t0) cc_final: 0.6573 (m-30) REVERT: z 36 THR cc_start: 0.8850 (OUTLIER) cc_final: 0.8542 (p) REVERT: z 180 LYS cc_start: 0.7886 (OUTLIER) cc_final: 0.7248 (tttm) REVERT: z 181 LYS cc_start: 0.7004 (mttt) cc_final: 0.6115 (mmmt) REVERT: z 190 MET cc_start: 0.8424 (mmt) cc_final: 0.8113 (mmp) REVERT: z 272 LYS cc_start: 0.7793 (mmtp) cc_final: 0.7571 (mtpp) REVERT: z 307 LYS cc_start: 0.7905 (mmtp) cc_final: 0.6781 (ttpt) REVERT: z 359 LYS cc_start: 0.7893 (mttt) cc_final: 0.7026 (mtmm) REVERT: z 388 LYS cc_start: 0.7463 (OUTLIER) cc_final: 0.6929 (mtpt) REVERT: z 430 LYS cc_start: 0.8330 (tppt) cc_final: 0.7732 (mmmt) REVERT: z 487 MET cc_start: 0.7173 (OUTLIER) cc_final: 0.5845 (ppp) REVERT: z 492 VAL cc_start: 0.8176 (p) cc_final: 0.7471 (p) REVERT: T 48 ASN cc_start: 0.6340 (OUTLIER) cc_final: 0.6067 (t0) REVERT: T 49 VAL cc_start: 0.8644 (OUTLIER) cc_final: 0.8429 (t) REVERT: T 69 GLU cc_start: 0.8027 (OUTLIER) cc_final: 0.7715 (pt0) REVERT: T 77 ARG cc_start: 0.7275 (mtt90) cc_final: 0.7059 (mtt90) REVERT: T 94 GLN cc_start: 0.5834 (mp10) cc_final: 0.5565 (mt0) REVERT: T 167 PHE cc_start: 0.8295 (m-80) cc_final: 0.8063 (m-80) REVERT: T 200 TYR cc_start: 0.7772 (m-80) cc_final: 0.7430 (m-80) REVERT: T 233 MET cc_start: 0.7365 (tpt) cc_final: 0.7117 (tpt) outliers start: 315 outliers final: 165 residues processed: 1180 average time/residue: 1.5282 time to fit residues: 2352.4813 Evaluate side-chains 1134 residues out of total 7485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 215 poor density : 919 time to evaluate : 6.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 63 LYS Chi-restraints excluded: chain A residue 119 SER Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 166 ASP Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 284 ASN Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 97 ASP Chi-restraints excluded: chain B residue 101 SER Chi-restraints excluded: chain B residue 132 GLU Chi-restraints excluded: chain B residue 134 THR Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain B residue 310 MET Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 400 THR Chi-restraints excluded: chain B residue 405 ARG Chi-restraints excluded: chain B residue 413 SER Chi-restraints excluded: chain B residue 416 LEU Chi-restraints excluded: chain B residue 437 GLU Chi-restraints excluded: chain B residue 460 ASP Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 73 ASP Chi-restraints excluded: chain D residue 82 GLN Chi-restraints excluded: chain D residue 136 SER Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 184 SER Chi-restraints excluded: chain D residue 186 MET Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 217 THR Chi-restraints excluded: chain D residue 273 ASP Chi-restraints excluded: chain D residue 400 GLU Chi-restraints excluded: chain D residue 404 SER Chi-restraints excluded: chain D residue 430 ILE Chi-restraints excluded: chain D residue 446 MET Chi-restraints excluded: chain D residue 536 VAL Chi-restraints excluded: chain E residue 23 ASP Chi-restraints excluded: chain E residue 188 ILE Chi-restraints excluded: chain E residue 194 LEU Chi-restraints excluded: chain E residue 198 ASP Chi-restraints excluded: chain E residue 245 ASP Chi-restraints excluded: chain E residue 269 THR Chi-restraints excluded: chain E residue 308 ASP Chi-restraints excluded: chain E residue 418 VAL Chi-restraints excluded: chain G residue 7 VAL Chi-restraints excluded: chain G residue 8 LEU Chi-restraints excluded: chain G residue 71 GLN Chi-restraints excluded: chain G residue 81 ILE Chi-restraints excluded: chain G residue 83 ILE Chi-restraints excluded: chain G residue 96 THR Chi-restraints excluded: chain G residue 146 ILE Chi-restraints excluded: chain G residue 210 GLU Chi-restraints excluded: chain G residue 252 SER Chi-restraints excluded: chain G residue 255 ASP Chi-restraints excluded: chain G residue 265 THR Chi-restraints excluded: chain G residue 332 VAL Chi-restraints excluded: chain G residue 373 THR Chi-restraints excluded: chain G residue 440 VAL Chi-restraints excluded: chain G residue 463 LEU Chi-restraints excluded: chain G residue 477 THR Chi-restraints excluded: chain G residue 508 THR Chi-restraints excluded: chain H residue 142 THR Chi-restraints excluded: chain H residue 151 GLN Chi-restraints excluded: chain H residue 251 ASP Chi-restraints excluded: chain H residue 340 ASP Chi-restraints excluded: chain H residue 344 ARG Chi-restraints excluded: chain H residue 356 GLU Chi-restraints excluded: chain H residue 362 THR Chi-restraints excluded: chain H residue 388 SER Chi-restraints excluded: chain H residue 400 ILE Chi-restraints excluded: chain H residue 427 ILE Chi-restraints excluded: chain N residue 43 LYS Chi-restraints excluded: chain N residue 83 ASN Chi-restraints excluded: chain Q residue 43 THR Chi-restraints excluded: chain Q residue 105 LEU Chi-restraints excluded: chain Q residue 146 LEU Chi-restraints excluded: chain Q residue 182 LEU Chi-restraints excluded: chain Q residue 212 ILE Chi-restraints excluded: chain Q residue 286 THR Chi-restraints excluded: chain Q residue 366 GLU Chi-restraints excluded: chain Q residue 480 LEU Chi-restraints excluded: chain Q residue 486 VAL Chi-restraints excluded: chain Q residue 517 THR Chi-restraints excluded: chain Z residue 17 GLN Chi-restraints excluded: chain Z residue 107 ASP Chi-restraints excluded: chain Z residue 246 SER Chi-restraints excluded: chain Z residue 340 SER Chi-restraints excluded: chain Z residue 373 THR Chi-restraints excluded: chain Z residue 407 VAL Chi-restraints excluded: chain Z residue 408 VAL Chi-restraints excluded: chain Z residue 430 LYS Chi-restraints excluded: chain Z residue 479 VAL Chi-restraints excluded: chain Z residue 488 VAL Chi-restraints excluded: chain a residue 23 MET Chi-restraints excluded: chain a residue 166 ASP Chi-restraints excluded: chain a residue 321 LYS Chi-restraints excluded: chain a residue 329 SER Chi-restraints excluded: chain a residue 361 LEU Chi-restraints excluded: chain a residue 367 THR Chi-restraints excluded: chain a residue 391 SER Chi-restraints excluded: chain b residue 51 ILE Chi-restraints excluded: chain b residue 66 ASP Chi-restraints excluded: chain b residue 134 THR Chi-restraints excluded: chain b residue 153 VAL Chi-restraints excluded: chain b residue 165 THR Chi-restraints excluded: chain b residue 182 LEU Chi-restraints excluded: chain b residue 214 LEU Chi-restraints excluded: chain b residue 236 LYS Chi-restraints excluded: chain b residue 323 LEU Chi-restraints excluded: chain b residue 353 MET Chi-restraints excluded: chain b residue 371 CYS Chi-restraints excluded: chain b residue 387 GLU Chi-restraints excluded: chain d residue 67 ASP Chi-restraints excluded: chain d residue 71 THR Chi-restraints excluded: chain d residue 115 SER Chi-restraints excluded: chain d residue 134 SER Chi-restraints excluded: chain d residue 136 SER Chi-restraints excluded: chain d residue 157 LEU Chi-restraints excluded: chain d residue 158 SER Chi-restraints excluded: chain d residue 168 THR Chi-restraints excluded: chain d residue 184 SER Chi-restraints excluded: chain d residue 233 VAL Chi-restraints excluded: chain d residue 239 THR Chi-restraints excluded: chain d residue 385 THR Chi-restraints excluded: chain d residue 394 ASN Chi-restraints excluded: chain d residue 395 LYS Chi-restraints excluded: chain d residue 430 ILE Chi-restraints excluded: chain d residue 536 VAL Chi-restraints excluded: chain e residue 122 GLN Chi-restraints excluded: chain e residue 298 ASN Chi-restraints excluded: chain e residue 308 ASP Chi-restraints excluded: chain e residue 330 ILE Chi-restraints excluded: chain e residue 418 VAL Chi-restraints excluded: chain e residue 474 MET Chi-restraints excluded: chain e residue 498 THR Chi-restraints excluded: chain g residue 17 GLU Chi-restraints excluded: chain g residue 39 THR Chi-restraints excluded: chain g residue 83 ILE Chi-restraints excluded: chain g residue 96 THR Chi-restraints excluded: chain g residue 110 GLU Chi-restraints excluded: chain g residue 153 LEU Chi-restraints excluded: chain g residue 161 THR Chi-restraints excluded: chain g residue 310 THR Chi-restraints excluded: chain g residue 367 LYS Chi-restraints excluded: chain g residue 397 VAL Chi-restraints excluded: chain g residue 415 GLU Chi-restraints excluded: chain g residue 432 VAL Chi-restraints excluded: chain g residue 440 VAL Chi-restraints excluded: chain g residue 460 ILE Chi-restraints excluded: chain g residue 471 THR Chi-restraints excluded: chain g residue 486 THR Chi-restraints excluded: chain h residue 32 ILE Chi-restraints excluded: chain h residue 38 THR Chi-restraints excluded: chain h residue 85 SER Chi-restraints excluded: chain h residue 177 LYS Chi-restraints excluded: chain h residue 211 VAL Chi-restraints excluded: chain h residue 221 SER Chi-restraints excluded: chain h residue 234 ASN Chi-restraints excluded: chain h residue 254 GLU Chi-restraints excluded: chain h residue 356 GLU Chi-restraints excluded: chain h residue 395 ILE Chi-restraints excluded: chain h residue 405 VAL Chi-restraints excluded: chain h residue 427 ILE Chi-restraints excluded: chain h residue 473 THR Chi-restraints excluded: chain n residue 12 VAL Chi-restraints excluded: chain n residue 83 ASN Chi-restraints excluded: chain q residue 3 LEU Chi-restraints excluded: chain q residue 43 THR Chi-restraints excluded: chain q residue 45 THR Chi-restraints excluded: chain q residue 55 MET Chi-restraints excluded: chain q residue 130 GLU Chi-restraints excluded: chain q residue 150 SER Chi-restraints excluded: chain q residue 170 SER Chi-restraints excluded: chain q residue 200 ASP Chi-restraints excluded: chain q residue 212 ILE Chi-restraints excluded: chain q residue 226 GLU Chi-restraints excluded: chain q residue 234 VAL Chi-restraints excluded: chain q residue 312 LEU Chi-restraints excluded: chain q residue 385 MET Chi-restraints excluded: chain q residue 480 LEU Chi-restraints excluded: chain q residue 498 LEU Chi-restraints excluded: chain z residue 4 VAL Chi-restraints excluded: chain z residue 5 LYS Chi-restraints excluded: chain z residue 15 ARG Chi-restraints excluded: chain z residue 36 THR Chi-restraints excluded: chain z residue 88 THR Chi-restraints excluded: chain z residue 149 ILE Chi-restraints excluded: chain z residue 179 ILE Chi-restraints excluded: chain z residue 180 LYS Chi-restraints excluded: chain z residue 246 SER Chi-restraints excluded: chain z residue 358 GLU Chi-restraints excluded: chain z residue 388 LYS Chi-restraints excluded: chain z residue 408 VAL Chi-restraints excluded: chain z residue 442 ASP Chi-restraints excluded: chain z residue 464 VAL Chi-restraints excluded: chain z residue 487 MET Chi-restraints excluded: chain z residue 488 VAL Chi-restraints excluded: chain T residue 48 ASN Chi-restraints excluded: chain T residue 49 VAL Chi-restraints excluded: chain T residue 69 GLU Chi-restraints excluded: chain T residue 84 ILE Chi-restraints excluded: chain T residue 143 THR Chi-restraints excluded: chain T residue 161 ASP Chi-restraints excluded: chain T residue 232 THR Chi-restraints excluded: chain T residue 391 ARG Chi-restraints excluded: chain T residue 395 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 885 random chunks: chunk 287 optimal weight: 3.9990 chunk 770 optimal weight: 0.8980 chunk 169 optimal weight: 5.9990 chunk 502 optimal weight: 7.9990 chunk 211 optimal weight: 6.9990 chunk 856 optimal weight: 8.9990 chunk 710 optimal weight: 1.9990 chunk 396 optimal weight: 7.9990 chunk 71 optimal weight: 9.9990 chunk 283 optimal weight: 3.9990 chunk 449 optimal weight: 2.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 502 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** G 235 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** ** Q 365 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 161 HIS ** a 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 492 ASN b 195 ASN b 464 GLN d 318 ASN e 122 GLN ** 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 130 GLN ** q 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 37 HIS T 52 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7460 moved from start: 0.2193 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= 0.310 Angle : 0.604 13.143 94470 Z= 0.299 Chirality : 0.043 0.206 11206 Planarity : 0.004 0.061 12067 Dihedral : 7.950 174.038 9743 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.35 % Favored : 96.60 % Rotamer: Outliers : 4.01 % Allowed : 19.21 % Favored : 76.78 % 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: 0.25 (0.09), residues: 8920 helix: 1.05 (0.08), residues: 4582 sheet: -0.46 (0.14), residues: 1230 loop : -0.81 (0.11), residues: 3108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP N 101 HIS 0.012 0.001 HIS G 111 PHE 0.032 0.002 PHE a 167 TYR 0.023 0.002 TYR g 303 ARG 0.009 0.000 ARG a 370 *********************** 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 1244 residues out of total 7485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 299 poor density : 945 time to evaluate : 6.235 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 PHE cc_start: 0.7638 (t80) cc_final: 0.7280 (t80) REVERT: A 51 ASP cc_start: 0.6286 (t0) cc_final: 0.5802 (t70) REVERT: A 102 LYS cc_start: 0.7548 (OUTLIER) cc_final: 0.7344 (ttmt) REVERT: A 123 LEU cc_start: 0.8198 (OUTLIER) cc_final: 0.7762 (tp) REVERT: A 230 VAL cc_start: 0.7237 (OUTLIER) cc_final: 0.6937 (t) REVERT: A 321 LYS cc_start: 0.7873 (mtmt) cc_final: 0.7552 (tptt) REVERT: A 354 GLU cc_start: 0.6530 (mm-30) cc_final: 0.5860 (tp30) REVERT: A 384 MET cc_start: 0.8134 (ttt) cc_final: 0.7859 (ttt) REVERT: A 389 GLU cc_start: 0.7063 (tt0) cc_final: 0.6859 (tt0) REVERT: A 430 MET cc_start: 0.5826 (mmm) cc_final: 0.5196 (mmm) REVERT: A 459 ASP cc_start: 0.8307 (t0) cc_final: 0.7988 (t0) REVERT: B 87 MET cc_start: 0.7816 (ttp) cc_final: 0.7574 (ttp) REVERT: B 132 GLU cc_start: 0.7511 (OUTLIER) cc_final: 0.7158 (mp0) REVERT: B 248 LYS cc_start: 0.7997 (mtpt) cc_final: 0.7649 (mtmt) REVERT: B 301 GLU cc_start: 0.7552 (tt0) cc_final: 0.7111 (tt0) REVERT: B 347 LYS cc_start: 0.8279 (mmtm) cc_final: 0.7484 (mppt) REVERT: B 402 LYS cc_start: 0.7624 (mtmm) cc_final: 0.6993 (mptp) REVERT: B 414 GLU cc_start: 0.6597 (mp0) cc_final: 0.6096 (mp0) REVERT: B 445 MET cc_start: 0.7772 (tpp) cc_final: 0.7292 (tpp) REVERT: B 456 TYR cc_start: 0.8721 (m-80) cc_final: 0.8335 (m-10) REVERT: D 32 GLN cc_start: 0.7542 (mt0) cc_final: 0.7317 (mm-40) REVERT: D 65 LYS cc_start: 0.8324 (mtmm) cc_final: 0.8038 (mtpt) REVERT: D 67 ASP cc_start: 0.7677 (m-30) cc_final: 0.7415 (m-30) REVERT: D 82 GLN cc_start: 0.8261 (OUTLIER) cc_final: 0.7723 (mm-40) REVERT: D 222 GLU cc_start: 0.7416 (tt0) cc_final: 0.6757 (mt-10) REVERT: D 224 VAL cc_start: 0.8179 (t) cc_final: 0.7862 (m) REVERT: D 257 LYS cc_start: 0.7751 (mmtm) cc_final: 0.7339 (ttpp) REVERT: D 326 LYS cc_start: 0.8576 (pttt) cc_final: 0.8253 (ptmt) REVERT: D 384 LYS cc_start: 0.7685 (mptt) cc_final: 0.6955 (mppt) REVERT: D 400 GLU cc_start: 0.7280 (OUTLIER) cc_final: 0.6836 (mm-30) REVERT: D 458 MET cc_start: 0.8262 (mmm) cc_final: 0.7912 (mpp) REVERT: D 459 GLU cc_start: 0.6586 (mt-10) cc_final: 0.6284 (tp30) REVERT: D 496 ARG cc_start: 0.8042 (ttp80) cc_final: 0.7733 (tmm160) REVERT: E 20 LYS cc_start: 0.7997 (tttp) cc_final: 0.7748 (ttpt) REVERT: E 21 ASP cc_start: 0.7524 (t0) cc_final: 0.7303 (t0) REVERT: E 48 MET cc_start: 0.8461 (tpt) cc_final: 0.8213 (mmm) REVERT: E 93 GLU cc_start: 0.6901 (mm-30) cc_final: 0.6530 (mm-30) REVERT: E 121 GLU cc_start: 0.7139 (tt0) cc_final: 0.6704 (tt0) REVERT: E 125 ASP cc_start: 0.7905 (m-30) cc_final: 0.7627 (m-30) REVERT: E 188 ILE cc_start: 0.8444 (OUTLIER) cc_final: 0.8123 (mt) REVERT: E 198 ASP cc_start: 0.7590 (OUTLIER) cc_final: 0.7357 (t70) REVERT: E 263 LYS cc_start: 0.7808 (ttmt) cc_final: 0.7079 (tttt) REVERT: E 283 GLU cc_start: 0.8031 (mm-30) cc_final: 0.7748 (mt-10) REVERT: E 290 GLN cc_start: 0.7360 (tp-100) cc_final: 0.6985 (tm-30) REVERT: E 439 LYS cc_start: 0.7743 (mtmm) cc_final: 0.7468 (mptt) REVERT: E 446 TYR cc_start: 0.8148 (m-80) cc_final: 0.7589 (m-80) REVERT: E 502 LYS cc_start: 0.7428 (tttt) cc_final: 0.7165 (tttm) REVERT: G 8 LEU cc_start: 0.6260 (OUTLIER) cc_final: 0.5957 (mm) REVERT: G 15 LYS cc_start: 0.7373 (mmmt) cc_final: 0.6665 (mtmm) REVERT: G 17 GLU cc_start: 0.6913 (mp0) cc_final: 0.6421 (mp0) REVERT: G 54 MET cc_start: 0.8090 (OUTLIER) cc_final: 0.7662 (mtp) REVERT: G 71 GLN cc_start: 0.8372 (OUTLIER) cc_final: 0.8062 (tt0) REVERT: G 81 ILE cc_start: 0.8539 (OUTLIER) cc_final: 0.8245 (mp) REVERT: G 82 GLU cc_start: 0.7741 (mm-30) cc_final: 0.7430 (mm-30) REVERT: G 110 GLU cc_start: 0.7714 (tt0) cc_final: 0.7270 (tp30) REVERT: G 210 GLU cc_start: 0.7932 (OUTLIER) cc_final: 0.7700 (mp0) REVERT: G 234 LYS cc_start: 0.7223 (tptp) cc_final: 0.6797 (tptt) REVERT: G 248 LYS cc_start: 0.8472 (mtpt) cc_final: 0.7762 (mmpt) REVERT: G 255 ASP cc_start: 0.6938 (OUTLIER) cc_final: 0.6684 (m-30) REVERT: G 270 MET cc_start: 0.7623 (mtp) cc_final: 0.7375 (mtp) REVERT: G 276 GLN cc_start: 0.7481 (tt0) cc_final: 0.7147 (tm-30) REVERT: G 277 GLN cc_start: 0.7529 (tp40) cc_final: 0.6799 (mp10) REVERT: G 367 LYS cc_start: 0.8349 (pttt) cc_final: 0.8062 (pttp) REVERT: G 429 MET cc_start: 0.7256 (mtm) cc_final: 0.6923 (mtm) REVERT: G 476 GLU cc_start: 0.7290 (OUTLIER) cc_final: 0.6961 (mt-10) REVERT: G 477 THR cc_start: 0.8520 (OUTLIER) cc_final: 0.8115 (t) REVERT: G 483 GLU cc_start: 0.5910 (OUTLIER) cc_final: 0.5057 (mp0) REVERT: G 511 GLU cc_start: 0.7566 (mm-30) cc_final: 0.7260 (mp0) REVERT: H 151 GLN cc_start: 0.7516 (OUTLIER) cc_final: 0.7203 (tt0) REVERT: H 172 LYS cc_start: 0.7819 (pttt) cc_final: 0.7591 (ptpt) REVERT: H 279 GLU cc_start: 0.7264 (tp30) cc_final: 0.6869 (mt-10) REVERT: H 317 GLU cc_start: 0.7470 (mp0) cc_final: 0.7258 (tt0) REVERT: H 356 GLU cc_start: 0.7553 (OUTLIER) cc_final: 0.7340 (mt-10) REVERT: H 368 LYS cc_start: 0.8118 (mttt) cc_final: 0.7596 (mmtm) REVERT: H 383 GLU cc_start: 0.7680 (mm-30) cc_final: 0.7460 (mm-30) REVERT: H 440 LYS cc_start: 0.7542 (mmtp) cc_final: 0.7226 (mtpt) REVERT: H 482 GLU cc_start: 0.7977 (mt-10) cc_final: 0.7731 (mt-10) REVERT: H 497 MET cc_start: 0.7370 (tpp) cc_final: 0.6793 (tpt) REVERT: Q 31 ARG cc_start: 0.7371 (mmp-170) cc_final: 0.6704 (mtt90) REVERT: Q 55 MET cc_start: 0.7904 (OUTLIER) cc_final: 0.7609 (mtt) REVERT: Q 193 ASP cc_start: 0.6878 (m-30) cc_final: 0.6514 (m-30) REVERT: Q 249 MET cc_start: 0.7411 (ptp) cc_final: 0.7083 (mmm) REVERT: Q 281 LYS cc_start: 0.7685 (ttmt) cc_final: 0.7407 (tptp) REVERT: Q 286 THR cc_start: 0.8662 (OUTLIER) cc_final: 0.8343 (p) REVERT: Q 296 LYS cc_start: 0.7820 (pttm) cc_final: 0.7417 (pttt) REVERT: Q 318 LYS cc_start: 0.8158 (pttm) cc_final: 0.7589 (ptmm) REVERT: Q 322 ARG cc_start: 0.7364 (mtt90) cc_final: 0.7115 (mtp180) REVERT: Q 344 MET cc_start: 0.8643 (ttm) cc_final: 0.8366 (tpp) REVERT: Q 354 GLU cc_start: 0.7681 (tm-30) cc_final: 0.7388 (tm-30) REVERT: Q 481 ASP cc_start: 0.7620 (t0) cc_final: 0.7411 (t0) REVERT: Z 17 GLN cc_start: 0.7030 (OUTLIER) cc_final: 0.6156 (pp30) REVERT: Z 44 MET cc_start: 0.9142 (mmm) cc_final: 0.8864 (mmt) REVERT: Z 108 LEU cc_start: 0.7871 (tt) cc_final: 0.7579 (tp) REVERT: Z 163 GLU cc_start: 0.6970 (tp30) cc_final: 0.6330 (tp30) REVERT: Z 195 GLU cc_start: 0.7948 (pt0) cc_final: 0.7423 (pt0) REVERT: Z 223 LYS cc_start: 0.7820 (mptt) cc_final: 0.7447 (mmtt) REVERT: Z 241 LYS cc_start: 0.8566 (ttmt) cc_final: 0.7699 (pttp) REVERT: Z 264 ARG cc_start: 0.7377 (mtp85) cc_final: 0.6990 (mtp-110) REVERT: Z 272 LYS cc_start: 0.7433 (mmtp) cc_final: 0.6902 (mtpp) REVERT: Z 303 ASP cc_start: 0.7251 (t70) cc_final: 0.6500 (m-30) REVERT: Z 307 LYS cc_start: 0.7790 (mmtp) cc_final: 0.7462 (mtpt) REVERT: Z 322 GLU cc_start: 0.7432 (tt0) cc_final: 0.7045 (tt0) REVERT: Z 340 SER cc_start: 0.7419 (OUTLIER) cc_final: 0.7174 (p) REVERT: Z 487 MET cc_start: 0.7007 (OUTLIER) cc_final: 0.6471 (ppp) REVERT: Z 495 TRP cc_start: 0.8033 (m100) cc_final: 0.7466 (m100) REVERT: Z 496 ASP cc_start: 0.7561 (m-30) cc_final: 0.7271 (m-30) REVERT: a 23 MET cc_start: 0.5743 (OUTLIER) cc_final: 0.5388 (ttp) REVERT: a 265 GLN cc_start: 0.7162 (pt0) cc_final: 0.6831 (tp40) REVERT: a 361 LEU cc_start: 0.8694 (OUTLIER) cc_final: 0.8358 (pt) REVERT: a 382 ASP cc_start: 0.7674 (m-30) cc_final: 0.7393 (m-30) REVERT: a 384 MET cc_start: 0.8012 (ttt) cc_final: 0.7722 (ttt) REVERT: b 93 ASP cc_start: 0.7269 (m-30) cc_final: 0.6535 (m-30) REVERT: b 223 LYS cc_start: 0.8351 (mttm) cc_final: 0.7977 (mtpt) REVERT: b 236 LYS cc_start: 0.7973 (OUTLIER) cc_final: 0.7480 (mtmm) REVERT: b 316 ASP cc_start: 0.7257 (t0) cc_final: 0.6886 (m-30) REVERT: b 387 GLU cc_start: 0.7359 (OUTLIER) cc_final: 0.7134 (tt0) REVERT: b 407 VAL cc_start: 0.7935 (t) cc_final: 0.7717 (m) REVERT: b 445 MET cc_start: 0.8076 (tpp) cc_final: 0.7770 (tpp) REVERT: b 516 ARG cc_start: 0.7661 (mtp85) cc_final: 0.7316 (mtp180) REVERT: b 522 LYS cc_start: 0.8019 (mttt) cc_final: 0.7160 (mppt) REVERT: d 42 LYS cc_start: 0.7204 (tttp) cc_final: 0.6394 (tptt) REVERT: d 46 ASP cc_start: 0.7909 (m-30) cc_final: 0.7495 (m-30) REVERT: d 60 MET cc_start: 0.8397 (ttp) cc_final: 0.7918 (ttp) REVERT: d 63 ASP cc_start: 0.7191 (m-30) cc_final: 0.6971 (m-30) REVERT: d 81 MET cc_start: 0.8220 (OUTLIER) cc_final: 0.7892 (ptt) REVERT: d 93 GLU cc_start: 0.7113 (mm-30) cc_final: 0.6700 (mm-30) REVERT: d 132 ILE cc_start: 0.8279 (mt) cc_final: 0.8005 (mp) REVERT: d 334 GLU cc_start: 0.7529 (tp30) cc_final: 0.7189 (tp30) REVERT: d 384 LYS cc_start: 0.7494 (mmtp) cc_final: 0.7031 (mmpt) REVERT: e 27 ARG cc_start: 0.8015 (ttp-170) cc_final: 0.7330 (ttt180) REVERT: e 29 MET cc_start: 0.8066 (mtp) cc_final: 0.7413 (mtp) REVERT: e 93 GLU cc_start: 0.7078 (mm-30) cc_final: 0.6684 (mt-10) REVERT: e 96 LYS cc_start: 0.7737 (tttm) cc_final: 0.7062 (ttmt) REVERT: e 126 ARG cc_start: 0.7331 (mtm180) cc_final: 0.6708 (mtp85) REVERT: e 146 GLU cc_start: 0.6988 (mt-10) cc_final: 0.6708 (mt-10) REVERT: e 150 LYS cc_start: 0.7657 (ttmt) cc_final: 0.7240 (ttpt) REVERT: e 231 ASP cc_start: 0.7550 (t0) cc_final: 0.7348 (t0) REVERT: e 360 GLN cc_start: 0.7979 (tt0) cc_final: 0.7357 (tp40) REVERT: e 371 MET cc_start: 0.8451 (mtt) cc_final: 0.8080 (mmm) REVERT: e 464 GLU cc_start: 0.6704 (tt0) cc_final: 0.6270 (tm-30) REVERT: e 474 MET cc_start: 0.7922 (OUTLIER) cc_final: 0.5840 (tmm) REVERT: e 478 ARG cc_start: 0.7318 (ttp-170) cc_final: 0.7003 (ttm170) REVERT: e 502 LYS cc_start: 0.7038 (tttm) cc_final: 0.6658 (ttmp) REVERT: e 515 GLN cc_start: 0.7711 (tp-100) cc_final: 0.7218 (tp40) REVERT: e 532 ASP cc_start: 0.8386 (t0) cc_final: 0.8091 (t0) REVERT: g 110 GLU cc_start: 0.8237 (OUTLIER) cc_final: 0.7305 (tt0) REVERT: g 117 MET cc_start: 0.8722 (OUTLIER) cc_final: 0.8373 (ttp) REVERT: g 186 GLU cc_start: 0.6959 (tt0) cc_final: 0.6511 (tt0) REVERT: g 191 LYS cc_start: 0.7748 (mtpt) cc_final: 0.7211 (mptt) REVERT: g 192 GLU cc_start: 0.6871 (tt0) cc_final: 0.6120 (pp20) REVERT: g 202 GLU cc_start: 0.6997 (mm-30) cc_final: 0.6584 (mm-30) REVERT: g 274 TYR cc_start: 0.8002 (t80) cc_final: 0.7681 (t80) REVERT: g 277 GLN cc_start: 0.7053 (tp-100) cc_final: 0.6263 (pt0) REVERT: g 294 LYS cc_start: 0.8150 (mmtp) cc_final: 0.7751 (mmtp) REVERT: g 367 LYS cc_start: 0.8450 (OUTLIER) cc_final: 0.8079 (pptt) REVERT: g 381 LYS cc_start: 0.7868 (tppt) cc_final: 0.7428 (mptt) REVERT: g 415 GLU cc_start: 0.7252 (OUTLIER) cc_final: 0.6970 (mm-30) REVERT: g 476 GLU cc_start: 0.7099 (pm20) cc_final: 0.6758 (mm-30) REVERT: h 10 LYS cc_start: 0.8131 (ttmt) cc_final: 0.7447 (ttpt) REVERT: h 17 GLN cc_start: 0.8142 (tt0) cc_final: 0.7912 (tt0) REVERT: h 119 GLN cc_start: 0.7940 (mm-40) cc_final: 0.7525 (mm110) REVERT: h 153 LYS cc_start: 0.7928 (mttm) cc_final: 0.7397 (mptt) REVERT: h 217 LYS cc_start: 0.8977 (ttpt) cc_final: 0.8673 (ttpt) REVERT: h 247 LYS cc_start: 0.8385 (pttp) cc_final: 0.8048 (ptpp) REVERT: h 254 GLU cc_start: 0.8052 (OUTLIER) cc_final: 0.7844 (tp30) REVERT: h 276 ASP cc_start: 0.7353 (t0) cc_final: 0.7054 (m-30) REVERT: h 308 MET cc_start: 0.8796 (mtp) cc_final: 0.8453 (mtp) REVERT: h 320 LYS cc_start: 0.7692 (mmtt) cc_final: 0.7447 (mtmm) REVERT: h 344 ARG cc_start: 0.7328 (ttm110) cc_final: 0.6513 (mtm-85) REVERT: h 356 GLU cc_start: 0.7371 (OUTLIER) cc_final: 0.6937 (mt-10) REVERT: h 368 LYS cc_start: 0.7761 (mttt) cc_final: 0.7114 (mtpp) REVERT: h 379 GLU cc_start: 0.8091 (tm-30) cc_final: 0.7534 (tm-30) REVERT: h 383 GLU cc_start: 0.7516 (mm-30) cc_final: 0.7130 (mm-30) REVERT: h 440 LYS cc_start: 0.8258 (tptt) cc_final: 0.7876 (tppt) REVERT: h 517 ASP cc_start: 0.8686 (p0) cc_final: 0.8019 (p0) REVERT: n 83 ASN cc_start: 0.2362 (OUTLIER) cc_final: 0.1307 (m110) REVERT: q 3 LEU cc_start: 0.5372 (OUTLIER) cc_final: 0.4647 (tt) REVERT: q 17 GLU cc_start: 0.7462 (tt0) cc_final: 0.7189 (tm-30) REVERT: q 31 ARG cc_start: 0.7577 (mmp-170) cc_final: 0.6919 (mmt-90) REVERT: q 55 MET cc_start: 0.7807 (OUTLIER) cc_final: 0.7395 (mtt) REVERT: q 117 GLU cc_start: 0.7226 (tt0) cc_final: 0.6679 (mt-10) REVERT: q 212 ILE cc_start: 0.7987 (OUTLIER) cc_final: 0.7699 (mm) REVERT: q 238 LYS cc_start: 0.7396 (mmtp) cc_final: 0.6993 (mmtp) REVERT: q 277 ASP cc_start: 0.8611 (t70) cc_final: 0.8192 (t0) REVERT: q 312 LEU cc_start: 0.8535 (OUTLIER) cc_final: 0.8332 (mt) REVERT: q 319 TRP cc_start: 0.7174 (m100) cc_final: 0.6360 (m100) REVERT: q 406 LYS cc_start: 0.7708 (ptmt) cc_final: 0.6797 (mmtm) REVERT: q 483 GLU cc_start: 0.7340 (mp0) cc_final: 0.6963 (mm-30) REVERT: q 498 LEU cc_start: 0.8930 (OUTLIER) cc_final: 0.8578 (mt) REVERT: q 505 TYR cc_start: 0.8167 (t80) cc_final: 0.7696 (t80) REVERT: z 5 LYS cc_start: 0.8095 (OUTLIER) cc_final: 0.7771 (mmtt) REVERT: z 10 LYS cc_start: 0.8046 (mtmt) cc_final: 0.7345 (pmtt) REVERT: z 15 ARG cc_start: 0.7673 (OUTLIER) cc_final: 0.6626 (mtm-85) REVERT: z 32 ASP cc_start: 0.7047 (t0) cc_final: 0.6574 (m-30) REVERT: z 36 THR cc_start: 0.8846 (OUTLIER) cc_final: 0.8529 (p) REVERT: z 180 LYS cc_start: 0.7882 (OUTLIER) cc_final: 0.7243 (tttm) REVERT: z 181 LYS cc_start: 0.6902 (mttt) cc_final: 0.6049 (mmmt) REVERT: z 190 MET cc_start: 0.8438 (mmt) cc_final: 0.8028 (mmp) REVERT: z 192 GLU cc_start: 0.7581 (tp30) cc_final: 0.7268 (tp30) REVERT: z 272 LYS cc_start: 0.7838 (mmtp) cc_final: 0.7611 (mtpp) REVERT: z 307 LYS cc_start: 0.7901 (mmtp) cc_final: 0.6770 (ttpt) REVERT: z 323 ARG cc_start: 0.8195 (OUTLIER) cc_final: 0.7421 (mtt-85) REVERT: z 359 LYS cc_start: 0.7875 (mttt) cc_final: 0.7022 (mtmm) REVERT: z 430 LYS cc_start: 0.8318 (tppt) cc_final: 0.7729 (mmmt) REVERT: z 487 MET cc_start: 0.7166 (OUTLIER) cc_final: 0.6067 (ppp) REVERT: z 492 VAL cc_start: 0.8180 (p) cc_final: 0.7560 (p) REVERT: T 48 ASN cc_start: 0.6364 (OUTLIER) cc_final: 0.6105 (t0) REVERT: T 49 VAL cc_start: 0.8640 (OUTLIER) cc_final: 0.8420 (t) REVERT: T 69 GLU cc_start: 0.8010 (OUTLIER) cc_final: 0.7705 (pt0) REVERT: T 77 ARG cc_start: 0.7308 (mtt90) cc_final: 0.7059 (mtt90) REVERT: T 94 GLN cc_start: 0.5912 (mp10) cc_final: 0.5624 (mt0) outliers start: 299 outliers final: 173 residues processed: 1171 average time/residue: 1.5066 time to fit residues: 2305.9311 Evaluate side-chains 1144 residues out of total 7485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 224 poor density : 920 time to evaluate : 6.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 102 LYS Chi-restraints excluded: chain A residue 119 SER Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 166 ASP Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 284 ASN Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 97 ASP Chi-restraints excluded: chain B residue 132 GLU Chi-restraints excluded: chain B residue 134 THR Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain B residue 310 MET Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 413 SER Chi-restraints excluded: chain B residue 416 LEU Chi-restraints excluded: chain B residue 434 VAL Chi-restraints excluded: chain B residue 437 GLU Chi-restraints excluded: chain B residue 460 ASP Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 73 ASP Chi-restraints excluded: chain D residue 79 LYS Chi-restraints excluded: chain D residue 82 GLN Chi-restraints excluded: chain D residue 136 SER Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 158 SER Chi-restraints excluded: chain D residue 184 SER Chi-restraints excluded: chain D residue 186 MET Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 217 THR Chi-restraints excluded: chain D residue 268 ASP Chi-restraints excluded: chain D residue 273 ASP Chi-restraints excluded: chain D residue 400 GLU Chi-restraints excluded: chain D residue 404 SER Chi-restraints excluded: chain D residue 430 ILE Chi-restraints excluded: chain D residue 446 MET Chi-restraints excluded: chain D residue 447 GLU Chi-restraints excluded: chain D residue 536 VAL Chi-restraints excluded: chain E residue 23 ASP Chi-restraints excluded: chain E residue 188 ILE Chi-restraints excluded: chain E residue 194 LEU Chi-restraints excluded: chain E residue 198 ASP Chi-restraints excluded: chain E residue 245 ASP Chi-restraints excluded: chain E residue 269 THR Chi-restraints excluded: chain E residue 306 PHE Chi-restraints excluded: chain E residue 308 ASP Chi-restraints excluded: chain E residue 418 VAL Chi-restraints excluded: chain E residue 522 GLN Chi-restraints excluded: chain G residue 7 VAL Chi-restraints excluded: chain G residue 8 LEU Chi-restraints excluded: chain G residue 54 MET Chi-restraints excluded: chain G residue 71 GLN Chi-restraints excluded: chain G residue 81 ILE Chi-restraints excluded: chain G residue 83 ILE Chi-restraints excluded: chain G residue 146 ILE Chi-restraints excluded: chain G residue 210 GLU Chi-restraints excluded: chain G residue 252 SER Chi-restraints excluded: chain G residue 255 ASP Chi-restraints excluded: chain G residue 265 THR Chi-restraints excluded: chain G residue 292 THR Chi-restraints excluded: chain G residue 332 VAL Chi-restraints excluded: chain G residue 373 THR Chi-restraints excluded: chain G residue 440 VAL Chi-restraints excluded: chain G residue 463 LEU Chi-restraints excluded: chain G residue 476 GLU Chi-restraints excluded: chain G residue 477 THR Chi-restraints excluded: chain G residue 483 GLU Chi-restraints excluded: chain G residue 508 THR Chi-restraints excluded: chain H residue 120 ILE Chi-restraints excluded: chain H residue 142 THR Chi-restraints excluded: chain H residue 151 GLN Chi-restraints excluded: chain H residue 356 GLU Chi-restraints excluded: chain H residue 362 THR Chi-restraints excluded: chain H residue 388 SER Chi-restraints excluded: chain H residue 400 ILE Chi-restraints excluded: chain H residue 427 ILE Chi-restraints excluded: chain N residue 78 VAL Chi-restraints excluded: chain N residue 83 ASN Chi-restraints excluded: chain Q residue 55 MET Chi-restraints excluded: chain Q residue 105 LEU Chi-restraints excluded: chain Q residue 146 LEU Chi-restraints excluded: chain Q residue 182 LEU Chi-restraints excluded: chain Q residue 212 ILE Chi-restraints excluded: chain Q residue 286 THR Chi-restraints excluded: chain Q residue 316 ASN Chi-restraints excluded: chain Q residue 366 GLU Chi-restraints excluded: chain Q residue 480 LEU Chi-restraints excluded: chain Q residue 486 VAL Chi-restraints excluded: chain Q residue 517 THR Chi-restraints excluded: chain Z residue 17 GLN Chi-restraints excluded: chain Z residue 38 LEU Chi-restraints excluded: chain Z residue 107 ASP Chi-restraints excluded: chain Z residue 246 SER Chi-restraints excluded: chain Z residue 340 SER Chi-restraints excluded: chain Z residue 373 THR Chi-restraints excluded: chain Z residue 407 VAL Chi-restraints excluded: chain Z residue 408 VAL Chi-restraints excluded: chain Z residue 430 LYS Chi-restraints excluded: chain Z residue 479 VAL Chi-restraints excluded: chain Z residue 487 MET Chi-restraints excluded: chain Z residue 488 VAL Chi-restraints excluded: chain a residue 23 MET Chi-restraints excluded: chain a residue 166 ASP Chi-restraints excluded: chain a residue 321 LYS Chi-restraints excluded: chain a residue 329 SER Chi-restraints excluded: chain a residue 361 LEU Chi-restraints excluded: chain a residue 367 THR Chi-restraints excluded: chain a residue 370 ARG Chi-restraints excluded: chain a residue 391 SER Chi-restraints excluded: chain a residue 508 ILE Chi-restraints excluded: chain b residue 51 ILE Chi-restraints excluded: chain b residue 66 ASP Chi-restraints excluded: chain b residue 134 THR Chi-restraints excluded: chain b residue 153 VAL Chi-restraints excluded: chain b residue 165 THR Chi-restraints excluded: chain b residue 182 LEU Chi-restraints excluded: chain b residue 214 LEU Chi-restraints excluded: chain b residue 236 LYS Chi-restraints excluded: chain b residue 353 MET Chi-restraints excluded: chain b residue 371 CYS Chi-restraints excluded: chain b residue 387 GLU Chi-restraints excluded: chain d residue 67 ASP Chi-restraints excluded: chain d residue 71 THR Chi-restraints excluded: chain d residue 81 MET Chi-restraints excluded: chain d residue 115 SER Chi-restraints excluded: chain d residue 134 SER Chi-restraints excluded: chain d residue 136 SER Chi-restraints excluded: chain d residue 158 SER Chi-restraints excluded: chain d residue 168 THR Chi-restraints excluded: chain d residue 184 SER Chi-restraints excluded: chain d residue 233 VAL Chi-restraints excluded: chain d residue 239 THR Chi-restraints excluded: chain d residue 377 THR Chi-restraints excluded: chain d residue 385 THR Chi-restraints excluded: chain d residue 394 ASN Chi-restraints excluded: chain d residue 395 LYS Chi-restraints excluded: chain d residue 404 SER Chi-restraints excluded: chain d residue 430 ILE Chi-restraints excluded: chain d residue 536 VAL Chi-restraints excluded: chain e residue 298 ASN Chi-restraints excluded: chain e residue 308 ASP Chi-restraints excluded: chain e residue 330 ILE Chi-restraints excluded: chain e residue 418 VAL Chi-restraints excluded: chain e residue 474 MET Chi-restraints excluded: chain e residue 498 THR Chi-restraints excluded: chain g residue 17 GLU Chi-restraints excluded: chain g residue 39 THR Chi-restraints excluded: chain g residue 83 ILE Chi-restraints excluded: chain g residue 93 ASP Chi-restraints excluded: chain g residue 96 THR Chi-restraints excluded: chain g residue 110 GLU Chi-restraints excluded: chain g residue 117 MET Chi-restraints excluded: chain g residue 161 THR Chi-restraints excluded: chain g residue 310 THR Chi-restraints excluded: chain g residue 367 LYS Chi-restraints excluded: chain g residue 397 VAL Chi-restraints excluded: chain g residue 415 GLU Chi-restraints excluded: chain g residue 432 VAL Chi-restraints excluded: chain g residue 440 VAL Chi-restraints excluded: chain g residue 460 ILE Chi-restraints excluded: chain g residue 471 THR Chi-restraints excluded: chain g residue 486 THR Chi-restraints excluded: chain h residue 32 ILE Chi-restraints excluded: chain h residue 38 THR Chi-restraints excluded: chain h residue 85 SER Chi-restraints excluded: chain h residue 177 LYS Chi-restraints excluded: chain h residue 211 VAL Chi-restraints excluded: chain h residue 221 SER Chi-restraints excluded: chain h residue 254 GLU Chi-restraints excluded: chain h residue 356 GLU Chi-restraints excluded: chain h residue 395 ILE Chi-restraints excluded: chain h residue 405 VAL Chi-restraints excluded: chain h residue 427 ILE Chi-restraints excluded: chain h residue 473 THR Chi-restraints excluded: chain n residue 12 VAL Chi-restraints excluded: chain n residue 83 ASN Chi-restraints excluded: chain q residue 3 LEU Chi-restraints excluded: chain q residue 43 THR Chi-restraints excluded: chain q residue 45 THR Chi-restraints excluded: chain q residue 55 MET Chi-restraints excluded: chain q residue 150 SER Chi-restraints excluded: chain q residue 181 LYS Chi-restraints excluded: chain q residue 200 ASP Chi-restraints excluded: chain q residue 212 ILE Chi-restraints excluded: chain q residue 226 GLU Chi-restraints excluded: chain q residue 234 VAL Chi-restraints excluded: chain q residue 312 LEU Chi-restraints excluded: chain q residue 385 MET Chi-restraints excluded: chain q residue 480 LEU Chi-restraints excluded: chain q residue 498 LEU Chi-restraints excluded: chain z residue 4 VAL Chi-restraints excluded: chain z residue 5 LYS Chi-restraints excluded: chain z residue 15 ARG Chi-restraints excluded: chain z residue 36 THR Chi-restraints excluded: chain z residue 88 THR Chi-restraints excluded: chain z residue 149 ILE Chi-restraints excluded: chain z residue 179 ILE Chi-restraints excluded: chain z residue 180 LYS Chi-restraints excluded: chain z residue 246 SER Chi-restraints excluded: chain z residue 323 ARG Chi-restraints excluded: chain z residue 408 VAL Chi-restraints excluded: chain z residue 442 ASP Chi-restraints excluded: chain z residue 464 VAL Chi-restraints excluded: chain z residue 487 MET Chi-restraints excluded: chain z residue 488 VAL Chi-restraints excluded: chain T residue 48 ASN Chi-restraints excluded: chain T residue 49 VAL Chi-restraints excluded: chain T residue 69 GLU Chi-restraints excluded: chain T residue 84 ILE Chi-restraints excluded: chain T residue 143 THR Chi-restraints excluded: chain T residue 161 ASP Chi-restraints excluded: chain T residue 232 THR Chi-restraints excluded: chain T residue 391 ARG Chi-restraints excluded: chain T residue 395 LEU Chi-restraints excluded: chain T residue 415 MET 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: 0.9990 chunk 487 optimal weight: 9.9990 chunk 625 optimal weight: 0.8980 chunk 484 optimal weight: 2.9990 chunk 720 optimal weight: 4.9990 chunk 478 optimal weight: 2.9990 chunk 852 optimal weight: 3.9990 chunk 533 optimal weight: 8.9990 chunk 520 optimal weight: 3.9990 chunk 393 optimal weight: 2.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 235 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** ** 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 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 492 ASN b 195 ASN e 122 GLN ** 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 130 GLN ** q 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 37 HIS T 52 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7449 moved from start: 0.2279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 69953 Z= 0.258 Angle : 0.582 11.201 94470 Z= 0.288 Chirality : 0.043 0.194 11206 Planarity : 0.004 0.049 12067 Dihedral : 7.666 170.267 9742 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.32 % Favored : 96.66 % Rotamer: Outliers : 3.76 % Allowed : 19.82 % Favored : 76.42 % 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: 0.38 (0.09), residues: 8920 helix: 1.17 (0.08), residues: 4578 sheet: -0.39 (0.14), residues: 1229 loop : -0.76 (0.11), residues: 3113 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP N 101 HIS 0.012 0.001 HIS G 111 PHE 0.027 0.001 PHE a 167 TYR 0.022 0.001 TYR g 303 ARG 0.009 0.000 ARG G 216 *********************** 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 1242 residues out of total 7485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 280 poor density : 962 time to evaluate : 7.473 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 PHE cc_start: 0.7640 (t80) cc_final: 0.7294 (t80) REVERT: A 51 ASP cc_start: 0.6229 (t0) cc_final: 0.5954 (t70) REVERT: A 123 LEU cc_start: 0.8071 (OUTLIER) cc_final: 0.7648 (tp) REVERT: A 230 VAL cc_start: 0.7225 (OUTLIER) cc_final: 0.6924 (t) REVERT: A 321 LYS cc_start: 0.7853 (mtmt) cc_final: 0.7533 (tptt) REVERT: A 354 GLU cc_start: 0.6518 (mm-30) cc_final: 0.5841 (tp30) REVERT: A 384 MET cc_start: 0.8156 (ttt) cc_final: 0.7886 (ttt) REVERT: A 430 MET cc_start: 0.5751 (mmm) cc_final: 0.5153 (mmm) REVERT: A 459 ASP cc_start: 0.8301 (t0) cc_final: 0.7981 (t0) REVERT: B 87 MET cc_start: 0.7834 (ttp) cc_final: 0.7426 (ttp) REVERT: B 114 GLU cc_start: 0.7634 (OUTLIER) cc_final: 0.7387 (pt0) REVERT: B 132 GLU cc_start: 0.7492 (OUTLIER) cc_final: 0.7155 (mp0) REVERT: B 248 LYS cc_start: 0.7934 (mtpt) cc_final: 0.7604 (mtmt) REVERT: B 301 GLU cc_start: 0.7540 (tt0) cc_final: 0.7108 (tt0) REVERT: B 347 LYS cc_start: 0.8308 (mmtm) cc_final: 0.7505 (mppt) REVERT: B 402 LYS cc_start: 0.7629 (mtmm) cc_final: 0.6995 (mptp) REVERT: B 405 ARG cc_start: 0.7632 (OUTLIER) cc_final: 0.7136 (mtt180) REVERT: B 414 GLU cc_start: 0.6598 (mp0) cc_final: 0.6100 (mp0) REVERT: B 445 MET cc_start: 0.7744 (tpp) cc_final: 0.7258 (tpp) REVERT: B 456 TYR cc_start: 0.8709 (m-80) cc_final: 0.8279 (m-10) REVERT: D 65 LYS cc_start: 0.8330 (mtmm) cc_final: 0.8051 (mtpt) REVERT: D 67 ASP cc_start: 0.7660 (m-30) cc_final: 0.7395 (m-30) REVERT: D 82 GLN cc_start: 0.8282 (OUTLIER) cc_final: 0.7703 (mm-40) REVERT: D 222 GLU cc_start: 0.7414 (tt0) cc_final: 0.6754 (mt-10) REVERT: D 224 VAL cc_start: 0.8115 (t) cc_final: 0.7799 (m) REVERT: D 257 LYS cc_start: 0.7738 (mmtm) cc_final: 0.7318 (ttpp) REVERT: D 291 LYS cc_start: 0.7917 (OUTLIER) cc_final: 0.7658 (tttp) REVERT: D 326 LYS cc_start: 0.8573 (pttt) cc_final: 0.8256 (ptmt) REVERT: D 384 LYS cc_start: 0.7673 (mptt) cc_final: 0.7423 (mptm) REVERT: D 400 GLU cc_start: 0.7272 (OUTLIER) cc_final: 0.6815 (mm-30) REVERT: D 458 MET cc_start: 0.8253 (mmm) cc_final: 0.7918 (mpp) REVERT: D 459 GLU cc_start: 0.6562 (mt-10) cc_final: 0.6285 (tp30) REVERT: E 20 LYS cc_start: 0.7969 (tttp) cc_final: 0.7741 (ttpt) REVERT: E 21 ASP cc_start: 0.7531 (t0) cc_final: 0.7313 (t0) REVERT: E 48 MET cc_start: 0.8430 (tpt) cc_final: 0.8128 (mmm) REVERT: E 93 GLU cc_start: 0.6972 (mm-30) cc_final: 0.6583 (mm-30) REVERT: E 121 GLU cc_start: 0.7127 (tt0) cc_final: 0.6701 (tt0) REVERT: E 125 ASP cc_start: 0.7864 (m-30) cc_final: 0.7594 (m-30) REVERT: E 188 ILE cc_start: 0.8407 (OUTLIER) cc_final: 0.8126 (mt) REVERT: E 198 ASP cc_start: 0.7674 (OUTLIER) cc_final: 0.7343 (t70) REVERT: E 263 LYS cc_start: 0.7805 (ttmt) cc_final: 0.7074 (tttt) REVERT: E 283 GLU cc_start: 0.7920 (mm-30) cc_final: 0.7661 (mt-10) REVERT: E 290 GLN cc_start: 0.7355 (tp-100) cc_final: 0.6979 (tm-30) REVERT: E 439 LYS cc_start: 0.7569 (mtmm) cc_final: 0.7310 (mptt) REVERT: E 446 TYR cc_start: 0.8159 (m-80) cc_final: 0.7601 (m-80) REVERT: E 502 LYS cc_start: 0.7401 (tttt) cc_final: 0.7140 (tttm) REVERT: G 15 LYS cc_start: 0.7387 (mmmt) cc_final: 0.6729 (mtmm) REVERT: G 17 GLU cc_start: 0.6657 (mp0) cc_final: 0.6178 (mp0) REVERT: G 54 MET cc_start: 0.8057 (OUTLIER) cc_final: 0.7571 (mtp) REVERT: G 71 GLN cc_start: 0.8328 (OUTLIER) cc_final: 0.8000 (tt0) REVERT: G 81 ILE cc_start: 0.8475 (OUTLIER) cc_final: 0.8181 (mp) REVERT: G 82 GLU cc_start: 0.7734 (mm-30) cc_final: 0.7463 (mm-30) REVERT: G 110 GLU cc_start: 0.7710 (tt0) cc_final: 0.7250 (tp30) REVERT: G 234 LYS cc_start: 0.7168 (tptp) cc_final: 0.6766 (tptt) REVERT: G 248 LYS cc_start: 0.8398 (mtpt) cc_final: 0.7635 (mmpt) REVERT: G 255 ASP cc_start: 0.6946 (OUTLIER) cc_final: 0.6704 (m-30) REVERT: G 270 MET cc_start: 0.7608 (mtp) cc_final: 0.7375 (mtp) REVERT: G 276 GLN cc_start: 0.7460 (tt0) cc_final: 0.7141 (tm-30) REVERT: G 277 GLN cc_start: 0.7567 (tp40) cc_final: 0.6895 (mp10) REVERT: G 367 LYS cc_start: 0.8340 (pttt) cc_final: 0.8092 (pttp) REVERT: G 429 MET cc_start: 0.7228 (mtm) cc_final: 0.6890 (mtm) REVERT: G 476 GLU cc_start: 0.7277 (OUTLIER) cc_final: 0.6921 (mt-10) REVERT: G 477 THR cc_start: 0.8560 (OUTLIER) cc_final: 0.8192 (t) REVERT: G 483 GLU cc_start: 0.5926 (OUTLIER) cc_final: 0.5094 (mp0) REVERT: G 511 GLU cc_start: 0.7560 (mm-30) cc_final: 0.7245 (mp0) REVERT: H 151 GLN cc_start: 0.7615 (OUTLIER) cc_final: 0.7359 (tt0) REVERT: H 172 LYS cc_start: 0.7797 (pttt) cc_final: 0.7501 (ptpt) REVERT: H 279 GLU cc_start: 0.7248 (tp30) cc_final: 0.6868 (mt-10) REVERT: H 317 GLU cc_start: 0.7512 (mp0) cc_final: 0.7288 (tt0) REVERT: H 349 GLU cc_start: 0.7915 (tt0) cc_final: 0.7653 (tt0) REVERT: H 368 LYS cc_start: 0.8123 (mttt) cc_final: 0.7599 (mmtm) REVERT: H 383 GLU cc_start: 0.7658 (mm-30) cc_final: 0.7389 (mm-30) REVERT: H 440 LYS cc_start: 0.7620 (mmtp) cc_final: 0.7324 (mtpt) REVERT: H 482 GLU cc_start: 0.7973 (mt-10) cc_final: 0.7718 (mt-10) REVERT: H 497 MET cc_start: 0.7335 (tpp) cc_final: 0.6793 (tpt) REVERT: Q 31 ARG cc_start: 0.7349 (mmp-170) cc_final: 0.6680 (mtt180) REVERT: Q 55 MET cc_start: 0.7760 (OUTLIER) cc_final: 0.7534 (mtt) REVERT: Q 193 ASP cc_start: 0.6938 (m-30) cc_final: 0.6628 (m-30) REVERT: Q 200 ASP cc_start: 0.8003 (m-30) cc_final: 0.7737 (m-30) REVERT: Q 249 MET cc_start: 0.7419 (ptp) cc_final: 0.6926 (mmm) REVERT: Q 281 LYS cc_start: 0.7697 (ttmt) cc_final: 0.7418 (tptp) REVERT: Q 286 THR cc_start: 0.8611 (OUTLIER) cc_final: 0.8352 (p) REVERT: Q 296 LYS cc_start: 0.7829 (pttm) cc_final: 0.7406 (pttt) REVERT: Q 318 LYS cc_start: 0.8118 (pttm) cc_final: 0.7666 (ptmm) REVERT: Q 354 GLU cc_start: 0.7665 (tm-30) cc_final: 0.7366 (tm-30) REVERT: Q 481 ASP cc_start: 0.7633 (t0) cc_final: 0.7418 (t0) REVERT: Z 17 GLN cc_start: 0.7033 (OUTLIER) cc_final: 0.6197 (pp30) REVERT: Z 44 MET cc_start: 0.9145 (mmm) cc_final: 0.8790 (mmm) REVERT: Z 108 LEU cc_start: 0.7845 (tt) cc_final: 0.7551 (tp) REVERT: Z 163 GLU cc_start: 0.6979 (tp30) cc_final: 0.6315 (tp30) REVERT: Z 190 MET cc_start: 0.7939 (mmp) cc_final: 0.7648 (mmp) REVERT: Z 195 GLU cc_start: 0.7942 (pt0) cc_final: 0.7384 (pt0) REVERT: Z 223 LYS cc_start: 0.7799 (mptt) cc_final: 0.7422 (mmtt) REVERT: Z 241 LYS cc_start: 0.8512 (ttmt) cc_final: 0.7629 (pttp) REVERT: Z 264 ARG cc_start: 0.7348 (mtp85) cc_final: 0.6973 (mtp-110) REVERT: Z 272 LYS cc_start: 0.7436 (mmtp) cc_final: 0.6933 (mtpp) REVERT: Z 303 ASP cc_start: 0.7206 (t70) cc_final: 0.6472 (m-30) REVERT: Z 307 LYS cc_start: 0.7794 (mmtp) cc_final: 0.7514 (mtpt) REVERT: Z 322 GLU cc_start: 0.7440 (tt0) cc_final: 0.7067 (tt0) REVERT: Z 487 MET cc_start: 0.6988 (OUTLIER) cc_final: 0.6466 (ppp) REVERT: Z 495 TRP cc_start: 0.8007 (m100) cc_final: 0.7449 (m100) REVERT: Z 496 ASP cc_start: 0.7506 (m-30) cc_final: 0.7212 (m-30) REVERT: a 23 MET cc_start: 0.5775 (OUTLIER) cc_final: 0.5434 (ttp) REVERT: a 265 GLN cc_start: 0.7193 (pt0) cc_final: 0.6862 (tp40) REVERT: a 354 GLU cc_start: 0.7163 (OUTLIER) cc_final: 0.6846 (tt0) REVERT: a 361 LEU cc_start: 0.8699 (OUTLIER) cc_final: 0.8412 (pt) REVERT: a 384 MET cc_start: 0.8031 (ttt) cc_final: 0.7777 (ttt) REVERT: b 93 ASP cc_start: 0.7289 (m-30) cc_final: 0.6531 (m-30) REVERT: b 223 LYS cc_start: 0.8316 (mttm) cc_final: 0.7972 (mtpt) REVERT: b 236 LYS cc_start: 0.7958 (OUTLIER) cc_final: 0.7463 (mtmm) REVERT: b 316 ASP cc_start: 0.7193 (t0) cc_final: 0.6833 (m-30) REVERT: b 321 GLU cc_start: 0.6908 (mt-10) cc_final: 0.6633 (tt0) REVERT: b 387 GLU cc_start: 0.7345 (OUTLIER) cc_final: 0.7122 (tt0) REVERT: b 407 VAL cc_start: 0.7947 (t) cc_final: 0.7733 (m) REVERT: b 445 MET cc_start: 0.8044 (tpp) cc_final: 0.7749 (tpp) REVERT: b 516 ARG cc_start: 0.7630 (mtp85) cc_final: 0.7205 (mtp85) REVERT: b 522 LYS cc_start: 0.8028 (mttt) cc_final: 0.7167 (mppt) REVERT: d 42 LYS cc_start: 0.7245 (tttp) cc_final: 0.6448 (tptt) REVERT: d 46 ASP cc_start: 0.7919 (m-30) cc_final: 0.7517 (m-30) REVERT: d 60 MET cc_start: 0.8321 (ttp) cc_final: 0.7844 (ttp) REVERT: d 63 ASP cc_start: 0.7182 (m-30) cc_final: 0.6969 (m-30) REVERT: d 81 MET cc_start: 0.8300 (OUTLIER) cc_final: 0.7950 (ptt) REVERT: d 93 GLU cc_start: 0.7099 (mm-30) cc_final: 0.6689 (mm-30) REVERT: d 132 ILE cc_start: 0.8278 (mt) cc_final: 0.8005 (mp) REVERT: d 334 GLU cc_start: 0.7529 (tp30) cc_final: 0.7185 (tp30) REVERT: d 384 LYS cc_start: 0.7477 (mmtp) cc_final: 0.7025 (mmpt) REVERT: e 27 ARG cc_start: 0.8013 (ttp-170) cc_final: 0.7379 (ttt180) REVERT: e 29 MET cc_start: 0.8004 (mtp) cc_final: 0.7389 (mtp) REVERT: e 58 ASP cc_start: 0.7233 (m-30) cc_final: 0.6906 (m-30) REVERT: e 93 GLU cc_start: 0.7045 (mm-30) cc_final: 0.6639 (mt-10) REVERT: e 96 LYS cc_start: 0.7688 (tttm) cc_final: 0.6991 (ttmt) REVERT: e 121 GLU cc_start: 0.6952 (tt0) cc_final: 0.6677 (tt0) REVERT: e 126 ARG cc_start: 0.7302 (mtm180) cc_final: 0.6742 (mtp85) REVERT: e 146 GLU cc_start: 0.7002 (mt-10) cc_final: 0.6723 (mt-10) REVERT: e 150 LYS cc_start: 0.7672 (ttmt) cc_final: 0.7271 (ttpt) REVERT: e 360 GLN cc_start: 0.7960 (tt0) cc_final: 0.7370 (tp40) REVERT: e 371 MET cc_start: 0.8440 (mtt) cc_final: 0.8051 (mmm) REVERT: e 464 GLU cc_start: 0.6731 (tt0) cc_final: 0.6111 (mm-30) REVERT: e 478 ARG cc_start: 0.7298 (ttp-170) cc_final: 0.6943 (ttm170) REVERT: e 502 LYS cc_start: 0.7013 (tttm) cc_final: 0.6639 (ttmp) REVERT: e 515 GLN cc_start: 0.7684 (tp-100) cc_final: 0.7217 (tp40) REVERT: e 532 ASP cc_start: 0.8339 (t0) cc_final: 0.8059 (t0) REVERT: g 110 GLU cc_start: 0.8207 (OUTLIER) cc_final: 0.7260 (tt0) REVERT: g 191 LYS cc_start: 0.7899 (mtpt) cc_final: 0.7379 (mptt) REVERT: g 192 GLU cc_start: 0.6897 (tt0) cc_final: 0.6164 (pp20) REVERT: g 202 GLU cc_start: 0.7022 (mm-30) cc_final: 0.6596 (mm-30) REVERT: g 274 TYR cc_start: 0.7998 (t80) cc_final: 0.7684 (t80) REVERT: g 277 GLN cc_start: 0.7056 (tp-100) cc_final: 0.6252 (pt0) REVERT: g 294 LYS cc_start: 0.8126 (mmtp) cc_final: 0.7761 (mmtp) REVERT: g 367 LYS cc_start: 0.8449 (OUTLIER) cc_final: 0.8054 (pptt) REVERT: g 381 LYS cc_start: 0.7847 (tppt) cc_final: 0.7409 (mptt) REVERT: g 415 GLU cc_start: 0.7276 (OUTLIER) cc_final: 0.6973 (mm-30) REVERT: g 476 GLU cc_start: 0.7095 (pm20) cc_final: 0.6740 (mm-30) REVERT: h 10 LYS cc_start: 0.8146 (ttmt) cc_final: 0.7452 (ttpt) REVERT: h 17 GLN cc_start: 0.8130 (tt0) cc_final: 0.7901 (tt0) REVERT: h 51 ASP cc_start: 0.7685 (p0) cc_final: 0.7484 (p0) REVERT: h 119 GLN cc_start: 0.7990 (mm-40) cc_final: 0.7588 (mm110) REVERT: h 149 VAL cc_start: 0.8417 (OUTLIER) cc_final: 0.7910 (t) REVERT: h 153 LYS cc_start: 0.7919 (mttm) cc_final: 0.7389 (mptt) REVERT: h 217 LYS cc_start: 0.8969 (ttpt) cc_final: 0.8677 (ttpt) REVERT: h 247 LYS cc_start: 0.8418 (pttp) cc_final: 0.8075 (ptpp) REVERT: h 254 GLU cc_start: 0.8040 (OUTLIER) cc_final: 0.7836 (tp30) REVERT: h 276 ASP cc_start: 0.7340 (t0) cc_final: 0.7054 (m-30) REVERT: h 320 LYS cc_start: 0.7669 (mmtt) cc_final: 0.7439 (mtmm) REVERT: h 344 ARG cc_start: 0.7332 (ttm110) cc_final: 0.6502 (mtm-85) REVERT: h 350 GLU cc_start: 0.8138 (OUTLIER) cc_final: 0.7865 (tt0) REVERT: h 356 GLU cc_start: 0.7360 (OUTLIER) cc_final: 0.6753 (mt-10) REVERT: h 368 LYS cc_start: 0.7690 (mttt) cc_final: 0.7033 (mtpp) REVERT: h 379 GLU cc_start: 0.8083 (tm-30) cc_final: 0.7635 (tm-30) REVERT: h 440 LYS cc_start: 0.8217 (tptt) cc_final: 0.7811 (tppt) REVERT: h 517 ASP cc_start: 0.8674 (p0) cc_final: 0.8039 (p0) REVERT: n 83 ASN cc_start: 0.2465 (OUTLIER) cc_final: 0.1349 (m110) REVERT: q 3 LEU cc_start: 0.5423 (OUTLIER) cc_final: 0.4700 (tt) REVERT: q 17 GLU cc_start: 0.7438 (tt0) cc_final: 0.7157 (tm-30) REVERT: q 31 ARG cc_start: 0.7562 (mmp-170) cc_final: 0.6912 (mmt-90) REVERT: q 55 MET cc_start: 0.7786 (OUTLIER) cc_final: 0.7361 (mtt) REVERT: q 117 GLU cc_start: 0.7212 (tt0) cc_final: 0.6669 (mt-10) REVERT: q 212 ILE cc_start: 0.7985 (OUTLIER) cc_final: 0.7733 (mm) REVERT: q 238 LYS cc_start: 0.7512 (mmtp) cc_final: 0.6991 (mmtp) REVERT: q 277 ASP cc_start: 0.8573 (t70) cc_final: 0.8178 (t0) REVERT: q 312 LEU cc_start: 0.8516 (OUTLIER) cc_final: 0.8310 (mt) REVERT: q 319 TRP cc_start: 0.7113 (m100) cc_final: 0.6326 (m100) REVERT: q 406 LYS cc_start: 0.7623 (ptmt) cc_final: 0.6740 (mmtm) REVERT: q 483 GLU cc_start: 0.7314 (mp0) cc_final: 0.6963 (mm-30) REVERT: q 498 LEU cc_start: 0.8964 (OUTLIER) cc_final: 0.8647 (mt) REVERT: q 505 TYR cc_start: 0.8144 (t80) cc_final: 0.7730 (t80) REVERT: z 5 LYS cc_start: 0.8076 (OUTLIER) cc_final: 0.7748 (mmtt) REVERT: z 10 LYS cc_start: 0.8025 (mtmt) cc_final: 0.7386 (pmtt) REVERT: z 32 ASP cc_start: 0.7039 (t0) cc_final: 0.6572 (m-30) REVERT: z 36 THR cc_start: 0.8797 (OUTLIER) cc_final: 0.8468 (p) REVERT: z 181 LYS cc_start: 0.6922 (mttt) cc_final: 0.6059 (mmmt) REVERT: z 190 MET cc_start: 0.8429 (mmt) cc_final: 0.8088 (mmp) REVERT: z 272 LYS cc_start: 0.7894 (mmtp) cc_final: 0.7623 (mtpp) REVERT: z 307 LYS cc_start: 0.7913 (mmtp) cc_final: 0.6738 (ttpt) REVERT: z 323 ARG cc_start: 0.8201 (OUTLIER) cc_final: 0.7334 (mtt-85) REVERT: z 359 LYS cc_start: 0.7802 (mttt) cc_final: 0.6958 (mtmm) REVERT: z 388 LYS cc_start: 0.7423 (OUTLIER) cc_final: 0.6775 (mtpt) REVERT: z 430 LYS cc_start: 0.8282 (tppt) cc_final: 0.7721 (mmmt) REVERT: z 487 MET cc_start: 0.7105 (OUTLIER) cc_final: 0.6028 (ppp) REVERT: z 492 VAL cc_start: 0.8104 (p) cc_final: 0.7467 (p) REVERT: T 49 VAL cc_start: 0.8530 (OUTLIER) cc_final: 0.8311 (t) REVERT: T 69 GLU cc_start: 0.7992 (OUTLIER) cc_final: 0.7697 (pt0) REVERT: T 77 ARG cc_start: 0.7325 (mtt90) cc_final: 0.7057 (mtt90) REVERT: T 94 GLN cc_start: 0.5843 (mp10) cc_final: 0.5577 (mt0) REVERT: T 167 PHE cc_start: 0.8151 (m-80) cc_final: 0.7839 (m-80) REVERT: T 233 MET cc_start: 0.7257 (tpt) cc_final: 0.6974 (tpt) outliers start: 280 outliers final: 168 residues processed: 1178 average time/residue: 1.5265 time to fit residues: 2362.4273 Evaluate side-chains 1138 residues out of total 7485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 216 poor density : 922 time to evaluate : 6.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 119 SER Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 166 ASP Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 284 ASN Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 97 ASP Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 114 GLU Chi-restraints excluded: chain B residue 132 GLU Chi-restraints excluded: chain B residue 134 THR Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain B residue 310 MET Chi-restraints excluded: chain B residue 405 ARG Chi-restraints excluded: chain B residue 413 SER Chi-restraints excluded: chain B residue 416 LEU Chi-restraints excluded: chain B residue 434 VAL Chi-restraints excluded: chain B residue 437 GLU Chi-restraints excluded: chain B residue 460 ASP Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 73 ASP Chi-restraints excluded: chain D residue 79 LYS Chi-restraints excluded: chain D residue 82 GLN Chi-restraints excluded: chain D residue 136 SER Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 158 SER Chi-restraints excluded: chain D residue 184 SER Chi-restraints excluded: chain D residue 186 MET Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 217 THR Chi-restraints excluded: chain D residue 268 ASP Chi-restraints excluded: chain D residue 273 ASP Chi-restraints excluded: chain D residue 291 LYS Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 400 GLU Chi-restraints excluded: chain D residue 404 SER Chi-restraints excluded: chain D residue 430 ILE Chi-restraints excluded: chain D residue 446 MET Chi-restraints excluded: chain D residue 447 GLU Chi-restraints excluded: chain D residue 536 VAL Chi-restraints excluded: chain E residue 23 ASP Chi-restraints excluded: chain E residue 188 ILE Chi-restraints excluded: chain E residue 198 ASP Chi-restraints excluded: chain E residue 245 ASP Chi-restraints excluded: chain E residue 269 THR Chi-restraints excluded: chain E residue 306 PHE Chi-restraints excluded: chain E residue 308 ASP Chi-restraints excluded: chain E residue 418 VAL Chi-restraints excluded: chain G residue 7 VAL Chi-restraints excluded: chain G residue 54 MET Chi-restraints excluded: chain G residue 71 GLN Chi-restraints excluded: chain G residue 81 ILE Chi-restraints excluded: chain G residue 83 ILE Chi-restraints excluded: chain G residue 96 THR Chi-restraints excluded: chain G residue 146 ILE Chi-restraints excluded: chain G residue 252 SER Chi-restraints excluded: chain G residue 255 ASP Chi-restraints excluded: chain G residue 265 THR Chi-restraints excluded: chain G residue 292 THR Chi-restraints excluded: chain G residue 373 THR Chi-restraints excluded: chain G residue 440 VAL Chi-restraints excluded: chain G residue 476 GLU Chi-restraints excluded: chain G residue 477 THR Chi-restraints excluded: chain G residue 483 GLU Chi-restraints excluded: chain G residue 508 THR Chi-restraints excluded: chain H residue 120 ILE Chi-restraints excluded: chain H residue 142 THR Chi-restraints excluded: chain H residue 151 GLN Chi-restraints excluded: chain H residue 362 THR Chi-restraints excluded: chain H residue 400 ILE Chi-restraints excluded: chain H residue 427 ILE Chi-restraints excluded: chain N residue 78 VAL Chi-restraints excluded: chain N residue 83 ASN Chi-restraints excluded: chain Q residue 55 MET Chi-restraints excluded: chain Q residue 105 LEU Chi-restraints excluded: chain Q residue 146 LEU Chi-restraints excluded: chain Q residue 182 LEU Chi-restraints excluded: chain Q residue 212 ILE Chi-restraints excluded: chain Q residue 286 THR Chi-restraints excluded: chain Q residue 316 ASN Chi-restraints excluded: chain Q residue 366 GLU Chi-restraints excluded: chain Q residue 480 LEU Chi-restraints excluded: chain Q residue 486 VAL Chi-restraints excluded: chain Q residue 517 THR Chi-restraints excluded: chain Z residue 17 GLN Chi-restraints excluded: chain Z residue 107 ASP Chi-restraints excluded: chain Z residue 246 SER Chi-restraints excluded: chain Z residue 373 THR Chi-restraints excluded: chain Z residue 380 ASN Chi-restraints excluded: chain Z residue 407 VAL Chi-restraints excluded: chain Z residue 408 VAL Chi-restraints excluded: chain Z residue 430 LYS Chi-restraints excluded: chain Z residue 479 VAL Chi-restraints excluded: chain Z residue 487 MET Chi-restraints excluded: chain Z residue 488 VAL Chi-restraints excluded: chain a residue 23 MET Chi-restraints excluded: chain a residue 166 ASP Chi-restraints excluded: chain a residue 321 LYS Chi-restraints excluded: chain a residue 329 SER Chi-restraints excluded: chain a residue 354 GLU Chi-restraints excluded: chain a residue 361 LEU Chi-restraints excluded: chain a residue 367 THR Chi-restraints excluded: chain a residue 370 ARG Chi-restraints excluded: chain a residue 391 SER Chi-restraints excluded: chain a residue 508 ILE Chi-restraints excluded: chain b residue 51 ILE Chi-restraints excluded: chain b residue 66 ASP Chi-restraints excluded: chain b residue 134 THR Chi-restraints excluded: chain b residue 153 VAL Chi-restraints excluded: chain b residue 165 THR Chi-restraints excluded: chain b residue 182 LEU Chi-restraints excluded: chain b residue 214 LEU Chi-restraints excluded: chain b residue 236 LYS Chi-restraints excluded: chain b residue 353 MET Chi-restraints excluded: chain b residue 371 CYS Chi-restraints excluded: chain b residue 387 GLU Chi-restraints excluded: chain d residue 67 ASP Chi-restraints excluded: chain d residue 71 THR Chi-restraints excluded: chain d residue 81 MET Chi-restraints excluded: chain d residue 115 SER Chi-restraints excluded: chain d residue 134 SER Chi-restraints excluded: chain d residue 136 SER Chi-restraints excluded: chain d residue 158 SER Chi-restraints excluded: chain d residue 168 THR Chi-restraints excluded: chain d residue 184 SER Chi-restraints excluded: chain d residue 233 VAL Chi-restraints excluded: chain d residue 239 THR Chi-restraints excluded: chain d residue 385 THR Chi-restraints excluded: chain d residue 394 ASN Chi-restraints excluded: chain d residue 395 LYS Chi-restraints excluded: chain d residue 404 SER Chi-restraints excluded: chain d residue 430 ILE Chi-restraints excluded: chain d residue 536 VAL Chi-restraints excluded: chain e residue 298 ASN Chi-restraints excluded: chain e residue 308 ASP Chi-restraints excluded: chain e residue 319 LEU Chi-restraints excluded: chain e residue 330 ILE Chi-restraints excluded: chain e residue 418 VAL Chi-restraints excluded: chain e residue 498 THR Chi-restraints excluded: chain g residue 17 GLU Chi-restraints excluded: chain g residue 39 THR Chi-restraints excluded: chain g residue 83 ILE Chi-restraints excluded: chain g residue 93 ASP Chi-restraints excluded: chain g residue 96 THR Chi-restraints excluded: chain g residue 110 GLU Chi-restraints excluded: chain g residue 161 THR Chi-restraints excluded: chain g residue 310 THR Chi-restraints excluded: chain g residue 367 LYS Chi-restraints excluded: chain g residue 397 VAL Chi-restraints excluded: chain g residue 415 GLU Chi-restraints excluded: chain g residue 432 VAL Chi-restraints excluded: chain g residue 440 VAL Chi-restraints excluded: chain g residue 460 ILE Chi-restraints excluded: chain g residue 471 THR Chi-restraints excluded: chain g residue 486 THR Chi-restraints excluded: chain h residue 32 ILE Chi-restraints excluded: chain h residue 38 THR Chi-restraints excluded: chain h residue 85 SER Chi-restraints excluded: chain h residue 149 VAL Chi-restraints excluded: chain h residue 200 VAL Chi-restraints excluded: chain h residue 211 VAL Chi-restraints excluded: chain h residue 221 SER Chi-restraints excluded: chain h residue 254 GLU Chi-restraints excluded: chain h residue 350 GLU Chi-restraints excluded: chain h residue 356 GLU Chi-restraints excluded: chain h residue 395 ILE Chi-restraints excluded: chain h residue 405 VAL Chi-restraints excluded: chain h residue 427 ILE Chi-restraints excluded: chain n residue 12 VAL Chi-restraints excluded: chain n residue 83 ASN Chi-restraints excluded: chain q residue 3 LEU Chi-restraints excluded: chain q residue 43 THR Chi-restraints excluded: chain q residue 45 THR Chi-restraints excluded: chain q residue 55 MET Chi-restraints excluded: chain q residue 130 GLU Chi-restraints excluded: chain q residue 150 SER Chi-restraints excluded: chain q residue 170 SER Chi-restraints excluded: chain q residue 181 LYS Chi-restraints excluded: chain q residue 200 ASP Chi-restraints excluded: chain q residue 212 ILE Chi-restraints excluded: chain q residue 226 GLU Chi-restraints excluded: chain q residue 234 VAL Chi-restraints excluded: chain q residue 312 LEU Chi-restraints excluded: chain q residue 385 MET Chi-restraints excluded: chain q residue 480 LEU Chi-restraints excluded: chain q residue 498 LEU Chi-restraints excluded: chain z residue 4 VAL Chi-restraints excluded: chain z residue 5 LYS Chi-restraints excluded: chain z residue 36 THR Chi-restraints excluded: chain z residue 88 THR Chi-restraints excluded: chain z residue 149 ILE Chi-restraints excluded: chain z residue 179 ILE Chi-restraints excluded: chain z residue 246 SER Chi-restraints excluded: chain z residue 323 ARG Chi-restraints excluded: chain z residue 388 LYS Chi-restraints excluded: chain z residue 408 VAL Chi-restraints excluded: chain z residue 442 ASP Chi-restraints excluded: chain z residue 464 VAL Chi-restraints excluded: chain z residue 487 MET Chi-restraints excluded: chain z residue 488 VAL Chi-restraints excluded: chain T residue 12 CYS Chi-restraints excluded: chain T residue 49 VAL Chi-restraints excluded: chain T residue 69 GLU Chi-restraints excluded: chain T residue 84 ILE Chi-restraints excluded: chain T residue 143 THR Chi-restraints excluded: chain T residue 395 LEU Chi-restraints excluded: chain T residue 415 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 885 random chunks: chunk 527 optimal weight: 3.9990 chunk 340 optimal weight: 0.8980 chunk 509 optimal weight: 0.5980 chunk 256 optimal weight: 5.9990 chunk 167 optimal weight: 5.9990 chunk 165 optimal weight: 4.9990 chunk 542 optimal weight: 1.9990 chunk 581 optimal weight: 6.9990 chunk 421 optimal weight: 3.9990 chunk 79 optimal weight: 3.9990 chunk 670 optimal weight: 6.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 235 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** ** 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 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 492 ASN b 195 ASN e 72 ASN e 122 GLN ** 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 130 GLN ** q 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 37 HIS T 52 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7451 moved from start: 0.2346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 69953 Z= 0.271 Angle : 0.589 11.641 94470 Z= 0.291 Chirality : 0.043 0.238 11206 Planarity : 0.004 0.045 12067 Dihedral : 7.518 169.025 9741 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.46 % Favored : 96.51 % Rotamer: Outliers : 3.78 % Allowed : 20.09 % Favored : 76.13 % 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: 0.39 (0.09), residues: 8920 helix: 1.15 (0.08), residues: 4580 sheet: -0.37 (0.14), residues: 1229 loop : -0.71 (0.11), residues: 3111 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP N 101 HIS 0.012 0.001 HIS G 111 PHE 0.027 0.002 PHE a 167 TYR 0.021 0.001 TYR Q 505 ARG 0.008 0.000 ARG a 370 *********************** 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 1216 residues out of total 7485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 282 poor density : 934 time to evaluate : 6.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 PHE cc_start: 0.7687 (t80) cc_final: 0.7333 (t80) REVERT: A 51 ASP cc_start: 0.6228 (t0) cc_final: 0.5988 (t70) REVERT: A 66 GLU cc_start: 0.7544 (mp0) cc_final: 0.7322 (mp0) REVERT: A 123 LEU cc_start: 0.8180 (OUTLIER) cc_final: 0.7753 (tp) REVERT: A 230 VAL cc_start: 0.7239 (OUTLIER) cc_final: 0.6934 (t) REVERT: A 321 LYS cc_start: 0.7847 (mtmt) cc_final: 0.7530 (tptt) REVERT: A 328 LEU cc_start: 0.7594 (OUTLIER) cc_final: 0.7166 (mm) REVERT: A 354 GLU cc_start: 0.6513 (mm-30) cc_final: 0.5831 (tp30) REVERT: A 355 ARG cc_start: 0.7650 (ttt90) cc_final: 0.7375 (ttt-90) REVERT: A 384 MET cc_start: 0.8098 (ttt) cc_final: 0.7847 (ttt) REVERT: A 430 MET cc_start: 0.5722 (mmm) cc_final: 0.5140 (mmm) REVERT: A 459 ASP cc_start: 0.8305 (t0) cc_final: 0.7992 (t0) REVERT: B 87 MET cc_start: 0.7845 (ttp) cc_final: 0.7413 (ttp) REVERT: B 132 GLU cc_start: 0.7487 (OUTLIER) cc_final: 0.7155 (mp0) REVERT: B 248 LYS cc_start: 0.7917 (mtpt) cc_final: 0.7599 (mtmt) REVERT: B 301 GLU cc_start: 0.7558 (tt0) cc_final: 0.7117 (tt0) REVERT: B 347 LYS cc_start: 0.8296 (mmtm) cc_final: 0.7744 (mppt) REVERT: B 402 LYS cc_start: 0.7638 (mtmm) cc_final: 0.6994 (mptp) REVERT: B 405 ARG cc_start: 0.7559 (OUTLIER) cc_final: 0.7109 (mtt180) REVERT: B 414 GLU cc_start: 0.6594 (mp0) cc_final: 0.6087 (mp0) REVERT: B 456 TYR cc_start: 0.8684 (m-80) cc_final: 0.8231 (m-10) REVERT: B 496 SER cc_start: 0.8725 (OUTLIER) cc_final: 0.8493 (m) REVERT: D 65 LYS cc_start: 0.8280 (mtmm) cc_final: 0.7981 (mtpt) REVERT: D 67 ASP cc_start: 0.7637 (m-30) cc_final: 0.7378 (m-30) REVERT: D 82 GLN cc_start: 0.8280 (OUTLIER) cc_final: 0.7698 (mm-40) REVERT: D 222 GLU cc_start: 0.7411 (tt0) cc_final: 0.6749 (mt-10) REVERT: D 224 VAL cc_start: 0.8117 (t) cc_final: 0.7816 (m) REVERT: D 257 LYS cc_start: 0.7738 (mmtm) cc_final: 0.7326 (ttpp) REVERT: D 291 LYS cc_start: 0.7841 (OUTLIER) cc_final: 0.7580 (tttp) REVERT: D 326 LYS cc_start: 0.8574 (pttt) cc_final: 0.8260 (ptmt) REVERT: D 384 LYS cc_start: 0.7675 (mptt) cc_final: 0.7423 (mptm) REVERT: D 458 MET cc_start: 0.8236 (mmm) cc_final: 0.7926 (mpp) REVERT: D 459 GLU cc_start: 0.6646 (mt-10) cc_final: 0.6364 (tp30) REVERT: E 20 LYS cc_start: 0.7960 (tttp) cc_final: 0.7734 (ttpt) REVERT: E 21 ASP cc_start: 0.7535 (t0) cc_final: 0.7333 (t0) REVERT: E 48 MET cc_start: 0.8439 (tpt) cc_final: 0.8192 (mmm) REVERT: E 93 GLU cc_start: 0.6969 (mm-30) cc_final: 0.6577 (mm-30) REVERT: E 121 GLU cc_start: 0.7108 (tt0) cc_final: 0.6684 (tt0) REVERT: E 125 ASP cc_start: 0.7871 (m-30) cc_final: 0.7597 (m-30) REVERT: E 188 ILE cc_start: 0.8399 (OUTLIER) cc_final: 0.8147 (mt) REVERT: E 198 ASP cc_start: 0.7630 (OUTLIER) cc_final: 0.7299 (t70) REVERT: E 245 ASP cc_start: 0.7546 (OUTLIER) cc_final: 0.7311 (m-30) REVERT: E 263 LYS cc_start: 0.7808 (ttmt) cc_final: 0.7080 (tttt) REVERT: E 283 GLU cc_start: 0.7898 (mm-30) cc_final: 0.7655 (mt-10) REVERT: E 290 GLN cc_start: 0.7361 (tp-100) cc_final: 0.6971 (tm-30) REVERT: E 439 LYS cc_start: 0.7528 (mtmm) cc_final: 0.7291 (mptt) REVERT: E 446 TYR cc_start: 0.8162 (m-80) cc_final: 0.7604 (m-80) REVERT: E 502 LYS cc_start: 0.7400 (tttt) cc_final: 0.7152 (tttm) REVERT: G 15 LYS cc_start: 0.7413 (mmmt) cc_final: 0.6710 (mtmm) REVERT: G 17 GLU cc_start: 0.6634 (mp0) cc_final: 0.6155 (mp0) REVERT: G 54 MET cc_start: 0.8063 (OUTLIER) cc_final: 0.7571 (mtp) REVERT: G 71 GLN cc_start: 0.8331 (OUTLIER) cc_final: 0.8003 (tt0) REVERT: G 81 ILE cc_start: 0.8478 (OUTLIER) cc_final: 0.8190 (mp) REVERT: G 82 GLU cc_start: 0.7698 (mm-30) cc_final: 0.7426 (mm-30) REVERT: G 110 GLU cc_start: 0.7735 (tt0) cc_final: 0.7246 (tp30) REVERT: G 133 MET cc_start: 0.8105 (mtm) cc_final: 0.7825 (mtm) REVERT: G 234 LYS cc_start: 0.7166 (tptp) cc_final: 0.6783 (tptt) REVERT: G 248 LYS cc_start: 0.8403 (mtpt) cc_final: 0.7626 (mmpt) REVERT: G 255 ASP cc_start: 0.6991 (OUTLIER) cc_final: 0.6749 (m-30) REVERT: G 270 MET cc_start: 0.7635 (mtp) cc_final: 0.7392 (mtp) REVERT: G 276 GLN cc_start: 0.7476 (tt0) cc_final: 0.7152 (tm-30) REVERT: G 277 GLN cc_start: 0.7565 (tp40) cc_final: 0.6889 (mp10) REVERT: G 429 MET cc_start: 0.7205 (mtm) cc_final: 0.6853 (mtm) REVERT: G 476 GLU cc_start: 0.7341 (OUTLIER) cc_final: 0.6993 (mt-10) REVERT: G 477 THR cc_start: 0.8564 (OUTLIER) cc_final: 0.8185 (t) REVERT: G 483 GLU cc_start: 0.6027 (OUTLIER) cc_final: 0.5192 (mp0) REVERT: G 511 GLU cc_start: 0.7544 (mm-30) cc_final: 0.7227 (mp0) REVERT: H 151 GLN cc_start: 0.7524 (OUTLIER) cc_final: 0.7305 (tt0) REVERT: H 172 LYS cc_start: 0.7804 (pttt) cc_final: 0.7505 (ptpt) REVERT: H 279 GLU cc_start: 0.7238 (tp30) cc_final: 0.6861 (mt-10) REVERT: H 317 GLU cc_start: 0.7511 (mp0) cc_final: 0.7285 (tt0) REVERT: H 344 ARG cc_start: 0.7773 (OUTLIER) cc_final: 0.7552 (mtp85) REVERT: H 356 GLU cc_start: 0.7529 (OUTLIER) cc_final: 0.7308 (mt-10) REVERT: H 368 LYS cc_start: 0.8120 (mttt) cc_final: 0.7598 (mmtm) REVERT: H 383 GLU cc_start: 0.7674 (mm-30) cc_final: 0.7347 (mm-30) REVERT: H 440 LYS cc_start: 0.7621 (mmtp) cc_final: 0.7325 (mtpt) REVERT: H 482 GLU cc_start: 0.7968 (mt-10) cc_final: 0.7714 (mt-10) REVERT: H 497 MET cc_start: 0.7338 (tpp) cc_final: 0.6795 (tpt) REVERT: Q 31 ARG cc_start: 0.7319 (mmp-170) cc_final: 0.6638 (mtt180) REVERT: Q 55 MET cc_start: 0.7764 (OUTLIER) cc_final: 0.7531 (mtt) REVERT: Q 193 ASP cc_start: 0.6989 (m-30) cc_final: 0.6686 (m-30) REVERT: Q 200 ASP cc_start: 0.8012 (m-30) cc_final: 0.7738 (m-30) REVERT: Q 249 MET cc_start: 0.7419 (ptp) cc_final: 0.6928 (mmm) REVERT: Q 281 LYS cc_start: 0.7700 (ttmt) cc_final: 0.7413 (tptp) REVERT: Q 296 LYS cc_start: 0.7864 (pttm) cc_final: 0.7425 (pttt) REVERT: Q 318 LYS cc_start: 0.8150 (pttm) cc_final: 0.7707 (ptmm) REVERT: Q 354 GLU cc_start: 0.7613 (tm-30) cc_final: 0.7321 (tm-30) REVERT: Q 434 GLU cc_start: 0.7065 (pt0) cc_final: 0.6642 (mm-30) REVERT: Q 481 ASP cc_start: 0.7645 (t0) cc_final: 0.7433 (t0) REVERT: Z 17 GLN cc_start: 0.7059 (OUTLIER) cc_final: 0.6215 (pp30) REVERT: Z 44 MET cc_start: 0.9142 (mmm) cc_final: 0.8783 (mmm) REVERT: Z 108 LEU cc_start: 0.7843 (tt) cc_final: 0.7541 (tp) REVERT: Z 163 GLU cc_start: 0.7020 (tp30) cc_final: 0.6408 (tp30) REVERT: Z 190 MET cc_start: 0.7941 (mmp) cc_final: 0.7704 (mmp) REVERT: Z 195 GLU cc_start: 0.7853 (pt0) cc_final: 0.7361 (pt0) REVERT: Z 223 LYS cc_start: 0.7802 (mptt) cc_final: 0.7420 (mmtt) REVERT: Z 241 LYS cc_start: 0.8517 (ttmt) cc_final: 0.7634 (pttp) REVERT: Z 264 ARG cc_start: 0.7397 (mtp85) cc_final: 0.7017 (mtp-110) REVERT: Z 272 LYS cc_start: 0.7434 (mmtp) cc_final: 0.6935 (mtpp) REVERT: Z 303 ASP cc_start: 0.7275 (t70) cc_final: 0.6481 (m-30) REVERT: Z 307 LYS cc_start: 0.7774 (mmtp) cc_final: 0.7499 (mtpt) REVERT: Z 322 GLU cc_start: 0.7485 (tt0) cc_final: 0.7140 (tt0) REVERT: Z 340 SER cc_start: 0.7479 (OUTLIER) cc_final: 0.7156 (p) REVERT: Z 487 MET cc_start: 0.6989 (OUTLIER) cc_final: 0.6464 (ppp) REVERT: Z 495 TRP cc_start: 0.8002 (m100) cc_final: 0.7443 (m100) REVERT: Z 496 ASP cc_start: 0.7516 (m-30) cc_final: 0.7222 (m-30) REVERT: a 1 MET cc_start: 0.4949 (OUTLIER) cc_final: 0.4709 (ptt) REVERT: a 23 MET cc_start: 0.5781 (OUTLIER) cc_final: 0.5427 (ttp) REVERT: a 265 GLN cc_start: 0.7139 (pt0) cc_final: 0.6837 (tp40) REVERT: a 361 LEU cc_start: 0.8708 (OUTLIER) cc_final: 0.8423 (pt) REVERT: a 384 MET cc_start: 0.7954 (ttt) cc_final: 0.7696 (ttt) REVERT: b 93 ASP cc_start: 0.7283 (m-30) cc_final: 0.6552 (m-30) REVERT: b 223 LYS cc_start: 0.8362 (mttm) cc_final: 0.7974 (mtpt) REVERT: b 236 LYS cc_start: 0.7964 (OUTLIER) cc_final: 0.7581 (mtmm) REVERT: b 316 ASP cc_start: 0.7188 (t0) cc_final: 0.6827 (m-30) REVERT: b 321 GLU cc_start: 0.6865 (mt-10) cc_final: 0.6603 (tt0) REVERT: b 387 GLU cc_start: 0.7348 (OUTLIER) cc_final: 0.7124 (tt0) REVERT: b 445 MET cc_start: 0.7959 (tpp) cc_final: 0.7753 (tpp) REVERT: b 516 ARG cc_start: 0.7628 (mtp85) cc_final: 0.7201 (mtp85) REVERT: b 522 LYS cc_start: 0.8088 (mttt) cc_final: 0.7235 (mppt) REVERT: d 42 LYS cc_start: 0.7219 (tttp) cc_final: 0.6435 (tptt) REVERT: d 46 ASP cc_start: 0.7930 (m-30) cc_final: 0.7542 (m-30) REVERT: d 60 MET cc_start: 0.8321 (ttp) cc_final: 0.7866 (ttp) REVERT: d 63 ASP cc_start: 0.7182 (m-30) cc_final: 0.6972 (m-30) REVERT: d 81 MET cc_start: 0.8334 (OUTLIER) cc_final: 0.8005 (ptt) REVERT: d 93 GLU cc_start: 0.7098 (mm-30) cc_final: 0.6688 (mm-30) REVERT: d 132 ILE cc_start: 0.8248 (mt) cc_final: 0.7981 (mp) REVERT: d 334 GLU cc_start: 0.7540 (tp30) cc_final: 0.7188 (tp30) REVERT: d 384 LYS cc_start: 0.7449 (mmtp) cc_final: 0.6985 (mmpt) REVERT: d 489 LYS cc_start: 0.7378 (ptmt) cc_final: 0.6839 (pttt) REVERT: d 497 LYS cc_start: 0.7824 (mtpp) cc_final: 0.7137 (mttm) REVERT: e 27 ARG cc_start: 0.8028 (ttp-170) cc_final: 0.7359 (ttt180) REVERT: e 29 MET cc_start: 0.8001 (mtp) cc_final: 0.7384 (mtp) REVERT: e 58 ASP cc_start: 0.7258 (m-30) cc_final: 0.6962 (m-30) REVERT: e 93 GLU cc_start: 0.7063 (mm-30) cc_final: 0.6652 (mt-10) REVERT: e 96 LYS cc_start: 0.7737 (tttm) cc_final: 0.7058 (ttmt) REVERT: e 121 GLU cc_start: 0.6947 (tt0) cc_final: 0.6601 (tt0) REVERT: e 122 GLN cc_start: 0.7190 (OUTLIER) cc_final: 0.6672 (mp10) REVERT: e 126 ARG cc_start: 0.7296 (mtm180) cc_final: 0.6738 (mtp85) REVERT: e 146 GLU cc_start: 0.7002 (mt-10) cc_final: 0.6725 (mt-10) REVERT: e 150 LYS cc_start: 0.7675 (ttmt) cc_final: 0.7267 (ttpt) REVERT: e 360 GLN cc_start: 0.7962 (tt0) cc_final: 0.7381 (tp40) REVERT: e 464 GLU cc_start: 0.6735 (tt0) cc_final: 0.6159 (mm-30) REVERT: e 474 MET cc_start: 0.8136 (tmm) cc_final: 0.7905 (tmm) REVERT: e 478 ARG cc_start: 0.7313 (ttp-170) cc_final: 0.7056 (ttm170) REVERT: e 502 LYS cc_start: 0.6998 (tttm) cc_final: 0.6626 (ttmp) REVERT: e 515 GLN cc_start: 0.7685 (tp-100) cc_final: 0.7238 (tp40) REVERT: e 532 ASP cc_start: 0.8333 (t0) cc_final: 0.8057 (t0) REVERT: g 110 GLU cc_start: 0.8229 (OUTLIER) cc_final: 0.7311 (tt0) REVERT: g 192 GLU cc_start: 0.6879 (tt0) cc_final: 0.6187 (pp20) REVERT: g 202 GLU cc_start: 0.7106 (mm-30) cc_final: 0.6665 (mm-30) REVERT: g 274 TYR cc_start: 0.7993 (t80) cc_final: 0.7676 (t80) REVERT: g 277 GLN cc_start: 0.7062 (tp-100) cc_final: 0.6251 (pt0) REVERT: g 294 LYS cc_start: 0.8118 (mmtp) cc_final: 0.7760 (mmtp) REVERT: g 367 LYS cc_start: 0.8445 (OUTLIER) cc_final: 0.8062 (pptt) REVERT: g 381 LYS cc_start: 0.7853 (tppt) cc_final: 0.7411 (mptt) REVERT: g 415 GLU cc_start: 0.7275 (OUTLIER) cc_final: 0.6964 (mm-30) REVERT: g 476 GLU cc_start: 0.7100 (pm20) cc_final: 0.6736 (mm-30) REVERT: h 10 LYS cc_start: 0.8133 (ttmt) cc_final: 0.7425 (ttpt) REVERT: h 17 GLN cc_start: 0.8129 (tt0) cc_final: 0.7908 (tt0) REVERT: h 119 GLN cc_start: 0.7976 (mm-40) cc_final: 0.7586 (mm110) REVERT: h 149 VAL cc_start: 0.8351 (OUTLIER) cc_final: 0.8100 (t) REVERT: h 153 LYS cc_start: 0.7920 (mttm) cc_final: 0.7422 (mptt) REVERT: h 217 LYS cc_start: 0.8928 (ttpt) cc_final: 0.8627 (ttpt) REVERT: h 247 LYS cc_start: 0.8420 (pttp) cc_final: 0.8070 (ptpp) REVERT: h 276 ASP cc_start: 0.7342 (t0) cc_final: 0.7056 (m-30) REVERT: h 320 LYS cc_start: 0.7661 (mmtt) cc_final: 0.7441 (mtmm) REVERT: h 344 ARG cc_start: 0.7359 (ttm110) cc_final: 0.6597 (mtm-85) REVERT: h 350 GLU cc_start: 0.7990 (OUTLIER) cc_final: 0.7733 (tt0) REVERT: h 356 GLU cc_start: 0.7361 (OUTLIER) cc_final: 0.6917 (mt-10) REVERT: h 368 LYS cc_start: 0.7705 (mttt) cc_final: 0.7045 (mtpp) REVERT: h 379 GLU cc_start: 0.8100 (tm-30) cc_final: 0.7510 (tm-30) REVERT: h 383 GLU cc_start: 0.7471 (mm-30) cc_final: 0.7132 (mm-30) REVERT: h 440 LYS cc_start: 0.8221 (tptt) cc_final: 0.7809 (tppt) REVERT: h 517 ASP cc_start: 0.8666 (p0) cc_final: 0.8049 (p0) REVERT: n 83 ASN cc_start: 0.2619 (OUTLIER) cc_final: 0.1537 (m110) REVERT: q 3 LEU cc_start: 0.5425 (OUTLIER) cc_final: 0.4642 (tt) REVERT: q 17 GLU cc_start: 0.7438 (tt0) cc_final: 0.7156 (tm-30) REVERT: q 31 ARG cc_start: 0.7569 (mmp-170) cc_final: 0.6913 (mmt-90) REVERT: q 55 MET cc_start: 0.7789 (OUTLIER) cc_final: 0.7366 (mtt) REVERT: q 117 GLU cc_start: 0.7135 (tt0) cc_final: 0.6582 (mt-10) REVERT: q 175 ASN cc_start: 0.8696 (OUTLIER) cc_final: 0.8472 (p0) REVERT: q 212 ILE cc_start: 0.8012 (OUTLIER) cc_final: 0.7704 (mm) REVERT: q 238 LYS cc_start: 0.7523 (mmtp) cc_final: 0.6955 (mmtp) REVERT: q 277 ASP cc_start: 0.8542 (t70) cc_final: 0.8132 (t0) REVERT: q 312 LEU cc_start: 0.8488 (OUTLIER) cc_final: 0.8283 (mt) REVERT: q 319 TRP cc_start: 0.7149 (m100) cc_final: 0.6349 (m100) REVERT: q 406 LYS cc_start: 0.7618 (ptmt) cc_final: 0.6735 (mmtm) REVERT: q 483 GLU cc_start: 0.7279 (mp0) cc_final: 0.6952 (mm-30) REVERT: q 498 LEU cc_start: 0.9038 (OUTLIER) cc_final: 0.8727 (mt) REVERT: q 505 TYR cc_start: 0.8144 (t80) cc_final: 0.7718 (t80) REVERT: z 10 LYS cc_start: 0.8008 (mtmt) cc_final: 0.7398 (pmtt) REVERT: z 32 ASP cc_start: 0.7014 (t0) cc_final: 0.6550 (m-30) REVERT: z 36 THR cc_start: 0.8803 (OUTLIER) cc_final: 0.8474 (p) REVERT: z 180 LYS cc_start: 0.7861 (OUTLIER) cc_final: 0.7232 (tttm) REVERT: z 181 LYS cc_start: 0.6952 (mttt) cc_final: 0.6114 (mmmt) REVERT: z 190 MET cc_start: 0.8473 (mmt) cc_final: 0.8002 (mmp) REVERT: z 272 LYS cc_start: 0.7897 (mmtp) cc_final: 0.7626 (mtpp) REVERT: z 307 LYS cc_start: 0.7918 (mmtp) cc_final: 0.6735 (ttpt) REVERT: z 323 ARG cc_start: 0.8236 (OUTLIER) cc_final: 0.7366 (mtt-85) REVERT: z 359 LYS cc_start: 0.7789 (mttt) cc_final: 0.6953 (mtmm) REVERT: z 388 LYS cc_start: 0.7425 (OUTLIER) cc_final: 0.6777 (mtpt) REVERT: z 430 LYS cc_start: 0.8306 (tppt) cc_final: 0.7740 (mmmt) REVERT: z 487 MET cc_start: 0.7105 (OUTLIER) cc_final: 0.6005 (ppp) REVERT: z 492 VAL cc_start: 0.8178 (p) cc_final: 0.7545 (p) REVERT: T 39 ASP cc_start: 0.4975 (OUTLIER) cc_final: 0.4253 (m-30) REVERT: T 49 VAL cc_start: 0.8583 (OUTLIER) cc_final: 0.8368 (t) REVERT: T 69 GLU cc_start: 0.8003 (OUTLIER) cc_final: 0.7707 (pt0) REVERT: T 77 ARG cc_start: 0.7237 (mtt90) cc_final: 0.6950 (mtt90) REVERT: T 94 GLN cc_start: 0.6019 (mp10) cc_final: 0.5604 (mt0) REVERT: T 167 PHE cc_start: 0.8151 (m-80) cc_final: 0.7821 (m-80) REVERT: T 233 MET cc_start: 0.7269 (tpt) cc_final: 0.6967 (tpt) outliers start: 282 outliers final: 173 residues processed: 1147 average time/residue: 1.5306 time to fit residues: 2298.5058 Evaluate side-chains 1141 residues out of total 7485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 226 poor density : 915 time to evaluate : 6.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 119 SER Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 166 ASP Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 284 ASN Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 132 GLU Chi-restraints excluded: chain B residue 134 THR Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain B residue 310 MET Chi-restraints excluded: chain B residue 405 ARG Chi-restraints excluded: chain B residue 413 SER Chi-restraints excluded: chain B residue 416 LEU Chi-restraints excluded: chain B residue 434 VAL Chi-restraints excluded: chain B residue 437 GLU Chi-restraints excluded: chain B residue 460 ASP Chi-restraints excluded: chain B residue 496 SER Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 73 ASP Chi-restraints excluded: chain D residue 82 GLN Chi-restraints excluded: chain D residue 136 SER Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 158 SER Chi-restraints excluded: chain D residue 184 SER Chi-restraints excluded: chain D residue 186 MET Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 217 THR Chi-restraints excluded: chain D residue 268 ASP Chi-restraints excluded: chain D residue 273 ASP Chi-restraints excluded: chain D residue 291 LYS Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 404 SER Chi-restraints excluded: chain D residue 430 ILE Chi-restraints excluded: chain D residue 446 MET Chi-restraints excluded: chain D residue 447 GLU Chi-restraints excluded: chain E residue 31 LEU Chi-restraints excluded: chain E residue 188 ILE Chi-restraints excluded: chain E residue 198 ASP Chi-restraints excluded: chain E residue 229 ILE Chi-restraints excluded: chain E residue 245 ASP Chi-restraints excluded: chain E residue 269 THR Chi-restraints excluded: chain E residue 306 PHE Chi-restraints excluded: chain E residue 308 ASP Chi-restraints excluded: chain E residue 418 VAL Chi-restraints excluded: chain G residue 7 VAL Chi-restraints excluded: chain G residue 54 MET Chi-restraints excluded: chain G residue 71 GLN Chi-restraints excluded: chain G residue 81 ILE Chi-restraints excluded: chain G residue 83 ILE Chi-restraints excluded: chain G residue 96 THR Chi-restraints excluded: chain G residue 146 ILE Chi-restraints excluded: chain G residue 252 SER Chi-restraints excluded: chain G residue 255 ASP Chi-restraints excluded: chain G residue 265 THR Chi-restraints excluded: chain G residue 292 THR Chi-restraints excluded: chain G residue 332 VAL Chi-restraints excluded: chain G residue 373 THR Chi-restraints excluded: chain G residue 440 VAL Chi-restraints excluded: chain G residue 471 THR Chi-restraints excluded: chain G residue 476 GLU Chi-restraints excluded: chain G residue 477 THR Chi-restraints excluded: chain G residue 483 GLU Chi-restraints excluded: chain G residue 508 THR Chi-restraints excluded: chain H residue 120 ILE Chi-restraints excluded: chain H residue 142 THR Chi-restraints excluded: chain H residue 151 GLN Chi-restraints excluded: chain H residue 310 CYS Chi-restraints excluded: chain H residue 344 ARG Chi-restraints excluded: chain H residue 356 GLU Chi-restraints excluded: chain H residue 362 THR Chi-restraints excluded: chain H residue 388 SER Chi-restraints excluded: chain H residue 400 ILE Chi-restraints excluded: chain H residue 427 ILE Chi-restraints excluded: chain N residue 78 VAL Chi-restraints excluded: chain N residue 83 ASN Chi-restraints excluded: chain Q residue 55 MET Chi-restraints excluded: chain Q residue 105 LEU Chi-restraints excluded: chain Q residue 146 LEU Chi-restraints excluded: chain Q residue 182 LEU Chi-restraints excluded: chain Q residue 212 ILE Chi-restraints excluded: chain Q residue 366 GLU Chi-restraints excluded: chain Q residue 480 LEU Chi-restraints excluded: chain Q residue 486 VAL Chi-restraints excluded: chain Q residue 517 THR Chi-restraints excluded: chain Z residue 17 GLN Chi-restraints excluded: chain Z residue 107 ASP Chi-restraints excluded: chain Z residue 159 LYS Chi-restraints excluded: chain Z residue 246 SER Chi-restraints excluded: chain Z residue 340 SER Chi-restraints excluded: chain Z residue 373 THR Chi-restraints excluded: chain Z residue 380 ASN Chi-restraints excluded: chain Z residue 407 VAL Chi-restraints excluded: chain Z residue 408 VAL Chi-restraints excluded: chain Z residue 430 LYS Chi-restraints excluded: chain Z residue 479 VAL Chi-restraints excluded: chain Z residue 487 MET Chi-restraints excluded: chain Z residue 488 VAL Chi-restraints excluded: chain a residue 1 MET Chi-restraints excluded: chain a residue 23 MET Chi-restraints excluded: chain a residue 166 ASP Chi-restraints excluded: chain a residue 321 LYS Chi-restraints excluded: chain a residue 329 SER Chi-restraints excluded: chain a residue 361 LEU Chi-restraints excluded: chain a residue 367 THR Chi-restraints excluded: chain a residue 391 SER Chi-restraints excluded: chain a residue 508 ILE Chi-restraints excluded: chain b residue 51 ILE Chi-restraints excluded: chain b residue 66 ASP Chi-restraints excluded: chain b residue 134 THR Chi-restraints excluded: chain b residue 153 VAL Chi-restraints excluded: chain b residue 165 THR Chi-restraints excluded: chain b residue 182 LEU Chi-restraints excluded: chain b residue 214 LEU Chi-restraints excluded: chain b residue 236 LYS Chi-restraints excluded: chain b residue 333 SER Chi-restraints excluded: chain b residue 353 MET Chi-restraints excluded: chain b residue 371 CYS Chi-restraints excluded: chain b residue 387 GLU Chi-restraints excluded: chain d residue 67 ASP Chi-restraints excluded: chain d residue 71 THR Chi-restraints excluded: chain d residue 81 MET Chi-restraints excluded: chain d residue 115 SER Chi-restraints excluded: chain d residue 134 SER Chi-restraints excluded: chain d residue 136 SER Chi-restraints excluded: chain d residue 158 SER Chi-restraints excluded: chain d residue 168 THR Chi-restraints excluded: chain d residue 184 SER Chi-restraints excluded: chain d residue 233 VAL Chi-restraints excluded: chain d residue 239 THR Chi-restraints excluded: chain d residue 368 ASN Chi-restraints excluded: chain d residue 385 THR Chi-restraints excluded: chain d residue 394 ASN Chi-restraints excluded: chain d residue 395 LYS Chi-restraints excluded: chain d residue 404 SER Chi-restraints excluded: chain d residue 430 ILE Chi-restraints excluded: chain d residue 536 VAL Chi-restraints excluded: chain e residue 72 ASN Chi-restraints excluded: chain e residue 122 GLN Chi-restraints excluded: chain e residue 298 ASN Chi-restraints excluded: chain e residue 308 ASP Chi-restraints excluded: chain e residue 319 LEU Chi-restraints excluded: chain e residue 330 ILE Chi-restraints excluded: chain e residue 418 VAL Chi-restraints excluded: chain e residue 498 THR Chi-restraints excluded: chain g residue 17 GLU Chi-restraints excluded: chain g residue 39 THR Chi-restraints excluded: chain g residue 83 ILE Chi-restraints excluded: chain g residue 93 ASP Chi-restraints excluded: chain g residue 96 THR Chi-restraints excluded: chain g residue 110 GLU Chi-restraints excluded: chain g residue 161 THR Chi-restraints excluded: chain g residue 310 THR Chi-restraints excluded: chain g residue 367 LYS Chi-restraints excluded: chain g residue 397 VAL Chi-restraints excluded: chain g residue 415 GLU Chi-restraints excluded: chain g residue 432 VAL Chi-restraints excluded: chain g residue 440 VAL Chi-restraints excluded: chain g residue 460 ILE Chi-restraints excluded: chain g residue 471 THR Chi-restraints excluded: chain g residue 486 THR Chi-restraints excluded: chain h residue 32 ILE Chi-restraints excluded: chain h residue 38 THR Chi-restraints excluded: chain h residue 85 SER Chi-restraints excluded: chain h residue 149 VAL Chi-restraints excluded: chain h residue 200 VAL Chi-restraints excluded: chain h residue 211 VAL Chi-restraints excluded: chain h residue 221 SER Chi-restraints excluded: chain h residue 350 GLU Chi-restraints excluded: chain h residue 356 GLU Chi-restraints excluded: chain h residue 395 ILE Chi-restraints excluded: chain h residue 405 VAL Chi-restraints excluded: chain h residue 427 ILE Chi-restraints excluded: chain h residue 473 THR Chi-restraints excluded: chain n residue 12 VAL Chi-restraints excluded: chain n residue 83 ASN Chi-restraints excluded: chain q residue 3 LEU Chi-restraints excluded: chain q residue 43 THR Chi-restraints excluded: chain q residue 45 THR Chi-restraints excluded: chain q residue 55 MET Chi-restraints excluded: chain q residue 150 SER Chi-restraints excluded: chain q residue 170 SER Chi-restraints excluded: chain q residue 175 ASN Chi-restraints excluded: chain q residue 181 LYS Chi-restraints excluded: chain q residue 200 ASP Chi-restraints excluded: chain q residue 212 ILE Chi-restraints excluded: chain q residue 226 GLU Chi-restraints excluded: chain q residue 234 VAL Chi-restraints excluded: chain q residue 312 LEU Chi-restraints excluded: chain q residue 385 MET Chi-restraints excluded: chain q residue 480 LEU Chi-restraints excluded: chain q residue 498 LEU Chi-restraints excluded: chain z residue 4 VAL Chi-restraints excluded: chain z residue 36 THR Chi-restraints excluded: chain z residue 88 THR Chi-restraints excluded: chain z residue 149 ILE Chi-restraints excluded: chain z residue 179 ILE Chi-restraints excluded: chain z residue 180 LYS Chi-restraints excluded: chain z residue 246 SER Chi-restraints excluded: chain z residue 323 ARG Chi-restraints excluded: chain z residue 388 LYS Chi-restraints excluded: chain z residue 408 VAL Chi-restraints excluded: chain z residue 442 ASP Chi-restraints excluded: chain z residue 464 VAL Chi-restraints excluded: chain z residue 487 MET Chi-restraints excluded: chain z residue 488 VAL Chi-restraints excluded: chain T residue 12 CYS Chi-restraints excluded: chain T residue 39 ASP Chi-restraints excluded: chain T residue 49 VAL Chi-restraints excluded: chain T residue 69 GLU Chi-restraints excluded: chain T residue 84 ILE Chi-restraints excluded: chain T residue 143 THR Chi-restraints excluded: chain T residue 177 ASP Chi-restraints excluded: chain T residue 395 LEU Chi-restraints excluded: chain T residue 415 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 885 random chunks: chunk 775 optimal weight: 3.9990 chunk 817 optimal weight: 9.9990 chunk 745 optimal weight: 10.0000 chunk 794 optimal weight: 0.9990 chunk 816 optimal weight: 4.9990 chunk 478 optimal weight: 4.9990 chunk 346 optimal weight: 0.6980 chunk 624 optimal weight: 0.9980 chunk 243 optimal weight: 5.9990 chunk 718 optimal weight: 0.9990 chunk 751 optimal weight: 2.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 350 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** G 235 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** ** H 331 GLN ** 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 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 492 ASN ** b 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 195 ASN e 72 ASN e 122 GLN g 157 ASN ** g 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 107 GLN h 130 GLN h 470 GLN ** q 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 52 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7448 moved from start: 0.2361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.128 69953 Z= 0.251 Angle : 0.688 59.190 94470 Z= 0.366 Chirality : 0.042 0.257 11206 Planarity : 0.004 0.081 12067 Dihedral : 7.512 168.942 9741 Min Nonbonded Distance : 1.694 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.48 % Favored : 96.50 % Rotamer: Outliers : 3.49 % Allowed : 20.66 % Favored : 75.85 % Cbeta Deviations : 0.01 % 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: 0.41 (0.09), residues: 8920 helix: 1.17 (0.08), residues: 4578 sheet: -0.37 (0.14), residues: 1229 loop : -0.70 (0.11), residues: 3113 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP N 101 HIS 0.011 0.001 HIS Z 161 PHE 0.025 0.001 PHE a 167 TYR 0.018 0.001 TYR Q 505 ARG 0.008 0.000 ARG Q 322 *********************** 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 1181 residues out of total 7485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 260 poor density : 921 time to evaluate : 6.245 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 PHE cc_start: 0.7684 (t80) cc_final: 0.7333 (t80) REVERT: A 51 ASP cc_start: 0.6224 (t0) cc_final: 0.5982 (t70) REVERT: A 66 GLU cc_start: 0.7544 (mp0) cc_final: 0.7310 (mp0) REVERT: A 123 LEU cc_start: 0.8071 (OUTLIER) cc_final: 0.7643 (tp) REVERT: A 230 VAL cc_start: 0.7236 (OUTLIER) cc_final: 0.6931 (t) REVERT: A 321 LYS cc_start: 0.7843 (mtmt) cc_final: 0.7528 (tptt) REVERT: A 328 LEU cc_start: 0.7592 (OUTLIER) cc_final: 0.7133 (mm) REVERT: A 354 GLU cc_start: 0.6508 (mm-30) cc_final: 0.5828 (tp30) REVERT: A 355 ARG cc_start: 0.7646 (ttt90) cc_final: 0.7378 (ttt-90) REVERT: A 384 MET cc_start: 0.8087 (ttt) cc_final: 0.7844 (ttt) REVERT: A 430 MET cc_start: 0.5720 (mmm) cc_final: 0.5140 (mmm) REVERT: A 459 ASP cc_start: 0.8304 (t0) cc_final: 0.7989 (t0) REVERT: B 87 MET cc_start: 0.7842 (ttp) cc_final: 0.7409 (ttp) REVERT: B 132 GLU cc_start: 0.7487 (OUTLIER) cc_final: 0.7152 (mp0) REVERT: B 248 LYS cc_start: 0.7919 (mtpt) cc_final: 0.7599 (mtmt) REVERT: B 301 GLU cc_start: 0.7557 (tt0) cc_final: 0.7113 (tt0) REVERT: B 347 LYS cc_start: 0.8296 (mmtm) cc_final: 0.7743 (mppt) REVERT: B 402 LYS cc_start: 0.7634 (mtmm) cc_final: 0.6992 (mptp) REVERT: B 405 ARG cc_start: 0.7558 (OUTLIER) cc_final: 0.7106 (mtt180) REVERT: B 414 GLU cc_start: 0.6583 (mp0) cc_final: 0.6079 (mp0) REVERT: B 456 TYR cc_start: 0.8685 (m-80) cc_final: 0.8235 (m-10) REVERT: B 496 SER cc_start: 0.8722 (OUTLIER) cc_final: 0.8490 (m) REVERT: D 65 LYS cc_start: 0.8279 (mtmm) cc_final: 0.7982 (mtpt) REVERT: D 67 ASP cc_start: 0.7638 (m-30) cc_final: 0.7375 (m-30) REVERT: D 82 GLN cc_start: 0.8282 (OUTLIER) cc_final: 0.7693 (mm-40) REVERT: D 222 GLU cc_start: 0.7407 (tt0) cc_final: 0.6746 (mt-10) REVERT: D 224 VAL cc_start: 0.8115 (t) cc_final: 0.7823 (m) REVERT: D 257 LYS cc_start: 0.7734 (mmtm) cc_final: 0.7324 (ttpp) REVERT: D 291 LYS cc_start: 0.7838 (OUTLIER) cc_final: 0.7573 (tttp) REVERT: D 326 LYS cc_start: 0.8573 (pttt) cc_final: 0.8258 (ptmt) REVERT: D 384 LYS cc_start: 0.7673 (mptt) cc_final: 0.7371 (mptm) REVERT: D 400 GLU cc_start: 0.7113 (OUTLIER) cc_final: 0.6640 (mm-30) REVERT: D 458 MET cc_start: 0.8232 (mmm) cc_final: 0.7924 (mpp) REVERT: D 459 GLU cc_start: 0.6641 (mt-10) cc_final: 0.6358 (tp30) REVERT: E 20 LYS cc_start: 0.7957 (tttp) cc_final: 0.7734 (ttpt) REVERT: E 48 MET cc_start: 0.8433 (tpt) cc_final: 0.8131 (mmm) REVERT: E 93 GLU cc_start: 0.6962 (mm-30) cc_final: 0.6558 (mm-30) REVERT: E 121 GLU cc_start: 0.7103 (tt0) cc_final: 0.6679 (tt0) REVERT: E 125 ASP cc_start: 0.7867 (m-30) cc_final: 0.7594 (m-30) REVERT: E 188 ILE cc_start: 0.8396 (OUTLIER) cc_final: 0.8145 (mt) REVERT: E 198 ASP cc_start: 0.7626 (OUTLIER) cc_final: 0.7296 (t70) REVERT: E 263 LYS cc_start: 0.7807 (ttmt) cc_final: 0.7077 (tttt) REVERT: E 283 GLU cc_start: 0.7895 (mm-30) cc_final: 0.7648 (mt-10) REVERT: E 290 GLN cc_start: 0.7359 (tp-100) cc_final: 0.6968 (tm-30) REVERT: E 439 LYS cc_start: 0.7525 (mtmm) cc_final: 0.7290 (mptt) REVERT: E 446 TYR cc_start: 0.8159 (m-80) cc_final: 0.7605 (m-80) REVERT: E 502 LYS cc_start: 0.7415 (tttt) cc_final: 0.7150 (tttm) REVERT: G 15 LYS cc_start: 0.7404 (mmmt) cc_final: 0.6714 (mtmm) REVERT: G 17 GLU cc_start: 0.6629 (mp0) cc_final: 0.6149 (mp0) REVERT: G 54 MET cc_start: 0.8061 (OUTLIER) cc_final: 0.7568 (mtp) REVERT: G 71 GLN cc_start: 0.8329 (OUTLIER) cc_final: 0.7999 (tt0) REVERT: G 81 ILE cc_start: 0.8474 (OUTLIER) cc_final: 0.8187 (mp) REVERT: G 82 GLU cc_start: 0.7695 (mm-30) cc_final: 0.7422 (mm-30) REVERT: G 110 GLU cc_start: 0.7728 (tt0) cc_final: 0.7239 (tp30) REVERT: G 133 MET cc_start: 0.8101 (mtm) cc_final: 0.7823 (mtm) REVERT: G 234 LYS cc_start: 0.7156 (tptp) cc_final: 0.6779 (tptt) REVERT: G 248 LYS cc_start: 0.8394 (mtpt) cc_final: 0.7623 (mmpt) REVERT: G 255 ASP cc_start: 0.6986 (OUTLIER) cc_final: 0.6746 (m-30) REVERT: G 270 MET cc_start: 0.7631 (mtp) cc_final: 0.7412 (mtp) REVERT: G 276 GLN cc_start: 0.7469 (tt0) cc_final: 0.7150 (tm-30) REVERT: G 277 GLN cc_start: 0.7560 (tp40) cc_final: 0.6887 (mp10) REVERT: G 429 MET cc_start: 0.7205 (mtm) cc_final: 0.6852 (mtm) REVERT: G 476 GLU cc_start: 0.7336 (OUTLIER) cc_final: 0.6990 (mt-10) REVERT: G 477 THR cc_start: 0.8562 (OUTLIER) cc_final: 0.8184 (t) REVERT: G 483 GLU cc_start: 0.6021 (OUTLIER) cc_final: 0.5189 (mp0) REVERT: G 511 GLU cc_start: 0.7538 (mm-30) cc_final: 0.7225 (mp0) REVERT: H 151 GLN cc_start: 0.7522 (OUTLIER) cc_final: 0.7302 (tt0) REVERT: H 172 LYS cc_start: 0.7797 (pttt) cc_final: 0.7503 (ptpt) REVERT: H 279 GLU cc_start: 0.7230 (tp30) cc_final: 0.6837 (mt-10) REVERT: H 317 GLU cc_start: 0.7510 (mp0) cc_final: 0.7281 (tt0) REVERT: H 349 GLU cc_start: 0.7913 (tt0) cc_final: 0.7648 (tt0) REVERT: H 356 GLU cc_start: 0.7524 (OUTLIER) cc_final: 0.7307 (mt-10) REVERT: H 368 LYS cc_start: 0.8120 (mttt) cc_final: 0.7596 (mmtm) REVERT: H 383 GLU cc_start: 0.7668 (mm-30) cc_final: 0.7350 (mm-30) REVERT: H 384 GLU cc_start: 0.7089 (OUTLIER) cc_final: 0.6625 (mm-30) REVERT: H 440 LYS cc_start: 0.7621 (mmtp) cc_final: 0.7324 (mtpt) REVERT: H 482 GLU cc_start: 0.7965 (mt-10) cc_final: 0.7711 (mt-10) REVERT: H 497 MET cc_start: 0.7335 (tpp) cc_final: 0.6793 (tpt) REVERT: Q 31 ARG cc_start: 0.7306 (mmp-170) cc_final: 0.6638 (mtt180) REVERT: Q 55 MET cc_start: 0.7768 (OUTLIER) cc_final: 0.7523 (mtt) REVERT: Q 113 GLU cc_start: 0.6373 (mt-10) cc_final: 0.6116 (mt-10) REVERT: Q 193 ASP cc_start: 0.6985 (m-30) cc_final: 0.6698 (m-30) REVERT: Q 200 ASP cc_start: 0.7998 (m-30) cc_final: 0.7736 (m-30) REVERT: Q 249 MET cc_start: 0.7418 (ptp) cc_final: 0.6926 (mmm) REVERT: Q 281 LYS cc_start: 0.7698 (ttmt) cc_final: 0.7411 (tptp) REVERT: Q 296 LYS cc_start: 0.7861 (pttm) cc_final: 0.7423 (pttt) REVERT: Q 318 LYS cc_start: 0.8143 (pttm) cc_final: 0.7704 (ptmm) REVERT: Q 354 GLU cc_start: 0.7610 (tm-30) cc_final: 0.7324 (tm-30) REVERT: Q 434 GLU cc_start: 0.7054 (pt0) cc_final: 0.6639 (mm-30) REVERT: Q 481 ASP cc_start: 0.7644 (t0) cc_final: 0.7422 (t0) REVERT: Z 17 GLN cc_start: 0.7054 (OUTLIER) cc_final: 0.6211 (pp30) REVERT: Z 44 MET cc_start: 0.9140 (mmm) cc_final: 0.8783 (mmm) REVERT: Z 108 LEU cc_start: 0.7841 (tt) cc_final: 0.7539 (tp) REVERT: Z 163 GLU cc_start: 0.7017 (tp30) cc_final: 0.6402 (tp30) REVERT: Z 195 GLU cc_start: 0.7870 (pt0) cc_final: 0.7359 (pt0) REVERT: Z 223 LYS cc_start: 0.7798 (mptt) cc_final: 0.7419 (mmtt) REVERT: Z 241 LYS cc_start: 0.8512 (ttmt) cc_final: 0.7632 (pttp) REVERT: Z 264 ARG cc_start: 0.7395 (mtp85) cc_final: 0.7016 (mtp-110) REVERT: Z 272 LYS cc_start: 0.7433 (mmtp) cc_final: 0.6932 (mtpp) REVERT: Z 303 ASP cc_start: 0.7264 (t70) cc_final: 0.6480 (m-30) REVERT: Z 307 LYS cc_start: 0.7776 (mmtp) cc_final: 0.7497 (mtpt) REVERT: Z 322 GLU cc_start: 0.7479 (tt0) cc_final: 0.7135 (tt0) REVERT: Z 340 SER cc_start: 0.7415 (OUTLIER) cc_final: 0.7089 (p) REVERT: Z 487 MET cc_start: 0.6987 (OUTLIER) cc_final: 0.6462 (ppp) REVERT: Z 495 TRP cc_start: 0.8000 (m100) cc_final: 0.7441 (m100) REVERT: Z 496 ASP cc_start: 0.7511 (m-30) cc_final: 0.7212 (m-30) REVERT: a 1 MET cc_start: 0.4948 (OUTLIER) cc_final: 0.4709 (ptt) REVERT: a 23 MET cc_start: 0.5779 (OUTLIER) cc_final: 0.5422 (ttp) REVERT: a 265 GLN cc_start: 0.7140 (pt0) cc_final: 0.6837 (tp40) REVERT: a 354 GLU cc_start: 0.7144 (OUTLIER) cc_final: 0.6788 (tt0) REVERT: a 361 LEU cc_start: 0.8705 (OUTLIER) cc_final: 0.8420 (pt) REVERT: a 384 MET cc_start: 0.7951 (ttt) cc_final: 0.7692 (ttt) REVERT: a 481 LYS cc_start: 0.7482 (OUTLIER) cc_final: 0.7150 (mttt) REVERT: b 93 ASP cc_start: 0.7279 (m-30) cc_final: 0.6546 (m-30) REVERT: b 223 LYS cc_start: 0.8360 (mttm) cc_final: 0.7973 (mtpt) REVERT: b 236 LYS cc_start: 0.7962 (OUTLIER) cc_final: 0.7579 (mtmm) REVERT: b 316 ASP cc_start: 0.7180 (t0) cc_final: 0.6823 (m-30) REVERT: b 321 GLU cc_start: 0.6858 (mt-10) cc_final: 0.6598 (tt0) REVERT: b 387 GLU cc_start: 0.7345 (OUTLIER) cc_final: 0.7120 (tt0) REVERT: b 445 MET cc_start: 0.7959 (tpp) cc_final: 0.7754 (tpp) REVERT: b 516 ARG cc_start: 0.7628 (mtp85) cc_final: 0.7375 (mtp180) REVERT: b 522 LYS cc_start: 0.8084 (mttt) cc_final: 0.7232 (mppt) REVERT: d 42 LYS cc_start: 0.7221 (tttp) cc_final: 0.6434 (tptt) REVERT: d 46 ASP cc_start: 0.7929 (m-30) cc_final: 0.7539 (m-30) REVERT: d 60 MET cc_start: 0.8319 (ttp) cc_final: 0.7864 (ttp) REVERT: d 63 ASP cc_start: 0.7183 (m-30) cc_final: 0.6970 (m-30) REVERT: d 81 MET cc_start: 0.8335 (OUTLIER) cc_final: 0.8000 (ptt) REVERT: d 93 GLU cc_start: 0.7092 (mm-30) cc_final: 0.6685 (mm-30) REVERT: d 132 ILE cc_start: 0.8245 (mt) cc_final: 0.7979 (mp) REVERT: d 334 GLU cc_start: 0.7535 (tp30) cc_final: 0.7184 (tp30) REVERT: d 384 LYS cc_start: 0.7447 (mmtp) cc_final: 0.6982 (mmpt) REVERT: d 489 LYS cc_start: 0.7375 (ptmt) cc_final: 0.6837 (pttt) REVERT: d 497 LYS cc_start: 0.7818 (mtpp) cc_final: 0.7132 (mttm) REVERT: e 27 ARG cc_start: 0.8027 (ttp-170) cc_final: 0.7358 (ttt180) REVERT: e 29 MET cc_start: 0.7997 (mtp) cc_final: 0.7383 (mtp) REVERT: e 93 GLU cc_start: 0.7057 (mm-30) cc_final: 0.6647 (mt-10) REVERT: e 96 LYS cc_start: 0.7732 (tttm) cc_final: 0.7056 (ttmt) REVERT: e 121 GLU cc_start: 0.7000 (tt0) cc_final: 0.6719 (tt0) REVERT: e 126 ARG cc_start: 0.7286 (mtm180) cc_final: 0.6726 (mtp85) REVERT: e 146 GLU cc_start: 0.6997 (mt-10) cc_final: 0.6723 (mt-10) REVERT: e 150 LYS cc_start: 0.7673 (ttmt) cc_final: 0.7265 (ttpt) REVERT: e 360 GLN cc_start: 0.7958 (tt0) cc_final: 0.7380 (tp40) REVERT: e 464 GLU cc_start: 0.6728 (tt0) cc_final: 0.6157 (mm-30) REVERT: e 478 ARG cc_start: 0.7308 (ttp-170) cc_final: 0.6969 (ttm170) REVERT: e 502 LYS cc_start: 0.6994 (tttm) cc_final: 0.6609 (ttmp) REVERT: e 515 GLN cc_start: 0.7684 (tp-100) cc_final: 0.7237 (tp40) REVERT: e 532 ASP cc_start: 0.8329 (t0) cc_final: 0.8056 (t0) REVERT: g 50 LEU cc_start: 0.8359 (OUTLIER) cc_final: 0.8098 (mt) REVERT: g 110 GLU cc_start: 0.8216 (OUTLIER) cc_final: 0.7312 (tt0) REVERT: g 192 GLU cc_start: 0.6873 (tt0) cc_final: 0.6188 (pp20) REVERT: g 202 GLU cc_start: 0.7101 (mm-30) cc_final: 0.6659 (mm-30) REVERT: g 274 TYR cc_start: 0.7989 (t80) cc_final: 0.7678 (t80) REVERT: g 277 GLN cc_start: 0.7061 (tp-100) cc_final: 0.6248 (pt0) REVERT: g 294 LYS cc_start: 0.8116 (mmtp) cc_final: 0.7758 (mmtp) REVERT: g 367 LYS cc_start: 0.8443 (OUTLIER) cc_final: 0.8061 (pptt) REVERT: g 381 LYS cc_start: 0.7851 (tppt) cc_final: 0.7412 (mptt) REVERT: g 415 GLU cc_start: 0.7275 (OUTLIER) cc_final: 0.6959 (mm-30) REVERT: g 476 GLU cc_start: 0.7098 (pm20) cc_final: 0.6730 (mm-30) REVERT: h 10 LYS cc_start: 0.8126 (ttmt) cc_final: 0.7424 (ttpt) REVERT: h 17 GLN cc_start: 0.8124 (tt0) cc_final: 0.7898 (tt0) REVERT: h 119 GLN cc_start: 0.7975 (mm-40) cc_final: 0.7583 (mm110) REVERT: h 149 VAL cc_start: 0.8349 (OUTLIER) cc_final: 0.8098 (t) REVERT: h 153 LYS cc_start: 0.7918 (mttm) cc_final: 0.7420 (mptt) REVERT: h 217 LYS cc_start: 0.8927 (ttpt) cc_final: 0.8626 (ttpt) REVERT: h 247 LYS cc_start: 0.8419 (pttp) cc_final: 0.8070 (ptpp) REVERT: h 276 ASP cc_start: 0.7339 (t0) cc_final: 0.7054 (m-30) REVERT: h 320 LYS cc_start: 0.7659 (mmtt) cc_final: 0.7438 (mtmm) REVERT: h 344 ARG cc_start: 0.7363 (ttm110) cc_final: 0.6605 (mtm-85) REVERT: h 350 GLU cc_start: 0.7989 (OUTLIER) cc_final: 0.7732 (tt0) REVERT: h 356 GLU cc_start: 0.7357 (OUTLIER) cc_final: 0.6915 (mt-10) REVERT: h 368 LYS cc_start: 0.7699 (mttt) cc_final: 0.7043 (mtpp) REVERT: h 379 GLU cc_start: 0.8098 (tm-30) cc_final: 0.7505 (tm-30) REVERT: h 383 GLU cc_start: 0.7464 (mm-30) cc_final: 0.7126 (mm-30) REVERT: h 440 LYS cc_start: 0.8215 (tptt) cc_final: 0.7807 (tppt) REVERT: h 517 ASP cc_start: 0.8666 (p0) cc_final: 0.8046 (p0) REVERT: n 83 ASN cc_start: 0.2618 (OUTLIER) cc_final: 0.1536 (m110) REVERT: q 3 LEU cc_start: 0.5356 (OUTLIER) cc_final: 0.4636 (tt) REVERT: q 17 GLU cc_start: 0.7437 (tt0) cc_final: 0.7154 (tm-30) REVERT: q 31 ARG cc_start: 0.7566 (mmp-170) cc_final: 0.6910 (mmt-90) REVERT: q 55 MET cc_start: 0.7784 (OUTLIER) cc_final: 0.7353 (mtt) REVERT: q 117 GLU cc_start: 0.7125 (tt0) cc_final: 0.6577 (mt-10) REVERT: q 175 ASN cc_start: 0.8695 (OUTLIER) cc_final: 0.8470 (p0) REVERT: q 212 ILE cc_start: 0.8014 (OUTLIER) cc_final: 0.7711 (mm) REVERT: q 238 LYS cc_start: 0.7458 (mmtp) cc_final: 0.7002 (mmtp) REVERT: q 277 ASP cc_start: 0.8537 (t70) cc_final: 0.8126 (t0) REVERT: q 312 LEU cc_start: 0.8485 (OUTLIER) cc_final: 0.8278 (mt) REVERT: q 319 TRP cc_start: 0.7147 (m100) cc_final: 0.6349 (m100) REVERT: q 406 LYS cc_start: 0.7613 (ptmt) cc_final: 0.6732 (mmtm) REVERT: q 483 GLU cc_start: 0.7277 (mp0) cc_final: 0.6951 (mm-30) REVERT: q 498 LEU cc_start: 0.9037 (OUTLIER) cc_final: 0.8724 (mt) REVERT: q 505 TYR cc_start: 0.8143 (t80) cc_final: 0.7712 (t80) REVERT: z 10 LYS cc_start: 0.8017 (mtmt) cc_final: 0.7399 (pmtt) REVERT: z 32 ASP cc_start: 0.7012 (t0) cc_final: 0.6546 (m-30) REVERT: z 36 THR cc_start: 0.8801 (OUTLIER) cc_final: 0.8470 (p) REVERT: z 180 LYS cc_start: 0.7859 (OUTLIER) cc_final: 0.7234 (tttm) REVERT: z 181 LYS cc_start: 0.6950 (mttt) cc_final: 0.6110 (mmmt) REVERT: z 190 MET cc_start: 0.8471 (mmt) cc_final: 0.7987 (mmp) REVERT: z 192 GLU cc_start: 0.7633 (tp30) cc_final: 0.7360 (tp30) REVERT: z 272 LYS cc_start: 0.7894 (mmtp) cc_final: 0.7624 (mtpp) REVERT: z 307 LYS cc_start: 0.7915 (mmtp) cc_final: 0.6734 (ttpt) REVERT: z 323 ARG cc_start: 0.8233 (OUTLIER) cc_final: 0.7462 (mtt-85) REVERT: z 359 LYS cc_start: 0.7786 (mttt) cc_final: 0.6956 (mtmm) REVERT: z 430 LYS cc_start: 0.8284 (tppt) cc_final: 0.7737 (mmmt) REVERT: z 487 MET cc_start: 0.7099 (OUTLIER) cc_final: 0.6018 (ppp) REVERT: z 492 VAL cc_start: 0.8172 (p) cc_final: 0.7535 (p) REVERT: T 39 ASP cc_start: 0.4970 (OUTLIER) cc_final: 0.4254 (m-30) REVERT: T 49 VAL cc_start: 0.8575 (OUTLIER) cc_final: 0.8366 (t) REVERT: T 69 GLU cc_start: 0.7993 (OUTLIER) cc_final: 0.7694 (pt0) REVERT: T 77 ARG cc_start: 0.7243 (mtt90) cc_final: 0.6943 (mtt90) REVERT: T 94 GLN cc_start: 0.6016 (mp10) cc_final: 0.5604 (mt0) REVERT: T 167 PHE cc_start: 0.8149 (m-80) cc_final: 0.7813 (m-80) REVERT: T 233 MET cc_start: 0.7273 (tpt) cc_final: 0.6961 (tpt) outliers start: 260 outliers final: 179 residues processed: 1120 average time/residue: 1.5408 time to fit residues: 2267.0927 Evaluate side-chains 1148 residues out of total 7485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 233 poor density : 915 time to evaluate : 6.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 119 SER Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 166 ASP Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 284 ASN Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 132 GLU Chi-restraints excluded: chain B residue 134 THR Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain B residue 310 MET Chi-restraints excluded: chain B residue 405 ARG Chi-restraints excluded: chain B residue 413 SER Chi-restraints excluded: chain B residue 416 LEU Chi-restraints excluded: chain B residue 437 GLU Chi-restraints excluded: chain B residue 460 ASP Chi-restraints excluded: chain B residue 496 SER Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 73 ASP Chi-restraints excluded: chain D residue 82 GLN Chi-restraints excluded: chain D residue 136 SER Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 158 SER Chi-restraints excluded: chain D residue 184 SER Chi-restraints excluded: chain D residue 186 MET Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 217 THR Chi-restraints excluded: chain D residue 268 ASP Chi-restraints excluded: chain D residue 273 ASP Chi-restraints excluded: chain D residue 291 LYS Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 400 GLU Chi-restraints excluded: chain D residue 404 SER Chi-restraints excluded: chain D residue 430 ILE Chi-restraints excluded: chain D residue 446 MET Chi-restraints excluded: chain D residue 447 GLU Chi-restraints excluded: chain D residue 536 VAL Chi-restraints excluded: chain E residue 31 LEU Chi-restraints excluded: chain E residue 188 ILE Chi-restraints excluded: chain E residue 198 ASP Chi-restraints excluded: chain E residue 229 ILE Chi-restraints excluded: chain E residue 245 ASP Chi-restraints excluded: chain E residue 269 THR Chi-restraints excluded: chain E residue 306 PHE Chi-restraints excluded: chain E residue 308 ASP Chi-restraints excluded: chain E residue 418 VAL Chi-restraints excluded: chain G residue 7 VAL Chi-restraints excluded: chain G residue 54 MET Chi-restraints excluded: chain G residue 71 GLN Chi-restraints excluded: chain G residue 81 ILE Chi-restraints excluded: chain G residue 83 ILE Chi-restraints excluded: chain G residue 96 THR Chi-restraints excluded: chain G residue 146 ILE Chi-restraints excluded: chain G residue 252 SER Chi-restraints excluded: chain G residue 255 ASP Chi-restraints excluded: chain G residue 265 THR Chi-restraints excluded: chain G residue 292 THR Chi-restraints excluded: chain G residue 332 VAL Chi-restraints excluded: chain G residue 373 THR Chi-restraints excluded: chain G residue 440 VAL Chi-restraints excluded: chain G residue 471 THR Chi-restraints excluded: chain G residue 476 GLU Chi-restraints excluded: chain G residue 477 THR Chi-restraints excluded: chain G residue 483 GLU Chi-restraints excluded: chain G residue 508 THR Chi-restraints excluded: chain H residue 120 ILE Chi-restraints excluded: chain H residue 142 THR Chi-restraints excluded: chain H residue 151 GLN Chi-restraints excluded: chain H residue 310 CYS Chi-restraints excluded: chain H residue 356 GLU Chi-restraints excluded: chain H residue 362 THR Chi-restraints excluded: chain H residue 384 GLU Chi-restraints excluded: chain H residue 388 SER Chi-restraints excluded: chain H residue 400 ILE Chi-restraints excluded: chain H residue 427 ILE Chi-restraints excluded: chain N residue 43 LYS Chi-restraints excluded: chain N residue 78 VAL Chi-restraints excluded: chain N residue 83 ASN Chi-restraints excluded: chain Q residue 55 MET Chi-restraints excluded: chain Q residue 105 LEU Chi-restraints excluded: chain Q residue 146 LEU Chi-restraints excluded: chain Q residue 182 LEU Chi-restraints excluded: chain Q residue 212 ILE Chi-restraints excluded: chain Q residue 316 ASN Chi-restraints excluded: chain Q residue 366 GLU Chi-restraints excluded: chain Q residue 480 LEU Chi-restraints excluded: chain Q residue 486 VAL Chi-restraints excluded: chain Q residue 517 THR Chi-restraints excluded: chain Z residue 17 GLN Chi-restraints excluded: chain Z residue 38 LEU Chi-restraints excluded: chain Z residue 107 ASP Chi-restraints excluded: chain Z residue 159 LYS Chi-restraints excluded: chain Z residue 246 SER Chi-restraints excluded: chain Z residue 340 SER Chi-restraints excluded: chain Z residue 373 THR Chi-restraints excluded: chain Z residue 380 ASN Chi-restraints excluded: chain Z residue 407 VAL Chi-restraints excluded: chain Z residue 408 VAL Chi-restraints excluded: chain Z residue 430 LYS Chi-restraints excluded: chain Z residue 479 VAL Chi-restraints excluded: chain Z residue 487 MET Chi-restraints excluded: chain Z residue 488 VAL Chi-restraints excluded: chain a residue 1 MET Chi-restraints excluded: chain a residue 23 MET Chi-restraints excluded: chain a residue 166 ASP Chi-restraints excluded: chain a residue 321 LYS Chi-restraints excluded: chain a residue 329 SER Chi-restraints excluded: chain a residue 354 GLU Chi-restraints excluded: chain a residue 361 LEU Chi-restraints excluded: chain a residue 367 THR Chi-restraints excluded: chain a residue 391 SER Chi-restraints excluded: chain a residue 481 LYS Chi-restraints excluded: chain a residue 508 ILE Chi-restraints excluded: chain a residue 528 ASP Chi-restraints excluded: chain b residue 51 ILE Chi-restraints excluded: chain b residue 66 ASP Chi-restraints excluded: chain b residue 134 THR Chi-restraints excluded: chain b residue 153 VAL Chi-restraints excluded: chain b residue 165 THR Chi-restraints excluded: chain b residue 182 LEU Chi-restraints excluded: chain b residue 214 LEU Chi-restraints excluded: chain b residue 236 LYS Chi-restraints excluded: chain b residue 333 SER Chi-restraints excluded: chain b residue 353 MET Chi-restraints excluded: chain b residue 371 CYS Chi-restraints excluded: chain b residue 387 GLU Chi-restraints excluded: chain d residue 67 ASP Chi-restraints excluded: chain d residue 71 THR Chi-restraints excluded: chain d residue 81 MET Chi-restraints excluded: chain d residue 115 SER Chi-restraints excluded: chain d residue 134 SER Chi-restraints excluded: chain d residue 136 SER Chi-restraints excluded: chain d residue 158 SER Chi-restraints excluded: chain d residue 168 THR Chi-restraints excluded: chain d residue 184 SER Chi-restraints excluded: chain d residue 233 VAL Chi-restraints excluded: chain d residue 239 THR Chi-restraints excluded: chain d residue 385 THR Chi-restraints excluded: chain d residue 394 ASN Chi-restraints excluded: chain d residue 395 LYS Chi-restraints excluded: chain d residue 404 SER Chi-restraints excluded: chain d residue 430 ILE Chi-restraints excluded: chain d residue 536 VAL Chi-restraints excluded: chain e residue 298 ASN Chi-restraints excluded: chain e residue 308 ASP Chi-restraints excluded: chain e residue 319 LEU Chi-restraints excluded: chain e residue 330 ILE Chi-restraints excluded: chain e residue 418 VAL Chi-restraints excluded: chain e residue 498 THR Chi-restraints excluded: chain g residue 17 GLU Chi-restraints excluded: chain g residue 39 THR Chi-restraints excluded: chain g residue 50 LEU Chi-restraints excluded: chain g residue 83 ILE Chi-restraints excluded: chain g residue 93 ASP Chi-restraints excluded: chain g residue 96 THR Chi-restraints excluded: chain g residue 110 GLU Chi-restraints excluded: chain g residue 161 THR Chi-restraints excluded: chain g residue 310 THR Chi-restraints excluded: chain g residue 367 LYS Chi-restraints excluded: chain g residue 397 VAL Chi-restraints excluded: chain g residue 403 LEU Chi-restraints excluded: chain g residue 415 GLU Chi-restraints excluded: chain g residue 432 VAL Chi-restraints excluded: chain g residue 440 VAL Chi-restraints excluded: chain g residue 460 ILE Chi-restraints excluded: chain g residue 471 THR Chi-restraints excluded: chain g residue 486 THR Chi-restraints excluded: chain h residue 32 ILE Chi-restraints excluded: chain h residue 38 THR Chi-restraints excluded: chain h residue 85 SER Chi-restraints excluded: chain h residue 149 VAL Chi-restraints excluded: chain h residue 200 VAL Chi-restraints excluded: chain h residue 211 VAL Chi-restraints excluded: chain h residue 221 SER Chi-restraints excluded: chain h residue 350 GLU Chi-restraints excluded: chain h residue 356 GLU Chi-restraints excluded: chain h residue 395 ILE Chi-restraints excluded: chain h residue 405 VAL Chi-restraints excluded: chain h residue 427 ILE Chi-restraints excluded: chain h residue 473 THR Chi-restraints excluded: chain n residue 12 VAL Chi-restraints excluded: chain n residue 83 ASN Chi-restraints excluded: chain q residue 3 LEU Chi-restraints excluded: chain q residue 43 THR Chi-restraints excluded: chain q residue 45 THR Chi-restraints excluded: chain q residue 55 MET Chi-restraints excluded: chain q residue 130 GLU Chi-restraints excluded: chain q residue 150 SER Chi-restraints excluded: chain q residue 170 SER Chi-restraints excluded: chain q residue 175 ASN Chi-restraints excluded: chain q residue 181 LYS Chi-restraints excluded: chain q residue 200 ASP Chi-restraints excluded: chain q residue 212 ILE Chi-restraints excluded: chain q residue 226 GLU Chi-restraints excluded: chain q residue 234 VAL Chi-restraints excluded: chain q residue 312 LEU Chi-restraints excluded: chain q residue 322 ARG Chi-restraints excluded: chain q residue 385 MET Chi-restraints excluded: chain q residue 480 LEU Chi-restraints excluded: chain q residue 498 LEU Chi-restraints excluded: chain z residue 4 VAL Chi-restraints excluded: chain z residue 36 THR Chi-restraints excluded: chain z residue 88 THR Chi-restraints excluded: chain z residue 149 ILE Chi-restraints excluded: chain z residue 179 ILE Chi-restraints excluded: chain z residue 180 LYS Chi-restraints excluded: chain z residue 246 SER Chi-restraints excluded: chain z residue 323 ARG Chi-restraints excluded: chain z residue 408 VAL Chi-restraints excluded: chain z residue 442 ASP Chi-restraints excluded: chain z residue 464 VAL Chi-restraints excluded: chain z residue 487 MET Chi-restraints excluded: chain z residue 488 VAL Chi-restraints excluded: chain T residue 12 CYS Chi-restraints excluded: chain T residue 39 ASP Chi-restraints excluded: chain T residue 49 VAL Chi-restraints excluded: chain T residue 69 GLU Chi-restraints excluded: chain T residue 84 ILE Chi-restraints excluded: chain T residue 143 THR Chi-restraints excluded: chain T residue 395 LEU Chi-restraints excluded: chain T residue 415 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 885 random chunks: chunk 792 optimal weight: 1.9990 chunk 521 optimal weight: 4.9990 chunk 840 optimal weight: 1.9990 chunk 513 optimal weight: 2.9990 chunk 398 optimal weight: 7.9990 chunk 584 optimal weight: 0.0870 chunk 881 optimal weight: 9.9990 chunk 811 optimal weight: 5.9990 chunk 702 optimal weight: 0.8980 chunk 72 optimal weight: 10.0000 chunk 542 optimal weight: 1.9990 overall best weight: 1.3964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 350 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** G 235 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** ** H 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 365 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 161 HIS a 164 ASN ** a 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 492 ASN ** b 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 195 ASN e 72 ASN ** e 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 130 GLN h 470 GLN ** q 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 52 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7448 moved from start: 0.2365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.128 69953 Z= 0.251 Angle : 0.688 59.040 94470 Z= 0.365 Chirality : 0.042 0.256 11206 Planarity : 0.004 0.085 12067 Dihedral : 7.512 168.942 9741 Min Nonbonded Distance : 1.697 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.48 % Favored : 96.50 % Rotamer: Outliers : 3.21 % Allowed : 20.90 % Favored : 75.89 % Cbeta Deviations : 0.01 % 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: 0.41 (0.09), residues: 8920 helix: 1.17 (0.08), residues: 4578 sheet: -0.37 (0.14), residues: 1229 loop : -0.70 (0.11), residues: 3113 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP N 101 HIS 0.011 0.001 HIS Z 161 PHE 0.025 0.001 PHE a 167 TYR 0.018 0.001 TYR Q 505 ARG 0.008 0.000 ARG Q 322 ********************** 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 1154 residues out of total 7485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 239 poor density : 915 time to evaluate : 6.280 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 PHE cc_start: 0.7685 (t80) cc_final: 0.7333 (t80) REVERT: A 51 ASP cc_start: 0.6224 (t0) cc_final: 0.5976 (t70) REVERT: A 66 GLU cc_start: 0.7544 (mp0) cc_final: 0.7310 (mp0) REVERT: A 123 LEU cc_start: 0.8071 (OUTLIER) cc_final: 0.7643 (tp) REVERT: A 230 VAL cc_start: 0.7236 (OUTLIER) cc_final: 0.6931 (t) REVERT: A 321 LYS cc_start: 0.7843 (mtmt) cc_final: 0.7528 (tptt) REVERT: A 328 LEU cc_start: 0.7591 (OUTLIER) cc_final: 0.7132 (mm) REVERT: A 354 GLU cc_start: 0.6509 (mm-30) cc_final: 0.5828 (tp30) REVERT: A 355 ARG cc_start: 0.7646 (ttt90) cc_final: 0.7377 (ttt-90) REVERT: A 384 MET cc_start: 0.8087 (ttt) cc_final: 0.7844 (ttt) REVERT: A 430 MET cc_start: 0.5721 (mmm) cc_final: 0.5141 (mmm) REVERT: A 459 ASP cc_start: 0.8304 (t0) cc_final: 0.7989 (t0) REVERT: B 87 MET cc_start: 0.7843 (ttp) cc_final: 0.7409 (ttp) REVERT: B 132 GLU cc_start: 0.7486 (OUTLIER) cc_final: 0.7152 (mp0) REVERT: B 248 LYS cc_start: 0.7919 (mtpt) cc_final: 0.7598 (mtmt) REVERT: B 301 GLU cc_start: 0.7557 (tt0) cc_final: 0.7113 (tt0) REVERT: B 347 LYS cc_start: 0.8296 (mmtm) cc_final: 0.7743 (mppt) REVERT: B 402 LYS cc_start: 0.7634 (mtmm) cc_final: 0.6992 (mptp) REVERT: B 405 ARG cc_start: 0.7559 (OUTLIER) cc_final: 0.7106 (mtt180) REVERT: B 414 GLU cc_start: 0.6583 (mp0) cc_final: 0.6078 (mp0) REVERT: B 456 TYR cc_start: 0.8685 (m-80) cc_final: 0.8235 (m-10) REVERT: B 496 SER cc_start: 0.8721 (OUTLIER) cc_final: 0.8491 (m) REVERT: D 65 LYS cc_start: 0.8279 (mtmm) cc_final: 0.7982 (mtpt) REVERT: D 67 ASP cc_start: 0.7638 (m-30) cc_final: 0.7375 (m-30) REVERT: D 82 GLN cc_start: 0.8282 (OUTLIER) cc_final: 0.7693 (mm-40) REVERT: D 222 GLU cc_start: 0.7407 (tt0) cc_final: 0.6746 (mt-10) REVERT: D 224 VAL cc_start: 0.8124 (t) cc_final: 0.7823 (m) REVERT: D 257 LYS cc_start: 0.7734 (mmtm) cc_final: 0.7324 (ttpp) REVERT: D 291 LYS cc_start: 0.7838 (OUTLIER) cc_final: 0.7572 (tttp) REVERT: D 326 LYS cc_start: 0.8574 (pttt) cc_final: 0.8258 (ptmt) REVERT: D 384 LYS cc_start: 0.7674 (mptt) cc_final: 0.7371 (mptm) REVERT: D 400 GLU cc_start: 0.7113 (OUTLIER) cc_final: 0.6640 (mm-30) REVERT: D 458 MET cc_start: 0.8232 (mmm) cc_final: 0.7925 (mpp) REVERT: D 459 GLU cc_start: 0.6641 (mt-10) cc_final: 0.6358 (tp30) REVERT: E 20 LYS cc_start: 0.7955 (tttp) cc_final: 0.7734 (ttpt) REVERT: E 48 MET cc_start: 0.8434 (tpt) cc_final: 0.8130 (mmm) REVERT: E 93 GLU cc_start: 0.6964 (mm-30) cc_final: 0.6558 (mm-30) REVERT: E 121 GLU cc_start: 0.7103 (tt0) cc_final: 0.6679 (tt0) REVERT: E 125 ASP cc_start: 0.7866 (m-30) cc_final: 0.7594 (m-30) REVERT: E 188 ILE cc_start: 0.8396 (OUTLIER) cc_final: 0.8145 (mt) REVERT: E 198 ASP cc_start: 0.7627 (OUTLIER) cc_final: 0.7296 (t70) REVERT: E 263 LYS cc_start: 0.7807 (ttmt) cc_final: 0.7077 (tttt) REVERT: E 283 GLU cc_start: 0.7895 (mm-30) cc_final: 0.7648 (mt-10) REVERT: E 290 GLN cc_start: 0.7359 (tp-100) cc_final: 0.6968 (tm-30) REVERT: E 439 LYS cc_start: 0.7526 (mtmm) cc_final: 0.7290 (mptt) REVERT: E 446 TYR cc_start: 0.8159 (m-80) cc_final: 0.7605 (m-80) REVERT: E 502 LYS cc_start: 0.7415 (tttt) cc_final: 0.7150 (tttm) REVERT: G 15 LYS cc_start: 0.7403 (mmmt) cc_final: 0.6714 (mtmm) REVERT: G 17 GLU cc_start: 0.6629 (mp0) cc_final: 0.6149 (mp0) REVERT: G 54 MET cc_start: 0.8061 (OUTLIER) cc_final: 0.7568 (mtp) REVERT: G 71 GLN cc_start: 0.8329 (OUTLIER) cc_final: 0.7999 (tt0) REVERT: G 81 ILE cc_start: 0.8474 (OUTLIER) cc_final: 0.8187 (mp) REVERT: G 82 GLU cc_start: 0.7694 (mm-30) cc_final: 0.7422 (mm-30) REVERT: G 110 GLU cc_start: 0.7724 (tt0) cc_final: 0.7239 (tp30) REVERT: G 133 MET cc_start: 0.8102 (mtm) cc_final: 0.7823 (mtm) REVERT: G 234 LYS cc_start: 0.7156 (tptp) cc_final: 0.6779 (tptt) REVERT: G 248 LYS cc_start: 0.8393 (mtpt) cc_final: 0.7623 (mmpt) REVERT: G 255 ASP cc_start: 0.6986 (OUTLIER) cc_final: 0.6747 (m-30) REVERT: G 270 MET cc_start: 0.7631 (mtp) cc_final: 0.7412 (mtp) REVERT: G 276 GLN cc_start: 0.7470 (tt0) cc_final: 0.7150 (tm-30) REVERT: G 277 GLN cc_start: 0.7560 (tp40) cc_final: 0.6887 (mp10) REVERT: G 429 MET cc_start: 0.7205 (mtm) cc_final: 0.6852 (mtm) REVERT: G 476 GLU cc_start: 0.7336 (OUTLIER) cc_final: 0.6991 (mt-10) REVERT: G 477 THR cc_start: 0.8562 (OUTLIER) cc_final: 0.8184 (t) REVERT: G 483 GLU cc_start: 0.6021 (OUTLIER) cc_final: 0.5189 (mp0) REVERT: G 511 GLU cc_start: 0.7538 (mm-30) cc_final: 0.7225 (mp0) REVERT: H 151 GLN cc_start: 0.7522 (OUTLIER) cc_final: 0.7302 (tt0) REVERT: H 172 LYS cc_start: 0.7796 (pttt) cc_final: 0.7514 (ptpt) REVERT: H 279 GLU cc_start: 0.7228 (tp30) cc_final: 0.6837 (mt-10) REVERT: H 317 GLU cc_start: 0.7509 (mp0) cc_final: 0.7281 (tt0) REVERT: H 349 GLU cc_start: 0.7912 (tt0) cc_final: 0.7648 (tt0) REVERT: H 356 GLU cc_start: 0.7523 (OUTLIER) cc_final: 0.7307 (mt-10) REVERT: H 368 LYS cc_start: 0.8120 (mttt) cc_final: 0.7596 (mmtm) REVERT: H 383 GLU cc_start: 0.7667 (mm-30) cc_final: 0.7350 (mm-30) REVERT: H 384 GLU cc_start: 0.7088 (OUTLIER) cc_final: 0.6625 (mm-30) REVERT: H 440 LYS cc_start: 0.7621 (mmtp) cc_final: 0.7324 (mtpt) REVERT: H 482 GLU cc_start: 0.7964 (mt-10) cc_final: 0.7711 (mt-10) REVERT: H 497 MET cc_start: 0.7335 (tpp) cc_final: 0.6793 (tpt) REVERT: Q 31 ARG cc_start: 0.7306 (mmp-170) cc_final: 0.6638 (mtt180) REVERT: Q 55 MET cc_start: 0.7759 (OUTLIER) cc_final: 0.7523 (mtt) REVERT: Q 113 GLU cc_start: 0.6373 (mt-10) cc_final: 0.6116 (mt-10) REVERT: Q 193 ASP cc_start: 0.6985 (m-30) cc_final: 0.6698 (m-30) REVERT: Q 200 ASP cc_start: 0.7998 (m-30) cc_final: 0.7736 (m-30) REVERT: Q 249 MET cc_start: 0.7418 (ptp) cc_final: 0.6926 (mmm) REVERT: Q 281 LYS cc_start: 0.7698 (ttmt) cc_final: 0.7411 (tptp) REVERT: Q 296 LYS cc_start: 0.7860 (pttm) cc_final: 0.7423 (pttt) REVERT: Q 318 LYS cc_start: 0.8144 (pttm) cc_final: 0.7704 (ptmm) REVERT: Q 354 GLU cc_start: 0.7610 (tm-30) cc_final: 0.7324 (tm-30) REVERT: Q 434 GLU cc_start: 0.7054 (pt0) cc_final: 0.6639 (mm-30) REVERT: Q 481 ASP cc_start: 0.7644 (t0) cc_final: 0.7422 (t0) REVERT: Z 17 GLN cc_start: 0.7053 (OUTLIER) cc_final: 0.6211 (pp30) REVERT: Z 44 MET cc_start: 0.9140 (mmm) cc_final: 0.8783 (mmm) REVERT: Z 108 LEU cc_start: 0.7841 (tt) cc_final: 0.7539 (tp) REVERT: Z 163 GLU cc_start: 0.7017 (tp30) cc_final: 0.6402 (tp30) REVERT: Z 195 GLU cc_start: 0.7871 (pt0) cc_final: 0.7359 (pt0) REVERT: Z 223 LYS cc_start: 0.7799 (mptt) cc_final: 0.7419 (mmtt) REVERT: Z 241 LYS cc_start: 0.8512 (ttmt) cc_final: 0.7632 (pttp) REVERT: Z 264 ARG cc_start: 0.7394 (mtp85) cc_final: 0.7015 (mtp-110) REVERT: Z 272 LYS cc_start: 0.7433 (mmtp) cc_final: 0.6932 (mtpp) REVERT: Z 303 ASP cc_start: 0.7264 (t70) cc_final: 0.6480 (m-30) REVERT: Z 307 LYS cc_start: 0.7775 (mmtp) cc_final: 0.7497 (mtpt) REVERT: Z 322 GLU cc_start: 0.7478 (tt0) cc_final: 0.7135 (tt0) REVERT: Z 340 SER cc_start: 0.7415 (OUTLIER) cc_final: 0.7088 (p) REVERT: Z 487 MET cc_start: 0.6987 (OUTLIER) cc_final: 0.6462 (ppp) REVERT: Z 495 TRP cc_start: 0.7999 (m100) cc_final: 0.7441 (m100) REVERT: Z 496 ASP cc_start: 0.7511 (m-30) cc_final: 0.7212 (m-30) REVERT: a 1 MET cc_start: 0.4948 (OUTLIER) cc_final: 0.4709 (ptt) REVERT: a 23 MET cc_start: 0.5779 (OUTLIER) cc_final: 0.5423 (ttp) REVERT: a 265 GLN cc_start: 0.7140 (pt0) cc_final: 0.6837 (tp40) REVERT: a 354 GLU cc_start: 0.7145 (OUTLIER) cc_final: 0.6788 (tt0) REVERT: a 361 LEU cc_start: 0.8705 (OUTLIER) cc_final: 0.8420 (pt) REVERT: a 384 MET cc_start: 0.7951 (ttt) cc_final: 0.7692 (ttt) REVERT: a 481 LYS cc_start: 0.7482 (OUTLIER) cc_final: 0.7150 (mttt) REVERT: b 93 ASP cc_start: 0.7278 (m-30) cc_final: 0.6547 (m-30) REVERT: b 223 LYS cc_start: 0.8361 (mttm) cc_final: 0.7973 (mtpt) REVERT: b 236 LYS cc_start: 0.7962 (OUTLIER) cc_final: 0.7579 (mtmm) REVERT: b 316 ASP cc_start: 0.7181 (t0) cc_final: 0.6823 (m-30) REVERT: b 321 GLU cc_start: 0.6857 (mt-10) cc_final: 0.6598 (tt0) REVERT: b 387 GLU cc_start: 0.7345 (OUTLIER) cc_final: 0.7119 (tt0) REVERT: b 445 MET cc_start: 0.7960 (tpp) cc_final: 0.7753 (tpp) REVERT: b 516 ARG cc_start: 0.7754 (mtp85) cc_final: 0.7236 (mtp85) REVERT: b 522 LYS cc_start: 0.8084 (mttt) cc_final: 0.7231 (mppt) REVERT: d 42 LYS cc_start: 0.7221 (tttp) cc_final: 0.6433 (tptt) REVERT: d 46 ASP cc_start: 0.7929 (m-30) cc_final: 0.7539 (m-30) REVERT: d 60 MET cc_start: 0.8318 (ttp) cc_final: 0.7864 (ttp) REVERT: d 63 ASP cc_start: 0.7182 (m-30) cc_final: 0.6970 (m-30) REVERT: d 81 MET cc_start: 0.8335 (OUTLIER) cc_final: 0.8000 (ptt) REVERT: d 93 GLU cc_start: 0.7093 (mm-30) cc_final: 0.6685 (mm-30) REVERT: d 132 ILE cc_start: 0.8245 (mt) cc_final: 0.7979 (mp) REVERT: d 334 GLU cc_start: 0.7534 (tp30) cc_final: 0.7184 (tp30) REVERT: d 384 LYS cc_start: 0.7447 (mmtp) cc_final: 0.6982 (mmpt) REVERT: d 489 LYS cc_start: 0.7375 (ptmt) cc_final: 0.6837 (pttt) REVERT: d 497 LYS cc_start: 0.7817 (mtpp) cc_final: 0.7131 (mttm) REVERT: e 27 ARG cc_start: 0.8028 (ttp-170) cc_final: 0.7359 (ttt180) REVERT: e 29 MET cc_start: 0.7998 (mtp) cc_final: 0.7383 (mtp) REVERT: e 93 GLU cc_start: 0.7057 (mm-30) cc_final: 0.6648 (mt-10) REVERT: e 96 LYS cc_start: 0.7733 (tttm) cc_final: 0.7055 (ttmt) REVERT: e 121 GLU cc_start: 0.7000 (tt0) cc_final: 0.6719 (tt0) REVERT: e 126 ARG cc_start: 0.7286 (mtm180) cc_final: 0.6726 (mtp85) REVERT: e 146 GLU cc_start: 0.6998 (mt-10) cc_final: 0.6723 (mt-10) REVERT: e 150 LYS cc_start: 0.7673 (ttmt) cc_final: 0.7265 (ttpt) REVERT: e 360 GLN cc_start: 0.7959 (tt0) cc_final: 0.7380 (tp40) REVERT: e 464 GLU cc_start: 0.6726 (tt0) cc_final: 0.6157 (mm-30) REVERT: e 478 ARG cc_start: 0.7308 (ttp-170) cc_final: 0.6969 (ttm170) REVERT: e 502 LYS cc_start: 0.6994 (tttm) cc_final: 0.6608 (ttmp) REVERT: e 515 GLN cc_start: 0.7684 (tp-100) cc_final: 0.7236 (tp40) REVERT: e 532 ASP cc_start: 0.8330 (t0) cc_final: 0.8056 (t0) REVERT: g 50 LEU cc_start: 0.8359 (OUTLIER) cc_final: 0.8098 (mt) REVERT: g 110 GLU cc_start: 0.8216 (OUTLIER) cc_final: 0.7312 (tt0) REVERT: g 192 GLU cc_start: 0.6873 (tt0) cc_final: 0.6188 (pp20) REVERT: g 202 GLU cc_start: 0.7101 (mm-30) cc_final: 0.6659 (mm-30) REVERT: g 274 TYR cc_start: 0.7995 (t80) cc_final: 0.7678 (t80) REVERT: g 277 GLN cc_start: 0.7060 (tp-100) cc_final: 0.6248 (pt0) REVERT: g 294 LYS cc_start: 0.8116 (mmtp) cc_final: 0.7758 (mmtp) REVERT: g 367 LYS cc_start: 0.8443 (OUTLIER) cc_final: 0.8060 (pptt) REVERT: g 381 LYS cc_start: 0.7852 (tppt) cc_final: 0.7411 (mptt) REVERT: g 415 GLU cc_start: 0.7274 (OUTLIER) cc_final: 0.6959 (mm-30) REVERT: g 476 GLU cc_start: 0.7099 (pm20) cc_final: 0.6729 (mm-30) REVERT: h 10 LYS cc_start: 0.8126 (ttmt) cc_final: 0.7424 (ttpt) REVERT: h 17 GLN cc_start: 0.8124 (tt0) cc_final: 0.7898 (tt0) REVERT: h 119 GLN cc_start: 0.7975 (mm-40) cc_final: 0.7584 (mm110) REVERT: h 149 VAL cc_start: 0.8349 (OUTLIER) cc_final: 0.8098 (t) REVERT: h 153 LYS cc_start: 0.7918 (mttm) cc_final: 0.7420 (mptt) REVERT: h 217 LYS cc_start: 0.8926 (ttpt) cc_final: 0.8626 (ttpt) REVERT: h 247 LYS cc_start: 0.8419 (pttp) cc_final: 0.8070 (ptpp) REVERT: h 276 ASP cc_start: 0.7339 (t0) cc_final: 0.7054 (m-30) REVERT: h 320 LYS cc_start: 0.7659 (mmtt) cc_final: 0.7437 (mtmm) REVERT: h 344 ARG cc_start: 0.7362 (ttm110) cc_final: 0.6605 (mtm-85) REVERT: h 350 GLU cc_start: 0.7989 (OUTLIER) cc_final: 0.7732 (tt0) REVERT: h 356 GLU cc_start: 0.7357 (OUTLIER) cc_final: 0.6915 (mt-10) REVERT: h 368 LYS cc_start: 0.7698 (mttt) cc_final: 0.7043 (mtpp) REVERT: h 379 GLU cc_start: 0.8099 (tm-30) cc_final: 0.7506 (tm-30) REVERT: h 383 GLU cc_start: 0.7463 (mm-30) cc_final: 0.7125 (mm-30) REVERT: h 440 LYS cc_start: 0.8215 (tptt) cc_final: 0.7806 (tppt) REVERT: h 517 ASP cc_start: 0.8664 (p0) cc_final: 0.8046 (p0) REVERT: n 83 ASN cc_start: 0.2617 (OUTLIER) cc_final: 0.1536 (m110) REVERT: q 3 LEU cc_start: 0.5356 (OUTLIER) cc_final: 0.4636 (tt) REVERT: q 17 GLU cc_start: 0.7437 (tt0) cc_final: 0.7154 (tm-30) REVERT: q 31 ARG cc_start: 0.7566 (mmp-170) cc_final: 0.6911 (mmt-90) REVERT: q 55 MET cc_start: 0.7783 (OUTLIER) cc_final: 0.7354 (mtt) REVERT: q 117 GLU cc_start: 0.7125 (tt0) cc_final: 0.6577 (mt-10) REVERT: q 175 ASN cc_start: 0.8695 (OUTLIER) cc_final: 0.8470 (p0) REVERT: q 212 ILE cc_start: 0.8013 (OUTLIER) cc_final: 0.7711 (mm) REVERT: q 238 LYS cc_start: 0.7458 (mmtp) cc_final: 0.7002 (mmtp) REVERT: q 277 ASP cc_start: 0.8537 (t70) cc_final: 0.8126 (t0) REVERT: q 312 LEU cc_start: 0.8485 (OUTLIER) cc_final: 0.8278 (mt) REVERT: q 319 TRP cc_start: 0.7147 (m100) cc_final: 0.6348 (m100) REVERT: q 406 LYS cc_start: 0.7613 (ptmt) cc_final: 0.6732 (mmtm) REVERT: q 483 GLU cc_start: 0.7277 (mp0) cc_final: 0.6951 (mm-30) REVERT: q 498 LEU cc_start: 0.9037 (OUTLIER) cc_final: 0.8724 (mt) REVERT: q 505 TYR cc_start: 0.8142 (t80) cc_final: 0.7713 (t80) REVERT: z 10 LYS cc_start: 0.8017 (mtmt) cc_final: 0.7399 (pmtt) REVERT: z 32 ASP cc_start: 0.7012 (t0) cc_final: 0.6546 (m-30) REVERT: z 36 THR cc_start: 0.8800 (OUTLIER) cc_final: 0.8471 (p) REVERT: z 180 LYS cc_start: 0.7858 (OUTLIER) cc_final: 0.7234 (tttm) REVERT: z 181 LYS cc_start: 0.6950 (mttt) cc_final: 0.6109 (mmmt) REVERT: z 190 MET cc_start: 0.8471 (mmt) cc_final: 0.7987 (mmp) REVERT: z 192 GLU cc_start: 0.7634 (tp30) cc_final: 0.7360 (tp30) REVERT: z 272 LYS cc_start: 0.7894 (mmtp) cc_final: 0.7624 (mtpp) REVERT: z 307 LYS cc_start: 0.7915 (mmtp) cc_final: 0.6734 (ttpt) REVERT: z 323 ARG cc_start: 0.8234 (OUTLIER) cc_final: 0.7462 (mtt-85) REVERT: z 359 LYS cc_start: 0.7786 (mttt) cc_final: 0.6956 (mtmm) REVERT: z 430 LYS cc_start: 0.8284 (tppt) cc_final: 0.7737 (mmmt) REVERT: z 487 MET cc_start: 0.7100 (OUTLIER) cc_final: 0.6018 (ppp) REVERT: z 492 VAL cc_start: 0.8172 (p) cc_final: 0.7535 (p) REVERT: T 39 ASP cc_start: 0.4969 (OUTLIER) cc_final: 0.4254 (m-30) REVERT: T 49 VAL cc_start: 0.8573 (OUTLIER) cc_final: 0.8366 (t) REVERT: T 69 GLU cc_start: 0.7993 (OUTLIER) cc_final: 0.7694 (pt0) REVERT: T 77 ARG cc_start: 0.7242 (mtt90) cc_final: 0.6943 (mtt90) REVERT: T 94 GLN cc_start: 0.6016 (mp10) cc_final: 0.5604 (mt0) REVERT: T 167 PHE cc_start: 0.8150 (m-80) cc_final: 0.7813 (m-80) REVERT: T 233 MET cc_start: 0.7272 (tpt) cc_final: 0.6961 (tpt) outliers start: 239 outliers final: 179 residues processed: 1101 average time/residue: 1.5392 time to fit residues: 2224.4956 Evaluate side-chains 1148 residues out of total 7485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 233 poor density : 915 time to evaluate : 6.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 119 SER Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 166 ASP Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 284 ASN Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 132 GLU Chi-restraints excluded: chain B residue 134 THR Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain B residue 310 MET Chi-restraints excluded: chain B residue 405 ARG Chi-restraints excluded: chain B residue 413 SER Chi-restraints excluded: chain B residue 416 LEU Chi-restraints excluded: chain B residue 437 GLU Chi-restraints excluded: chain B residue 460 ASP Chi-restraints excluded: chain B residue 496 SER Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 73 ASP Chi-restraints excluded: chain D residue 82 GLN Chi-restraints excluded: chain D residue 136 SER Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 158 SER Chi-restraints excluded: chain D residue 184 SER Chi-restraints excluded: chain D residue 186 MET Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 217 THR Chi-restraints excluded: chain D residue 268 ASP Chi-restraints excluded: chain D residue 273 ASP Chi-restraints excluded: chain D residue 291 LYS Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 400 GLU Chi-restraints excluded: chain D residue 404 SER Chi-restraints excluded: chain D residue 430 ILE Chi-restraints excluded: chain D residue 446 MET Chi-restraints excluded: chain D residue 447 GLU Chi-restraints excluded: chain D residue 536 VAL Chi-restraints excluded: chain E residue 31 LEU Chi-restraints excluded: chain E residue 188 ILE Chi-restraints excluded: chain E residue 198 ASP Chi-restraints excluded: chain E residue 229 ILE Chi-restraints excluded: chain E residue 245 ASP Chi-restraints excluded: chain E residue 269 THR Chi-restraints excluded: chain E residue 306 PHE Chi-restraints excluded: chain E residue 308 ASP Chi-restraints excluded: chain E residue 418 VAL Chi-restraints excluded: chain G residue 7 VAL Chi-restraints excluded: chain G residue 54 MET Chi-restraints excluded: chain G residue 71 GLN Chi-restraints excluded: chain G residue 81 ILE Chi-restraints excluded: chain G residue 83 ILE Chi-restraints excluded: chain G residue 96 THR Chi-restraints excluded: chain G residue 146 ILE Chi-restraints excluded: chain G residue 252 SER Chi-restraints excluded: chain G residue 255 ASP Chi-restraints excluded: chain G residue 265 THR Chi-restraints excluded: chain G residue 292 THR Chi-restraints excluded: chain G residue 332 VAL Chi-restraints excluded: chain G residue 373 THR Chi-restraints excluded: chain G residue 440 VAL Chi-restraints excluded: chain G residue 471 THR Chi-restraints excluded: chain G residue 476 GLU Chi-restraints excluded: chain G residue 477 THR Chi-restraints excluded: chain G residue 483 GLU Chi-restraints excluded: chain G residue 508 THR Chi-restraints excluded: chain H residue 120 ILE Chi-restraints excluded: chain H residue 142 THR Chi-restraints excluded: chain H residue 151 GLN Chi-restraints excluded: chain H residue 310 CYS Chi-restraints excluded: chain H residue 356 GLU Chi-restraints excluded: chain H residue 362 THR Chi-restraints excluded: chain H residue 384 GLU Chi-restraints excluded: chain H residue 388 SER Chi-restraints excluded: chain H residue 400 ILE Chi-restraints excluded: chain H residue 427 ILE Chi-restraints excluded: chain N residue 43 LYS Chi-restraints excluded: chain N residue 78 VAL Chi-restraints excluded: chain N residue 83 ASN Chi-restraints excluded: chain Q residue 55 MET Chi-restraints excluded: chain Q residue 105 LEU Chi-restraints excluded: chain Q residue 146 LEU Chi-restraints excluded: chain Q residue 182 LEU Chi-restraints excluded: chain Q residue 212 ILE Chi-restraints excluded: chain Q residue 316 ASN Chi-restraints excluded: chain Q residue 366 GLU Chi-restraints excluded: chain Q residue 480 LEU Chi-restraints excluded: chain Q residue 486 VAL Chi-restraints excluded: chain Q residue 517 THR Chi-restraints excluded: chain Z residue 17 GLN Chi-restraints excluded: chain Z residue 38 LEU Chi-restraints excluded: chain Z residue 107 ASP Chi-restraints excluded: chain Z residue 159 LYS Chi-restraints excluded: chain Z residue 246 SER Chi-restraints excluded: chain Z residue 340 SER Chi-restraints excluded: chain Z residue 373 THR Chi-restraints excluded: chain Z residue 380 ASN Chi-restraints excluded: chain Z residue 407 VAL Chi-restraints excluded: chain Z residue 408 VAL Chi-restraints excluded: chain Z residue 430 LYS Chi-restraints excluded: chain Z residue 479 VAL Chi-restraints excluded: chain Z residue 487 MET Chi-restraints excluded: chain Z residue 488 VAL Chi-restraints excluded: chain a residue 1 MET Chi-restraints excluded: chain a residue 23 MET Chi-restraints excluded: chain a residue 166 ASP Chi-restraints excluded: chain a residue 321 LYS Chi-restraints excluded: chain a residue 329 SER Chi-restraints excluded: chain a residue 354 GLU Chi-restraints excluded: chain a residue 361 LEU Chi-restraints excluded: chain a residue 367 THR Chi-restraints excluded: chain a residue 391 SER Chi-restraints excluded: chain a residue 481 LYS Chi-restraints excluded: chain a residue 508 ILE Chi-restraints excluded: chain a residue 528 ASP Chi-restraints excluded: chain b residue 51 ILE Chi-restraints excluded: chain b residue 66 ASP Chi-restraints excluded: chain b residue 134 THR Chi-restraints excluded: chain b residue 153 VAL Chi-restraints excluded: chain b residue 165 THR Chi-restraints excluded: chain b residue 182 LEU Chi-restraints excluded: chain b residue 214 LEU Chi-restraints excluded: chain b residue 236 LYS Chi-restraints excluded: chain b residue 333 SER Chi-restraints excluded: chain b residue 353 MET Chi-restraints excluded: chain b residue 371 CYS Chi-restraints excluded: chain b residue 387 GLU Chi-restraints excluded: chain d residue 67 ASP Chi-restraints excluded: chain d residue 71 THR Chi-restraints excluded: chain d residue 81 MET Chi-restraints excluded: chain d residue 115 SER Chi-restraints excluded: chain d residue 134 SER Chi-restraints excluded: chain d residue 136 SER Chi-restraints excluded: chain d residue 158 SER Chi-restraints excluded: chain d residue 168 THR Chi-restraints excluded: chain d residue 184 SER Chi-restraints excluded: chain d residue 233 VAL Chi-restraints excluded: chain d residue 239 THR Chi-restraints excluded: chain d residue 385 THR Chi-restraints excluded: chain d residue 394 ASN Chi-restraints excluded: chain d residue 395 LYS Chi-restraints excluded: chain d residue 404 SER Chi-restraints excluded: chain d residue 430 ILE Chi-restraints excluded: chain d residue 536 VAL Chi-restraints excluded: chain e residue 298 ASN Chi-restraints excluded: chain e residue 308 ASP Chi-restraints excluded: chain e residue 319 LEU Chi-restraints excluded: chain e residue 330 ILE Chi-restraints excluded: chain e residue 418 VAL Chi-restraints excluded: chain e residue 498 THR Chi-restraints excluded: chain g residue 17 GLU Chi-restraints excluded: chain g residue 39 THR Chi-restraints excluded: chain g residue 50 LEU Chi-restraints excluded: chain g residue 83 ILE Chi-restraints excluded: chain g residue 93 ASP Chi-restraints excluded: chain g residue 96 THR Chi-restraints excluded: chain g residue 110 GLU Chi-restraints excluded: chain g residue 161 THR Chi-restraints excluded: chain g residue 310 THR Chi-restraints excluded: chain g residue 367 LYS Chi-restraints excluded: chain g residue 397 VAL Chi-restraints excluded: chain g residue 403 LEU Chi-restraints excluded: chain g residue 415 GLU Chi-restraints excluded: chain g residue 432 VAL Chi-restraints excluded: chain g residue 440 VAL Chi-restraints excluded: chain g residue 460 ILE Chi-restraints excluded: chain g residue 471 THR Chi-restraints excluded: chain g residue 486 THR Chi-restraints excluded: chain h residue 32 ILE Chi-restraints excluded: chain h residue 38 THR Chi-restraints excluded: chain h residue 85 SER Chi-restraints excluded: chain h residue 149 VAL Chi-restraints excluded: chain h residue 200 VAL Chi-restraints excluded: chain h residue 211 VAL Chi-restraints excluded: chain h residue 221 SER Chi-restraints excluded: chain h residue 350 GLU Chi-restraints excluded: chain h residue 356 GLU Chi-restraints excluded: chain h residue 395 ILE Chi-restraints excluded: chain h residue 405 VAL Chi-restraints excluded: chain h residue 427 ILE Chi-restraints excluded: chain h residue 473 THR Chi-restraints excluded: chain n residue 12 VAL Chi-restraints excluded: chain n residue 83 ASN Chi-restraints excluded: chain q residue 3 LEU Chi-restraints excluded: chain q residue 43 THR Chi-restraints excluded: chain q residue 45 THR Chi-restraints excluded: chain q residue 55 MET Chi-restraints excluded: chain q residue 130 GLU Chi-restraints excluded: chain q residue 150 SER Chi-restraints excluded: chain q residue 170 SER Chi-restraints excluded: chain q residue 175 ASN Chi-restraints excluded: chain q residue 181 LYS Chi-restraints excluded: chain q residue 200 ASP Chi-restraints excluded: chain q residue 212 ILE Chi-restraints excluded: chain q residue 226 GLU Chi-restraints excluded: chain q residue 234 VAL Chi-restraints excluded: chain q residue 312 LEU Chi-restraints excluded: chain q residue 322 ARG Chi-restraints excluded: chain q residue 385 MET Chi-restraints excluded: chain q residue 480 LEU Chi-restraints excluded: chain q residue 498 LEU Chi-restraints excluded: chain z residue 4 VAL Chi-restraints excluded: chain z residue 36 THR Chi-restraints excluded: chain z residue 88 THR Chi-restraints excluded: chain z residue 149 ILE Chi-restraints excluded: chain z residue 179 ILE Chi-restraints excluded: chain z residue 180 LYS Chi-restraints excluded: chain z residue 246 SER Chi-restraints excluded: chain z residue 323 ARG Chi-restraints excluded: chain z residue 408 VAL Chi-restraints excluded: chain z residue 442 ASP Chi-restraints excluded: chain z residue 464 VAL Chi-restraints excluded: chain z residue 487 MET Chi-restraints excluded: chain z residue 488 VAL Chi-restraints excluded: chain T residue 12 CYS Chi-restraints excluded: chain T residue 39 ASP Chi-restraints excluded: chain T residue 49 VAL Chi-restraints excluded: chain T residue 69 GLU Chi-restraints excluded: chain T residue 84 ILE Chi-restraints excluded: chain T residue 143 THR Chi-restraints excluded: chain T residue 395 LEU Chi-restraints excluded: chain T residue 415 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 885 random chunks: chunk 430 optimal weight: 0.8980 chunk 557 optimal weight: 7.9990 chunk 747 optimal weight: 9.9990 chunk 215 optimal weight: 0.6980 chunk 647 optimal weight: 4.9990 chunk 103 optimal weight: 9.9990 chunk 195 optimal weight: 0.9990 chunk 703 optimal weight: 0.0980 chunk 294 optimal weight: 0.9990 chunk 722 optimal weight: 5.9990 chunk 89 optimal weight: 0.8980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN D 350 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** G 235 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** H 331 GLN ** Q 365 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 161 HIS a 164 ASN ** a 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 492 ASN ** b 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 195 ASN e 72 ASN ** 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 130 GLN h 470 GLN ** q 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 52 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.131365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.115265 restraints weight = 98423.740| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 1.55 r_work: 0.3166 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3050 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3078 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3078 r_free = 0.3078 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3078 r_free = 0.3078 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3078 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.2365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.138 69953 Z= 0.204 Angle : 0.668 59.199 94470 Z= 0.351 Chirality : 0.041 0.298 11206 Planarity : 0.004 0.078 12067 Dihedral : 7.498 168.621 9741 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.49 % Favored : 96.49 % Rotamer: Outliers : 3.40 % Allowed : 20.77 % Favored : 75.83 % 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: 0.46 (0.09), residues: 8920 helix: 1.22 (0.08), residues: 4578 sheet: -0.37 (0.14), residues: 1229 loop : -0.68 (0.11), residues: 3113 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP N 101 HIS 0.013 0.001 HIS Z 161 PHE 0.025 0.001 PHE a 167 TYR 0.018 0.001 TYR Q 505 ARG 0.010 0.000 ARG a 189 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 30996.80 seconds wall clock time: 536 minutes 52.72 seconds (32212.72 seconds total)