Starting phenix.real_space_refine on Sat Feb 17 23:30:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nvm_12606/02_2024/7nvm_12606_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nvm_12606/02_2024/7nvm_12606.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nvm_12606/02_2024/7nvm_12606.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nvm_12606/02_2024/7nvm_12606.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nvm_12606/02_2024/7nvm_12606_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nvm_12606/02_2024/7nvm_12606_updated.pdb" } resolution = 3.1 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= 0.006 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 429 5.16 5 C 44388 2.51 5 N 12337 2.21 5 O 13742 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 ARG 11": "NH1" <-> "NH2" Residue "A GLU 15": "OE1" <-> "OE2" Residue "A GLU 106": "OE1" <-> "OE2" Residue "A GLU 134": "OE1" <-> "OE2" Residue "A GLU 142": "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 341": "OE1" <-> "OE2" Residue "A GLU 349": "OE1" <-> "OE2" Residue "A ARG 355": "NH1" <-> "NH2" Residue "A GLU 360": "OE1" <-> "OE2" Residue "A ARG 370": "NH1" <-> "NH2" Residue "A ARG 443": "NH1" <-> "NH2" Residue "A GLU 473": "OE1" <-> "OE2" Residue "A ARG 480": "NH1" <-> "NH2" Residue "A ARG 496": "NH1" <-> "NH2" Residue "A GLU 505": "OE1" <-> "OE2" Residue "B GLU 19": "OE1" <-> "OE2" Residue "B ARG 20": "NH1" <-> "NH2" Residue "B GLU 94": "OE1" <-> "OE2" Residue "B GLU 114": "OE1" <-> "OE2" Residue "B GLU 152": "OE1" <-> "OE2" 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 321": "OE1" <-> "OE2" Residue "B ARG 388": "NH1" <-> "NH2" Residue "B ARG 405": "NH1" <-> "NH2" Residue "B GLU 414": "OE1" <-> "OE2" 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 "B GLU 495": "OE1" <-> "OE2" 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 101": "OE1" <-> "OE2" Residue "D GLU 142": "OE1" <-> "OE2" Residue "D ARG 153": "NH1" <-> "NH2" Residue "D ARG 206": "NH1" <-> "NH2" Residue "D GLU 222": "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 334": "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 GLU 459": "OE1" <-> "OE2" Residue "D ARG 483": "NH1" <-> "NH2" Residue "D GLU 505": "OE1" <-> "OE2" Residue "D GLU 524": "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 ARG 142": "NH1" <-> "NH2" Residue "E GLU 163": "OE1" <-> "OE2" Residue "E ARG 183": "NH1" <-> "NH2" Residue "E ARG 201": "NH1" <-> "NH2" Residue "E ARG 202": "NH1" <-> "NH2" Residue "E GLU 207": "OE1" <-> "OE2" Residue "E GLU 212": "OE1" <-> "OE2" Residue "E ARG 218": "NH1" <-> "NH2" Residue "E GLU 220": "OE1" <-> "OE2" Residue "E GLU 244": "OE1" <-> "OE2" Residue "E GLU 256": "OE1" <-> "OE2" Residue "E GLU 287": "OE1" <-> "OE2" Residue "E GLU 294": "OE1" <-> "OE2" Residue "E GLU 329": "OE1" <-> "OE2" Residue "E GLU 361": "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 476": "OE1" <-> "OE2" Residue "E ARG 478": "NH1" <-> "NH2" Residue "E ARG 480": "NH1" <-> "NH2" Residue "G GLU 69": "OE1" <-> "OE2" 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 GLU 251": "OE1" <-> "OE2" 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 ARG 438": "NH1" <-> "NH2" Residue "G GLU 445": "OE1" <-> "OE2" Residue "G GLU 473": "OE1" <-> "OE2" Residue "G GLU 476": "OE1" <-> "OE2" Residue "G GLU 492": "OE1" <-> "OE2" Residue "G GLU 497": "OE1" <-> "OE2" Residue "H GLU 11": "OE1" <-> "OE2" Residue "H ARG 37": "NH1" <-> "NH2" Residue "H ARG 43": "NH1" <-> "NH2" Residue "H ARG 53": "NH1" <-> "NH2" Residue "H ARG 123": "NH1" <-> "NH2" Residue "H GLU 150": "OE1" <-> "OE2" Residue "H GLU 156": "OE1" <-> "OE2" Residue "H GLU 226": "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 GLU 317": "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 GLU 6": "OE1" <-> "OE2" Residue "N ARG 38": "NH1" <-> "NH2" Residue "N ARG 45": "NH1" <-> "NH2" Residue "N ARG 53": "NH1" <-> "NH2" Residue "N GLU 88": "OE1" <-> "OE2" Residue "N ARG 103": "NH1" <-> "NH2" Residue "Q ARG 31": "NH1" <-> "NH2" Residue "Q ARG 44": "NH1" <-> "NH2" Residue "Q GLU 61": "OE1" <-> "OE2" Residue "Q GLU 113": "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 272": "OE1" <-> "OE2" Residue "Q ARG 314": "NH1" <-> "NH2" Residue "Q ARG 322": "NH1" <-> "NH2" Residue "Q GLU 342": "OE1" <-> "OE2" Residue "Q GLU 366": "OE1" <-> "OE2" Residue "Q ARG 404": "NH1" <-> "NH2" Residue "Q ARG 407": "NH1" <-> "NH2" Residue "Q GLU 416": "OE1" <-> "OE2" Residue "Q GLU 462": "OE1" <-> "OE2" Residue "Q GLU 473": "OE1" <-> "OE2" Residue "Q GLU 483": "OE1" <-> "OE2" Residue "Q GLU 485": "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 66": "OE1" <-> "OE2" Residue "Z GLU 124": "OE1" <-> "OE2" Residue "Z ARG 141": "NH1" <-> "NH2" Residue "Z ARG 145": "NH1" <-> "NH2" Residue "Z ARG 157": "NH1" <-> "NH2" Residue "Z GLU 195": "OE1" <-> "OE2" Residue "Z ARG 208": "NH1" <-> "NH2" Residue "Z GLU 226": "OE1" <-> "OE2" Residue "Z GLU 243": "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 ARG 370": "NH1" <-> "NH2" Residue "Z GLU 415": "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 106": "OE1" <-> "OE2" Residue "a GLU 134": "OE1" <-> "OE2" Residue "a GLU 142": "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 341": "OE1" <-> "OE2" Residue "a GLU 349": "OE1" <-> "OE2" Residue "a ARG 355": "NH1" <-> "NH2" Residue "a GLU 360": "OE1" <-> "OE2" Residue "a ARG 370": "NH1" <-> "NH2" Residue "a ARG 443": "NH1" <-> "NH2" Residue "a GLU 473": "OE1" <-> "OE2" Residue "a ARG 480": "NH1" <-> "NH2" Residue "a ARG 496": "NH1" <-> "NH2" Residue "a GLU 505": "OE1" <-> "OE2" Residue "b GLU 19": "OE1" <-> "OE2" Residue "b ARG 20": "NH1" <-> "NH2" Residue "b GLU 94": "OE1" <-> "OE2" Residue "b GLU 114": "OE1" <-> "OE2" Residue "b GLU 152": "OE1" <-> "OE2" 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 321": "OE1" <-> "OE2" Residue "b ARG 388": "NH1" <-> "NH2" Residue "b ARG 405": "NH1" <-> "NH2" Residue "b GLU 414": "OE1" <-> "OE2" 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 "b GLU 495": "OE1" <-> "OE2" Residue "d ARG 89": "NH1" <-> "NH2" Residue "d GLU 93": "OE1" <-> "OE2" Residue "d GLU 135": "OE1" <-> "OE2" Residue "d ARG 153": "NH1" <-> "NH2" Residue "d ARG 206": "NH1" <-> "NH2" Residue "d GLU 222": "OE1" <-> "OE2" Residue "d ARG 274": "NH1" <-> "NH2" Residue "d ARG 277": "NH1" <-> "NH2" Residue "d GLU 279": "OE1" <-> "OE2" Residue "d ARG 280": "NH1" <-> "NH2" Residue "d ARG 306": "NH1" <-> "NH2" Residue "d GLU 331": "OE1" <-> "OE2" Residue "d ARG 419": "NH1" <-> "NH2" Residue "d GLU 429": "OE1" <-> "OE2" Residue "d ARG 435": "NH1" <-> "NH2" Residue "d ARG 452": "NH1" <-> "NH2" Residue "d GLU 459": "OE1" <-> "OE2" Residue "d GLU 467": "OE1" <-> "OE2" Residue "d ARG 483": "NH1" <-> "NH2" Residue "d GLU 505": "OE1" <-> "OE2" Residue "d GLU 506": "OE1" <-> "OE2" Residue "d ARG 527": "NH1" <-> "NH2" Residue "e TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 ARG 142": "NH1" <-> "NH2" Residue "e ARG 183": "NH1" <-> "NH2" Residue "e ARG 201": "NH1" <-> "NH2" Residue "e ARG 202": "NH1" <-> "NH2" Residue "e GLU 207": "OE1" <-> "OE2" Residue "e GLU 212": "OE1" <-> "OE2" Residue "e ARG 218": "NH1" <-> "NH2" Residue "e GLU 220": "OE1" <-> "OE2" Residue "e GLU 244": "OE1" <-> "OE2" Residue "e GLU 256": "OE1" <-> "OE2" Residue "e GLU 287": "OE1" <-> "OE2" Residue "e GLU 294": "OE1" <-> "OE2" Residue "e GLU 329": "OE1" <-> "OE2" Residue "e GLU 361": "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 476": "OE1" <-> "OE2" Residue "e ARG 478": "NH1" <-> "NH2" Residue "e ARG 480": "NH1" <-> "NH2" Residue "e GLU 540": "OE1" <-> "OE2" Residue "e GLU 541": "OE1" <-> "OE2" Residue "g GLU 17": "OE1" <-> "OE2" Residue "g GLU 69": "OE1" <-> "OE2" 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 GLU 251": "OE1" <-> "OE2" Residue "g ARG 260": "NH1" <-> "NH2" Residue "g GLU 261": "OE1" <-> "OE2" Residue "g GLU 271": "OE1" <-> "OE2" Residue "g GLU 280": "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 ARG 438": "NH1" <-> "NH2" Residue "g GLU 473": "OE1" <-> "OE2" Residue "h GLU 11": "OE1" <-> "OE2" Residue "h ARG 37": "NH1" <-> "NH2" Residue "h ARG 43": "NH1" <-> "NH2" Residue "h ARG 53": "NH1" <-> "NH2" Residue "h ARG 123": "NH1" <-> "NH2" Residue "h GLU 150": "OE1" <-> "OE2" Residue "h GLU 156": "OE1" <-> "OE2" Residue "h GLU 226": "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 GLU 317": "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 GLU 6": "OE1" <-> "OE2" Residue "n ARG 38": "NH1" <-> "NH2" Residue "n ARG 45": "NH1" <-> "NH2" Residue "n ARG 53": "NH1" <-> "NH2" Residue "n GLU 88": "OE1" <-> "OE2" Residue "n ARG 103": "NH1" <-> "NH2" Residue "q ARG 31": "NH1" <-> "NH2" Residue "q ARG 44": "NH1" <-> "NH2" Residue "q GLU 61": "OE1" <-> "OE2" Residue "q GLU 113": "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 272": "OE1" <-> "OE2" Residue "q ARG 314": "NH1" <-> "NH2" Residue "q ARG 322": "NH1" <-> "NH2" Residue "q GLU 342": "OE1" <-> "OE2" Residue "q GLU 366": "OE1" <-> "OE2" Residue "q ARG 404": "NH1" <-> "NH2" Residue "q ARG 407": "NH1" <-> "NH2" Residue "q GLU 416": "OE1" <-> "OE2" Residue "q GLU 462": "OE1" <-> "OE2" Residue "q GLU 473": "OE1" <-> "OE2" Residue "q GLU 483": "OE1" <-> "OE2" Residue "q GLU 485": "OE1" <-> "OE2" Residue "q GLU 494": "OE1" <-> "OE2" Residue "q ARG 520": "NH1" <-> "NH2" Residue "z ARG 15": "NH1" <-> "NH2" Residue "z ARG 28": "NH1" <-> "NH2" Residue "z ARG 35": "NH1" <-> "NH2" Residue "z GLU 66": "OE1" <-> "OE2" Residue "z GLU 124": "OE1" <-> "OE2" Residue "z ARG 141": "NH1" <-> "NH2" Residue "z ARG 145": "NH1" <-> "NH2" Residue "z ARG 157": "NH1" <-> "NH2" Residue "z GLU 195": "OE1" <-> "OE2" Residue "z ARG 208": "NH1" <-> "NH2" Residue "z GLU 226": "OE1" <-> "OE2" Residue "z GLU 243": "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 ARG 370": "NH1" <-> "NH2" Residue "z GLU 415": "OE1" <-> "OE2" Residue "z ARG 432": "NH1" <-> "NH2" Residue "z GLU 469": "OE1" <-> "OE2" Residue "z GLU 485": "OE1" <-> "OE2" Residue "K GLU 72": "OE1" <-> "OE2" Residue "K GLU 99": "OE1" <-> "OE2" Residue "K GLU 100": "OE1" <-> "OE2" Residue "K GLU 117": "OE1" <-> "OE2" Residue "K GLU 207": "OE1" <-> "OE2" Residue "K GLU 226": "OE1" <-> "OE2" Residue "K ARG 335": "NH1" <-> "NH2" Residue "K ARG 372": "NH1" <-> "NH2" Residue "P GLU 9": "OE1" <-> "OE2" Residue "P GLU 65": "OE1" <-> "OE2" Residue "P GLU 66": "OE1" <-> "OE2" Residue "P GLU 93": "OE1" <-> "OE2" Residue "P GLU 105": "OE1" <-> "OE2" Residue "P ARG 161": "NH1" <-> "NH2" Residue "P GLU 171": "OE1" <-> "OE2" Residue "P ARG 191": "NH1" <-> "NH2" Residue "P GLU 193": "OE1" <-> "OE2" Residue "P GLU 210": "OE1" <-> "OE2" Time to flip residues: 0.18s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 71008 Number of models: 1 Model: "" Number of chains: 52 Chain: "A" Number of atoms: 4069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 536, 4069 Classifications: {'peptide': 536} Link IDs: {'PTRANS': 14, 'TRANS': 521} 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: 3923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 520, 3923 Classifications: {'peptide': 520} Link IDs: {'PTRANS': 14, 'TRANS': 505} Chain: "E" Number of atoms: 4132 Number of conformers: 2 Conformer: "B" Number of residues, atoms: 535, 4121 Classifications: {'peptide': 535} Link IDs: {'PTRANS': 18, 'TRANS': 516} Conformer: "C" Number of residues, atoms: 535, 4121 Classifications: {'peptide': 535} Link IDs: {'PTRANS': 18, 'TRANS': 516} bond proxies already assigned to first conformer: 4158 Chain: "G" Number of atoms: 4089 Number of conformers: 1 Conformer: "" Number of residues, atoms: 526, 4089 Classifications: {'peptide': 526} Link IDs: {'PTRANS': 17, 'TRANS': 508} Chain: "H" Number of atoms: 4054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 528, 4054 Classifications: {'peptide': 528} Link IDs: {'PTRANS': 16, 'TRANS': 511} Chain: "N" Number of atoms: 924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 924 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 1, 'TRANS': 117} Chain: "Q" Number of atoms: 4086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 538, 4086 Classifications: {'peptide': 538} Link IDs: {'PTRANS': 18, 'TRANS': 519} Chain: "Z" Number of atoms: 4022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 4022 Classifications: {'peptide': 525} Link IDs: {'PTRANS': 14, 'TRANS': 510} Chain: "a" Number of atoms: 4041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 532, 4041 Classifications: {'peptide': 532} Link IDs: {'PTRANS': 13, 'TRANS': 518} Chain: "b" Number of atoms: 3943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 3943 Classifications: {'peptide': 525} Link IDs: {'PTRANS': 10, 'TRANS': 514} Chain: "d" Number of atoms: 3917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 520, 3917 Classifications: {'peptide': 520} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 505} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "e" Number of atoms: 4169 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 540, 4158 Classifications: {'peptide': 540} Link IDs: {'PTRANS': 18, 'TRANS': 521} Conformer: "B" Number of residues, atoms: 540, 4158 Classifications: {'peptide': 540} Link IDs: {'PTRANS': 18, 'TRANS': 521} bond proxies already assigned to first conformer: 4195 Chain: "g" Number of atoms: 4169 Number of conformers: 1 Conformer: "" Number of residues, atoms: 538, 4169 Classifications: {'peptide': 538} Link IDs: {'PTRANS': 17, 'TRANS': 520} Chain: "h" Number of atoms: 4032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 4032 Classifications: {'peptide': 525} Link IDs: {'PTRANS': 16, 'TRANS': 508} Chain: "n" Number of atoms: 924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 924 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 1, 'TRANS': 117} Chain: "q" Number of atoms: 4053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 4053 Classifications: {'peptide': 533} Link IDs: {'PTRANS': 16, 'TRANS': 516} Chain: "z" Number of atoms: 4033 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 4033 Classifications: {'peptide': 527} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 512} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "K" Number of atoms: 2459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2459 Classifications: {'peptide': 317} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 16, 'TRANS': 300} Chain breaks: 3 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "P" Number of atoms: 1486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1486 Classifications: {'peptide': 190} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 179} Chain breaks: 1 Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 49 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 40 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} Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N BPHE E 9 " occ=0.38 ... (20 atoms not shown) pdb=" CZ CPHE E 9 " occ=0.62 residue: pdb=" N APHE e 9 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE e 9 " occ=0.50 Time building chain proxies: 30.56, per 1000 atoms: 0.43 Number of scatterers: 71008 At special positions: 0 Unit cell: (185.5, 171.72, 188.68, 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 429 16.00 P 32 15.00 Al 16 13.00 Mg 16 11.99 F 48 9.00 O 13742 8.00 N 12337 7.00 C 44388 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=2.04 Simple disulfide: pdb=" SG CYS n 22 " - pdb=" SG CYS n 95 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 21.90 Conformation dependent library (CDL) restraints added in 12.5 seconds 18354 Ramachandran restraints generated. 9177 Oldfield, 0 Emsley, 9177 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 17152 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 333 helices and 112 sheets defined 49.0% alpha, 11.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 12.63 Creating SS restraints... Processing helix chain 'A' and resid 14 through 35 removed outlier: 3.873A pdb=" N LYS A 33 " --> pdb=" O ASN A 30 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N SER A 34 " --> 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: 3.930A pdb=" N LEU A 75 " --> pdb=" O ALA A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 109 removed outlier: 3.897A 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 142 No H-bonds generated for 'chain 'A' and resid 140 through 142' Processing helix chain 'A' and resid 146 through 156 Processing helix chain 'A' and resid 163 through 179 removed outlier: 3.777A pdb=" N ASP A 166 " --> pdb=" O ILE A 163 " (cutoff:3.500A) removed outlier: 5.113A pdb=" N ALA A 169 " --> pdb=" O ASP A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 186 No H-bonds generated for 'chain 'A' and resid 184 through 186' 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: 4.636A pdb=" N ASP A 261 " --> pdb=" O GLU A 258 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N ILE A 270 " --> pdb=" O GLU A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 303 removed outlier: 3.632A 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: 4.783A pdb=" N THR A 428 " --> pdb=" O GLU A 424 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N SER A 429 " --> pdb=" O ASN A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 455 removed outlier: 3.742A pdb=" N LEU A 446 " --> pdb=" O ALA A 442 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N VAL A 447 " --> pdb=" O ARG A 443 " (cutoff:3.500A) removed outlier: 4.950A 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: 4.169A pdb=" N LYS A 481 " --> pdb=" O PRO A 478 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N ASN A 482 " --> pdb=" O GLU A 479 " (cutoff:3.500A) removed outlier: 3.724A 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 526 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: 3.876A 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: 3.726A pdb=" N HIS B 174 " --> pdb=" O LEU B 171 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LYS B 176 " --> pdb=" O THR B 173 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N ASP B 177 " --> pdb=" O HIS B 174 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ARG B 189 " --> pdb=" O ALA B 186 " (cutoff:3.500A) 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: 3.911A 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 426 Processing helix chain 'B' and resid 431 through 454 Proline residue: B 447 - end of helix removed outlier: 3.819A 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: 4.898A pdb=" N THR D 50 " --> pdb=" O ASP D 46 " (cutoff:3.500A) removed outlier: 5.678A 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: 3.968A 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: 3.799A pdb=" N VAL D 191 " --> pdb=" O SER D 187 " (cutoff:3.500A) 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: 4.029A pdb=" N ASP D 273 " --> pdb=" O TYR D 269 " (cutoff:3.500A) removed outlier: 4.189A 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: 4.014A pdb=" N VAL D 460 " --> pdb=" O ASP D 456 " (cutoff:3.500A) removed outlier: 4.819A 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 512 through 531 Processing helix chain 'E' and resid 31 through 51 removed outlier: 4.523A pdb=" N THR E 50 " --> pdb=" O ASN E 46 " (cutoff:3.500A) removed outlier: 4.963A 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: 3.654A 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: 4.580A pdb=" N SER E 175 " --> pdb=" O THR E 171 " (cutoff:3.500A) Processing helix chain 'E' and resid 177 through 195 removed outlier: 3.778A pdb=" N SER E 180 " --> pdb=" O VAL E 177 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N ARG E 183 " --> pdb=" O SER E 180 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N GLU E 187 " --> pdb=" O GLN E 184 " (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 437 Processing helix chain 'E' and resid 442 through 465 removed outlier: 4.060A pdb=" N TYR E 446 " --> pdb=" O LEU E 443 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ALA E 447 " --> pdb=" O GLU E 444 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLU E 456 " --> pdb=" O ASP E 453 " (cutoff:3.500A) removed outlier: 3.663A 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: 3.829A pdb=" N ILE G 37 " --> pdb=" O ILE G 33 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N THR G 39 " --> pdb=" O ASP G 35 " (cutoff:3.500A) removed outlier: 5.761A 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: 3.839A pdb=" N HIS G 111 " --> pdb=" O SER G 107 " (cutoff:3.500A) removed outlier: 3.879A 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 removed outlier: 3.516A pdb=" N SER G 159 " --> pdb=" O ILE G 155 " (cutoff:3.500A) Processing helix chain 'G' and resid 164 through 183 removed outlier: 3.653A pdb=" N ARG G 167 " --> pdb=" O ALA G 164 " (cutoff:3.500A) removed outlier: 5.766A 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: 4.526A 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: 3.778A pdb=" N LYS G 427 " --> pdb=" O THR G 423 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N ALA G 428 " --> pdb=" O GLU G 424 " (cutoff:3.500A) Processing helix chain 'G' and resid 434 through 455 removed outlier: 3.979A pdb=" N GLU G 445 " --> pdb=" O ALA G 441 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N VAL G 446 " --> pdb=" O GLN G 442 " (cutoff:3.500A) removed outlier: 5.346A 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: 3.686A 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: 3.807A pdb=" N VAL H 36 " --> pdb=" O ILE H 32 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N THR H 38 " --> pdb=" O GLU H 34 " (cutoff:3.500A) removed outlier: 6.535A 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: 3.605A 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 removed outlier: 3.581A pdb=" N LEU H 155 " --> pdb=" O GLN H 151 " (cutoff:3.500A) Processing helix chain 'H' and resid 169 through 183 removed outlier: 6.207A pdb=" N ALA H 173 " --> pdb=" O GLN H 170 " (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 205 through 207 No H-bonds generated for 'chain 'H' and resid 205 through 207' 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: 3.858A pdb=" N THR H 426 " --> pdb=" O ASP H 422 " (cutoff:3.500A) Processing helix chain 'H' and resid 430 through 453 removed outlier: 3.755A pdb=" N LEU H 434 " --> pdb=" O LYS H 430 " (cutoff:3.500A) removed outlier: 3.646A 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: 5.029A 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 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: 4.567A pdb=" N THR Q 45 " --> pdb=" O GLN Q 41 " (cutoff:3.500A) removed outlier: 5.879A 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: 4.628A pdb=" N THR Q 166 " --> pdb=" O SER Q 162 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N SER Q 167 " --> pdb=" O LEU Q 163 " (cutoff:3.500A) removed outlier: 3.722A 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: 4.754A pdb=" N SER Q 269 " --> pdb=" O LEU Q 265 " (cutoff:3.500A) removed outlier: 4.849A 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 427 Processing helix chain 'Q' and resid 434 through 456 removed outlier: 3.791A pdb=" N PHE Q 445 " --> pdb=" O PHE Q 441 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N GLU Q 446 " --> pdb=" O ALA Q 442 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ALA Q 447 " --> pdb=" O GLU Q 443 " (cutoff:3.500A) removed outlier: 4.509A 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: 3.915A 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: 4.909A pdb=" N THR Z 36 " --> pdb=" O ASP Z 32 " (cutoff:3.500A) removed outlier: 4.781A 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: 3.841A 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: 4.013A pdb=" N THR Z 158 " --> pdb=" O THR Z 154 " (cutoff:3.500A) Processing helix chain 'Z' and resid 162 through 178 removed outlier: 4.008A 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: 3.754A pdb=" N ARG Z 270 " --> pdb=" O PHE Z 266 " (cutoff:3.500A) Processing helix chain 'Z' and resid 299 through 307 Processing helix chain 'Z' and resid 318 through 327 removed outlier: 4.405A 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: 3.695A pdb=" N LEU Z 445 " --> pdb=" O ASP Z 442 " (cutoff:3.500A) removed outlier: 3.596A 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 472 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 516 Processing helix chain 'a' and resid 14 through 35 removed outlier: 3.504A pdb=" N ARG a 18 " --> pdb=" O GLU a 15 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LYS a 33 " --> pdb=" O ASN a 30 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N SER a 34 " --> 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: 4.042A pdb=" N LEU a 75 " --> pdb=" O ALA a 71 " (cutoff:3.500A) Processing helix chain 'a' and resid 90 through 109 removed outlier: 3.924A 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 146 through 156 Processing helix chain 'a' and resid 163 through 178 removed outlier: 3.673A pdb=" N ASP a 166 " --> pdb=" O ILE a 163 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N ALA a 169 " --> pdb=" O ASP a 166 " (cutoff:3.500A) Processing helix chain 'a' and resid 184 through 186 No H-bonds generated for 'chain 'a' and resid 184 through 186' 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: 4.755A pdb=" N ASP a 261 " --> pdb=" O GLU a 258 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N ILE a 270 " --> pdb=" O GLU a 267 " (cutoff:3.500A) Processing helix chain 'a' and resid 294 through 303 removed outlier: 3.774A 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: 4.607A pdb=" N THR a 428 " --> pdb=" O GLU a 424 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N SER a 429 " --> pdb=" O ASN a 425 " (cutoff:3.500A) Processing helix chain 'a' and resid 433 through 455 removed outlier: 3.712A pdb=" N LEU a 446 " --> pdb=" O ALA a 442 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N VAL a 447 " --> pdb=" O ARG a 443 " (cutoff:3.500A) removed outlier: 4.854A 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: 4.042A pdb=" N LYS a 481 " --> pdb=" O PRO a 478 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N ASN a 482 " --> pdb=" O GLU a 479 " (cutoff:3.500A) removed outlier: 3.747A 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 526 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 Processing helix chain 'b' and resid 123 through 144 Processing helix chain 'b' and resid 152 through 168 Processing helix chain 'b' and resid 171 through 190 removed outlier: 3.686A pdb=" N HIS b 174 " --> pdb=" O LEU b 171 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LYS b 176 " --> pdb=" O THR b 173 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N ASP b 177 " --> pdb=" O HIS b 174 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ARG b 189 " --> pdb=" O ALA b 186 " (cutoff:3.500A) 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: 3.921A 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 Proline residue: b 447 - end of helix removed outlier: 3.843A 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 49 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: 3.809A pdb=" N VAL d 110 " --> pdb=" O THR d 106 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N LYS d 122 " --> pdb=" O ASP d 118 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU d 123 " --> pdb=" O SER d 119 " (cutoff:3.500A) Processing helix chain 'd' and resid 132 through 151 Processing helix chain 'd' and resid 160 through 172 Processing helix chain 'd' and resid 175 through 177 No H-bonds generated for 'chain 'd' and resid 175 through 177' Processing helix chain 'd' and resid 180 through 193 Proline residue: d 185 - end of helix removed outlier: 3.745A 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: 3.762A pdb=" N LEU d 276 " --> pdb=" O MET d 272 " (cutoff:3.500A) removed outlier: 4.271A 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 416 Processing helix chain 'd' and resid 427 through 441 Processing helix chain 'd' and resid 446 through 466 removed outlier: 4.317A pdb=" N VAL d 460 " --> pdb=" O ASP d 456 " (cutoff:3.500A) removed outlier: 4.933A 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 505 No H-bonds generated for 'chain 'd' and resid 503 through 505' Processing helix chain 'd' and resid 512 through 530 removed outlier: 4.890A pdb=" N SER d 517 " --> pdb=" O LEU d 513 " (cutoff:3.500A) Processing helix chain 'e' and resid 31 through 51 removed outlier: 4.434A pdb=" N THR e 50 " --> pdb=" O ASN e 46 " (cutoff:3.500A) removed outlier: 4.820A 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: 3.838A 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: 4.465A pdb=" N SER e 175 " --> pdb=" O THR e 171 " (cutoff:3.500A) Processing helix chain 'e' and resid 177 through 195 removed outlier: 3.760A pdb=" N SER e 180 " --> pdb=" O VAL e 177 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N ARG e 183 " --> pdb=" O SER e 180 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N GLU e 187 " --> pdb=" O GLN e 184 " (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 437 Processing helix chain 'e' and resid 442 through 465 removed outlier: 3.937A pdb=" N TYR e 446 " --> pdb=" O LEU e 443 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ALA e 447 " --> pdb=" O GLU e 444 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLU e 456 " --> pdb=" O ASP e 453 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ILE e 458 " --> pdb=" O LEU e 455 " (cutoff:3.500A) Proline residue: e 459 - end of helix removed outlier: 3.541A pdb=" N ASN e 465 " --> pdb=" O LEU e 462 " (cutoff:3.500A) 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: 3.761A pdb=" N ILE g 37 " --> pdb=" O ILE g 33 " (cutoff:3.500A) removed outlier: 5.215A pdb=" N THR g 39 " --> pdb=" O ASP g 35 " (cutoff:3.500A) removed outlier: 5.927A 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: 3.769A 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 removed outlier: 3.515A pdb=" N SER g 159 " --> pdb=" O ILE g 155 " (cutoff:3.500A) Processing helix chain 'g' and resid 164 through 167 removed outlier: 3.971A pdb=" N ARG g 167 " --> pdb=" O ALA g 164 " (cutoff:3.500A) No H-bonds generated for 'chain 'g' and resid 164 through 167' Processing helix chain 'g' and resid 169 through 183 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 261 through 285 removed outlier: 4.751A pdb=" N THR g 265 " --> pdb=" O GLU g 261 " (cutoff:3.500A) removed outlier: 4.414A 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 381 through 403 Processing helix chain 'g' and resid 413 through 428 removed outlier: 3.855A pdb=" N LYS g 427 " --> pdb=" O THR g 423 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N ALA g 428 " --> pdb=" O GLU g 424 " (cutoff:3.500A) Processing helix chain 'g' and resid 434 through 442 Processing helix chain 'g' and resid 444 through 455 removed outlier: 3.623A pdb=" N ILE g 447 " --> pdb=" O LEU g 444 " (cutoff:3.500A) Proline residue: g 448 - end of helix Processing helix chain 'g' and resid 459 through 471 removed outlier: 3.706A 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 517 Processing helix chain 'h' and resid 19 through 39 removed outlier: 3.793A pdb=" N VAL h 36 " --> pdb=" O ILE h 32 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N THR h 38 " --> pdb=" O GLU h 34 " (cutoff:3.500A) removed outlier: 6.510A 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: 3.569A 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 removed outlier: 3.577A pdb=" N LEU h 155 " --> pdb=" O GLN h 151 " (cutoff:3.500A) Processing helix chain 'h' and resid 169 through 183 removed outlier: 6.212A pdb=" N ALA h 173 " --> pdb=" O GLN h 170 " (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 205 through 207 No H-bonds generated for 'chain 'h' and resid 205 through 207' 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: 3.848A pdb=" N THR h 426 " --> pdb=" O ASP h 422 " (cutoff:3.500A) Processing helix chain 'h' and resid 430 through 453 removed outlier: 3.689A pdb=" N LEU h 434 " --> pdb=" O LYS h 430 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLU h 443 " --> pdb=" O ALA h 439 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N ILE h 444 " --> pdb=" O LYS h 440 " (cutoff:3.500A) removed outlier: 5.105A 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 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: 4.540A pdb=" N THR q 45 " --> pdb=" O GLN q 41 " (cutoff:3.500A) removed outlier: 5.842A 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: 4.620A pdb=" N THR q 166 " --> pdb=" O SER q 162 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N SER q 167 " --> pdb=" O LEU q 163 " (cutoff:3.500A) removed outlier: 3.611A 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: 4.767A pdb=" N SER q 269 " --> pdb=" O LEU q 265 " (cutoff:3.500A) removed outlier: 4.843A 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: 3.676A pdb=" N THR q 429 " --> pdb=" O SER q 425 " (cutoff:3.500A) Processing helix chain 'q' and resid 434 through 456 removed outlier: 3.759A pdb=" N PHE q 445 " --> pdb=" O PHE q 441 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N GLU q 446 " --> pdb=" O ALA q 442 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N ALA q 447 " --> pdb=" O GLU q 443 " (cutoff:3.500A) removed outlier: 4.526A 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: 3.840A 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: 5.036A pdb=" N THR z 36 " --> pdb=" O ASP z 32 " (cutoff:3.500A) removed outlier: 4.967A 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: 3.862A 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: 4.013A pdb=" N THR z 158 " --> pdb=" O THR z 154 " (cutoff:3.500A) Processing helix chain 'z' and resid 162 through 178 removed outlier: 4.035A 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: 3.693A pdb=" N ARG z 270 " --> pdb=" O PHE z 266 " (cutoff:3.500A) Processing helix chain 'z' and resid 299 through 307 Processing helix chain 'z' and resid 318 through 327 removed outlier: 4.431A 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: 3.570A pdb=" N LEU z 445 " --> pdb=" O ASP z 442 " (cutoff:3.500A) removed outlier: 3.622A 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 472 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 516 Processing helix chain 'K' and resid 59 through 66 removed outlier: 3.836A pdb=" N ILE K 64 " --> pdb=" O SER K 60 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N THR K 66 " --> pdb=" O ARG K 62 " (cutoff:3.500A) Processing helix chain 'K' and resid 79 through 89 Processing helix chain 'K' and resid 113 through 125 Processing helix chain 'K' and resid 137 through 144 Processing helix chain 'K' and resid 182 through 191 removed outlier: 4.209A pdb=" N TYR K 188 " --> pdb=" O ASP K 184 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N LEU K 189 " --> pdb=" O LEU K 185 " (cutoff:3.500A) Processing helix chain 'K' and resid 203 through 214 Processing helix chain 'K' and resid 223 through 227 Processing helix chain 'K' and resid 264 through 267 No H-bonds generated for 'chain 'K' and resid 264 through 267' Processing helix chain 'K' and resid 274 through 283 Processing helix chain 'K' and resid 290 through 295 Processing helix chain 'K' and resid 302 through 307 Proline residue: K 307 - end of helix Processing helix chain 'K' and resid 311 through 320 Processing helix chain 'K' and resid 338 through 348 Processing helix chain 'K' and resid 351 through 355 Processing helix chain 'K' and resid 359 through 371 Proline residue: K 367 - end of helix Processing helix chain 'P' and resid 9 through 17 Processing helix chain 'P' and resid 53 through 59 removed outlier: 3.645A pdb=" N HIS P 59 " --> pdb=" O GLU P 55 " (cutoff:3.500A) Processing helix chain 'P' and resid 65 through 88 removed outlier: 4.200A pdb=" N ALA P 70 " --> pdb=" O GLU P 66 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N MET P 73 " --> pdb=" O ARG P 69 " (cutoff:3.500A) Processing helix chain 'P' and resid 102 through 105 No H-bonds generated for 'chain 'P' and resid 102 through 105' Processing helix chain 'P' and resid 125 through 140 removed outlier: 3.743A pdb=" N ARG P 139 " --> pdb=" O SER P 135 " (cutoff:3.500A) Processing helix chain 'P' and resid 151 through 154 No H-bonds generated for 'chain 'P' and resid 151 through 154' Processing helix chain 'P' and resid 193 through 200 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: 6.663A pdb=" N VAL A 285 " --> pdb=" O ALA A 235 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N LEU A 237 " --> pdb=" O VAL A 285 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N LEU A 287 " --> pdb=" O LEU A 237 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N MET A 306 " --> pdb=" O ILE A 286 " (cutoff:3.500A) removed outlier: 7.711A pdb=" N THR A 288 " --> pdb=" O MET A 306 " (cutoff:3.500A) removed outlier: 6.379A 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 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: 6.068A pdb=" N CYS B 371 " --> pdb=" O HIS B 200 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N ILE B 202 " --> pdb=" O CYS B 371 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N ILE B 373 " --> pdb=" O ILE B 202 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N LYS B 204 " --> pdb=" O ILE B 373 " (cutoff:3.500A) removed outlier: 5.934A 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: 6.750A pdb=" N CYS B 289 " --> pdb=" O LEU B 238 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N ALA B 240 " --> pdb=" O CYS B 289 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N ILE B 291 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N MET B 310 " --> pdb=" O PHE B 290 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N ASN B 292 " --> pdb=" O MET B 310 " (cutoff:3.500A) removed outlier: 6.770A 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: 6.732A pdb=" N VAL D 386 " --> pdb=" O LYS D 209 " (cutoff:3.500A) removed outlier: 8.162A pdb=" N VAL D 211 " --> pdb=" O VAL D 386 " (cutoff:3.500A) removed outlier: 6.556A 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: 6.972A pdb=" N VAL D 297 " --> pdb=" O GLY D 247 " (cutoff:3.500A) removed outlier: 7.940A pdb=" N ILE D 249 " --> pdb=" O VAL D 297 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N LEU D 299 " --> pdb=" O ILE D 249 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N MET D 323 " --> pdb=" O LEU D 298 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N ILE D 300 " --> pdb=" O MET D 323 " (cutoff:3.500A) removed outlier: 6.401A 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 59 through 62 Processing sheet with id= V, first strand: chain 'E' and resid 209 through 215 removed outlier: 6.853A pdb=" N VAL E 383 " --> pdb=" O LYS E 210 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N GLU E 212 " --> pdb=" O VAL E 383 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N ILE E 385 " --> pdb=" O GLU E 212 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N LYS E 214 " --> pdb=" O ILE E 385 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N ILE E 387 " --> pdb=" O LYS E 214 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'E' and resid 228 through 230 Processing sheet with id= X, first strand: chain 'E' and resid 354 through 356 removed outlier: 6.891A pdb=" N LEU E 299 " --> pdb=" O ALA E 249 " (cutoff:3.500A) removed outlier: 7.979A pdb=" N LEU E 251 " --> pdb=" O LEU E 299 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N ILE E 301 " --> pdb=" O LEU E 251 " (cutoff:3.500A) removed outlier: 8.095A 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= Y, first strand: chain 'E' and resid 418 through 420 Processing sheet with id= Z, first strand: chain 'G' and resid 48 through 51 Processing sheet with id= AA, first strand: chain 'G' and resid 184 through 186 Processing sheet with id= AB, first strand: chain 'G' and resid 199 through 205 removed outlier: 6.683A pdb=" N CYS G 372 " --> pdb=" O ARG G 200 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N GLU G 202 " --> pdb=" O CYS G 372 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N ILE G 374 " --> pdb=" O GLU G 202 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N ILE G 204 " --> pdb=" O ILE G 374 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N LEU G 376 " --> pdb=" O ILE G 204 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N THR G 373 " --> pdb=" O LEU G 215 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'G' and resid 219 through 221 Processing sheet with id= AD, first strand: chain 'G' and resid 238 through 241 removed outlier: 6.802A pdb=" N VAL G 289 " --> pdb=" O VAL G 239 " (cutoff:3.500A) removed outlier: 8.390A pdb=" N LEU G 241 " --> pdb=" O VAL G 289 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N ILE G 291 " --> pdb=" O LEU G 241 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N THR G 310 " --> pdb=" O VAL G 290 " (cutoff:3.500A) removed outlier: 8.121A pdb=" N THR G 292 " --> pdb=" O THR G 310 " (cutoff:3.500A) removed outlier: 6.768A 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 407 through 409 Processing sheet with id= AF, first strand: chain 'G' and resid 478 through 480 Processing sheet with id= AG, first strand: chain 'H' and resid 14 through 17 Processing sheet with id= AH, first strand: chain 'H' and resid 47 through 50 Processing sheet with id= AI, first strand: chain 'H' and resid 195 through 201 removed outlier: 6.551A pdb=" N CYS H 370 " --> pdb=" O GLY H 196 " (cutoff:3.500A) removed outlier: 7.890A pdb=" N LYS H 198 " --> pdb=" O CYS H 370 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N PHE H 372 " --> pdb=" O LYS H 198 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N VAL H 200 " --> pdb=" O PHE H 372 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N LEU H 374 " --> pdb=" O VAL H 200 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'H' and resid 213 through 217 Processing sheet with id= AK, first strand: chain 'H' and resid 237 through 240 removed outlier: 6.787A pdb=" N VAL H 288 " --> pdb=" O ALA H 238 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N LEU H 240 " --> pdb=" O VAL H 288 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N LEU H 290 " --> pdb=" O LEU H 240 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N PHE H 309 " --> pdb=" O VAL H 289 " (cutoff:3.500A) removed outlier: 7.957A pdb=" N SER H 291 " --> pdb=" O PHE H 309 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ALA H 311 " --> pdb=" O SER H 291 " (cutoff:3.500A) No H-bonds generated for sheet with id= AK Processing sheet with id= AL, first strand: chain 'H' and resid 405 through 407 Processing sheet with id= AM, first strand: chain 'H' and resid 475 through 478 Processing sheet with id= AN, first strand: chain 'N' and resid 2 through 7 Processing sheet with id= AO, first strand: chain 'N' and resid 57 through 59 removed outlier: 7.103A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N SER N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N MET N 34 " --> pdb=" O SER N 50 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N THR N 52 " --> pdb=" O ASN N 32 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N ASN N 32 " --> pdb=" O THR N 52 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N ASN N 98 " --> pdb=" O ASN N 32 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N MET N 34 " --> pdb=" O LYS N 96 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N LYS N 96 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N TRP N 36 " --> pdb=" O TYR N 94 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N TYR N 94 " --> pdb=" O TRP N 36 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ARG N 38 " --> pdb=" O VAL N 92 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N VAL N 92 " --> pdb=" O ARG N 38 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'Q' and resid 20 through 23 Processing sheet with id= AQ, first strand: chain 'Q' and resid 54 through 57 Processing sheet with id= AR, first strand: chain 'Q' and resid 202 through 206 removed outlier: 6.419A pdb=" N SER Q 373 " --> pdb=" O ARG Q 203 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N CYS Q 205 " --> pdb=" O SER Q 373 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N ILE Q 375 " --> pdb=" O CYS Q 205 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain 'Q' and resid 220 through 223 Processing sheet with id= AT, first strand: chain 'Q' and resid 240 through 242 removed outlier: 6.039A pdb=" N MET Q 311 " --> pdb=" O VAL Q 291 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N THR Q 293 " --> pdb=" O MET Q 311 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N VAL Q 313 " --> pdb=" O THR Q 293 " (cutoff:3.500A) Processing sheet with id= AU, first strand: chain 'Q' and resid 408 through 410 Processing sheet with id= AV, first strand: chain 'Q' and resid 478 through 480 Processing sheet with id= AW, first strand: chain 'Z' and resid 12 through 15 Processing sheet with id= AX, first strand: chain 'Z' and resid 45 through 48 Processing sheet with id= AY, first strand: chain 'Z' and resid 191 through 196 removed outlier: 6.570A pdb=" N VAL Z 372 " --> pdb=" O GLU Z 192 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N MET Z 194 " --> pdb=" O VAL Z 372 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N LEU Z 374 " --> pdb=" O MET Z 194 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N MET Z 196 " --> pdb=" O LEU Z 374 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N ILE Z 376 " --> pdb=" O MET Z 196 " (cutoff:3.500A) Processing sheet with id= AZ, first strand: chain 'Z' and resid 210 through 212 Processing sheet with id= BA, first strand: chain 'Z' and resid 345 through 347 removed outlier: 6.512A pdb=" N GLY Z 288 " --> pdb=" O TYR Z 229 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N LEU Z 231 " --> pdb=" O GLY Z 288 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N VAL Z 290 " --> pdb=" O LEU Z 231 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N CYS Z 233 " --> pdb=" O VAL Z 290 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N ILE Z 292 " --> pdb=" O CYS Z 233 " (cutoff:3.500A) Processing sheet with id= BB, first strand: chain 'Z' and resid 477 through 479 Processing sheet with id= BC, first strand: chain 'a' and resid 9 through 13 Processing sheet with id= BD, first strand: chain 'a' and resid 43 through 46 Processing sheet with id= BE, first strand: chain 'a' and resid 180 through 182 Processing sheet with id= BF, first strand: chain 'a' and resid 196 through 199 Processing sheet with id= BG, first strand: chain 'a' and resid 213 through 216 Processing sheet with id= BH, first strand: chain 'a' and resid 346 through 348 removed outlier: 6.714A pdb=" N VAL a 285 " --> pdb=" O ALA a 235 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N LEU a 237 " --> pdb=" O VAL a 285 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N LEU a 287 " --> pdb=" O LEU a 237 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N MET a 306 " --> pdb=" O ILE a 286 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N THR a 288 " --> pdb=" O MET a 306 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N VAL a 308 " --> pdb=" O THR a 288 " (cutoff:3.500A) Processing sheet with id= BI, first strand: chain 'a' and resid 408 through 410 Processing sheet with id= BJ, first strand: chain 'a' and resid 486 through 489 Processing sheet with id= BK, first strand: chain 'b' and resid 17 through 19 Processing sheet with id= BL, first strand: chain 'b' and resid 50 through 53 Processing sheet with id= BM, first strand: chain 'b' and resid 199 through 205 removed outlier: 6.053A pdb=" N CYS b 371 " --> pdb=" O HIS b 200 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N ILE b 202 " --> pdb=" O CYS b 371 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N ILE b 373 " --> pdb=" O ILE b 202 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N LYS b 204 " --> pdb=" O ILE b 373 " (cutoff:3.500A) removed outlier: 5.935A 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: 6.759A pdb=" N CYS b 289 " --> pdb=" O LEU b 238 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N ALA b 240 " --> pdb=" O CYS b 289 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N ILE b 291 " --> pdb=" O ALA b 240 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N MET b 310 " --> pdb=" O PHE b 290 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N ASN b 292 " --> pdb=" O MET b 310 " (cutoff:3.500A) removed outlier: 6.642A 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: 6.746A pdb=" N VAL d 386 " --> pdb=" O LYS d 209 " (cutoff:3.500A) removed outlier: 8.072A pdb=" N VAL d 211 " --> pdb=" O VAL d 386 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N ILE d 388 " --> pdb=" O VAL d 211 " (cutoff:3.500A) No H-bonds generated for sheet with id= BS Processing sheet with id= BT, first strand: chain 'd' and resid 227 through 229 removed outlier: 3.517A pdb=" N LEU d 227 " --> pdb=" O ILE d 376 " (cutoff:3.500A) Processing sheet with id= BU, first strand: chain 'd' and resid 357 through 359 removed outlier: 6.786A pdb=" N VAL d 297 " --> pdb=" O GLY d 247 " (cutoff:3.500A) removed outlier: 7.856A pdb=" N ILE d 249 " --> pdb=" O VAL d 297 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N LEU d 299 " --> pdb=" O ILE d 249 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N MET d 323 " --> pdb=" O LEU d 298 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N ILE d 300 " --> pdb=" O MET d 323 " (cutoff:3.500A) removed outlier: 6.635A 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 59 through 62 Processing sheet with id= BY, first strand: chain 'e' and resid 209 through 215 removed outlier: 6.903A pdb=" N VAL e 383 " --> pdb=" O LYS e 210 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N GLU e 212 " --> pdb=" O VAL e 383 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N ILE e 385 " --> pdb=" O GLU e 212 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N LYS e 214 " --> pdb=" O ILE e 385 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N ILE e 387 " --> pdb=" O LYS e 214 " (cutoff:3.500A) Processing sheet with id= BZ, first strand: chain 'e' and resid 228 through 230 Processing sheet with id= CA, first strand: chain 'e' and resid 354 through 356 removed outlier: 6.965A pdb=" N LEU e 299 " --> pdb=" O ALA e 249 " (cutoff:3.500A) removed outlier: 8.034A pdb=" N LEU e 251 " --> pdb=" O LEU e 299 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N ILE e 301 " --> pdb=" O LEU e 251 " (cutoff:3.500A) removed outlier: 8.095A pdb=" N CYS e 302 " --> pdb=" O PRO e 320 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N VAL e 322 " --> pdb=" O CYS e 302 " (cutoff:3.500A) Processing sheet with id= CB, first strand: chain 'e' and resid 418 through 420 Processing sheet with id= CC, first strand: chain 'g' and resid 15 through 18 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 200 through 205 removed outlier: 3.961A pdb=" N GLY g 378 " --> 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= CF, first strand: chain 'g' and resid 218 through 220 Processing sheet with id= CG, first strand: chain 'g' and resid 238 through 241 removed outlier: 6.665A pdb=" N VAL g 289 " --> pdb=" O VAL g 239 " (cutoff:3.500A) removed outlier: 8.234A pdb=" N LEU g 241 " --> pdb=" O VAL g 289 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ILE g 291 " --> pdb=" O LEU g 241 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N THR g 310 " --> pdb=" O VAL g 290 " (cutoff:3.500A) removed outlier: 8.070A pdb=" N THR g 292 " --> pdb=" O THR g 310 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ILE g 312 " --> pdb=" O THR g 292 " (cutoff:3.500A) No H-bonds generated for sheet with id= CG Processing sheet with id= CH, first strand: chain 'g' and resid 407 through 409 Processing sheet with id= CI, first strand: chain 'g' and resid 478 through 481 removed outlier: 3.884A pdb=" N THR g 486 " --> pdb=" O ASN g 481 " (cutoff:3.500A) Processing sheet with id= CJ, first strand: chain 'h' and resid 14 through 17 Processing sheet with id= CK, first strand: chain 'h' and resid 47 through 50 Processing sheet with id= CL, first strand: chain 'h' and resid 195 through 201 removed outlier: 6.606A pdb=" N CYS h 370 " --> pdb=" O GLY h 196 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N LYS h 198 " --> pdb=" O CYS h 370 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N PHE h 372 " --> pdb=" O LYS h 198 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N VAL h 200 " --> pdb=" O PHE h 372 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N LEU h 374 " --> pdb=" O VAL h 200 " (cutoff:3.500A) Processing sheet with id= CM, first strand: chain 'h' and resid 213 through 217 Processing sheet with id= CN, first strand: chain 'h' and resid 237 through 240 removed outlier: 6.732A pdb=" N VAL h 288 " --> pdb=" O ALA h 238 " (cutoff:3.500A) removed outlier: 7.882A pdb=" N LEU h 240 " --> pdb=" O VAL h 288 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N LEU h 290 " --> pdb=" O LEU h 240 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N PHE h 309 " --> pdb=" O VAL h 289 " (cutoff:3.500A) removed outlier: 8.011A pdb=" N SER h 291 " --> pdb=" O PHE h 309 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ALA h 311 " --> pdb=" O SER h 291 " (cutoff:3.500A) No H-bonds generated for sheet with id= CN Processing sheet with id= CO, first strand: chain 'h' and resid 405 through 407 Processing sheet with id= CP, first strand: chain 'h' and resid 475 through 478 Processing sheet with id= CQ, first strand: chain 'n' and resid 2 through 7 Processing sheet with id= CR, first strand: chain 'n' and resid 57 through 59 removed outlier: 6.701A pdb=" N TRP n 36 " --> pdb=" O VAL n 48 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N SER n 50 " --> pdb=" O MET n 34 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N MET n 34 " --> pdb=" O SER n 50 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N THR n 52 " --> pdb=" O ASN n 32 " (cutoff:3.500A) removed outlier: 8.083A pdb=" N ASN n 32 " --> pdb=" O THR n 52 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N ASN n 98 " --> pdb=" O ASN n 32 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N MET n 34 " --> pdb=" O LYS n 96 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N LYS n 96 " --> pdb=" O MET n 34 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N TRP n 36 " --> pdb=" O TYR n 94 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N TYR n 94 " --> pdb=" O TRP n 36 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N ARG n 38 " --> pdb=" O VAL n 92 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N VAL n 92 " --> pdb=" O ARG n 38 " (cutoff:3.500A) Processing sheet with id= CS, first strand: chain 'q' and resid 20 through 23 Processing sheet with id= CT, first strand: chain 'q' and resid 54 through 57 Processing sheet with id= CU, first strand: chain 'q' and resid 202 through 206 removed outlier: 6.384A pdb=" N SER q 373 " --> pdb=" O ARG q 203 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N CYS q 205 " --> pdb=" O SER q 373 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N ILE q 375 " --> pdb=" O CYS q 205 " (cutoff:3.500A) Processing sheet with id= CV, first strand: chain 'q' and resid 220 through 223 Processing sheet with id= CW, first strand: chain 'q' and resid 240 through 242 removed outlier: 6.048A pdb=" N MET q 311 " --> pdb=" O VAL q 291 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N THR q 293 " --> pdb=" O MET q 311 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N VAL q 313 " --> pdb=" O THR q 293 " (cutoff:3.500A) Processing sheet with id= CX, first strand: chain 'q' and resid 408 through 410 Processing sheet with id= CY, first strand: chain 'q' and resid 478 through 480 Processing sheet with id= CZ, first strand: chain 'z' and resid 12 through 15 Processing sheet with id= DA, first strand: chain 'z' and resid 45 through 48 Processing sheet with id= DB, first strand: chain 'z' and resid 191 through 196 removed outlier: 6.507A pdb=" N VAL z 372 " --> pdb=" O GLU z 192 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N MET z 194 " --> pdb=" O VAL z 372 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N LEU z 374 " --> pdb=" O MET z 194 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N MET z 196 " --> pdb=" O LEU z 374 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N ILE z 376 " --> pdb=" O MET z 196 " (cutoff:3.500A) Processing sheet with id= DC, first strand: chain 'z' and resid 210 through 212 Processing sheet with id= DD, first strand: chain 'z' and resid 345 through 347 removed outlier: 6.580A pdb=" N GLY z 288 " --> pdb=" O TYR z 229 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N LEU z 231 " --> pdb=" O GLY z 288 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N VAL z 290 " --> pdb=" O LEU z 231 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N CYS z 233 " --> pdb=" O VAL z 290 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N ILE z 292 " --> pdb=" O CYS z 233 " (cutoff:3.500A) Processing sheet with id= DE, first strand: chain 'z' and resid 477 through 479 Processing sheet with id= DF, first strand: chain 'K' and resid 7 through 10 removed outlier: 7.345A pdb=" N ILE K 10 " --> pdb=" O PRO K 102 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N LEU K 104 " --> pdb=" O ILE K 10 " (cutoff:3.500A) Processing sheet with id= DG, first strand: chain 'K' and resid 160 through 165 Processing sheet with id= DH, first strand: chain 'P' and resid 145 through 150 removed outlier: 6.073A pdb=" N LEU P 170 " --> pdb=" O ILE P 174 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N ILE P 174 " --> pdb=" O LEU P 170 " (cutoff:3.500A) 3544 hydrogen bonds defined for protein. 9540 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 30.95 Time building geometry restraints manager: 24.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 22191 1.33 - 1.45: 8827 1.45 - 1.57: 40035 1.57 - 1.69: 96 1.69 - 1.81: 712 Bond restraints: 71861 Sorted by residual: bond pdb=" N SER H 525 " pdb=" CA SER H 525 " ideal model delta sigma weight residual 1.454 1.491 -0.037 1.21e-02 6.83e+03 9.24e+00 bond pdb=" N LYS e 535 " pdb=" CA LYS e 535 " ideal model delta sigma weight residual 1.452 1.493 -0.041 1.46e-02 4.69e+03 7.99e+00 bond pdb=" N GLU A 536 " pdb=" CA GLU A 536 " ideal model delta sigma weight residual 1.459 1.492 -0.033 1.20e-02 6.94e+03 7.40e+00 bond pdb=" N ILE d 430 " pdb=" CA ILE d 430 " ideal model delta sigma weight residual 1.459 1.493 -0.035 1.34e-02 5.57e+03 6.66e+00 bond pdb=" N LYS Q 528 " pdb=" CA LYS Q 528 " ideal model delta sigma weight residual 1.454 1.487 -0.033 1.29e-02 6.01e+03 6.60e+00 ... (remaining 71856 not shown) Histogram of bond angle deviations from ideal: 93.81 - 102.46: 330 102.46 - 111.10: 29432 111.10 - 119.74: 34406 119.74 - 128.39: 32519 128.39 - 137.03: 379 Bond angle restraints: 97066 Sorted by residual: angle pdb=" C ALA E 8 " pdb=" N CPHE E 9 " pdb=" CA CPHE E 9 " ideal model delta sigma weight residual 121.54 134.47 -12.93 1.91e+00 2.74e-01 4.58e+01 angle pdb=" C BPHE E 9 " pdb=" N ASP E 10 " pdb=" CA ASP E 10 " ideal model delta sigma weight residual 121.54 131.73 -10.19 1.91e+00 2.74e-01 2.85e+01 angle pdb=" N PRO K 332 " pdb=" CA PRO K 332 " pdb=" C PRO K 332 " ideal model delta sigma weight residual 110.70 116.89 -6.19 1.22e+00 6.72e-01 2.57e+01 angle pdb=" N PRO e 536 " pdb=" CA PRO e 536 " pdb=" C PRO e 536 " ideal model delta sigma weight residual 112.47 102.73 9.74 2.06e+00 2.36e-01 2.23e+01 angle pdb=" C APHE e 9 " pdb=" N ASP e 10 " pdb=" CA ASP e 10 " ideal model delta sigma weight residual 121.54 130.46 -8.92 1.91e+00 2.74e-01 2.18e+01 ... (remaining 97061 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.94: 42711 31.94 - 63.88: 1448 63.88 - 95.83: 140 95.83 - 127.77: 9 127.77 - 159.71: 13 Dihedral angle restraints: 44321 sinusoidal: 17808 harmonic: 26513 Sorted by residual: dihedral pdb=" O1B ADP h 601 " pdb=" O3A ADP h 601 " pdb=" PB ADP h 601 " pdb=" PA ADP h 601 " ideal model delta sinusoidal sigma weight residual -60.00 99.71 -159.71 1 2.00e+01 2.50e-03 4.65e+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 93.91 -153.91 1 2.00e+01 2.50e-03 4.56e+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 93.36 -153.36 1 2.00e+01 2.50e-03 4.55e+01 ... (remaining 44318 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 7759 0.043 - 0.086: 2720 0.086 - 0.130: 867 0.130 - 0.173: 147 0.173 - 0.216: 11 Chirality restraints: 11504 Sorted by residual: chirality pdb=" C2' ADP h 601 " pdb=" C1' ADP h 601 " pdb=" C3' ADP h 601 " pdb=" O2' ADP h 601 " both_signs ideal model delta sigma weight residual False -2.51 -2.73 0.22 2.00e-01 2.50e+01 1.17e+00 chirality pdb=" CA PRO K 333 " pdb=" N PRO K 333 " pdb=" C PRO K 333 " pdb=" CB PRO K 333 " both_signs ideal model delta sigma weight residual False 2.72 2.51 0.20 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" CA ILE Q 190 " pdb=" N ILE Q 190 " pdb=" C ILE Q 190 " pdb=" CB ILE Q 190 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.20 2.00e-01 2.50e+01 9.54e-01 ... (remaining 11501 not shown) Planarity restraints: 12403 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA e 8 " 0.035 2.00e-02 2.50e+03 7.38e-02 5.45e+01 pdb=" C ALA e 8 " -0.128 2.00e-02 2.50e+03 pdb=" O ALA e 8 " 0.048 2.00e-02 2.50e+03 pdb=" N APHE e 9 " 0.044 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA e 8 " 0.034 2.00e-02 2.50e+03 7.19e-02 5.17e+01 pdb=" C ALA e 8 " -0.124 2.00e-02 2.50e+03 pdb=" O ALA e 8 " 0.047 2.00e-02 2.50e+03 pdb=" N BPHE e 9 " 0.043 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA APHE e 9 " 0.025 2.00e-02 2.50e+03 5.21e-02 2.72e+01 pdb=" C APHE e 9 " -0.090 2.00e-02 2.50e+03 pdb=" O APHE e 9 " 0.034 2.00e-02 2.50e+03 pdb=" N ASP e 10 " 0.031 2.00e-02 2.50e+03 ... (remaining 12400 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.52: 542 2.52 - 3.11: 55234 3.11 - 3.71: 112366 3.71 - 4.30: 169085 4.30 - 4.90: 281269 Nonbonded interactions: 618496 Sorted by model distance: nonbonded pdb=" OD1 ASP Q 99 " pdb="MG MG Q 602 " model vdw 1.920 2.170 nonbonded pdb=" OD1 ASP q 99 " pdb="MG MG q 602 " model vdw 1.927 2.170 nonbonded pdb="MG MG D 602 " pdb=" F2 AF3 D 603 " model vdw 1.932 2.120 nonbonded pdb=" OD1 ASP b 97 " pdb="MG MG b 602 " model vdw 1.944 2.170 nonbonded pdb=" OD1 ASP B 97 " pdb="MG MG B 602 " model vdw 1.952 2.170 ... (remaining 618491 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' and (resid 4 through 535 or resid 601 through 603)) selection = chain 'a' } ncs_group { reference = (chain 'B' and (resid 2 through 526 or resid 601 through 603)) selection = chain 'b' } ncs_group { reference = (chain 'D' and ((resid 19 and (name N or name CA or name C or name O or name CB \ )) or resid 20 through 538 or resid 601 through 603)) selection = chain 'd' } ncs_group { reference = (chain 'E' and (resid 2 through 8 or resid 10 through 536 or resid 601 through 6 \ 03)) selection = (chain 'e' and (resid 2 through 8 or resid 10 through 536 or resid 601 through 6 \ 03)) } ncs_group { reference = (chain 'G' and (resid 8 through 528 or resid 601 through 603)) selection = (chain 'g' and (resid 8 through 528 or resid 601 through 603)) } ncs_group { reference = (chain 'H' and (resid 1 through 525 or resid 601 through 603)) selection = chain 'h' } ncs_group { reference = chain 'N' selection = chain 'n' } ncs_group { reference = (chain 'Q' and (resid 2 through 534 or resid 601 through 603)) selection = chain 'q' } ncs_group { reference = chain 'Z' selection = (chain 'z' and (resid 2 through 526 or resid 601 through 603)) } 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: 5.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.050 Extract box with map and model: 16.500 Check model and map are aligned: 0.830 Set scattering table: 0.500 Process input model: 161.180 Find NCS groups from input model: 6.620 Set up NCS constraints: 0.640 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 194.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7196 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 : 0.006 0.082 71861 Z= 0.370 Angle : 0.767 12.929 97066 Z= 0.414 Chirality : 0.049 0.216 11504 Planarity : 0.005 0.080 12403 Dihedral : 16.020 159.712 27163 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.24 % Favored : 95.65 % Rotamer: Outliers : 1.50 % Allowed : 12.43 % Favored : 86.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.37 % 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: -2.23 (0.08), residues: 9177 helix: -0.75 (0.07), residues: 4682 sheet: -1.34 (0.13), residues: 1217 loop : -2.47 (0.09), residues: 3278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP P 10 HIS 0.012 0.002 HIS K 371 PHE 0.025 0.002 PHE G 112 TYR 0.025 0.002 TYR g 126 ARG 0.036 0.001 ARG Z 28 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18354 Ramachandran restraints generated. 9177 Oldfield, 0 Emsley, 9177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18354 Ramachandran restraints generated. 9177 Oldfield, 0 Emsley, 9177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1772 residues out of total 7685 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 1657 time to evaluate : 6.550 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 SER cc_start: 0.8840 (t) cc_final: 0.8639 (p) REVERT: A 66 GLU cc_start: 0.7239 (tt0) cc_final: 0.6932 (tp30) REVERT: A 80 ASP cc_start: 0.7600 (t70) cc_final: 0.6907 (m-30) REVERT: A 81 LEU cc_start: 0.8632 (tp) cc_final: 0.8375 (tp) REVERT: A 84 LYS cc_start: 0.8034 (mtmm) cc_final: 0.7826 (mmmt) REVERT: A 156 MET cc_start: 0.7702 (mtm) cc_final: 0.7460 (mtp) REVERT: A 245 LYS cc_start: 0.8168 (tttt) cc_final: 0.7966 (tttm) REVERT: A 309 ARG cc_start: 0.8400 (ptt180) cc_final: 0.7857 (ptt180) REVERT: A 389 GLU cc_start: 0.7920 (tt0) cc_final: 0.7642 (tt0) REVERT: A 532 LYS cc_start: 0.8234 (tttt) cc_final: 0.7904 (ttpt) REVERT: B 22 GLU cc_start: 0.7317 (pm20) cc_final: 0.7080 (pm20) REVERT: B 94 GLU cc_start: 0.6329 (mm-30) cc_final: 0.5973 (tp30) REVERT: B 414 GLU cc_start: 0.7846 (mp0) cc_final: 0.7324 (mp0) REVERT: D 42 LYS cc_start: 0.8034 (tttp) cc_final: 0.7823 (tppt) REVERT: D 187 SER cc_start: 0.8646 (t) cc_final: 0.8187 (m) REVERT: D 193 LYS cc_start: 0.8032 (mttt) cc_final: 0.7621 (tttp) REVERT: D 302 LYS cc_start: 0.8256 (ttmm) cc_final: 0.7983 (tttm) REVERT: D 432 LEU cc_start: 0.8387 (OUTLIER) cc_final: 0.7971 (mt) REVERT: D 534 ASP cc_start: 0.8310 (t70) cc_final: 0.7958 (t0) REVERT: E 20 LYS cc_start: 0.7903 (tttp) cc_final: 0.7682 (tttm) REVERT: E 126 ARG cc_start: 0.7749 (mtm180) cc_final: 0.7385 (mtp180) REVERT: E 212 GLU cc_start: 0.6721 (mm-30) cc_final: 0.6470 (mm-30) REVERT: E 368 LYS cc_start: 0.8561 (ttpp) cc_final: 0.7851 (tptt) REVERT: E 392 LYS cc_start: 0.7330 (ptpt) cc_final: 0.7024 (pttt) REVERT: E 410 ARG cc_start: 0.7725 (tmm-80) cc_final: 0.7507 (tmm160) REVERT: E 514 LYS cc_start: 0.8959 (mtmt) cc_final: 0.8705 (mtmt) REVERT: E 535 LYS cc_start: 0.7779 (pttp) cc_final: 0.7283 (pttm) REVERT: G 152 MET cc_start: 0.7822 (mmm) cc_final: 0.7582 (mmt) REVERT: G 202 GLU cc_start: 0.7532 (mm-30) cc_final: 0.7316 (mm-30) REVERT: G 284 GLN cc_start: 0.7525 (tp-100) cc_final: 0.7279 (tp40) REVERT: G 382 GLU cc_start: 0.8216 (mp0) cc_final: 0.7990 (mp0) REVERT: G 464 THR cc_start: 0.8356 (m) cc_final: 0.8055 (p) REVERT: H 10 LYS cc_start: 0.7548 (ttpp) cc_final: 0.7237 (ttpt) REVERT: H 22 LEU cc_start: 0.7951 (OUTLIER) cc_final: 0.7659 (tp) REVERT: H 151 GLN cc_start: 0.7610 (tm-30) cc_final: 0.7174 (tt0) REVERT: H 177 LYS cc_start: 0.7745 (tttp) cc_final: 0.7376 (ttmt) REVERT: H 191 GLN cc_start: 0.8435 (OUTLIER) cc_final: 0.8171 (mt0) REVERT: H 344 ARG cc_start: 0.7374 (ttm110) cc_final: 0.6970 (mtp-110) REVERT: H 402 ASN cc_start: 0.7200 (t0) cc_final: 0.6953 (t0) REVERT: H 440 LYS cc_start: 0.8445 (tptt) cc_final: 0.8208 (tppt) REVERT: H 456 ASP cc_start: 0.7179 (p0) cc_final: 0.6904 (t0) REVERT: N 22 CYS cc_start: 0.5359 (t) cc_final: 0.5046 (t) REVERT: Q 31 ARG cc_start: 0.7440 (mmp-170) cc_final: 0.7050 (mmt90) REVERT: Q 37 LYS cc_start: 0.7879 (tttt) cc_final: 0.7666 (tttm) REVERT: Q 52 MET cc_start: 0.8652 (mmm) cc_final: 0.8381 (mmp) REVERT: Q 55 MET cc_start: 0.7975 (mtm) cc_final: 0.7745 (mtt) REVERT: Q 238 LYS cc_start: 0.7426 (mmtp) cc_final: 0.6407 (mttp) REVERT: Q 299 ASP cc_start: 0.7669 (m-30) cc_final: 0.7281 (m-30) REVERT: Q 318 LYS cc_start: 0.7321 (pttm) cc_final: 0.7023 (pttp) REVERT: Q 344 MET cc_start: 0.7855 (ttm) cc_final: 0.7649 (tpp) REVERT: Q 357 ASP cc_start: 0.7186 (t0) cc_final: 0.6733 (p0) REVERT: Q 386 ASP cc_start: 0.8265 (m-30) cc_final: 0.8043 (m-30) REVERT: Q 433 LEU cc_start: 0.7591 (mt) cc_final: 0.7116 (mp) REVERT: Q 494 GLU cc_start: 0.8161 (tm-30) cc_final: 0.7663 (mm-30) REVERT: Z 133 PHE cc_start: 0.7569 (t80) cc_final: 0.7154 (t80) REVERT: Z 153 ARG cc_start: 0.6863 (ttp-170) cc_final: 0.6584 (ttp-110) REVERT: Z 195 GLU cc_start: 0.8152 (pt0) cc_final: 0.7903 (pt0) REVERT: Z 251 LYS cc_start: 0.8839 (pttt) cc_final: 0.8639 (pttp) REVERT: Z 385 THR cc_start: 0.8297 (m) cc_final: 0.7662 (p) REVERT: a 47 ASP cc_start: 0.6892 (t0) cc_final: 0.6664 (t0) REVERT: a 63 LYS cc_start: 0.7550 (mtpt) cc_final: 0.7121 (ptpt) REVERT: a 123 LEU cc_start: 0.7980 (mt) cc_final: 0.7768 (mp) REVERT: a 209 MET cc_start: 0.7625 (mtm) cc_final: 0.7318 (mtp) REVERT: a 247 LYS cc_start: 0.7312 (pttm) cc_final: 0.6803 (pttp) REVERT: a 276 GLN cc_start: 0.7605 (mm110) cc_final: 0.7299 (mt0) REVERT: a 382 ASP cc_start: 0.7370 (m-30) cc_final: 0.6861 (m-30) REVERT: a 406 LYS cc_start: 0.5910 (mmpt) cc_final: 0.5534 (mmmt) REVERT: a 505 GLU cc_start: 0.7404 (mt-10) cc_final: 0.7109 (mt-10) REVERT: a 532 LYS cc_start: 0.8468 (tttt) cc_final: 0.8098 (tttm) REVERT: b 236 LYS cc_start: 0.7342 (mttm) cc_final: 0.7120 (mtmm) REVERT: b 242 THR cc_start: 0.8736 (p) cc_final: 0.8532 (p) REVERT: b 347 LYS cc_start: 0.8106 (mmtm) cc_final: 0.7651 (mtmm) REVERT: b 441 LYS cc_start: 0.7353 (mtmm) cc_final: 0.7111 (mmmt) REVERT: d 27 ARG cc_start: 0.6589 (mmm-85) cc_final: 0.6182 (mpp80) REVERT: d 196 ASP cc_start: 0.7884 (t0) cc_final: 0.7253 (p0) REVERT: d 222 GLU cc_start: 0.6446 (OUTLIER) cc_final: 0.6138 (mp0) REVERT: d 277 ARG cc_start: 0.7100 (ttm-80) cc_final: 0.6747 (ttm-80) REVERT: d 363 GLU cc_start: 0.7651 (tt0) cc_final: 0.7288 (pt0) REVERT: d 395 LYS cc_start: 0.7387 (tptt) cc_final: 0.7095 (mmmt) REVERT: d 418 LYS cc_start: 0.7471 (ttmt) cc_final: 0.7214 (tptp) REVERT: d 429 GLU cc_start: 0.7849 (mp0) cc_final: 0.7580 (mp0) REVERT: e 21 ASP cc_start: 0.7071 (m-30) cc_final: 0.6867 (m-30) REVERT: e 67 ASP cc_start: 0.7213 (m-30) cc_final: 0.6940 (t70) REVERT: e 132 ARG cc_start: 0.7474 (mmm-85) cc_final: 0.7217 (mtt180) REVERT: e 263 LYS cc_start: 0.7899 (ttmt) cc_final: 0.7530 (mtmt) REVERT: e 316 GLN cc_start: 0.8027 (OUTLIER) cc_final: 0.7665 (tt0) REVERT: e 444 GLU cc_start: 0.6929 (mm-30) cc_final: 0.6435 (mm-30) REVERT: e 501 MET cc_start: 0.5500 (mmp) cc_final: 0.5256 (mmt) REVERT: e 533 ILE cc_start: 0.8734 (mt) cc_final: 0.8516 (mp) REVERT: e 540 GLU cc_start: 0.5041 (OUTLIER) cc_final: 0.4547 (pt0) REVERT: g 8 LEU cc_start: 0.5221 (OUTLIER) cc_final: 0.4838 (tt) REVERT: g 21 LYS cc_start: 0.7703 (mmtm) cc_final: 0.6926 (mtmm) REVERT: g 31 LYS cc_start: 0.6994 (mtpt) cc_final: 0.6736 (mtmt) REVERT: g 44 LYS cc_start: 0.8482 (mttt) cc_final: 0.8222 (mmmt) REVERT: g 69 GLU cc_start: 0.7344 (mm-30) cc_final: 0.7130 (mm-30) REVERT: g 84 SER cc_start: 0.8395 (t) cc_final: 0.8013 (p) REVERT: g 200 ARG cc_start: 0.7819 (tpt170) cc_final: 0.7170 (tpt-90) REVERT: g 242 ASP cc_start: 0.7603 (m-30) cc_final: 0.6761 (m-30) REVERT: g 294 LYS cc_start: 0.8127 (mmmm) cc_final: 0.7815 (mmtp) REVERT: g 298 ASP cc_start: 0.7527 (m-30) cc_final: 0.7264 (m-30) REVERT: g 358 GLU cc_start: 0.7674 (mm-30) cc_final: 0.7379 (tp30) REVERT: g 368 ASP cc_start: 0.7558 (t70) cc_final: 0.7314 (t0) REVERT: h 1 MET cc_start: 0.3979 (tpt) cc_final: 0.3700 (mmm) REVERT: h 30 GLN cc_start: 0.8094 (mm-40) cc_final: 0.7823 (mt0) REVERT: h 153 LYS cc_start: 0.7633 (mmtt) cc_final: 0.7238 (mttp) REVERT: h 156 GLU cc_start: 0.7257 (mt-10) cc_final: 0.6802 (pt0) REVERT: h 220 PHE cc_start: 0.7869 (t80) cc_final: 0.7365 (t80) REVERT: h 320 LYS cc_start: 0.8392 (mtpp) cc_final: 0.8076 (mmmt) REVERT: h 338 SER cc_start: 0.7579 (OUTLIER) cc_final: 0.7296 (p) REVERT: h 356 GLU cc_start: 0.7686 (mm-30) cc_final: 0.7243 (mm-30) REVERT: h 368 LYS cc_start: 0.8421 (mttt) cc_final: 0.8068 (mmmt) REVERT: h 386 GLU cc_start: 0.7796 (tt0) cc_final: 0.7577 (tt0) REVERT: h 391 ASP cc_start: 0.7629 (m-30) cc_final: 0.7330 (m-30) REVERT: h 459 ASN cc_start: 0.7758 (m110) cc_final: 0.7250 (t0) REVERT: h 521 LYS cc_start: 0.8226 (mttt) cc_final: 0.7935 (mtmt) REVERT: q 20 LYS cc_start: 0.8345 (mttt) cc_final: 0.8120 (mtmt) REVERT: q 34 GLN cc_start: 0.7760 (tp-100) cc_final: 0.6877 (tp-100) REVERT: q 41 GLN cc_start: 0.7766 (mm-40) cc_final: 0.7534 (mt0) REVERT: q 235 LYS cc_start: 0.8385 (mptp) cc_final: 0.7899 (tttp) REVERT: q 281 LYS cc_start: 0.7782 (ttmt) cc_final: 0.7559 (tttm) REVERT: q 343 GLU cc_start: 0.7520 (mt-10) cc_final: 0.7278 (mm-30) REVERT: q 348 ASP cc_start: 0.6986 (m-30) cc_final: 0.6643 (m-30) REVERT: q 354 GLU cc_start: 0.8250 (tt0) cc_final: 0.7900 (tt0) REVERT: q 382 ASP cc_start: 0.7524 (m-30) cc_final: 0.7194 (m-30) REVERT: q 434 GLU cc_start: 0.6983 (pt0) cc_final: 0.6616 (pm20) REVERT: q 459 LYS cc_start: 0.8159 (mmtm) cc_final: 0.7949 (tppt) REVERT: q 522 ASP cc_start: 0.7447 (t70) cc_final: 0.7232 (t70) REVERT: q 526 MET cc_start: 0.8506 (mtp) cc_final: 0.8303 (mtt) REVERT: q 534 LYS cc_start: 0.3268 (OUTLIER) cc_final: 0.1155 (tttp) REVERT: z 114 LEU cc_start: 0.7815 (tp) cc_final: 0.7575 (tp) REVERT: z 175 SER cc_start: 0.8000 (t) cc_final: 0.7792 (p) REVERT: z 181 LYS cc_start: 0.7067 (mttt) cc_final: 0.6646 (mtpt) REVERT: z 240 GLU cc_start: 0.7758 (mm-30) cc_final: 0.7314 (pt0) REVERT: z 241 LYS cc_start: 0.8435 (ttmt) cc_final: 0.7883 (pttp) REVERT: z 258 LYS cc_start: 0.7884 (mttt) cc_final: 0.7646 (mtmt) REVERT: z 264 ARG cc_start: 0.7238 (mtp85) cc_final: 0.6707 (mtp85) REVERT: z 272 LYS cc_start: 0.7235 (mttt) cc_final: 0.6860 (mmpt) REVERT: z 315 ARG cc_start: 0.7389 (mtm180) cc_final: 0.7133 (mmt180) REVERT: z 359 LYS cc_start: 0.7814 (mttt) cc_final: 0.7458 (mtmt) REVERT: K 91 TYR cc_start: 0.6539 (OUTLIER) cc_final: 0.5672 (m-10) REVERT: K 154 ASP cc_start: 0.3953 (t70) cc_final: 0.3501 (t70) REVERT: K 187 ASP cc_start: 0.6298 (m-30) cc_final: 0.6094 (m-30) REVERT: K 312 ARG cc_start: 0.5413 (tpt-90) cc_final: 0.5053 (ttt180) REVERT: P 65 GLU cc_start: 0.4342 (mm-30) cc_final: 0.3786 (tt0) outliers start: 115 outliers final: 55 residues processed: 1756 average time/residue: 0.7600 time to fit residues: 2198.4165 Evaluate side-chains 1099 residues out of total 7685 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 1034 time to evaluate : 6.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 GLU Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 537 SER Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 55 SER Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 432 LEU Chi-restraints excluded: chain D residue 461 ILE Chi-restraints excluded: chain E residue 65 ASP Chi-restraints excluded: chain E residue 163 GLU Chi-restraints excluded: chain E residue 316 GLN Chi-restraints excluded: chain E residue 372 LEU Chi-restraints excluded: chain E residue 408 VAL Chi-restraints excluded: chain E residue 418 VAL Chi-restraints excluded: chain G residue 460 ILE Chi-restraints excluded: chain H residue 6 VAL Chi-restraints excluded: chain H residue 9 LEU Chi-restraints excluded: chain H residue 22 LEU Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 191 GLN Chi-restraints excluded: chain H residue 338 SER Chi-restraints excluded: chain H residue 362 THR Chi-restraints excluded: chain H residue 405 VAL Chi-restraints excluded: chain H residue 460 ILE Chi-restraints excluded: chain Q residue 105 LEU Chi-restraints excluded: chain Z residue 281 VAL Chi-restraints excluded: chain a residue 352 VAL Chi-restraints excluded: chain b residue 35 ILE Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain b residue 52 LEU Chi-restraints excluded: chain b residue 55 SER Chi-restraints excluded: chain b residue 513 VAL Chi-restraints excluded: chain d residue 222 GLU Chi-restraints excluded: chain d residue 374 LEU Chi-restraints excluded: chain d residue 385 THR Chi-restraints excluded: chain d residue 404 SER Chi-restraints excluded: chain e residue 316 GLN Chi-restraints excluded: chain e residue 408 VAL Chi-restraints excluded: chain e residue 442 THR Chi-restraints excluded: chain e residue 540 GLU Chi-restraints excluded: chain g residue 8 LEU Chi-restraints excluded: chain g residue 460 ILE Chi-restraints excluded: chain g residue 528 LYS Chi-restraints excluded: chain g residue 529 LYS Chi-restraints excluded: chain h residue 9 LEU Chi-restraints excluded: chain h residue 85 SER Chi-restraints excluded: chain h residue 226 GLU Chi-restraints excluded: chain h residue 322 THR Chi-restraints excluded: chain h residue 338 SER Chi-restraints excluded: chain h residue 362 THR Chi-restraints excluded: chain h residue 460 ILE Chi-restraints excluded: chain q residue 534 LYS Chi-restraints excluded: chain z residue 526 MET Chi-restraints excluded: chain K residue 82 MET Chi-restraints excluded: chain K residue 91 TYR Chi-restraints excluded: chain K residue 183 ARG Chi-restraints excluded: chain K residue 221 LEU Chi-restraints excluded: chain K residue 261 LEU Chi-restraints excluded: chain K residue 309 ILE Chi-restraints excluded: chain K residue 328 LYS Chi-restraints excluded: chain K residue 336 LYS Chi-restraints excluded: chain P residue 91 PHE Chi-restraints excluded: chain P residue 139 ARG Chi-restraints excluded: chain P residue 165 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 912 random chunks: chunk 770 optimal weight: 4.9990 chunk 691 optimal weight: 6.9990 chunk 383 optimal weight: 1.9990 chunk 236 optimal weight: 0.9990 chunk 466 optimal weight: 7.9990 chunk 369 optimal weight: 3.9990 chunk 714 optimal weight: 8.9990 chunk 276 optimal weight: 10.0000 chunk 434 optimal weight: 0.8980 chunk 532 optimal weight: 2.9990 chunk 828 optimal weight: 2.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 20 GLN A 103 ASN A 150 ASN ** A 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 217 ASN A 475 GLN A 482 ASN ** B 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 122 HIS B 228 GLN B 285 HIS B 294 GLN B 361 HIS B 381 GLN D 72 ASN D 138 GLN D 235 ASN D 271 GLN D 347 HIS D 482 ASN E 22 GLN E 55 ASN E 86 GLN E 139 GLN E 298 ASN E 316 GLN E 435 GLN E 445 GLN E 465 ASN E 504 GLN G 4 HIS G 61 ASN G 116 GLN ** G 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 269 GLN G 390 ASN G 392 GLN G 472 GLN G 504 GLN H 252 ASN H 272 ASN H 431 GLN H 470 GLN H 522 ASN Q 201 ASN ** Q 365 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 68 GLN ** Z 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 95 ASN Z 161 HIS ** Z 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 438 GLN Z 460 GLN a 20 GLN a 103 ASN a 113 HIS a 150 ASN a 475 GLN b 65 ASN ** b 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 228 GLN b 285 HIS b 294 GLN b 381 GLN b 419 HIS b 502 GLN d 80 GLN d 125 GLN d 189 ASN d 301 GLN d 366 ASN e 22 GLN e 86 GLN e 139 GLN e 316 GLN e 360 GLN e 465 ASN g 71 GLN g 87 GLN g 116 GLN ** g 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 235 ASN g 253 GLN g 276 GLN g 453 GLN g 504 GLN g 544 GLN h 264 GLN h 272 ASN h 459 ASN h 470 GLN ** h 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 172 GLN ** q 365 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** z 8 ASN z 71 HIS ** z 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 161 HIS z 438 GLN K 59 GLN K 111 ASN K 115 ASN K 371 HIS P 11 ASN P 59 HIS ** P 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 104 GLN P 157 ASN Total number of N/Q/H flips: 96 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7239 moved from start: 0.1503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 71861 Z= 0.250 Angle : 0.610 12.770 97066 Z= 0.307 Chirality : 0.043 0.171 11504 Planarity : 0.004 0.066 12403 Dihedral : 8.437 179.923 10102 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.44 % Favored : 96.51 % Rotamer: Outliers : 2.50 % Allowed : 14.10 % Favored : 83.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.37 % 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: -0.46 (0.08), residues: 9177 helix: 0.76 (0.07), residues: 4649 sheet: -0.93 (0.14), residues: 1234 loop : -1.53 (0.10), residues: 3294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP b 130 HIS 0.013 0.001 HIS K 371 PHE 0.018 0.001 PHE G 112 TYR 0.024 0.002 TYR P 169 ARG 0.012 0.001 ARG z 323 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18354 Ramachandran restraints generated. 9177 Oldfield, 0 Emsley, 9177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18354 Ramachandran restraints generated. 9177 Oldfield, 0 Emsley, 9177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1261 residues out of total 7685 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 192 poor density : 1069 time to evaluate : 6.489 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 GLU cc_start: 0.7346 (tt0) cc_final: 0.6854 (mm-30) REVERT: A 80 ASP cc_start: 0.7562 (t70) cc_final: 0.6933 (m-30) REVERT: A 84 LYS cc_start: 0.7976 (mtmm) cc_final: 0.7740 (mmmt) REVERT: A 123 LEU cc_start: 0.8330 (mt) cc_final: 0.8127 (mp) REVERT: A 189 ARG cc_start: 0.6363 (mtp85) cc_final: 0.6158 (mtp85) REVERT: A 245 LYS cc_start: 0.8090 (tttt) cc_final: 0.7832 (tttm) REVERT: A 261 ASP cc_start: 0.7331 (OUTLIER) cc_final: 0.7128 (m-30) REVERT: A 309 ARG cc_start: 0.8366 (ptt180) cc_final: 0.7689 (ptt180) REVERT: A 389 GLU cc_start: 0.7877 (tt0) cc_final: 0.7547 (tt0) REVERT: A 532 LYS cc_start: 0.8248 (tttt) cc_final: 0.7888 (ttpt) REVERT: B 414 GLU cc_start: 0.7700 (mp0) cc_final: 0.7279 (mp0) REVERT: B 445 MET cc_start: 0.8130 (OUTLIER) cc_final: 0.7805 (ttp) REVERT: D 42 LYS cc_start: 0.8062 (tttp) cc_final: 0.7831 (tppt) REVERT: D 187 SER cc_start: 0.8621 (t) cc_final: 0.7986 (m) REVERT: D 193 LYS cc_start: 0.7950 (mttt) cc_final: 0.7579 (tttp) REVERT: D 302 LYS cc_start: 0.8078 (ttmm) cc_final: 0.7754 (tttm) REVERT: D 309 LEU cc_start: 0.8664 (OUTLIER) cc_final: 0.8374 (tp) REVERT: D 534 ASP cc_start: 0.8223 (t0) cc_final: 0.7955 (t0) REVERT: E 20 LYS cc_start: 0.7917 (tttp) cc_final: 0.7708 (tttm) REVERT: E 126 ARG cc_start: 0.7889 (mtm180) cc_final: 0.7252 (mtp180) REVERT: E 163 GLU cc_start: 0.7866 (OUTLIER) cc_final: 0.6937 (mp0) REVERT: E 212 GLU cc_start: 0.6618 (mm-30) cc_final: 0.6397 (mm-30) REVERT: E 368 LYS cc_start: 0.8552 (ttpp) cc_final: 0.7915 (tptt) REVERT: E 514 LYS cc_start: 0.8949 (mtmt) cc_final: 0.8590 (mtpt) REVERT: E 532 ASP cc_start: 0.8095 (t0) cc_final: 0.7871 (t0) REVERT: E 535 LYS cc_start: 0.8139 (pttp) cc_final: 0.7657 (pttm) REVERT: G 133 MET cc_start: 0.7794 (mtt) cc_final: 0.7159 (mtt) REVERT: G 151 MET cc_start: 0.7917 (ttm) cc_final: 0.7566 (ttp) REVERT: G 152 MET cc_start: 0.7856 (mmm) cc_final: 0.7533 (mmt) REVERT: G 202 GLU cc_start: 0.7504 (mm-30) cc_final: 0.7288 (mm-30) REVERT: G 248 LYS cc_start: 0.7989 (mtpt) cc_final: 0.7757 (mtpt) REVERT: G 277 GLN cc_start: 0.6870 (tp-100) cc_final: 0.6521 (tt0) REVERT: G 284 GLN cc_start: 0.7575 (tp-100) cc_final: 0.7371 (tp40) REVERT: G 382 GLU cc_start: 0.8143 (mp0) cc_final: 0.7415 (mp0) REVERT: H 10 LYS cc_start: 0.7631 (ttpp) cc_final: 0.7306 (ttpt) REVERT: H 22 LEU cc_start: 0.7930 (OUTLIER) cc_final: 0.7666 (tp) REVERT: H 151 GLN cc_start: 0.7651 (tm-30) cc_final: 0.7205 (tt0) REVERT: H 177 LYS cc_start: 0.7643 (tttp) cc_final: 0.7278 (ttmt) REVERT: H 220 PHE cc_start: 0.8447 (t80) cc_final: 0.8158 (t80) REVERT: H 227 MET cc_start: 0.8780 (mtp) cc_final: 0.8568 (mtm) REVERT: H 240 LEU cc_start: 0.8576 (OUTLIER) cc_final: 0.8165 (mt) REVERT: H 344 ARG cc_start: 0.7492 (ttm110) cc_final: 0.7075 (mtp-110) REVERT: H 402 ASN cc_start: 0.7193 (t0) cc_final: 0.6993 (t0) REVERT: H 440 LYS cc_start: 0.8484 (tptt) cc_final: 0.8274 (tppt) REVERT: H 456 ASP cc_start: 0.7112 (p0) cc_final: 0.6754 (t0) REVERT: N 82 MET cc_start: 0.2267 (mmm) cc_final: 0.1905 (mmp) REVERT: Q 31 ARG cc_start: 0.7319 (mmp-170) cc_final: 0.6986 (mmt90) REVERT: Q 37 LYS cc_start: 0.7865 (tttt) cc_final: 0.7649 (tttm) REVERT: Q 52 MET cc_start: 0.8679 (mmm) cc_final: 0.8354 (mmp) REVERT: Q 55 MET cc_start: 0.7939 (mtm) cc_final: 0.7611 (mtt) REVERT: Q 238 LYS cc_start: 0.7420 (mmtp) cc_final: 0.6731 (mptt) REVERT: Q 299 ASP cc_start: 0.7681 (m-30) cc_final: 0.7225 (m-30) REVERT: Q 354 GLU cc_start: 0.7720 (tt0) cc_final: 0.7492 (tt0) REVERT: Q 357 ASP cc_start: 0.7058 (t0) cc_final: 0.6654 (p0) REVERT: Q 386 ASP cc_start: 0.8233 (m-30) cc_final: 0.8020 (m-30) REVERT: Q 433 LEU cc_start: 0.7599 (mt) cc_final: 0.7303 (mp) REVERT: Q 494 GLU cc_start: 0.8131 (tm-30) cc_final: 0.7899 (mm-30) REVERT: Z 15 ARG cc_start: 0.7259 (mtt180) cc_final: 0.7028 (tpp80) REVERT: Z 217 ARG cc_start: 0.7754 (mtp85) cc_final: 0.7095 (mmm160) REVERT: Z 258 LYS cc_start: 0.7814 (mttt) cc_final: 0.7598 (mttm) REVERT: Z 264 ARG cc_start: 0.7273 (mtp85) cc_final: 0.6393 (mtp-110) REVERT: a 47 ASP cc_start: 0.6976 (t0) cc_final: 0.6661 (t0) REVERT: a 63 LYS cc_start: 0.7527 (mtpt) cc_final: 0.7094 (ptpt) REVERT: a 156 MET cc_start: 0.8642 (OUTLIER) cc_final: 0.8415 (mtm) REVERT: a 209 MET cc_start: 0.7590 (mtm) cc_final: 0.7270 (mtp) REVERT: a 247 LYS cc_start: 0.7363 (pttm) cc_final: 0.6948 (pttp) REVERT: a 276 GLN cc_start: 0.7497 (mm110) cc_final: 0.7019 (mt0) REVERT: a 382 ASP cc_start: 0.7355 (m-30) cc_final: 0.7089 (m-30) REVERT: a 505 GLU cc_start: 0.7253 (mt-10) cc_final: 0.6930 (mt-10) REVERT: a 532 LYS cc_start: 0.8456 (tttt) cc_final: 0.8097 (tttm) REVERT: b 242 THR cc_start: 0.8665 (p) cc_final: 0.8432 (p) REVERT: b 347 LYS cc_start: 0.8236 (mmtm) cc_final: 0.7736 (mtmm) REVERT: b 414 GLU cc_start: 0.7923 (mp0) cc_final: 0.7657 (mp0) REVERT: d 27 ARG cc_start: 0.6636 (mmm-85) cc_final: 0.6373 (mpp80) REVERT: d 196 ASP cc_start: 0.7848 (t0) cc_final: 0.7131 (p0) REVERT: d 222 GLU cc_start: 0.6620 (mt-10) cc_final: 0.6226 (mp0) REVERT: d 277 ARG cc_start: 0.7187 (ttm-80) cc_final: 0.6807 (ttm-80) REVERT: d 363 GLU cc_start: 0.7702 (tt0) cc_final: 0.7251 (pt0) REVERT: d 429 GLU cc_start: 0.7866 (mp0) cc_final: 0.7429 (mp0) REVERT: e 67 ASP cc_start: 0.7125 (m-30) cc_final: 0.6838 (t70) REVERT: e 210 LYS cc_start: 0.8199 (tttp) cc_final: 0.7912 (tttt) REVERT: e 263 LYS cc_start: 0.7906 (ttmt) cc_final: 0.7491 (mtmt) REVERT: e 383 VAL cc_start: 0.8275 (OUTLIER) cc_final: 0.8066 (t) REVERT: e 501 MET cc_start: 0.5627 (mmp) cc_final: 0.5340 (mmt) REVERT: e 503 GLN cc_start: 0.7603 (tt0) cc_final: 0.7007 (mt0) REVERT: e 540 GLU cc_start: 0.5273 (OUTLIER) cc_final: 0.4712 (pt0) REVERT: g 21 LYS cc_start: 0.7615 (mmtm) cc_final: 0.6975 (mtmm) REVERT: g 31 LYS cc_start: 0.6970 (mtpt) cc_final: 0.6760 (mtmt) REVERT: g 44 LYS cc_start: 0.8417 (mttt) cc_final: 0.8162 (mmmt) REVERT: g 52 ASP cc_start: 0.6824 (t0) cc_final: 0.6584 (t70) REVERT: g 61 ASN cc_start: 0.8510 (OUTLIER) cc_final: 0.8135 (p0) REVERT: g 69 GLU cc_start: 0.7524 (mm-30) cc_final: 0.7145 (mm-30) REVERT: g 84 SER cc_start: 0.8323 (t) cc_final: 0.7833 (p) REVERT: g 133 MET cc_start: 0.7156 (mtt) cc_final: 0.6736 (mtt) REVERT: g 150 ASP cc_start: 0.6935 (OUTLIER) cc_final: 0.6272 (p0) REVERT: g 200 ARG cc_start: 0.7726 (tpt170) cc_final: 0.7180 (tpt-90) REVERT: g 229 MET cc_start: 0.8480 (mtt) cc_final: 0.8152 (mtt) REVERT: g 242 ASP cc_start: 0.7446 (OUTLIER) cc_final: 0.7051 (m-30) REVERT: g 294 LYS cc_start: 0.8185 (mmmm) cc_final: 0.7799 (mmtp) REVERT: g 358 GLU cc_start: 0.7597 (mm-30) cc_final: 0.7325 (tp30) REVERT: g 368 ASP cc_start: 0.7599 (t70) cc_final: 0.7381 (t0) REVERT: g 406 GLN cc_start: 0.7578 (mm-40) cc_final: 0.7150 (mp10) REVERT: h 30 GLN cc_start: 0.8064 (mm-40) cc_final: 0.7821 (mt0) REVERT: h 153 LYS cc_start: 0.7600 (mmtt) cc_final: 0.7244 (mttp) REVERT: h 156 GLU cc_start: 0.7242 (mt-10) cc_final: 0.6782 (pt0) REVERT: h 217 LYS cc_start: 0.8907 (ttpt) cc_final: 0.8213 (ttpt) REVERT: h 240 LEU cc_start: 0.8262 (OUTLIER) cc_final: 0.7814 (mt) REVERT: h 320 LYS cc_start: 0.8406 (mtpp) cc_final: 0.8056 (mmtp) REVERT: h 356 GLU cc_start: 0.7763 (mm-30) cc_final: 0.7189 (mm-30) REVERT: h 368 LYS cc_start: 0.8402 (mttt) cc_final: 0.8039 (mmmt) REVERT: h 459 ASN cc_start: 0.7648 (m-40) cc_final: 0.7365 (t0) REVERT: h 521 LYS cc_start: 0.8143 (mttt) cc_final: 0.7895 (mtmt) REVERT: q 20 LYS cc_start: 0.8281 (mttt) cc_final: 0.8065 (mtmt) REVERT: q 34 GLN cc_start: 0.7728 (tp-100) cc_final: 0.6789 (tp-100) REVERT: q 38 GLU cc_start: 0.7460 (mt-10) cc_final: 0.6914 (mt-10) REVERT: q 41 GLN cc_start: 0.7789 (mm-40) cc_final: 0.7544 (mt0) REVERT: q 175 ASN cc_start: 0.8818 (OUTLIER) cc_final: 0.8555 (p0) REVERT: q 235 LYS cc_start: 0.8319 (mptp) cc_final: 0.7874 (tttp) REVERT: q 254 LYS cc_start: 0.8182 (tttm) cc_final: 0.7911 (tptt) REVERT: q 281 LYS cc_start: 0.7919 (ttmt) cc_final: 0.7600 (tttm) REVERT: q 343 GLU cc_start: 0.7474 (mt-10) cc_final: 0.7270 (mm-30) REVERT: q 348 ASP cc_start: 0.6844 (m-30) cc_final: 0.6549 (m-30) REVERT: q 382 ASP cc_start: 0.7491 (m-30) cc_final: 0.7288 (m-30) REVERT: q 434 GLU cc_start: 0.7225 (pt0) cc_final: 0.6700 (pm20) REVERT: q 534 LYS cc_start: 0.3350 (OUTLIER) cc_final: 0.1460 (tttp) REVERT: z 175 SER cc_start: 0.8331 (t) cc_final: 0.8078 (p) REVERT: z 181 LYS cc_start: 0.7063 (mttt) cc_final: 0.6682 (mtpt) REVERT: z 192 GLU cc_start: 0.7884 (tp30) cc_final: 0.7585 (tp30) REVERT: z 240 GLU cc_start: 0.7642 (mm-30) cc_final: 0.7312 (pt0) REVERT: z 241 LYS cc_start: 0.8431 (ttmt) cc_final: 0.7819 (pttp) REVERT: z 258 LYS cc_start: 0.7866 (mttt) cc_final: 0.7617 (mtmt) REVERT: z 264 ARG cc_start: 0.7194 (mtp85) cc_final: 0.6751 (mtp85) REVERT: z 272 LYS cc_start: 0.7219 (mttt) cc_final: 0.6843 (mmpt) REVERT: z 281 VAL cc_start: 0.8575 (OUTLIER) cc_final: 0.8292 (m) REVERT: z 315 ARG cc_start: 0.7353 (mtm180) cc_final: 0.7147 (mmt180) REVERT: z 359 LYS cc_start: 0.7838 (mttt) cc_final: 0.7612 (mtmt) REVERT: K 101 HIS cc_start: 0.7283 (m-70) cc_final: 0.6919 (m170) REVERT: K 147 ARG cc_start: 0.8574 (OUTLIER) cc_final: 0.8223 (ptp90) REVERT: K 154 ASP cc_start: 0.3997 (t70) cc_final: 0.3395 (t70) REVERT: K 187 ASP cc_start: 0.6227 (m-30) cc_final: 0.6008 (m-30) REVERT: K 207 GLU cc_start: 0.2593 (OUTLIER) cc_final: 0.2255 (tt0) REVERT: K 313 MET cc_start: 0.6156 (mmm) cc_final: 0.5831 (tpt) REVERT: K 363 ASP cc_start: 0.7161 (m-30) cc_final: 0.6947 (m-30) REVERT: P 65 GLU cc_start: 0.4555 (mm-30) cc_final: 0.3695 (tt0) outliers start: 192 outliers final: 110 residues processed: 1212 average time/residue: 0.7577 time to fit residues: 1572.0973 Evaluate side-chains 1053 residues out of total 7685 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 925 time to evaluate : 6.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 284 ASN Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 494 LYS Chi-restraints excluded: chain A residue 537 SER Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 412 CYS Chi-restraints excluded: chain B residue 422 THR Chi-restraints excluded: chain B residue 445 MET Chi-restraints excluded: chain D residue 65 LYS Chi-restraints excluded: chain D residue 186 MET Chi-restraints excluded: chain D residue 230 THR Chi-restraints excluded: chain D residue 267 SER Chi-restraints excluded: chain D residue 309 LEU Chi-restraints excluded: chain D residue 332 ASP Chi-restraints excluded: chain D residue 377 THR Chi-restraints excluded: chain D residue 404 SER Chi-restraints excluded: chain D residue 461 ILE Chi-restraints excluded: chain E residue 23 ASP Chi-restraints excluded: chain E residue 65 ASP Chi-restraints excluded: chain E residue 163 GLU Chi-restraints excluded: chain E residue 220 GLU Chi-restraints excluded: chain E residue 287 GLU Chi-restraints excluded: chain E residue 418 VAL Chi-restraints excluded: chain E residue 494 LEU Chi-restraints excluded: chain G residue 161 THR Chi-restraints excluded: chain G residue 192 GLU Chi-restraints excluded: chain G residue 209 ILE Chi-restraints excluded: chain G residue 341 ASP Chi-restraints excluded: chain G residue 373 THR Chi-restraints excluded: chain G residue 460 ILE Chi-restraints excluded: chain H residue 9 LEU Chi-restraints excluded: chain H residue 22 LEU Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 130 GLN Chi-restraints excluded: chain H residue 239 LEU Chi-restraints excluded: chain H residue 240 LEU Chi-restraints excluded: chain H residue 351 THR Chi-restraints excluded: chain H residue 362 THR Chi-restraints excluded: chain H residue 400 ILE Chi-restraints excluded: chain H residue 405 VAL Chi-restraints excluded: chain H residue 460 ILE Chi-restraints excluded: chain Q residue 23 SER Chi-restraints excluded: chain Q residue 105 LEU Chi-restraints excluded: chain Q residue 170 SER Chi-restraints excluded: chain Q residue 212 ILE Chi-restraints excluded: chain Q residue 253 THR Chi-restraints excluded: chain Q residue 480 LEU Chi-restraints excluded: chain Z residue 176 ILE Chi-restraints excluded: chain Z residue 335 SER Chi-restraints excluded: chain a residue 55 THR Chi-restraints excluded: chain a residue 156 MET Chi-restraints excluded: chain a residue 167 PHE Chi-restraints excluded: chain a residue 352 VAL Chi-restraints excluded: chain a residue 358 ASP Chi-restraints excluded: chain b residue 212 SER Chi-restraints excluded: chain b residue 363 SER Chi-restraints excluded: chain b residue 446 LEU Chi-restraints excluded: chain d residue 265 VAL Chi-restraints excluded: chain d residue 324 VAL Chi-restraints excluded: chain d residue 366 ASN Chi-restraints excluded: chain d residue 377 THR Chi-restraints excluded: chain d residue 385 THR Chi-restraints excluded: chain e residue 6 THR Chi-restraints excluded: chain e residue 298 ASN Chi-restraints excluded: chain e residue 383 VAL Chi-restraints excluded: chain e residue 408 VAL Chi-restraints excluded: chain e residue 418 VAL Chi-restraints excluded: chain e residue 540 GLU Chi-restraints excluded: chain g residue 61 ASN Chi-restraints excluded: chain g residue 150 ASP Chi-restraints excluded: chain g residue 161 THR Chi-restraints excluded: chain g residue 192 GLU Chi-restraints excluded: chain g residue 242 ASP Chi-restraints excluded: chain g residue 284 GLN Chi-restraints excluded: chain g residue 288 ASP Chi-restraints excluded: chain g residue 341 ASP Chi-restraints excluded: chain g residue 365 ASP Chi-restraints excluded: chain g residue 460 ILE Chi-restraints excluded: chain g residue 471 THR Chi-restraints excluded: chain g residue 508 THR Chi-restraints excluded: chain g residue 528 LYS Chi-restraints excluded: chain h residue 7 ILE Chi-restraints excluded: chain h residue 9 LEU Chi-restraints excluded: chain h residue 85 SER Chi-restraints excluded: chain h residue 142 THR Chi-restraints excluded: chain h residue 211 VAL Chi-restraints excluded: chain h residue 240 LEU Chi-restraints excluded: chain h residue 251 ASP Chi-restraints excluded: chain h residue 362 THR Chi-restraints excluded: chain h residue 400 ILE Chi-restraints excluded: chain h residue 460 ILE Chi-restraints excluded: chain q residue 130 GLU Chi-restraints excluded: chain q residue 170 SER Chi-restraints excluded: chain q residue 175 ASN Chi-restraints excluded: chain q residue 212 ILE Chi-restraints excluded: chain q residue 218 LEU Chi-restraints excluded: chain q residue 253 THR Chi-restraints excluded: chain q residue 475 ASN Chi-restraints excluded: chain q residue 480 LEU Chi-restraints excluded: chain q residue 534 LYS Chi-restraints excluded: chain z residue 67 MET Chi-restraints excluded: chain z residue 88 THR Chi-restraints excluded: chain z residue 135 GLU Chi-restraints excluded: chain z residue 149 ILE Chi-restraints excluded: chain z residue 280 LYS Chi-restraints excluded: chain z residue 281 VAL Chi-restraints excluded: chain z residue 338 ASP Chi-restraints excluded: chain z residue 408 VAL Chi-restraints excluded: chain z residue 476 LEU Chi-restraints excluded: chain z residue 526 MET Chi-restraints excluded: chain K residue 67 LEU Chi-restraints excluded: chain K residue 115 ASN Chi-restraints excluded: chain K residue 141 SER Chi-restraints excluded: chain K residue 147 ARG Chi-restraints excluded: chain K residue 179 ASP Chi-restraints excluded: chain K residue 207 GLU Chi-restraints excluded: chain K residue 299 LEU Chi-restraints excluded: chain K residue 309 ILE Chi-restraints excluded: chain K residue 316 GLU Chi-restraints excluded: chain K residue 318 THR Chi-restraints excluded: chain K residue 336 LYS Chi-restraints excluded: chain P residue 53 LEU Chi-restraints excluded: chain P residue 91 PHE Chi-restraints excluded: chain P residue 95 LEU Chi-restraints excluded: chain P residue 139 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 912 random chunks: chunk 460 optimal weight: 6.9990 chunk 257 optimal weight: 9.9990 chunk 689 optimal weight: 9.9990 chunk 563 optimal weight: 6.9990 chunk 228 optimal weight: 9.9990 chunk 829 optimal weight: 5.9990 chunk 896 optimal weight: 5.9990 chunk 738 optimal weight: 2.9990 chunk 822 optimal weight: 9.9990 chunk 282 optimal weight: 3.9990 chunk 665 optimal weight: 5.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 65 ASN B 298 ASN B 419 HIS D 406 HIS E 278 GLN E 360 GLN E 516 GLN G 61 ASN ** G 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 390 ASN ** H 60 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 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 276 GLN a 458 GLN b 122 HIS ** b 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 302 GLN ** b 419 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 366 ASN d 406 HIS e 55 ASN e 435 GLN g 87 GLN g 226 HIS ** h 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 81 GLN q 80 HIS ** q 365 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** z 425 HIS K 111 ASN K 353 GLN ** P 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7325 moved from start: 0.1992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.071 71861 Z= 0.484 Angle : 0.718 13.870 97066 Z= 0.358 Chirality : 0.048 0.190 11504 Planarity : 0.005 0.075 12403 Dihedral : 8.072 176.804 10036 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.11 % Favored : 95.84 % Rotamer: Outliers : 3.44 % Allowed : 15.61 % Favored : 80.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.37 % 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: -0.48 (0.08), residues: 9177 helix: 0.63 (0.07), residues: 4618 sheet: -0.84 (0.14), residues: 1271 loop : -1.36 (0.10), residues: 3288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP P 10 HIS 0.009 0.002 HIS B 419 PHE 0.023 0.002 PHE h 220 TYR 0.023 0.002 TYR P 169 ARG 0.008 0.001 ARG E 202 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18354 Ramachandran restraints generated. 9177 Oldfield, 0 Emsley, 9177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18354 Ramachandran restraints generated. 9177 Oldfield, 0 Emsley, 9177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1227 residues out of total 7685 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 264 poor density : 963 time to evaluate : 7.062 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 GLU cc_start: 0.7429 (tt0) cc_final: 0.6912 (mm-30) REVERT: A 80 ASP cc_start: 0.7587 (t70) cc_final: 0.6877 (m-30) REVERT: A 84 LYS cc_start: 0.8124 (mtmm) cc_final: 0.7785 (mmmt) REVERT: A 156 MET cc_start: 0.8044 (mtp) cc_final: 0.7669 (mtp) REVERT: A 171 MET cc_start: 0.7193 (mtp) cc_final: 0.6925 (mtm) REVERT: A 245 LYS cc_start: 0.8161 (tttt) cc_final: 0.7799 (tttm) REVERT: A 251 GLN cc_start: 0.8206 (mt0) cc_final: 0.8004 (tt0) REVERT: A 309 ARG cc_start: 0.8335 (ptt180) cc_final: 0.7669 (ptt180) REVERT: A 337 GLU cc_start: 0.7619 (OUTLIER) cc_final: 0.7183 (mm-30) REVERT: A 344 MET cc_start: 0.7499 (mmt) cc_final: 0.7097 (mmm) REVERT: A 473 GLU cc_start: 0.7138 (tt0) cc_final: 0.6782 (tp30) REVERT: B 445 MET cc_start: 0.8306 (OUTLIER) cc_final: 0.7980 (ttp) REVERT: B 480 MET cc_start: 0.8355 (mmm) cc_final: 0.8084 (mmm) REVERT: D 42 LYS cc_start: 0.8103 (tttp) cc_final: 0.7787 (tppt) REVERT: D 187 SER cc_start: 0.8676 (t) cc_final: 0.8012 (m) REVERT: D 193 LYS cc_start: 0.8161 (mttt) cc_final: 0.7650 (tttp) REVERT: D 302 LYS cc_start: 0.8197 (ttmm) cc_final: 0.7760 (tttm) REVERT: D 374 LEU cc_start: 0.8781 (OUTLIER) cc_final: 0.8402 (tm) REVERT: D 533 ASP cc_start: 0.7569 (OUTLIER) cc_final: 0.7100 (p0) REVERT: D 534 ASP cc_start: 0.8321 (t0) cc_final: 0.8049 (t0) REVERT: E 4 MET cc_start: 0.6107 (mmp) cc_final: 0.5688 (mmp) REVERT: E 20 LYS cc_start: 0.7899 (tttp) cc_final: 0.7682 (tttm) REVERT: E 91 MET cc_start: 0.8695 (mmp) cc_final: 0.8482 (mmp) REVERT: E 149 ASP cc_start: 0.7733 (m-30) cc_final: 0.7186 (m-30) REVERT: E 368 LYS cc_start: 0.8566 (ttpp) cc_final: 0.7898 (tptt) REVERT: E 383 VAL cc_start: 0.8794 (OUTLIER) cc_final: 0.8573 (t) REVERT: E 392 LYS cc_start: 0.7253 (ptpt) cc_final: 0.6881 (pttt) REVERT: E 407 CYS cc_start: 0.8259 (m) cc_final: 0.7574 (m) REVERT: E 514 LYS cc_start: 0.8969 (mtmt) cc_final: 0.8632 (mttt) REVERT: E 529 LYS cc_start: 0.8724 (OUTLIER) cc_final: 0.8278 (tttm) REVERT: E 535 LYS cc_start: 0.8301 (pttp) cc_final: 0.7826 (pttm) REVERT: G 47 MET cc_start: 0.8571 (mmm) cc_final: 0.6602 (mmm) REVERT: G 152 MET cc_start: 0.7883 (mmm) cc_final: 0.7395 (mmt) REVERT: G 202 GLU cc_start: 0.7503 (mm-30) cc_final: 0.7247 (mm-30) REVERT: G 248 LYS cc_start: 0.8020 (mtpt) cc_final: 0.7791 (mtpt) REVERT: G 277 GLN cc_start: 0.6881 (tp-100) cc_final: 0.6367 (tt0) REVERT: H 10 LYS cc_start: 0.7700 (ttpp) cc_final: 0.7376 (ttpt) REVERT: H 22 LEU cc_start: 0.7971 (OUTLIER) cc_final: 0.7609 (tt) REVERT: H 151 GLN cc_start: 0.7663 (tm-30) cc_final: 0.7379 (tt0) REVERT: H 344 ARG cc_start: 0.7601 (ttm110) cc_final: 0.7176 (mtp-110) REVERT: H 402 ASN cc_start: 0.7373 (t0) cc_final: 0.7162 (t0) REVERT: H 413 GLU cc_start: 0.7994 (mp0) cc_final: 0.7771 (mp0) REVERT: H 440 LYS cc_start: 0.8625 (tptt) cc_final: 0.8221 (tttp) REVERT: H 456 ASP cc_start: 0.7340 (OUTLIER) cc_final: 0.6786 (t0) REVERT: N 22 CYS cc_start: 0.5499 (t) cc_final: 0.5289 (t) REVERT: N 82 MET cc_start: 0.2069 (mmm) cc_final: 0.1670 (mmp) REVERT: Q 31 ARG cc_start: 0.7433 (mmp-170) cc_final: 0.7072 (mmt90) REVERT: Q 52 MET cc_start: 0.8684 (mmm) cc_final: 0.8257 (mmp) REVERT: Q 55 MET cc_start: 0.7954 (mtm) cc_final: 0.7584 (mtm) REVERT: Q 238 LYS cc_start: 0.7458 (mmtp) cc_final: 0.6681 (mptt) REVERT: Q 299 ASP cc_start: 0.7752 (m-30) cc_final: 0.7278 (m-30) REVERT: Q 357 ASP cc_start: 0.7164 (t0) cc_final: 0.6709 (p0) REVERT: Q 393 ASP cc_start: 0.7464 (OUTLIER) cc_final: 0.6746 (m-30) REVERT: Z 258 LYS cc_start: 0.7923 (mttt) cc_final: 0.7691 (mttm) REVERT: Z 264 ARG cc_start: 0.7399 (mtp85) cc_final: 0.6532 (mtp-110) REVERT: a 43 LYS cc_start: 0.8380 (OUTLIER) cc_final: 0.8027 (mttp) REVERT: a 47 ASP cc_start: 0.7043 (t0) cc_final: 0.6770 (t0) REVERT: a 63 LYS cc_start: 0.7520 (mtpt) cc_final: 0.7104 (ptpt) REVERT: a 106 GLU cc_start: 0.7059 (OUTLIER) cc_final: 0.6786 (pt0) REVERT: a 209 MET cc_start: 0.7659 (mtm) cc_final: 0.7228 (mtp) REVERT: a 247 LYS cc_start: 0.7512 (pttm) cc_final: 0.7071 (pttp) REVERT: a 276 GLN cc_start: 0.7433 (OUTLIER) cc_final: 0.7040 (mt0) REVERT: a 382 ASP cc_start: 0.7435 (m-30) cc_final: 0.7014 (m-30) REVERT: a 443 ARG cc_start: 0.7419 (ttp80) cc_final: 0.6979 (ttp80) REVERT: a 532 LYS cc_start: 0.8540 (tttt) cc_final: 0.8177 (tttm) REVERT: b 242 THR cc_start: 0.8762 (p) cc_final: 0.8530 (p) REVERT: b 280 GLU cc_start: 0.7126 (tp30) cc_final: 0.6911 (tp30) REVERT: b 347 LYS cc_start: 0.8210 (mmtm) cc_final: 0.7705 (mtmt) REVERT: b 414 GLU cc_start: 0.8034 (mp0) cc_final: 0.7768 (mp0) REVERT: d 27 ARG cc_start: 0.6731 (mmm-85) cc_final: 0.6348 (mpp80) REVERT: d 46 ASP cc_start: 0.7028 (m-30) cc_final: 0.6745 (m-30) REVERT: d 101 GLU cc_start: 0.7175 (tt0) cc_final: 0.6958 (tt0) REVERT: d 277 ARG cc_start: 0.7306 (ttm-80) cc_final: 0.6918 (ttm-80) REVERT: d 363 GLU cc_start: 0.7733 (tt0) cc_final: 0.7319 (pt0) REVERT: d 429 GLU cc_start: 0.7805 (mp0) cc_final: 0.7256 (mp0) REVERT: d 505 GLU cc_start: 0.7681 (pp20) cc_final: 0.7223 (tp30) REVERT: e 21 ASP cc_start: 0.7314 (m-30) cc_final: 0.7056 (m-30) REVERT: e 67 ASP cc_start: 0.7244 (m-30) cc_final: 0.6853 (t70) REVERT: e 210 LYS cc_start: 0.8277 (tttp) cc_final: 0.7944 (tttt) REVERT: e 263 LYS cc_start: 0.7943 (ttmt) cc_final: 0.7590 (mtmt) REVERT: e 381 ARG cc_start: 0.7694 (OUTLIER) cc_final: 0.7394 (ttt-90) REVERT: e 501 MET cc_start: 0.5741 (mmp) cc_final: 0.5159 (mmt) REVERT: e 503 GLN cc_start: 0.7708 (tt0) cc_final: 0.7031 (mt0) REVERT: e 540 GLU cc_start: 0.5343 (OUTLIER) cc_final: 0.4733 (pt0) REVERT: g 21 LYS cc_start: 0.7554 (mmtm) cc_final: 0.6849 (mtmm) REVERT: g 31 LYS cc_start: 0.7286 (mtpt) cc_final: 0.6999 (mtmt) REVERT: g 52 ASP cc_start: 0.7008 (t0) cc_final: 0.6685 (t70) REVERT: g 61 ASN cc_start: 0.8535 (OUTLIER) cc_final: 0.8147 (p0) REVERT: g 84 SER cc_start: 0.8373 (t) cc_final: 0.7835 (p) REVERT: g 133 MET cc_start: 0.7249 (mtt) cc_final: 0.6762 (mtt) REVERT: g 200 ARG cc_start: 0.7780 (tpt170) cc_final: 0.7282 (tpt-90) REVERT: g 242 ASP cc_start: 0.7969 (OUTLIER) cc_final: 0.7314 (m-30) REVERT: g 358 GLU cc_start: 0.7557 (mm-30) cc_final: 0.7243 (tp30) REVERT: g 368 ASP cc_start: 0.7664 (t70) cc_final: 0.7419 (t0) REVERT: g 406 GLN cc_start: 0.7722 (mm-40) cc_final: 0.7344 (mp10) REVERT: h 153 LYS cc_start: 0.7642 (mmtt) cc_final: 0.7196 (mtmt) REVERT: h 156 GLU cc_start: 0.7309 (mt-10) cc_final: 0.6810 (pt0) REVERT: h 254 GLU cc_start: 0.7942 (OUTLIER) cc_final: 0.7701 (tp30) REVERT: h 320 LYS cc_start: 0.8442 (mtpp) cc_final: 0.7999 (mmmt) REVERT: h 356 GLU cc_start: 0.7794 (mm-30) cc_final: 0.7248 (mm-30) REVERT: h 368 LYS cc_start: 0.8355 (mttt) cc_final: 0.7811 (mmmt) REVERT: h 414 MET cc_start: 0.8604 (mmm) cc_final: 0.8309 (mmm) REVERT: h 459 ASN cc_start: 0.7703 (m-40) cc_final: 0.7243 (t0) REVERT: h 478 ASP cc_start: 0.7799 (t70) cc_final: 0.7564 (t0) REVERT: h 521 LYS cc_start: 0.8204 (mttt) cc_final: 0.7978 (mtmt) REVERT: q 20 LYS cc_start: 0.8399 (mttt) cc_final: 0.8073 (mtmt) REVERT: q 34 GLN cc_start: 0.7774 (tp-100) cc_final: 0.6955 (tp-100) REVERT: q 113 GLU cc_start: 0.7101 (OUTLIER) cc_final: 0.6896 (mt-10) REVERT: q 175 ASN cc_start: 0.8953 (OUTLIER) cc_final: 0.8730 (p0) REVERT: q 181 LYS cc_start: 0.7724 (mmmt) cc_final: 0.7454 (tppt) REVERT: q 254 LYS cc_start: 0.8332 (tttm) cc_final: 0.7997 (tttt) REVERT: q 281 LYS cc_start: 0.7996 (ttmt) cc_final: 0.7536 (tttm) REVERT: q 382 ASP cc_start: 0.7670 (m-30) cc_final: 0.7433 (m-30) REVERT: q 534 LYS cc_start: 0.2799 (OUTLIER) cc_final: 0.1153 (tttp) REVERT: z 144 ASP cc_start: 0.6842 (p0) cc_final: 0.6575 (p0) REVERT: z 181 LYS cc_start: 0.7231 (mttt) cc_final: 0.6777 (mtpt) REVERT: z 240 GLU cc_start: 0.7771 (mm-30) cc_final: 0.7327 (pt0) REVERT: z 241 LYS cc_start: 0.8548 (ttmt) cc_final: 0.7797 (pttp) REVERT: z 258 LYS cc_start: 0.8008 (mttt) cc_final: 0.7700 (mtmt) REVERT: z 264 ARG cc_start: 0.7371 (mtp85) cc_final: 0.6850 (mtp85) REVERT: z 338 ASP cc_start: 0.7676 (OUTLIER) cc_final: 0.7224 (m-30) REVERT: z 359 LYS cc_start: 0.7977 (mttt) cc_final: 0.7733 (mtmt) REVERT: K 101 HIS cc_start: 0.7302 (m-70) cc_final: 0.6983 (m170) REVERT: K 147 ARG cc_start: 0.8680 (OUTLIER) cc_final: 0.8382 (ptp90) REVERT: P 65 GLU cc_start: 0.4555 (mm-30) cc_final: 0.3746 (tt0) REVERT: P 116 ILE cc_start: 0.6756 (OUTLIER) cc_final: 0.6440 (mp) REVERT: P 139 ARG cc_start: 0.6206 (OUTLIER) cc_final: 0.5517 (mtp-110) outliers start: 264 outliers final: 175 residues processed: 1158 average time/residue: 0.6897 time to fit residues: 1354.6827 Evaluate side-chains 1091 residues out of total 7685 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 199 poor density : 892 time to evaluate : 6.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 GLU Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 284 ASN Chi-restraints excluded: chain A residue 337 GLU Chi-restraints excluded: chain A residue 350 GLU Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 528 ASP Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 134 THR Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain B residue 412 CYS Chi-restraints excluded: chain B residue 422 THR Chi-restraints excluded: chain B residue 445 MET Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 230 THR Chi-restraints excluded: chain D residue 267 SER Chi-restraints excluded: chain D residue 296 ASN Chi-restraints excluded: chain D residue 332 ASP Chi-restraints excluded: chain D residue 374 LEU Chi-restraints excluded: chain D residue 377 THR Chi-restraints excluded: chain D residue 404 SER Chi-restraints excluded: chain D residue 422 ILE Chi-restraints excluded: chain D residue 437 THR Chi-restraints excluded: chain D residue 442 THR Chi-restraints excluded: chain D residue 490 THR Chi-restraints excluded: chain D residue 519 LEU Chi-restraints excluded: chain D residue 533 ASP Chi-restraints excluded: chain E residue 23 ASP Chi-restraints excluded: chain E residue 47 THR Chi-restraints excluded: chain E residue 65 ASP Chi-restraints excluded: chain E residue 163 GLU Chi-restraints excluded: chain E residue 220 GLU Chi-restraints excluded: chain E residue 287 GLU Chi-restraints excluded: chain E residue 298 ASN Chi-restraints excluded: chain E residue 372 LEU Chi-restraints excluded: chain E residue 383 VAL Chi-restraints excluded: chain E residue 408 VAL Chi-restraints excluded: chain E residue 418 VAL Chi-restraints excluded: chain E residue 494 LEU Chi-restraints excluded: chain E residue 529 LYS Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 146 ILE Chi-restraints excluded: chain G residue 161 THR Chi-restraints excluded: chain G residue 192 GLU Chi-restraints excluded: chain G residue 209 ILE Chi-restraints excluded: chain G residue 255 ASP Chi-restraints excluded: chain G residue 341 ASP Chi-restraints excluded: chain G residue 373 THR Chi-restraints excluded: chain G residue 460 ILE Chi-restraints excluded: chain H residue 9 LEU Chi-restraints excluded: chain H residue 22 LEU Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 130 GLN Chi-restraints excluded: chain H residue 239 LEU Chi-restraints excluded: chain H residue 351 THR Chi-restraints excluded: chain H residue 362 THR Chi-restraints excluded: chain H residue 400 ILE Chi-restraints excluded: chain H residue 404 SER Chi-restraints excluded: chain H residue 405 VAL Chi-restraints excluded: chain H residue 427 ILE Chi-restraints excluded: chain H residue 456 ASP Chi-restraints excluded: chain Q residue 3 LEU Chi-restraints excluded: chain Q residue 23 SER Chi-restraints excluded: chain Q residue 105 LEU Chi-restraints excluded: chain Q residue 168 ILE Chi-restraints excluded: chain Q residue 170 SER Chi-restraints excluded: chain Q residue 175 ASN Chi-restraints excluded: chain Q residue 212 ILE Chi-restraints excluded: chain Q residue 253 THR Chi-restraints excluded: chain Q residue 289 ASN Chi-restraints excluded: chain Q residue 296 LYS Chi-restraints excluded: chain Q residue 393 ASP Chi-restraints excluded: chain Q residue 475 ASN Chi-restraints excluded: chain Q residue 480 LEU Chi-restraints excluded: chain Z residue 4 VAL Chi-restraints excluded: chain Z residue 108 LEU Chi-restraints excluded: chain Z residue 149 ILE Chi-restraints excluded: chain Z residue 176 ILE Chi-restraints excluded: chain Z residue 257 GLU Chi-restraints excluded: chain Z residue 281 VAL Chi-restraints excluded: chain Z residue 429 VAL Chi-restraints excluded: chain Z residue 488 VAL Chi-restraints excluded: chain Z residue 526 MET Chi-restraints excluded: chain a residue 43 LYS Chi-restraints excluded: chain a residue 55 THR Chi-restraints excluded: chain a residue 106 GLU Chi-restraints excluded: chain a residue 129 VAL Chi-restraints excluded: chain a residue 166 ASP Chi-restraints excluded: chain a residue 167 PHE Chi-restraints excluded: chain a residue 276 GLN Chi-restraints excluded: chain a residue 329 SER Chi-restraints excluded: chain a residue 358 ASP Chi-restraints excluded: chain a residue 467 LEU Chi-restraints excluded: chain a residue 486 ILE Chi-restraints excluded: chain b residue 52 LEU Chi-restraints excluded: chain b residue 212 SER Chi-restraints excluded: chain b residue 261 THR Chi-restraints excluded: chain b residue 363 SER Chi-restraints excluded: chain b residue 434 VAL Chi-restraints excluded: chain b residue 446 LEU Chi-restraints excluded: chain b residue 513 VAL Chi-restraints excluded: chain d residue 26 ASP Chi-restraints excluded: chain d residue 50 THR Chi-restraints excluded: chain d residue 265 VAL Chi-restraints excluded: chain d residue 311 ASP Chi-restraints excluded: chain d residue 324 VAL Chi-restraints excluded: chain d residue 374 LEU Chi-restraints excluded: chain d residue 377 THR Chi-restraints excluded: chain d residue 385 THR Chi-restraints excluded: chain d residue 411 VAL Chi-restraints excluded: chain d residue 468 ASN Chi-restraints excluded: chain e residue 6 THR Chi-restraints excluded: chain e residue 298 ASN Chi-restraints excluded: chain e residue 381 ARG Chi-restraints excluded: chain e residue 408 VAL Chi-restraints excluded: chain e residue 418 VAL Chi-restraints excluded: chain e residue 498 THR Chi-restraints excluded: chain e residue 540 GLU Chi-restraints excluded: chain g residue 41 LEU Chi-restraints excluded: chain g residue 61 ASN Chi-restraints excluded: chain g residue 73 GLN Chi-restraints excluded: chain g residue 83 ILE Chi-restraints excluded: chain g residue 161 THR Chi-restraints excluded: chain g residue 192 GLU Chi-restraints excluded: chain g residue 242 ASP Chi-restraints excluded: chain g residue 284 GLN Chi-restraints excluded: chain g residue 288 ASP Chi-restraints excluded: chain g residue 341 ASP Chi-restraints excluded: chain g residue 365 ASP Chi-restraints excluded: chain g residue 373 THR Chi-restraints excluded: chain g residue 460 ILE Chi-restraints excluded: chain g residue 471 THR Chi-restraints excluded: chain g residue 508 THR Chi-restraints excluded: chain g residue 528 LYS Chi-restraints excluded: chain h residue 7 ILE Chi-restraints excluded: chain h residue 9 LEU Chi-restraints excluded: chain h residue 85 SER Chi-restraints excluded: chain h residue 142 THR Chi-restraints excluded: chain h residue 211 VAL Chi-restraints excluded: chain h residue 219 THR Chi-restraints excluded: chain h residue 251 ASP Chi-restraints excluded: chain h residue 254 GLU Chi-restraints excluded: chain h residue 308 MET Chi-restraints excluded: chain h residue 362 THR Chi-restraints excluded: chain h residue 382 MET Chi-restraints excluded: chain h residue 400 ILE Chi-restraints excluded: chain h residue 404 SER Chi-restraints excluded: chain h residue 427 ILE Chi-restraints excluded: chain n residue 27 THR Chi-restraints excluded: chain q residue 113 GLU Chi-restraints excluded: chain q residue 130 GLU Chi-restraints excluded: chain q residue 146 LEU Chi-restraints excluded: chain q residue 170 SER Chi-restraints excluded: chain q residue 175 ASN Chi-restraints excluded: chain q residue 212 ILE Chi-restraints excluded: chain q residue 218 LEU Chi-restraints excluded: chain q residue 253 THR Chi-restraints excluded: chain q residue 318 LYS Chi-restraints excluded: chain q residue 355 VAL Chi-restraints excluded: chain q residue 357 ASP Chi-restraints excluded: chain q residue 385 MET Chi-restraints excluded: chain q residue 475 ASN Chi-restraints excluded: chain q residue 480 LEU Chi-restraints excluded: chain q residue 534 LYS Chi-restraints excluded: chain z residue 67 MET Chi-restraints excluded: chain z residue 135 GLU Chi-restraints excluded: chain z residue 149 ILE Chi-restraints excluded: chain z residue 159 LYS Chi-restraints excluded: chain z residue 280 LYS Chi-restraints excluded: chain z residue 281 VAL Chi-restraints excluded: chain z residue 286 ASP Chi-restraints excluded: chain z residue 338 ASP Chi-restraints excluded: chain z residue 340 SER Chi-restraints excluded: chain z residue 408 VAL Chi-restraints excluded: chain z residue 432 ARG Chi-restraints excluded: chain z residue 476 LEU Chi-restraints excluded: chain z residue 526 MET Chi-restraints excluded: chain K residue 66 THR Chi-restraints excluded: chain K residue 67 LEU Chi-restraints excluded: chain K residue 82 MET Chi-restraints excluded: chain K residue 141 SER Chi-restraints excluded: chain K residue 147 ARG Chi-restraints excluded: chain K residue 179 ASP Chi-restraints excluded: chain K residue 267 LEU Chi-restraints excluded: chain K residue 272 CYS Chi-restraints excluded: chain K residue 299 LEU Chi-restraints excluded: chain K residue 309 ILE Chi-restraints excluded: chain K residue 318 THR Chi-restraints excluded: chain K residue 336 LYS Chi-restraints excluded: chain P residue 53 LEU Chi-restraints excluded: chain P residue 91 PHE Chi-restraints excluded: chain P residue 95 LEU Chi-restraints excluded: chain P residue 116 ILE Chi-restraints excluded: chain P residue 139 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 912 random chunks: chunk 819 optimal weight: 0.9990 chunk 623 optimal weight: 4.9990 chunk 430 optimal weight: 9.9990 chunk 91 optimal weight: 3.9990 chunk 395 optimal weight: 4.9990 chunk 557 optimal weight: 0.9980 chunk 832 optimal weight: 5.9990 chunk 881 optimal weight: 3.9990 chunk 435 optimal weight: 0.8980 chunk 789 optimal weight: 0.6980 chunk 237 optimal weight: 7.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 502 GLN G 61 ASN ** G 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 60 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 ** Z 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 302 GLN ** b 419 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 453 ASN d 32 GLN d 366 ASN e 290 GLN h 30 GLN ** h 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 365 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** z 245 ASN K 115 ASN ** P 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7270 moved from start: 0.2161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 71861 Z= 0.206 Angle : 0.563 11.358 97066 Z= 0.282 Chirality : 0.042 0.159 11504 Planarity : 0.004 0.063 12403 Dihedral : 7.435 170.887 10027 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.29 % Favored : 96.66 % Rotamer: Outliers : 2.56 % Allowed : 16.78 % Favored : 80.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.37 % 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: 0.04 (0.09), residues: 9177 helix: 1.06 (0.08), residues: 4636 sheet: -0.70 (0.14), residues: 1303 loop : -1.11 (0.10), residues: 3238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP b 130 HIS 0.011 0.001 HIS Z 161 PHE 0.013 0.001 PHE a 167 TYR 0.027 0.001 TYR P 120 ARG 0.009 0.000 ARG B 481 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18354 Ramachandran restraints generated. 9177 Oldfield, 0 Emsley, 9177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18354 Ramachandran restraints generated. 9177 Oldfield, 0 Emsley, 9177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1168 residues out of total 7685 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 196 poor density : 972 time to evaluate : 7.181 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 GLU cc_start: 0.7397 (tt0) cc_final: 0.6887 (mm-30) REVERT: A 80 ASP cc_start: 0.7559 (t70) cc_final: 0.6911 (m-30) REVERT: A 81 LEU cc_start: 0.8554 (tp) cc_final: 0.8263 (tp) REVERT: A 84 LYS cc_start: 0.8059 (mtmm) cc_final: 0.7696 (mmmt) REVERT: A 171 MET cc_start: 0.6902 (mtp) cc_final: 0.6689 (mtp) REVERT: A 216 LEU cc_start: 0.8928 (mt) cc_final: 0.8574 (tp) REVERT: A 245 LYS cc_start: 0.8164 (tttt) cc_final: 0.7892 (tttm) REVERT: A 251 GLN cc_start: 0.8161 (mt0) cc_final: 0.7892 (tt0) REVERT: A 298 LYS cc_start: 0.8209 (mmtt) cc_final: 0.7914 (mmtm) REVERT: A 309 ARG cc_start: 0.8273 (ptt180) cc_final: 0.7624 (ptt180) REVERT: A 337 GLU cc_start: 0.7455 (OUTLIER) cc_final: 0.6798 (tm-30) REVERT: A 344 MET cc_start: 0.7463 (mmt) cc_final: 0.7073 (mmm) REVERT: A 359 ASP cc_start: 0.7882 (OUTLIER) cc_final: 0.7648 (t0) REVERT: A 473 GLU cc_start: 0.7227 (tt0) cc_final: 0.6793 (tp30) REVERT: D 42 LYS cc_start: 0.8022 (tttp) cc_final: 0.7814 (tppt) REVERT: D 187 SER cc_start: 0.8585 (t) cc_final: 0.7863 (m) REVERT: D 193 LYS cc_start: 0.8069 (mttt) cc_final: 0.7657 (tttp) REVERT: D 302 LYS cc_start: 0.8141 (ttmm) cc_final: 0.7688 (tttm) REVERT: D 534 ASP cc_start: 0.8287 (t0) cc_final: 0.8050 (t0) REVERT: E 4 MET cc_start: 0.5948 (mmp) cc_final: 0.5582 (mmp) REVERT: E 20 LYS cc_start: 0.7882 (tttp) cc_final: 0.7638 (tttm) REVERT: E 81 MET cc_start: 0.8195 (ttp) cc_final: 0.7993 (ttm) REVERT: E 149 ASP cc_start: 0.7678 (m-30) cc_final: 0.7135 (m-30) REVERT: E 368 LYS cc_start: 0.8592 (ttpp) cc_final: 0.7998 (tptt) REVERT: E 383 VAL cc_start: 0.8801 (OUTLIER) cc_final: 0.8591 (m) REVERT: E 468 MET cc_start: 0.7796 (mpp) cc_final: 0.7324 (mpp) REVERT: E 514 LYS cc_start: 0.8960 (mtmt) cc_final: 0.8758 (mtmt) REVERT: E 535 LYS cc_start: 0.8302 (pttp) cc_final: 0.7819 (pttm) REVERT: G 47 MET cc_start: 0.8517 (mmm) cc_final: 0.6653 (mmm) REVERT: G 133 MET cc_start: 0.7790 (mtt) cc_final: 0.7192 (mtt) REVERT: G 152 MET cc_start: 0.7868 (mmm) cc_final: 0.7185 (mmt) REVERT: G 202 GLU cc_start: 0.7530 (mm-30) cc_final: 0.7278 (mm-30) REVERT: G 248 LYS cc_start: 0.8046 (mtpt) cc_final: 0.7793 (mtpt) REVERT: G 277 GLN cc_start: 0.6924 (tp-100) cc_final: 0.6475 (tt0) REVERT: H 10 LYS cc_start: 0.7706 (ttpp) cc_final: 0.7335 (ttpt) REVERT: H 22 LEU cc_start: 0.7903 (OUTLIER) cc_final: 0.7555 (tt) REVERT: H 151 GLN cc_start: 0.7538 (tm-30) cc_final: 0.7244 (tt0) REVERT: H 344 ARG cc_start: 0.7648 (ttm110) cc_final: 0.7139 (mtt-85) REVERT: H 440 LYS cc_start: 0.8610 (tptt) cc_final: 0.8243 (tttp) REVERT: H 456 ASP cc_start: 0.7242 (OUTLIER) cc_final: 0.6727 (t0) REVERT: N 22 CYS cc_start: 0.5437 (t) cc_final: 0.5228 (t) REVERT: N 82 MET cc_start: 0.2007 (mmm) cc_final: 0.1692 (mmp) REVERT: Q 31 ARG cc_start: 0.7312 (mmp-170) cc_final: 0.6967 (mmt90) REVERT: Q 52 MET cc_start: 0.8719 (mmm) cc_final: 0.8299 (mmp) REVERT: Q 55 MET cc_start: 0.7916 (mtm) cc_final: 0.7554 (mtm) REVERT: Q 164 LEU cc_start: 0.8613 (OUTLIER) cc_final: 0.8379 (mt) REVERT: Q 238 LYS cc_start: 0.7514 (mmtp) cc_final: 0.6802 (mptt) REVERT: Q 299 ASP cc_start: 0.7686 (m-30) cc_final: 0.7187 (m-30) REVERT: Q 311 MET cc_start: 0.9045 (ttm) cc_final: 0.8754 (ttm) REVERT: Q 354 GLU cc_start: 0.7802 (tt0) cc_final: 0.7571 (tt0) REVERT: Q 357 ASP cc_start: 0.7087 (t0) cc_final: 0.6635 (p0) REVERT: Q 494 GLU cc_start: 0.8093 (tm-30) cc_final: 0.7811 (mp0) REVERT: Z 257 GLU cc_start: 0.8141 (OUTLIER) cc_final: 0.7800 (mm-30) REVERT: Z 258 LYS cc_start: 0.7875 (mttt) cc_final: 0.7655 (mttm) REVERT: Z 264 ARG cc_start: 0.7396 (mtp85) cc_final: 0.6499 (mtp-110) REVERT: a 63 LYS cc_start: 0.7542 (mtpt) cc_final: 0.7143 (ptpt) REVERT: a 106 GLU cc_start: 0.7108 (OUTLIER) cc_final: 0.6835 (pt0) REVERT: a 189 ARG cc_start: 0.6615 (ttm-80) cc_final: 0.6272 (ttm-80) REVERT: a 247 LYS cc_start: 0.7446 (pttm) cc_final: 0.7032 (pttp) REVERT: a 299 TYR cc_start: 0.7097 (m-80) cc_final: 0.6807 (m-80) REVERT: a 360 GLU cc_start: 0.8080 (mt-10) cc_final: 0.7339 (mt-10) REVERT: a 382 ASP cc_start: 0.7435 (m-30) cc_final: 0.7171 (m-30) REVERT: a 443 ARG cc_start: 0.7179 (ttp80) cc_final: 0.6711 (ttp80) REVERT: a 505 GLU cc_start: 0.7454 (mt-10) cc_final: 0.7085 (mt-10) REVERT: a 532 LYS cc_start: 0.8524 (tttt) cc_final: 0.8177 (tttm) REVERT: b 130 TRP cc_start: 0.7911 (m-10) cc_final: 0.7662 (m100) REVERT: b 347 LYS cc_start: 0.8234 (mmtm) cc_final: 0.7720 (mtmt) REVERT: b 414 GLU cc_start: 0.7959 (mp0) cc_final: 0.7753 (mp0) REVERT: d 27 ARG cc_start: 0.6687 (mmm-85) cc_final: 0.6437 (mpp80) REVERT: d 46 ASP cc_start: 0.6950 (m-30) cc_final: 0.6718 (m-30) REVERT: d 78 LEU cc_start: 0.8769 (mt) cc_final: 0.8357 (mt) REVERT: d 101 GLU cc_start: 0.7102 (tt0) cc_final: 0.6900 (tt0) REVERT: d 196 ASP cc_start: 0.7967 (t0) cc_final: 0.7266 (p0) REVERT: d 232 LYS cc_start: 0.8318 (ptmm) cc_final: 0.7983 (ptmm) REVERT: d 277 ARG cc_start: 0.7282 (ttm-80) cc_final: 0.6923 (ttm-80) REVERT: d 363 GLU cc_start: 0.7690 (tt0) cc_final: 0.7296 (pt0) REVERT: d 393 SER cc_start: 0.8621 (p) cc_final: 0.8410 (t) REVERT: d 429 GLU cc_start: 0.7919 (mp0) cc_final: 0.7291 (mp0) REVERT: d 431 GLU cc_start: 0.7752 (tp30) cc_final: 0.7504 (tp30) REVERT: d 505 GLU cc_start: 0.7434 (pp20) cc_final: 0.7065 (tp30) REVERT: d 524 GLU cc_start: 0.7670 (tp30) cc_final: 0.7427 (tp30) REVERT: e 67 ASP cc_start: 0.7236 (m-30) cc_final: 0.6838 (t70) REVERT: e 91 MET cc_start: 0.8377 (mmm) cc_final: 0.8146 (mmm) REVERT: e 160 LYS cc_start: 0.8084 (mmtt) cc_final: 0.7641 (mptt) REVERT: e 210 LYS cc_start: 0.8221 (tttp) cc_final: 0.7940 (tttt) REVERT: e 263 LYS cc_start: 0.7971 (ttmt) cc_final: 0.7620 (mtmt) REVERT: e 381 ARG cc_start: 0.7569 (OUTLIER) cc_final: 0.7086 (ttt-90) REVERT: e 501 MET cc_start: 0.5800 (mmp) cc_final: 0.5349 (mmt) REVERT: e 503 GLN cc_start: 0.7629 (tt0) cc_final: 0.7011 (mt0) REVERT: g 21 LYS cc_start: 0.7465 (mmtm) cc_final: 0.6814 (mtmm) REVERT: g 31 LYS cc_start: 0.7099 (mtpt) cc_final: 0.6783 (mtmt) REVERT: g 52 ASP cc_start: 0.6981 (t0) cc_final: 0.6683 (t70) REVERT: g 61 ASN cc_start: 0.8434 (OUTLIER) cc_final: 0.8039 (p0) REVERT: g 70 ILE cc_start: 0.8135 (mt) cc_final: 0.7926 (pt) REVERT: g 84 SER cc_start: 0.8250 (t) cc_final: 0.7784 (p) REVERT: g 133 MET cc_start: 0.7202 (mtt) cc_final: 0.6881 (mtp) REVERT: g 200 ARG cc_start: 0.7831 (tpt170) cc_final: 0.7353 (tpt-90) REVERT: g 242 ASP cc_start: 0.7789 (OUTLIER) cc_final: 0.7366 (m-30) REVERT: g 294 LYS cc_start: 0.8168 (mmmm) cc_final: 0.7718 (mmtp) REVERT: g 358 GLU cc_start: 0.7549 (mm-30) cc_final: 0.7298 (tp30) REVERT: g 368 ASP cc_start: 0.7468 (t70) cc_final: 0.7219 (t0) REVERT: h 30 GLN cc_start: 0.8351 (mm-40) cc_final: 0.8125 (mm-40) REVERT: h 81 ASP cc_start: 0.6453 (m-30) cc_final: 0.6068 (m-30) REVERT: h 153 LYS cc_start: 0.7684 (mmtt) cc_final: 0.7270 (mtmt) REVERT: h 156 GLU cc_start: 0.7282 (mt-10) cc_final: 0.6712 (pt0) REVERT: h 240 LEU cc_start: 0.8313 (OUTLIER) cc_final: 0.7914 (mt) REVERT: h 320 LYS cc_start: 0.8340 (mtpp) cc_final: 0.8061 (mmmt) REVERT: h 324 MET cc_start: 0.8118 (mmt) cc_final: 0.7846 (mmt) REVERT: h 356 GLU cc_start: 0.7802 (mm-30) cc_final: 0.7432 (mm-30) REVERT: h 368 LYS cc_start: 0.8265 (mttt) cc_final: 0.7823 (mmmt) REVERT: h 414 MET cc_start: 0.8640 (mmm) cc_final: 0.8332 (mmt) REVERT: h 459 ASN cc_start: 0.7738 (m-40) cc_final: 0.7280 (t0) REVERT: h 521 LYS cc_start: 0.8133 (mttt) cc_final: 0.7870 (mtmt) REVERT: q 20 LYS cc_start: 0.8455 (mttt) cc_final: 0.8141 (mtmt) REVERT: q 34 GLN cc_start: 0.7642 (tp-100) cc_final: 0.6781 (tp-100) REVERT: q 38 GLU cc_start: 0.7459 (mt-10) cc_final: 0.6922 (mt-10) REVERT: q 175 ASN cc_start: 0.8896 (OUTLIER) cc_final: 0.8628 (p0) REVERT: q 181 LYS cc_start: 0.7703 (mmmt) cc_final: 0.7446 (tppt) REVERT: q 254 LYS cc_start: 0.8047 (tttm) cc_final: 0.7577 (tptt) REVERT: q 281 LYS cc_start: 0.7939 (ttmt) cc_final: 0.7609 (tttm) REVERT: q 382 ASP cc_start: 0.7613 (m-30) cc_final: 0.7396 (m-30) REVERT: q 534 LYS cc_start: 0.2820 (OUTLIER) cc_final: 0.1207 (tttp) REVERT: z 127 LYS cc_start: 0.6609 (OUTLIER) cc_final: 0.6253 (tttt) REVERT: z 181 LYS cc_start: 0.7102 (mttt) cc_final: 0.6700 (mtpt) REVERT: z 192 GLU cc_start: 0.7877 (tp30) cc_final: 0.7459 (tp30) REVERT: z 221 MET cc_start: 0.8700 (mtt) cc_final: 0.8378 (mtt) REVERT: z 240 GLU cc_start: 0.7674 (mm-30) cc_final: 0.7271 (pt0) REVERT: z 241 LYS cc_start: 0.8522 (ttmt) cc_final: 0.7777 (pttp) REVERT: z 258 LYS cc_start: 0.7914 (mttt) cc_final: 0.7650 (mtmt) REVERT: z 264 ARG cc_start: 0.7272 (mtp85) cc_final: 0.6792 (mtp85) REVERT: z 338 ASP cc_start: 0.7697 (OUTLIER) cc_final: 0.7224 (m-30) REVERT: z 358 GLU cc_start: 0.8005 (tt0) cc_final: 0.7654 (mp0) REVERT: z 359 LYS cc_start: 0.7935 (mttt) cc_final: 0.7702 (mtmt) REVERT: z 432 ARG cc_start: 0.7590 (OUTLIER) cc_final: 0.7043 (ptm160) REVERT: K 101 HIS cc_start: 0.7321 (m-70) cc_final: 0.7064 (m170) REVERT: K 178 LEU cc_start: 0.5225 (pt) cc_final: 0.4855 (mp) REVERT: K 207 GLU cc_start: 0.2617 (OUTLIER) cc_final: 0.2365 (tt0) REVERT: P 139 ARG cc_start: 0.6069 (OUTLIER) cc_final: 0.5486 (mtp-110) outliers start: 196 outliers final: 130 residues processed: 1121 average time/residue: 0.7227 time to fit residues: 1379.3099 Evaluate side-chains 1061 residues out of total 7685 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 912 time to evaluate : 6.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 GLU Chi-restraints excluded: chain A residue 284 ASN Chi-restraints excluded: chain A residue 337 GLU Chi-restraints excluded: chain A residue 359 ASP Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 532 LYS Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 267 SER Chi-restraints excluded: chain D residue 296 ASN Chi-restraints excluded: chain D residue 332 ASP Chi-restraints excluded: chain D residue 377 THR Chi-restraints excluded: chain D residue 404 SER Chi-restraints excluded: chain D residue 519 LEU Chi-restraints excluded: chain E residue 23 ASP Chi-restraints excluded: chain E residue 65 ASP Chi-restraints excluded: chain E residue 121 GLU Chi-restraints excluded: chain E residue 220 GLU Chi-restraints excluded: chain E residue 287 GLU Chi-restraints excluded: chain E residue 298 ASN Chi-restraints excluded: chain E residue 372 LEU Chi-restraints excluded: chain E residue 383 VAL Chi-restraints excluded: chain E residue 418 VAL Chi-restraints excluded: chain G residue 146 ILE Chi-restraints excluded: chain G residue 161 THR Chi-restraints excluded: chain G residue 192 GLU Chi-restraints excluded: chain G residue 252 SER Chi-restraints excluded: chain G residue 255 ASP Chi-restraints excluded: chain G residue 341 ASP Chi-restraints excluded: chain G residue 373 THR Chi-restraints excluded: chain G residue 458 SER Chi-restraints excluded: chain G residue 460 ILE Chi-restraints excluded: chain H residue 9 LEU Chi-restraints excluded: chain H residue 22 LEU Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 130 GLN Chi-restraints excluded: chain H residue 239 LEU Chi-restraints excluded: chain H residue 351 THR Chi-restraints excluded: chain H residue 362 THR Chi-restraints excluded: chain H residue 400 ILE Chi-restraints excluded: chain H residue 405 VAL Chi-restraints excluded: chain H residue 427 ILE Chi-restraints excluded: chain H residue 456 ASP Chi-restraints excluded: chain N residue 115 VAL Chi-restraints excluded: chain Q residue 23 SER Chi-restraints excluded: chain Q residue 105 LEU Chi-restraints excluded: chain Q residue 164 LEU Chi-restraints excluded: chain Q residue 175 ASN Chi-restraints excluded: chain Q residue 212 ILE Chi-restraints excluded: chain Q residue 253 THR Chi-restraints excluded: chain Q residue 480 LEU Chi-restraints excluded: chain Z residue 4 VAL Chi-restraints excluded: chain Z residue 108 LEU Chi-restraints excluded: chain Z residue 176 ILE Chi-restraints excluded: chain Z residue 195 GLU Chi-restraints excluded: chain Z residue 257 GLU Chi-restraints excluded: chain Z residue 488 VAL Chi-restraints excluded: chain a residue 55 THR Chi-restraints excluded: chain a residue 106 GLU Chi-restraints excluded: chain a residue 167 PHE Chi-restraints excluded: chain a residue 352 VAL Chi-restraints excluded: chain a residue 358 ASP Chi-restraints excluded: chain a residue 486 ILE Chi-restraints excluded: chain b residue 212 SER Chi-restraints excluded: chain b residue 261 THR Chi-restraints excluded: chain b residue 363 SER Chi-restraints excluded: chain b residue 434 VAL Chi-restraints excluded: chain b residue 446 LEU Chi-restraints excluded: chain b residue 485 ILE Chi-restraints excluded: chain b residue 513 VAL Chi-restraints excluded: chain d residue 71 THR Chi-restraints excluded: chain d residue 94 LEU Chi-restraints excluded: chain d residue 265 VAL Chi-restraints excluded: chain d residue 311 ASP Chi-restraints excluded: chain d residue 366 ASN Chi-restraints excluded: chain d residue 374 LEU Chi-restraints excluded: chain d residue 377 THR Chi-restraints excluded: chain d residue 385 THR Chi-restraints excluded: chain d residue 468 ASN Chi-restraints excluded: chain e residue 205 ASP Chi-restraints excluded: chain e residue 298 ASN Chi-restraints excluded: chain e residue 372 LEU Chi-restraints excluded: chain e residue 381 ARG Chi-restraints excluded: chain e residue 383 VAL Chi-restraints excluded: chain e residue 408 VAL Chi-restraints excluded: chain e residue 418 VAL Chi-restraints excluded: chain g residue 61 ASN Chi-restraints excluded: chain g residue 73 GLN Chi-restraints excluded: chain g residue 161 THR Chi-restraints excluded: chain g residue 192 GLU Chi-restraints excluded: chain g residue 242 ASP Chi-restraints excluded: chain g residue 288 ASP Chi-restraints excluded: chain g residue 341 ASP Chi-restraints excluded: chain g residue 365 ASP Chi-restraints excluded: chain g residue 407 LEU Chi-restraints excluded: chain g residue 460 ILE Chi-restraints excluded: chain g residue 528 LYS Chi-restraints excluded: chain h residue 7 ILE Chi-restraints excluded: chain h residue 9 LEU Chi-restraints excluded: chain h residue 142 THR Chi-restraints excluded: chain h residue 211 VAL Chi-restraints excluded: chain h residue 240 LEU Chi-restraints excluded: chain h residue 251 ASP Chi-restraints excluded: chain h residue 308 MET Chi-restraints excluded: chain h residue 322 THR Chi-restraints excluded: chain h residue 362 THR Chi-restraints excluded: chain h residue 382 MET Chi-restraints excluded: chain h residue 400 ILE Chi-restraints excluded: chain h residue 404 SER Chi-restraints excluded: chain h residue 427 ILE Chi-restraints excluded: chain q residue 105 LEU Chi-restraints excluded: chain q residue 125 VAL Chi-restraints excluded: chain q residue 130 GLU Chi-restraints excluded: chain q residue 146 LEU Chi-restraints excluded: chain q residue 175 ASN Chi-restraints excluded: chain q residue 212 ILE Chi-restraints excluded: chain q residue 218 LEU Chi-restraints excluded: chain q residue 253 THR Chi-restraints excluded: chain q residue 385 MET Chi-restraints excluded: chain q residue 475 ASN Chi-restraints excluded: chain q residue 480 LEU Chi-restraints excluded: chain q residue 534 LYS Chi-restraints excluded: chain z residue 67 MET Chi-restraints excluded: chain z residue 127 LYS Chi-restraints excluded: chain z residue 135 GLU Chi-restraints excluded: chain z residue 149 ILE Chi-restraints excluded: chain z residue 159 LYS Chi-restraints excluded: chain z residue 235 VAL Chi-restraints excluded: chain z residue 280 LYS Chi-restraints excluded: chain z residue 338 ASP Chi-restraints excluded: chain z residue 408 VAL Chi-restraints excluded: chain z residue 432 ARG Chi-restraints excluded: chain z residue 526 MET Chi-restraints excluded: chain K residue 67 LEU Chi-restraints excluded: chain K residue 82 MET Chi-restraints excluded: chain K residue 141 SER Chi-restraints excluded: chain K residue 179 ASP Chi-restraints excluded: chain K residue 207 GLU Chi-restraints excluded: chain K residue 272 CYS Chi-restraints excluded: chain K residue 309 ILE Chi-restraints excluded: chain K residue 318 THR Chi-restraints excluded: chain K residue 336 LYS Chi-restraints excluded: chain P residue 53 LEU Chi-restraints excluded: chain P residue 91 PHE Chi-restraints excluded: chain P residue 95 LEU Chi-restraints excluded: chain P residue 139 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 912 random chunks: chunk 734 optimal weight: 1.9990 chunk 500 optimal weight: 0.9990 chunk 12 optimal weight: 8.9990 chunk 656 optimal weight: 8.9990 chunk 363 optimal weight: 0.8980 chunk 752 optimal weight: 2.9990 chunk 609 optimal weight: 2.9990 chunk 1 optimal weight: 0.9980 chunk 450 optimal weight: 10.0000 chunk 791 optimal weight: 0.0170 chunk 222 optimal weight: 8.9990 overall best weight: 0.9822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 138 GLN ** H 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 65 HIS ** Z 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 276 GLN d 32 GLN d 366 ASN ** h 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 365 HIS K 111 ASN ** P 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7248 moved from start: 0.2357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 71861 Z= 0.167 Angle : 0.533 11.070 97066 Z= 0.265 Chirality : 0.041 0.176 11504 Planarity : 0.004 0.054 12403 Dihedral : 6.911 158.074 10019 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.27 % Favored : 96.70 % Rotamer: Outliers : 2.59 % Allowed : 17.25 % Favored : 80.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.37 % 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: 0.35 (0.09), residues: 9177 helix: 1.32 (0.08), residues: 4632 sheet: -0.55 (0.14), residues: 1301 loop : -0.95 (0.11), residues: 3244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP b 130 HIS 0.004 0.001 HIS G 111 PHE 0.012 0.001 PHE a 167 TYR 0.019 0.001 TYR P 120 ARG 0.010 0.000 ARG B 481 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18354 Ramachandran restraints generated. 9177 Oldfield, 0 Emsley, 9177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18354 Ramachandran restraints generated. 9177 Oldfield, 0 Emsley, 9177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1186 residues out of total 7685 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 199 poor density : 987 time to evaluate : 6.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 GLU cc_start: 0.7435 (tt0) cc_final: 0.6865 (mm-30) REVERT: A 80 ASP cc_start: 0.7585 (t70) cc_final: 0.6930 (m-30) REVERT: A 81 LEU cc_start: 0.8560 (tp) cc_final: 0.8268 (tp) REVERT: A 84 LYS cc_start: 0.7988 (mtmm) cc_final: 0.7680 (mmmt) REVERT: A 216 LEU cc_start: 0.8913 (mt) cc_final: 0.8547 (tp) REVERT: A 245 LYS cc_start: 0.8135 (tttt) cc_final: 0.7819 (tttm) REVERT: A 251 GLN cc_start: 0.7983 (mt0) cc_final: 0.7783 (tt0) REVERT: A 337 GLU cc_start: 0.7458 (OUTLIER) cc_final: 0.6801 (tm-30) REVERT: A 344 MET cc_start: 0.7431 (mmt) cc_final: 0.7103 (mmm) REVERT: A 473 GLU cc_start: 0.7249 (tt0) cc_final: 0.6646 (tp30) REVERT: B 22 GLU cc_start: 0.7216 (pm20) cc_final: 0.6930 (pm20) REVERT: B 273 GLU cc_start: 0.7605 (tp30) cc_final: 0.7356 (mm-30) REVERT: D 187 SER cc_start: 0.8542 (t) cc_final: 0.7787 (m) REVERT: D 193 LYS cc_start: 0.8053 (mttt) cc_final: 0.7521 (tttp) REVERT: D 309 LEU cc_start: 0.8715 (OUTLIER) cc_final: 0.8408 (tp) REVERT: D 355 MET cc_start: 0.8645 (mmm) cc_final: 0.8321 (mmt) REVERT: D 374 LEU cc_start: 0.8737 (OUTLIER) cc_final: 0.8401 (tm) REVERT: E 4 MET cc_start: 0.5869 (mmp) cc_final: 0.5572 (mmp) REVERT: E 20 LYS cc_start: 0.7911 (tttp) cc_final: 0.7642 (tttm) REVERT: E 126 ARG cc_start: 0.7968 (mtm180) cc_final: 0.7367 (mtp180) REVERT: E 199 MET cc_start: 0.7880 (mmm) cc_final: 0.7425 (mmm) REVERT: E 220 GLU cc_start: 0.7517 (OUTLIER) cc_final: 0.7142 (pm20) REVERT: E 368 LYS cc_start: 0.8446 (ttpp) cc_final: 0.7893 (tptt) REVERT: E 468 MET cc_start: 0.7741 (mpp) cc_final: 0.7263 (mpp) REVERT: E 501 MET cc_start: 0.7285 (mmt) cc_final: 0.6922 (mmm) REVERT: E 514 LYS cc_start: 0.8950 (mtmt) cc_final: 0.8619 (mtpt) REVERT: E 535 LYS cc_start: 0.8298 (pttp) cc_final: 0.7825 (pttm) REVERT: G 47 MET cc_start: 0.8474 (mmm) cc_final: 0.6724 (mmm) REVERT: G 71 GLN cc_start: 0.7810 (tp40) cc_final: 0.7274 (tt0) REVERT: G 133 MET cc_start: 0.7721 (mtt) cc_final: 0.7142 (mtt) REVERT: G 152 MET cc_start: 0.7903 (mmm) cc_final: 0.7190 (mmt) REVERT: G 202 GLU cc_start: 0.7561 (mm-30) cc_final: 0.7314 (mm-30) REVERT: G 277 GLN cc_start: 0.6977 (tp-100) cc_final: 0.6514 (tt0) REVERT: G 284 GLN cc_start: 0.7895 (tp40) cc_final: 0.7591 (mt0) REVERT: H 10 LYS cc_start: 0.7719 (ttpp) cc_final: 0.7321 (ttpt) REVERT: H 22 LEU cc_start: 0.7866 (OUTLIER) cc_final: 0.7584 (tt) REVERT: H 156 GLU cc_start: 0.8075 (mt-10) cc_final: 0.7638 (mm-30) REVERT: H 344 ARG cc_start: 0.7683 (ttm110) cc_final: 0.7175 (mtt-85) REVERT: H 404 SER cc_start: 0.8710 (OUTLIER) cc_final: 0.8345 (p) REVERT: H 440 LYS cc_start: 0.8575 (tptt) cc_final: 0.8285 (tppt) REVERT: N 82 MET cc_start: 0.2007 (mmm) cc_final: 0.1698 (mmp) REVERT: Q 31 ARG cc_start: 0.7289 (mmp-170) cc_final: 0.6964 (mmt90) REVERT: Q 52 MET cc_start: 0.8718 (mmm) cc_final: 0.8320 (mmp) REVERT: Q 55 MET cc_start: 0.7901 (mtm) cc_final: 0.7540 (mtm) REVERT: Q 238 LYS cc_start: 0.7550 (mmtp) cc_final: 0.6341 (mptt) REVERT: Q 267 ASN cc_start: 0.8179 (m-40) cc_final: 0.7718 (m-40) REVERT: Q 299 ASP cc_start: 0.7767 (m-30) cc_final: 0.7250 (m-30) REVERT: Q 354 GLU cc_start: 0.7790 (tt0) cc_final: 0.7537 (tt0) REVERT: Q 357 ASP cc_start: 0.7029 (t0) cc_final: 0.6621 (p0) REVERT: Q 433 LEU cc_start: 0.7806 (mt) cc_final: 0.7524 (mp) REVERT: Z 195 GLU cc_start: 0.8133 (pt0) cc_final: 0.7867 (mt-10) REVERT: Z 257 GLU cc_start: 0.8168 (OUTLIER) cc_final: 0.7805 (mm-30) REVERT: Z 258 LYS cc_start: 0.7890 (mttt) cc_final: 0.7662 (mttm) REVERT: Z 264 ARG cc_start: 0.7411 (mtp85) cc_final: 0.6499 (mtp-110) REVERT: a 63 LYS cc_start: 0.7487 (mtpt) cc_final: 0.7112 (ptpt) REVERT: a 106 GLU cc_start: 0.7172 (OUTLIER) cc_final: 0.6900 (pt0) REVERT: a 247 LYS cc_start: 0.7380 (pttm) cc_final: 0.6976 (pttp) REVERT: a 299 TYR cc_start: 0.7066 (m-80) cc_final: 0.6784 (m-80) REVERT: a 360 GLU cc_start: 0.8063 (mt-10) cc_final: 0.7334 (mt-10) REVERT: a 382 ASP cc_start: 0.7481 (m-30) cc_final: 0.7202 (m-30) REVERT: a 443 ARG cc_start: 0.7209 (ttp80) cc_final: 0.6726 (ttp80) REVERT: a 505 GLU cc_start: 0.7260 (mt-10) cc_final: 0.6891 (mt-10) REVERT: a 532 LYS cc_start: 0.8436 (tttt) cc_final: 0.8054 (tttm) REVERT: b 130 TRP cc_start: 0.7929 (m-10) cc_final: 0.7720 (m100) REVERT: b 347 LYS cc_start: 0.8220 (mmtm) cc_final: 0.7679 (mtmt) REVERT: d 27 ARG cc_start: 0.6703 (mmm-85) cc_final: 0.6105 (mpp80) REVERT: d 78 LEU cc_start: 0.8722 (mt) cc_final: 0.8293 (mt) REVERT: d 93 GLU cc_start: 0.7454 (mm-30) cc_final: 0.7231 (mt-10) REVERT: d 104 ASP cc_start: 0.8670 (p0) cc_final: 0.8468 (p0) REVERT: d 196 ASP cc_start: 0.8022 (t0) cc_final: 0.7356 (p0) REVERT: d 209 LYS cc_start: 0.8103 (ttmm) cc_final: 0.7887 (ttmm) REVERT: d 232 LYS cc_start: 0.8360 (ptmm) cc_final: 0.8031 (ptmm) REVERT: d 277 ARG cc_start: 0.7203 (ttm-80) cc_final: 0.6919 (ttm-80) REVERT: d 363 GLU cc_start: 0.7666 (tt0) cc_final: 0.7264 (pt0) REVERT: d 429 GLU cc_start: 0.7911 (mp0) cc_final: 0.7267 (mp0) REVERT: d 505 GLU cc_start: 0.7353 (pp20) cc_final: 0.7014 (tp30) REVERT: d 524 GLU cc_start: 0.7685 (tp30) cc_final: 0.7436 (tp30) REVERT: e 67 ASP cc_start: 0.7209 (m-30) cc_final: 0.6837 (t70) REVERT: e 160 LYS cc_start: 0.8164 (mmtt) cc_final: 0.7683 (mptt) REVERT: e 210 LYS cc_start: 0.8261 (tttp) cc_final: 0.7959 (tttt) REVERT: e 263 LYS cc_start: 0.8014 (ttmt) cc_final: 0.7607 (mtmt) REVERT: e 381 ARG cc_start: 0.7441 (OUTLIER) cc_final: 0.6493 (ttm170) REVERT: e 503 GLN cc_start: 0.7620 (tt0) cc_final: 0.7010 (mt0) REVERT: g 21 LYS cc_start: 0.7441 (mmtm) cc_final: 0.6785 (mtmm) REVERT: g 31 LYS cc_start: 0.7076 (mtpt) cc_final: 0.6777 (mtmt) REVERT: g 52 ASP cc_start: 0.7014 (t0) cc_final: 0.6762 (t70) REVERT: g 84 SER cc_start: 0.8251 (t) cc_final: 0.7765 (p) REVERT: g 117 MET cc_start: 0.8217 (ttp) cc_final: 0.7916 (ttp) REVERT: g 133 MET cc_start: 0.7259 (mtt) cc_final: 0.6902 (mtp) REVERT: g 200 ARG cc_start: 0.7830 (tpt170) cc_final: 0.7373 (tpt-90) REVERT: g 242 ASP cc_start: 0.7756 (OUTLIER) cc_final: 0.7378 (m-30) REVERT: g 368 ASP cc_start: 0.7438 (t70) cc_final: 0.7202 (t0) REVERT: g 393 ASP cc_start: 0.7583 (t0) cc_final: 0.7277 (t0) REVERT: h 30 GLN cc_start: 0.8110 (mm-40) cc_final: 0.7880 (mm110) REVERT: h 81 ASP cc_start: 0.6447 (m-30) cc_final: 0.6070 (m-30) REVERT: h 153 LYS cc_start: 0.7645 (mmtt) cc_final: 0.7307 (mtmt) REVERT: h 156 GLU cc_start: 0.7290 (mt-10) cc_final: 0.6744 (pt0) REVERT: h 240 LEU cc_start: 0.8269 (OUTLIER) cc_final: 0.7897 (mt) REVERT: h 276 ASP cc_start: 0.7475 (t0) cc_final: 0.6908 (t0) REVERT: h 320 LYS cc_start: 0.8430 (mtpp) cc_final: 0.8133 (mmmt) REVERT: h 356 GLU cc_start: 0.7790 (mm-30) cc_final: 0.7461 (mm-30) REVERT: h 368 LYS cc_start: 0.8152 (mttt) cc_final: 0.7777 (mmmt) REVERT: h 414 MET cc_start: 0.8605 (mmm) cc_final: 0.8216 (mmt) REVERT: h 459 ASN cc_start: 0.7715 (m-40) cc_final: 0.7232 (t0) REVERT: h 521 LYS cc_start: 0.8145 (mttt) cc_final: 0.7898 (mtmt) REVERT: q 20 LYS cc_start: 0.8473 (mttt) cc_final: 0.8204 (mtmt) REVERT: q 34 GLN cc_start: 0.7614 (tp-100) cc_final: 0.6737 (tp-100) REVERT: q 38 GLU cc_start: 0.7505 (mt-10) cc_final: 0.7010 (mt-10) REVERT: q 254 LYS cc_start: 0.8002 (tttm) cc_final: 0.7547 (tptt) REVERT: q 281 LYS cc_start: 0.7899 (ttmt) cc_final: 0.7555 (ttpp) REVERT: q 357 ASP cc_start: 0.8047 (OUTLIER) cc_final: 0.7657 (t0) REVERT: q 382 ASP cc_start: 0.7527 (m-30) cc_final: 0.7309 (m-30) REVERT: q 522 ASP cc_start: 0.7233 (t70) cc_final: 0.7025 (t0) REVERT: q 534 LYS cc_start: 0.2852 (OUTLIER) cc_final: 0.1289 (tttp) REVERT: z 127 LYS cc_start: 0.6612 (OUTLIER) cc_final: 0.6274 (tttt) REVERT: z 175 SER cc_start: 0.8540 (t) cc_final: 0.8279 (p) REVERT: z 181 LYS cc_start: 0.7101 (mttt) cc_final: 0.6713 (mtpt) REVERT: z 192 GLU cc_start: 0.7736 (tp30) cc_final: 0.7325 (tp30) REVERT: z 221 MET cc_start: 0.8704 (mtt) cc_final: 0.8400 (mtt) REVERT: z 240 GLU cc_start: 0.7610 (mm-30) cc_final: 0.7211 (pt0) REVERT: z 241 LYS cc_start: 0.8448 (ttmt) cc_final: 0.7559 (ptmm) REVERT: z 258 LYS cc_start: 0.7930 (mttt) cc_final: 0.7632 (mtmm) REVERT: z 264 ARG cc_start: 0.7268 (mtp85) cc_final: 0.6776 (mtp85) REVERT: z 338 ASP cc_start: 0.7777 (OUTLIER) cc_final: 0.7325 (m-30) REVERT: z 358 GLU cc_start: 0.7975 (tt0) cc_final: 0.7625 (mp0) REVERT: z 359 LYS cc_start: 0.8016 (mttt) cc_final: 0.7731 (mtmt) REVERT: z 432 ARG cc_start: 0.7484 (OUTLIER) cc_final: 0.6928 (ptm160) REVERT: K 101 HIS cc_start: 0.7371 (m-70) cc_final: 0.7126 (m170) REVERT: K 132 MET cc_start: 0.8124 (ttp) cc_final: 0.7890 (ptm) REVERT: P 139 ARG cc_start: 0.5975 (OUTLIER) cc_final: 0.5323 (mtp-110) outliers start: 199 outliers final: 138 residues processed: 1130 average time/residue: 0.6852 time to fit residues: 1321.9777 Evaluate side-chains 1066 residues out of total 7685 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 155 poor density : 911 time to evaluate : 6.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ASP Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 284 ASN Chi-restraints excluded: chain A residue 337 GLU Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 532 LYS Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 422 THR Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 267 SER Chi-restraints excluded: chain D residue 296 ASN Chi-restraints excluded: chain D residue 309 LEU Chi-restraints excluded: chain D residue 332 ASP Chi-restraints excluded: chain D residue 374 LEU Chi-restraints excluded: chain D residue 377 THR Chi-restraints excluded: chain E residue 65 ASP Chi-restraints excluded: chain E residue 121 GLU Chi-restraints excluded: chain E residue 220 GLU Chi-restraints excluded: chain E residue 298 ASN Chi-restraints excluded: chain E residue 372 LEU Chi-restraints excluded: chain E residue 418 VAL Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 146 ILE Chi-restraints excluded: chain G residue 161 THR Chi-restraints excluded: chain G residue 192 GLU Chi-restraints excluded: chain G residue 252 SER Chi-restraints excluded: chain G residue 255 ASP Chi-restraints excluded: chain G residue 341 ASP Chi-restraints excluded: chain G residue 350 LEU Chi-restraints excluded: chain G residue 460 ILE Chi-restraints excluded: chain H residue 9 LEU Chi-restraints excluded: chain H residue 22 LEU Chi-restraints excluded: chain H residue 37 ARG Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 130 GLN Chi-restraints excluded: chain H residue 239 LEU Chi-restraints excluded: chain H residue 351 THR Chi-restraints excluded: chain H residue 400 ILE Chi-restraints excluded: chain H residue 404 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 115 VAL Chi-restraints excluded: chain Q residue 90 SER Chi-restraints excluded: chain Q residue 105 LEU Chi-restraints excluded: chain Q residue 175 ASN Chi-restraints excluded: chain Q residue 212 ILE Chi-restraints excluded: chain Q residue 253 THR Chi-restraints excluded: chain Q residue 289 ASN Chi-restraints excluded: chain Q residue 296 LYS Chi-restraints excluded: chain Q residue 480 LEU Chi-restraints excluded: chain Z residue 4 VAL Chi-restraints excluded: chain Z residue 108 LEU Chi-restraints excluded: chain Z residue 176 ILE Chi-restraints excluded: chain Z residue 257 GLU Chi-restraints excluded: chain Z residue 414 VAL Chi-restraints excluded: chain Z residue 488 VAL Chi-restraints excluded: chain Z residue 526 MET Chi-restraints excluded: chain a residue 55 THR Chi-restraints excluded: chain a residue 101 LEU Chi-restraints excluded: chain a residue 106 GLU Chi-restraints excluded: chain a residue 166 ASP Chi-restraints excluded: chain a residue 167 PHE Chi-restraints excluded: chain a residue 329 SER Chi-restraints excluded: chain a residue 352 VAL Chi-restraints excluded: chain a residue 358 ASP Chi-restraints excluded: chain a residue 486 ILE Chi-restraints excluded: chain b residue 184 VAL Chi-restraints excluded: chain b residue 212 SER Chi-restraints excluded: chain b residue 261 THR Chi-restraints excluded: chain b residue 363 SER Chi-restraints excluded: chain b residue 434 VAL Chi-restraints excluded: chain b residue 446 LEU Chi-restraints excluded: chain b residue 485 ILE Chi-restraints excluded: chain b residue 513 VAL Chi-restraints excluded: chain d residue 71 THR Chi-restraints excluded: chain d residue 94 LEU Chi-restraints excluded: chain d residue 265 VAL Chi-restraints excluded: chain d residue 311 ASP Chi-restraints excluded: chain d residue 324 VAL Chi-restraints excluded: chain d residue 374 LEU Chi-restraints excluded: chain d residue 385 THR Chi-restraints excluded: chain d residue 468 ASN Chi-restraints excluded: chain e residue 6 THR Chi-restraints excluded: chain e residue 205 ASP Chi-restraints excluded: chain e residue 215 VAL Chi-restraints excluded: chain e residue 298 ASN Chi-restraints excluded: chain e residue 372 LEU Chi-restraints excluded: chain e residue 381 ARG Chi-restraints excluded: chain e residue 383 VAL Chi-restraints excluded: chain e residue 408 VAL Chi-restraints excluded: chain e residue 418 VAL Chi-restraints excluded: chain g residue 73 GLN Chi-restraints excluded: chain g residue 83 ILE Chi-restraints excluded: chain g residue 161 THR Chi-restraints excluded: chain g residue 192 GLU Chi-restraints excluded: chain g residue 195 ILE Chi-restraints excluded: chain g residue 242 ASP Chi-restraints excluded: chain g residue 288 ASP Chi-restraints excluded: chain g residue 341 ASP Chi-restraints excluded: chain g residue 365 ASP Chi-restraints excluded: chain g residue 460 ILE Chi-restraints excluded: chain g residue 508 THR Chi-restraints excluded: chain g residue 528 LYS Chi-restraints excluded: chain h residue 9 LEU Chi-restraints excluded: chain h residue 34 GLU Chi-restraints excluded: chain h residue 85 SER Chi-restraints excluded: chain h residue 211 VAL Chi-restraints excluded: chain h residue 240 LEU Chi-restraints excluded: chain h residue 251 ASP Chi-restraints excluded: chain h residue 308 MET Chi-restraints excluded: chain h residue 322 THR Chi-restraints excluded: chain h residue 362 THR Chi-restraints excluded: chain h residue 382 MET Chi-restraints excluded: chain h residue 400 ILE Chi-restraints excluded: chain h residue 427 ILE Chi-restraints excluded: chain q residue 125 VAL Chi-restraints excluded: chain q residue 130 GLU Chi-restraints excluded: chain q residue 146 LEU Chi-restraints excluded: chain q residue 212 ILE Chi-restraints excluded: chain q residue 253 THR Chi-restraints excluded: chain q residue 355 VAL Chi-restraints excluded: chain q residue 357 ASP Chi-restraints excluded: chain q residue 385 MET Chi-restraints excluded: chain q residue 480 LEU Chi-restraints excluded: chain q residue 534 LYS Chi-restraints excluded: chain z residue 38 LEU Chi-restraints excluded: chain z residue 67 MET Chi-restraints excluded: chain z residue 127 LYS Chi-restraints excluded: chain z residue 135 GLU Chi-restraints excluded: chain z residue 149 ILE Chi-restraints excluded: chain z residue 159 LYS Chi-restraints excluded: chain z residue 195 GLU Chi-restraints excluded: chain z residue 235 VAL Chi-restraints excluded: chain z residue 280 LYS Chi-restraints excluded: chain z residue 338 ASP Chi-restraints excluded: chain z residue 340 SER Chi-restraints excluded: chain z residue 408 VAL Chi-restraints excluded: chain z residue 432 ARG Chi-restraints excluded: chain z residue 526 MET Chi-restraints excluded: chain K residue 67 LEU Chi-restraints excluded: chain K residue 141 SER Chi-restraints excluded: chain K residue 179 ASP Chi-restraints excluded: chain K residue 267 LEU Chi-restraints excluded: chain K residue 272 CYS Chi-restraints excluded: chain K residue 299 LEU Chi-restraints excluded: chain K residue 309 ILE Chi-restraints excluded: chain K residue 336 LYS Chi-restraints excluded: chain P residue 53 LEU Chi-restraints excluded: chain P residue 91 PHE Chi-restraints excluded: chain P residue 95 LEU Chi-restraints excluded: chain P residue 130 ILE Chi-restraints excluded: chain P residue 139 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 912 random chunks: chunk 296 optimal weight: 6.9990 chunk 793 optimal weight: 3.9990 chunk 174 optimal weight: 8.9990 chunk 517 optimal weight: 10.0000 chunk 217 optimal weight: 0.9980 chunk 882 optimal weight: 9.9990 chunk 732 optimal weight: 3.9990 chunk 408 optimal weight: 8.9990 chunk 73 optimal weight: 3.9990 chunk 291 optimal weight: 8.9990 chunk 463 optimal weight: 0.8980 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 223 GLN G 61 ASN ** Q 365 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 56 ASN a 193 ASN a 231 ASN ** b 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 366 ASN ** h 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 161 HIS ** P 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7291 moved from start: 0.2433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 71861 Z= 0.295 Angle : 0.590 10.608 97066 Z= 0.292 Chirality : 0.043 0.181 11504 Planarity : 0.004 0.053 12403 Dihedral : 6.948 158.261 10018 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.54 % Favored : 96.43 % Rotamer: Outliers : 3.01 % Allowed : 17.46 % Favored : 79.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.37 % 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: 0.26 (0.09), residues: 9177 helix: 1.21 (0.08), residues: 4614 sheet: -0.49 (0.14), residues: 1295 loop : -0.98 (0.10), residues: 3268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP P 10 HIS 0.016 0.001 HIS G 226 PHE 0.013 0.001 PHE a 167 TYR 0.028 0.001 TYR P 120 ARG 0.010 0.000 ARG B 481 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18354 Ramachandran restraints generated. 9177 Oldfield, 0 Emsley, 9177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18354 Ramachandran restraints generated. 9177 Oldfield, 0 Emsley, 9177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1145 residues out of total 7685 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 231 poor density : 914 time to evaluate : 6.423 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 GLU cc_start: 0.4910 (OUTLIER) cc_final: 0.3433 (tm-30) REVERT: A 66 GLU cc_start: 0.7512 (tt0) cc_final: 0.6856 (mm-30) REVERT: A 80 ASP cc_start: 0.7624 (t70) cc_final: 0.6924 (m-30) REVERT: A 81 LEU cc_start: 0.8552 (tp) cc_final: 0.8272 (tp) REVERT: A 84 LYS cc_start: 0.8107 (mtmm) cc_final: 0.7699 (mmmt) REVERT: A 171 MET cc_start: 0.6944 (mtp) cc_final: 0.6721 (mtp) REVERT: A 207 GLU cc_start: 0.8661 (OUTLIER) cc_final: 0.7434 (mp0) REVERT: A 245 LYS cc_start: 0.8202 (tttt) cc_final: 0.7854 (tttm) REVERT: A 251 GLN cc_start: 0.8047 (mt0) cc_final: 0.7789 (tt0) REVERT: A 337 GLU cc_start: 0.7483 (OUTLIER) cc_final: 0.6828 (tm-30) REVERT: A 344 MET cc_start: 0.7543 (mmt) cc_final: 0.7167 (mmm) REVERT: D 187 SER cc_start: 0.8628 (t) cc_final: 0.7897 (m) REVERT: D 193 LYS cc_start: 0.8066 (mttt) cc_final: 0.7575 (tttp) REVERT: D 232 LYS cc_start: 0.7922 (tppt) cc_final: 0.7479 (ptmt) REVERT: D 374 LEU cc_start: 0.8751 (OUTLIER) cc_final: 0.8384 (tm) REVERT: D 533 ASP cc_start: 0.7586 (OUTLIER) cc_final: 0.7148 (p0) REVERT: E 20 LYS cc_start: 0.7881 (tttp) cc_final: 0.7610 (tttm) REVERT: E 149 ASP cc_start: 0.7696 (m-30) cc_final: 0.7199 (m-30) REVERT: E 368 LYS cc_start: 0.8476 (ttpp) cc_final: 0.7889 (tptt) REVERT: E 501 MET cc_start: 0.7332 (mmt) cc_final: 0.6938 (mmm) REVERT: E 535 LYS cc_start: 0.8326 (pttp) cc_final: 0.7860 (pttm) REVERT: G 152 MET cc_start: 0.7877 (mmm) cc_final: 0.7267 (mmt) REVERT: G 200 ARG cc_start: 0.7624 (tpt170) cc_final: 0.7280 (tpt170) REVERT: G 277 GLN cc_start: 0.6944 (tp-100) cc_final: 0.6473 (tt0) REVERT: G 284 GLN cc_start: 0.7894 (tp40) cc_final: 0.7596 (mt0) REVERT: G 528 LYS cc_start: 0.6926 (mttm) cc_final: 0.6662 (mttm) REVERT: H 10 LYS cc_start: 0.7724 (ttpp) cc_final: 0.7326 (ttpt) REVERT: H 22 LEU cc_start: 0.7917 (OUTLIER) cc_final: 0.7645 (tt) REVERT: H 344 ARG cc_start: 0.7754 (ttm110) cc_final: 0.7191 (mtt-85) REVERT: H 404 SER cc_start: 0.8742 (OUTLIER) cc_final: 0.8467 (p) REVERT: H 440 LYS cc_start: 0.8623 (tptt) cc_final: 0.8249 (tttp) REVERT: N 82 MET cc_start: 0.1967 (mmm) cc_final: 0.1666 (mmp) REVERT: Q 31 ARG cc_start: 0.7347 (mmp-170) cc_final: 0.6963 (mmt90) REVERT: Q 52 MET cc_start: 0.8754 (mmm) cc_final: 0.8336 (mmp) REVERT: Q 55 MET cc_start: 0.7921 (mtm) cc_final: 0.7536 (mtm) REVERT: Q 238 LYS cc_start: 0.7203 (mmtp) cc_final: 0.6519 (mptt) REVERT: Q 299 ASP cc_start: 0.7773 (m-30) cc_final: 0.7251 (m-30) REVERT: Q 354 GLU cc_start: 0.7797 (tt0) cc_final: 0.7586 (tt0) REVERT: Q 357 ASP cc_start: 0.7108 (t0) cc_final: 0.6694 (p0) REVERT: Q 494 GLU cc_start: 0.8057 (tm-30) cc_final: 0.7832 (mp0) REVERT: Z 195 GLU cc_start: 0.8224 (pt0) cc_final: 0.7934 (mt-10) REVERT: Z 258 LYS cc_start: 0.7914 (mttt) cc_final: 0.7674 (mttm) REVERT: Z 264 ARG cc_start: 0.7411 (mtp85) cc_final: 0.6536 (mtp-110) REVERT: a 63 LYS cc_start: 0.7563 (mtpt) cc_final: 0.7187 (ptpt) REVERT: a 247 LYS cc_start: 0.7405 (pttm) cc_final: 0.6992 (pttp) REVERT: a 382 ASP cc_start: 0.7524 (m-30) cc_final: 0.6961 (m-30) REVERT: a 443 ARG cc_start: 0.7222 (ttp80) cc_final: 0.6787 (ttp80) REVERT: a 532 LYS cc_start: 0.8472 (tttt) cc_final: 0.8111 (tttm) REVERT: b 130 TRP cc_start: 0.7934 (m-10) cc_final: 0.7725 (m-10) REVERT: b 347 LYS cc_start: 0.8250 (mmtm) cc_final: 0.7703 (mtmt) REVERT: d 27 ARG cc_start: 0.6581 (mmm-85) cc_final: 0.6367 (mpp80) REVERT: d 104 ASP cc_start: 0.8751 (p0) cc_final: 0.8543 (p0) REVERT: d 232 LYS cc_start: 0.8322 (ptmm) cc_final: 0.8021 (ptmm) REVERT: d 277 ARG cc_start: 0.7214 (ttm-80) cc_final: 0.6918 (ttm-80) REVERT: d 363 GLU cc_start: 0.7713 (tt0) cc_final: 0.7294 (pt0) REVERT: d 429 GLU cc_start: 0.7919 (mp0) cc_final: 0.7241 (mp0) REVERT: d 431 GLU cc_start: 0.7784 (tp30) cc_final: 0.7538 (tp30) REVERT: d 505 GLU cc_start: 0.7427 (pp20) cc_final: 0.7025 (tp30) REVERT: d 524 GLU cc_start: 0.7679 (tp30) cc_final: 0.7438 (tp30) REVERT: e 67 ASP cc_start: 0.7241 (m-30) cc_final: 0.6856 (t70) REVERT: e 160 LYS cc_start: 0.8174 (mmtt) cc_final: 0.7720 (mptt) REVERT: e 210 LYS cc_start: 0.8262 (tttp) cc_final: 0.8034 (tttm) REVERT: e 263 LYS cc_start: 0.8020 (ttmt) cc_final: 0.7676 (mtmt) REVERT: e 381 ARG cc_start: 0.7670 (OUTLIER) cc_final: 0.6628 (ttm170) REVERT: e 503 GLN cc_start: 0.7678 (tt0) cc_final: 0.7017 (mt0) REVERT: g 21 LYS cc_start: 0.7551 (mmtm) cc_final: 0.6868 (mtmm) REVERT: g 31 LYS cc_start: 0.7152 (mtpt) cc_final: 0.6821 (mtmt) REVERT: g 84 SER cc_start: 0.8225 (t) cc_final: 0.7767 (p) REVERT: g 117 MET cc_start: 0.8316 (ttp) cc_final: 0.7998 (ttp) REVERT: g 133 MET cc_start: 0.7225 (mtt) cc_final: 0.6877 (mtp) REVERT: g 200 ARG cc_start: 0.7852 (tpt170) cc_final: 0.7375 (tpt-90) REVERT: g 242 ASP cc_start: 0.7874 (OUTLIER) cc_final: 0.7421 (m-30) REVERT: g 368 ASP cc_start: 0.7529 (t70) cc_final: 0.7312 (t0) REVERT: g 393 ASP cc_start: 0.7690 (t0) cc_final: 0.7437 (t0) REVERT: h 81 ASP cc_start: 0.6518 (m-30) cc_final: 0.6133 (m-30) REVERT: h 153 LYS cc_start: 0.7661 (mmtt) cc_final: 0.7290 (mtmt) REVERT: h 156 GLU cc_start: 0.7301 (mt-10) cc_final: 0.6718 (pt0) REVERT: h 239 LEU cc_start: 0.8752 (OUTLIER) cc_final: 0.8535 (mt) REVERT: h 320 LYS cc_start: 0.8448 (mtpp) cc_final: 0.8166 (mmmt) REVERT: h 338 SER cc_start: 0.8353 (m) cc_final: 0.8032 (t) REVERT: h 356 GLU cc_start: 0.7849 (mm-30) cc_final: 0.7441 (mm-30) REVERT: h 368 LYS cc_start: 0.8229 (mttt) cc_final: 0.7843 (mmmt) REVERT: h 459 ASN cc_start: 0.7705 (m-40) cc_final: 0.7261 (t0) REVERT: q 20 LYS cc_start: 0.8499 (mttt) cc_final: 0.8215 (mtmt) REVERT: q 34 GLN cc_start: 0.7637 (tp-100) cc_final: 0.6823 (tp-100) REVERT: q 175 ASN cc_start: 0.8853 (OUTLIER) cc_final: 0.8616 (p0) REVERT: q 181 LYS cc_start: 0.7751 (mmmt) cc_final: 0.7499 (tppt) REVERT: q 254 LYS cc_start: 0.8089 (tttm) cc_final: 0.7661 (tptt) REVERT: q 281 LYS cc_start: 0.7937 (ttmt) cc_final: 0.7581 (tttm) REVERT: q 357 ASP cc_start: 0.8083 (OUTLIER) cc_final: 0.7663 (t0) REVERT: q 382 ASP cc_start: 0.7607 (m-30) cc_final: 0.7381 (m-30) REVERT: q 522 ASP cc_start: 0.7253 (t70) cc_final: 0.7049 (t0) REVERT: q 534 LYS cc_start: 0.2916 (OUTLIER) cc_final: 0.1363 (tttp) REVERT: z 44 MET cc_start: 0.7501 (tpp) cc_final: 0.7135 (tpp) REVERT: z 127 LYS cc_start: 0.6654 (OUTLIER) cc_final: 0.6311 (tttt) REVERT: z 175 SER cc_start: 0.8509 (OUTLIER) cc_final: 0.7977 (p) REVERT: z 181 LYS cc_start: 0.7147 (mttt) cc_final: 0.6745 (mtpt) REVERT: z 240 GLU cc_start: 0.7660 (mm-30) cc_final: 0.7246 (pt0) REVERT: z 241 LYS cc_start: 0.8543 (ttmt) cc_final: 0.7811 (pttp) REVERT: z 258 LYS cc_start: 0.7989 (mttt) cc_final: 0.7716 (mtmt) REVERT: z 264 ARG cc_start: 0.7318 (mtp85) cc_final: 0.6805 (mtp85) REVERT: z 281 VAL cc_start: 0.8634 (OUTLIER) cc_final: 0.8293 (m) REVERT: z 338 ASP cc_start: 0.7720 (OUTLIER) cc_final: 0.7275 (m-30) REVERT: z 358 GLU cc_start: 0.8000 (tt0) cc_final: 0.7620 (mp0) REVERT: z 359 LYS cc_start: 0.8098 (mttt) cc_final: 0.7789 (mtmt) REVERT: z 432 ARG cc_start: 0.7585 (OUTLIER) cc_final: 0.7054 (ptm160) REVERT: K 101 HIS cc_start: 0.7346 (m-70) cc_final: 0.7111 (m170) REVERT: K 313 MET cc_start: 0.5572 (tpt) cc_final: 0.5315 (tpt) REVERT: P 139 ARG cc_start: 0.6067 (OUTLIER) cc_final: 0.5347 (mtp-110) outliers start: 231 outliers final: 171 residues processed: 1086 average time/residue: 0.6679 time to fit residues: 1233.3014 Evaluate side-chains 1074 residues out of total 7685 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 190 poor density : 884 time to evaluate : 6.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 GLU Chi-restraints excluded: chain A residue 10 ASP Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 284 ASN Chi-restraints excluded: chain A residue 337 GLU Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain A residue 359 ASP Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 532 LYS Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 416 LEU Chi-restraints excluded: chain B residue 422 THR Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 230 THR Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 267 SER Chi-restraints excluded: chain D residue 296 ASN Chi-restraints excluded: chain D residue 332 ASP Chi-restraints excluded: chain D residue 374 LEU Chi-restraints excluded: chain D residue 377 THR Chi-restraints excluded: chain D residue 404 SER Chi-restraints excluded: chain D residue 422 ILE Chi-restraints excluded: chain D residue 519 LEU Chi-restraints excluded: chain D residue 533 ASP Chi-restraints excluded: chain E residue 65 ASP Chi-restraints excluded: chain E residue 122 GLN Chi-restraints excluded: chain E residue 220 GLU Chi-restraints excluded: chain E residue 298 ASN Chi-restraints excluded: chain E residue 372 LEU Chi-restraints excluded: chain E residue 408 VAL Chi-restraints excluded: chain E residue 418 VAL Chi-restraints excluded: chain E residue 511 ILE Chi-restraints excluded: chain G residue 12 GLN Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 146 ILE Chi-restraints excluded: chain G residue 161 THR Chi-restraints excluded: chain G residue 192 GLU Chi-restraints excluded: chain G residue 209 ILE Chi-restraints excluded: chain G residue 252 SER Chi-restraints excluded: chain G residue 255 ASP Chi-restraints excluded: chain G residue 458 SER Chi-restraints excluded: chain G residue 460 ILE Chi-restraints excluded: chain H residue 9 LEU Chi-restraints excluded: chain H residue 22 LEU Chi-restraints excluded: chain H residue 37 ARG Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 130 GLN Chi-restraints excluded: chain H residue 239 LEU Chi-restraints excluded: chain H residue 351 THR Chi-restraints excluded: chain H residue 362 THR Chi-restraints excluded: chain H residue 400 ILE Chi-restraints excluded: chain H residue 404 SER Chi-restraints excluded: chain H residue 405 VAL Chi-restraints excluded: chain H residue 427 ILE Chi-restraints excluded: chain H residue 456 ASP Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 115 VAL Chi-restraints excluded: chain Q residue 3 LEU Chi-restraints excluded: chain Q residue 23 SER Chi-restraints excluded: chain Q residue 90 SER Chi-restraints excluded: chain Q residue 105 LEU Chi-restraints excluded: chain Q residue 175 ASN Chi-restraints excluded: chain Q residue 212 ILE Chi-restraints excluded: chain Q residue 253 THR Chi-restraints excluded: chain Q residue 289 ASN Chi-restraints excluded: chain Q residue 296 LYS Chi-restraints excluded: chain Q residue 480 LEU Chi-restraints excluded: chain Z residue 4 VAL Chi-restraints excluded: chain Z residue 57 THR Chi-restraints excluded: chain Z residue 108 LEU Chi-restraints excluded: chain Z residue 176 ILE Chi-restraints excluded: chain Z residue 257 GLU Chi-restraints excluded: chain Z residue 281 VAL Chi-restraints excluded: chain Z residue 414 VAL Chi-restraints excluded: chain Z residue 429 VAL Chi-restraints excluded: chain Z residue 488 VAL Chi-restraints excluded: chain Z residue 522 MET Chi-restraints excluded: chain Z residue 526 MET Chi-restraints excluded: chain a residue 55 THR Chi-restraints excluded: chain a residue 101 LEU Chi-restraints excluded: chain a residue 166 ASP Chi-restraints excluded: chain a residue 167 PHE Chi-restraints excluded: chain a residue 329 SER Chi-restraints excluded: chain a residue 352 VAL Chi-restraints excluded: chain a residue 358 ASP Chi-restraints excluded: chain a residue 486 ILE Chi-restraints excluded: chain b residue 30 ILE Chi-restraints excluded: chain b residue 184 VAL Chi-restraints excluded: chain b residue 212 SER Chi-restraints excluded: chain b residue 261 THR Chi-restraints excluded: chain b residue 363 SER Chi-restraints excluded: chain b residue 434 VAL Chi-restraints excluded: chain b residue 446 LEU Chi-restraints excluded: chain b residue 485 ILE Chi-restraints excluded: chain b residue 513 VAL Chi-restraints excluded: chain d residue 71 THR Chi-restraints excluded: chain d residue 94 LEU Chi-restraints excluded: chain d residue 265 VAL Chi-restraints excluded: chain d residue 311 ASP Chi-restraints excluded: chain d residue 324 VAL Chi-restraints excluded: chain d residue 366 ASN Chi-restraints excluded: chain d residue 374 LEU Chi-restraints excluded: chain d residue 377 THR Chi-restraints excluded: chain d residue 385 THR Chi-restraints excluded: chain d residue 468 ASN Chi-restraints excluded: chain d residue 478 THR Chi-restraints excluded: chain e residue 6 THR Chi-restraints excluded: chain e residue 205 ASP Chi-restraints excluded: chain e residue 215 VAL Chi-restraints excluded: chain e residue 298 ASN Chi-restraints excluded: chain e residue 372 LEU Chi-restraints excluded: chain e residue 381 ARG Chi-restraints excluded: chain e residue 408 VAL Chi-restraints excluded: chain e residue 418 VAL Chi-restraints excluded: chain g residue 73 GLN Chi-restraints excluded: chain g residue 153 LEU Chi-restraints excluded: chain g residue 161 THR Chi-restraints excluded: chain g residue 192 GLU Chi-restraints excluded: chain g residue 195 ILE Chi-restraints excluded: chain g residue 242 ASP Chi-restraints excluded: chain g residue 284 GLN Chi-restraints excluded: chain g residue 288 ASP Chi-restraints excluded: chain g residue 341 ASP Chi-restraints excluded: chain g residue 365 ASP Chi-restraints excluded: chain g residue 373 THR Chi-restraints excluded: chain g residue 407 LEU Chi-restraints excluded: chain g residue 460 ILE Chi-restraints excluded: chain g residue 471 THR Chi-restraints excluded: chain g residue 508 THR Chi-restraints excluded: chain g residue 528 LYS Chi-restraints excluded: chain h residue 9 LEU Chi-restraints excluded: chain h residue 34 GLU Chi-restraints excluded: chain h residue 38 THR Chi-restraints excluded: chain h residue 85 SER Chi-restraints excluded: chain h residue 142 THR Chi-restraints excluded: chain h residue 211 VAL Chi-restraints excluded: chain h residue 239 LEU Chi-restraints excluded: chain h residue 251 ASP Chi-restraints excluded: chain h residue 308 MET Chi-restraints excluded: chain h residue 322 THR Chi-restraints excluded: chain h residue 362 THR Chi-restraints excluded: chain h residue 382 MET Chi-restraints excluded: chain h residue 404 SER Chi-restraints excluded: chain h residue 427 ILE Chi-restraints excluded: chain q residue 125 VAL Chi-restraints excluded: chain q residue 130 GLU Chi-restraints excluded: chain q residue 170 SER Chi-restraints excluded: chain q residue 175 ASN Chi-restraints excluded: chain q residue 212 ILE Chi-restraints excluded: chain q residue 218 LEU Chi-restraints excluded: chain q residue 253 THR Chi-restraints excluded: chain q residue 355 VAL Chi-restraints excluded: chain q residue 357 ASP Chi-restraints excluded: chain q residue 385 MET Chi-restraints excluded: chain q residue 475 ASN Chi-restraints excluded: chain q residue 480 LEU Chi-restraints excluded: chain q residue 534 LYS Chi-restraints excluded: chain z residue 67 MET Chi-restraints excluded: chain z residue 127 LYS Chi-restraints excluded: chain z residue 135 GLU Chi-restraints excluded: chain z residue 149 ILE Chi-restraints excluded: chain z residue 159 LYS Chi-restraints excluded: chain z residue 175 SER Chi-restraints excluded: chain z residue 235 VAL Chi-restraints excluded: chain z residue 280 LYS Chi-restraints excluded: chain z residue 281 VAL Chi-restraints excluded: chain z residue 338 ASP Chi-restraints excluded: chain z residue 340 SER Chi-restraints excluded: chain z residue 408 VAL Chi-restraints excluded: chain z residue 432 ARG Chi-restraints excluded: chain z residue 526 MET Chi-restraints excluded: chain K residue 67 LEU Chi-restraints excluded: chain K residue 82 MET Chi-restraints excluded: chain K residue 115 ASN Chi-restraints excluded: chain K residue 141 SER Chi-restraints excluded: chain K residue 147 ARG Chi-restraints excluded: chain K residue 179 ASP Chi-restraints excluded: chain K residue 267 LEU Chi-restraints excluded: chain K residue 272 CYS Chi-restraints excluded: chain K residue 299 LEU Chi-restraints excluded: chain K residue 309 ILE Chi-restraints excluded: chain K residue 318 THR Chi-restraints excluded: chain K residue 336 LYS Chi-restraints excluded: chain P residue 53 LEU Chi-restraints excluded: chain P residue 91 PHE Chi-restraints excluded: chain P residue 95 LEU Chi-restraints excluded: chain P residue 139 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 912 random chunks: chunk 850 optimal weight: 7.9990 chunk 99 optimal weight: 6.9990 chunk 502 optimal weight: 9.9990 chunk 644 optimal weight: 7.9990 chunk 499 optimal weight: 7.9990 chunk 742 optimal weight: 1.9990 chunk 492 optimal weight: 0.7980 chunk 879 optimal weight: 7.9990 chunk 550 optimal weight: 7.9990 chunk 535 optimal weight: 6.9990 chunk 405 optimal weight: 6.9990 overall best weight: 4.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 450 ASN B 124 GLN D 138 GLN E 291 GLN G 61 ASN ** H 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 365 HIS ** Z 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 56 ASN ** b 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 486 GLN h 30 GLN ** h 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 80 HIS ** P 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7337 moved from start: 0.2573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.059 71861 Z= 0.457 Angle : 0.683 13.410 97066 Z= 0.340 Chirality : 0.047 0.179 11504 Planarity : 0.005 0.056 12403 Dihedral : 7.279 166.806 10018 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.01 % Allowed : 4.26 % Favored : 95.72 % Rotamer: Outliers : 3.42 % Allowed : 17.73 % Favored : 78.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.37 % 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: -0.13 (0.08), residues: 9177 helix: 0.83 (0.07), residues: 4621 sheet: -0.57 (0.14), residues: 1266 loop : -1.11 (0.10), residues: 3290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP P 10 HIS 0.006 0.001 HIS z 346 PHE 0.020 0.002 PHE H 220 TYR 0.023 0.002 TYR P 120 ARG 0.011 0.001 ARG B 481 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18354 Ramachandran restraints generated. 9177 Oldfield, 0 Emsley, 9177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18354 Ramachandran restraints generated. 9177 Oldfield, 0 Emsley, 9177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1154 residues out of total 7685 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 262 poor density : 892 time to evaluate : 6.525 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 GLU cc_start: 0.4873 (OUTLIER) cc_final: 0.3447 (tm-30) REVERT: A 80 ASP cc_start: 0.7635 (t70) cc_final: 0.6985 (m-30) REVERT: A 84 LYS cc_start: 0.8139 (mtmm) cc_final: 0.7689 (mmmt) REVERT: A 171 MET cc_start: 0.7167 (mtp) cc_final: 0.6923 (mtp) REVERT: A 207 GLU cc_start: 0.8677 (OUTLIER) cc_final: 0.7472 (mp0) REVERT: A 245 LYS cc_start: 0.8172 (tttt) cc_final: 0.7864 (tttm) REVERT: A 251 GLN cc_start: 0.8180 (mt0) cc_final: 0.7790 (tt0) REVERT: A 337 GLU cc_start: 0.7520 (OUTLIER) cc_final: 0.6871 (tm-30) REVERT: A 344 MET cc_start: 0.7560 (mmt) cc_final: 0.7223 (mmm) REVERT: A 416 GLU cc_start: 0.8343 (mp0) cc_final: 0.8115 (mp0) REVERT: A 505 GLU cc_start: 0.8064 (OUTLIER) cc_final: 0.7556 (mt-10) REVERT: B 273 GLU cc_start: 0.7653 (tp30) cc_final: 0.7169 (mt-10) REVERT: D 187 SER cc_start: 0.8689 (t) cc_final: 0.7970 (m) REVERT: D 193 LYS cc_start: 0.8076 (mttt) cc_final: 0.7493 (tttp) REVERT: D 232 LYS cc_start: 0.8105 (tppt) cc_final: 0.7661 (ptmt) REVERT: D 374 LEU cc_start: 0.8762 (OUTLIER) cc_final: 0.8390 (tm) REVERT: D 533 ASP cc_start: 0.7596 (OUTLIER) cc_final: 0.7159 (p0) REVERT: E 20 LYS cc_start: 0.7924 (tttp) cc_final: 0.7586 (tttm) REVERT: E 149 ASP cc_start: 0.7663 (m-30) cc_final: 0.7429 (m-30) REVERT: E 468 MET cc_start: 0.8028 (mpp) cc_final: 0.7561 (mpp) REVERT: E 501 MET cc_start: 0.7350 (mmt) cc_final: 0.6876 (mmm) REVERT: E 529 LYS cc_start: 0.8580 (OUTLIER) cc_final: 0.8112 (tttp) REVERT: E 535 LYS cc_start: 0.8416 (pttp) cc_final: 0.7954 (pttm) REVERT: G 47 MET cc_start: 0.8767 (mmm) cc_final: 0.6867 (mmm) REVERT: G 152 MET cc_start: 0.7850 (mmm) cc_final: 0.7347 (mmt) REVERT: G 200 ARG cc_start: 0.7639 (tpt170) cc_final: 0.7427 (tpt170) REVERT: G 277 GLN cc_start: 0.7018 (tp-100) cc_final: 0.6517 (tt0) REVERT: G 284 GLN cc_start: 0.7902 (tp40) cc_final: 0.7559 (mt0) REVERT: H 10 LYS cc_start: 0.7647 (ttpp) cc_final: 0.7232 (ttpt) REVERT: H 22 LEU cc_start: 0.7994 (OUTLIER) cc_final: 0.7693 (tt) REVERT: H 404 SER cc_start: 0.8829 (OUTLIER) cc_final: 0.8507 (p) REVERT: H 440 LYS cc_start: 0.8662 (tptt) cc_final: 0.8249 (tttp) REVERT: N 82 MET cc_start: 0.2018 (mmm) cc_final: 0.1744 (mmp) REVERT: Q 31 ARG cc_start: 0.7464 (mmp-170) cc_final: 0.7048 (mmt90) REVERT: Q 52 MET cc_start: 0.8734 (mmm) cc_final: 0.8310 (mmp) REVERT: Q 55 MET cc_start: 0.7907 (mtm) cc_final: 0.7485 (mtm) REVERT: Q 238 LYS cc_start: 0.7264 (mmtp) cc_final: 0.6481 (mptt) REVERT: Q 299 ASP cc_start: 0.7880 (m-30) cc_final: 0.7344 (m-30) REVERT: Q 354 GLU cc_start: 0.7898 (tt0) cc_final: 0.7665 (tp30) REVERT: Q 357 ASP cc_start: 0.7141 (t0) cc_final: 0.6670 (p0) REVERT: Q 494 GLU cc_start: 0.8087 (tm-30) cc_final: 0.7840 (mp0) REVERT: Z 195 GLU cc_start: 0.8248 (pt0) cc_final: 0.7962 (mt-10) REVERT: Z 221 MET cc_start: 0.8809 (mtt) cc_final: 0.8528 (mtt) REVERT: Z 258 LYS cc_start: 0.7932 (mttt) cc_final: 0.7695 (mttm) REVERT: Z 264 ARG cc_start: 0.7555 (mtp85) cc_final: 0.6531 (mtp85) REVERT: a 47 ASP cc_start: 0.7077 (t0) cc_final: 0.6778 (t0) REVERT: a 63 LYS cc_start: 0.7684 (mtpt) cc_final: 0.7292 (ptpt) REVERT: a 247 LYS cc_start: 0.7554 (pttm) cc_final: 0.7139 (pttp) REVERT: a 382 ASP cc_start: 0.7451 (m-30) cc_final: 0.7180 (m-30) REVERT: a 443 ARG cc_start: 0.7061 (ttp80) cc_final: 0.6833 (ttp80) REVERT: a 532 LYS cc_start: 0.8528 (tttt) cc_final: 0.8168 (tttm) REVERT: b 130 TRP cc_start: 0.8054 (m-10) cc_final: 0.7832 (m-10) REVERT: b 242 THR cc_start: 0.8816 (p) cc_final: 0.8576 (p) REVERT: b 347 LYS cc_start: 0.8300 (mmtm) cc_final: 0.7707 (mtmt) REVERT: d 27 ARG cc_start: 0.6586 (mmm-85) cc_final: 0.6330 (mpp80) REVERT: d 46 ASP cc_start: 0.7011 (m-30) cc_final: 0.6718 (m-30) REVERT: d 196 ASP cc_start: 0.8083 (t0) cc_final: 0.7369 (p0) REVERT: d 277 ARG cc_start: 0.7253 (ttm-80) cc_final: 0.6932 (ttm-80) REVERT: d 363 GLU cc_start: 0.7708 (tt0) cc_final: 0.7330 (pt0) REVERT: d 472 ASN cc_start: 0.8025 (OUTLIER) cc_final: 0.7428 (t0) REVERT: d 483 ARG cc_start: 0.8048 (OUTLIER) cc_final: 0.7815 (mtp85) REVERT: d 505 GLU cc_start: 0.7508 (pp20) cc_final: 0.7058 (tp30) REVERT: d 524 GLU cc_start: 0.7730 (tp30) cc_final: 0.7517 (tp30) REVERT: e 67 ASP cc_start: 0.7246 (m-30) cc_final: 0.6849 (t70) REVERT: e 160 LYS cc_start: 0.8311 (mmtt) cc_final: 0.7812 (mptt) REVERT: e 210 LYS cc_start: 0.8218 (tttp) cc_final: 0.7922 (ttpp) REVERT: e 263 LYS cc_start: 0.8020 (ttmt) cc_final: 0.7749 (ttmt) REVERT: e 381 ARG cc_start: 0.7734 (OUTLIER) cc_final: 0.7362 (ttt-90) REVERT: e 448 MET cc_start: 0.8007 (mtp) cc_final: 0.7494 (mtp) REVERT: e 503 GLN cc_start: 0.7715 (tt0) cc_final: 0.7036 (mt0) REVERT: g 21 LYS cc_start: 0.7595 (mmtm) cc_final: 0.6866 (mtmm) REVERT: g 31 LYS cc_start: 0.7324 (mtpt) cc_final: 0.7077 (mtmt) REVERT: g 61 ASN cc_start: 0.8488 (OUTLIER) cc_final: 0.8107 (p0) REVERT: g 84 SER cc_start: 0.8489 (t) cc_final: 0.7927 (p) REVERT: g 133 MET cc_start: 0.7170 (mtt) cc_final: 0.6798 (mtp) REVERT: g 200 ARG cc_start: 0.7853 (tpt170) cc_final: 0.7368 (tpt-90) REVERT: g 242 ASP cc_start: 0.7987 (OUTLIER) cc_final: 0.7478 (m-30) REVERT: g 368 ASP cc_start: 0.7599 (t70) cc_final: 0.7383 (t0) REVERT: h 81 ASP cc_start: 0.6520 (m-30) cc_final: 0.6084 (m-30) REVERT: h 106 LYS cc_start: 0.8096 (tttt) cc_final: 0.7491 (ttmt) REVERT: h 153 LYS cc_start: 0.7737 (mmtt) cc_final: 0.7264 (mtmt) REVERT: h 156 GLU cc_start: 0.7369 (mt-10) cc_final: 0.6753 (pt0) REVERT: h 320 LYS cc_start: 0.8474 (mtpp) cc_final: 0.8076 (mmmt) REVERT: h 338 SER cc_start: 0.8361 (m) cc_final: 0.7909 (t) REVERT: h 368 LYS cc_start: 0.8319 (mttt) cc_final: 0.7853 (mmmt) REVERT: h 459 ASN cc_start: 0.7703 (m-40) cc_final: 0.7320 (t0) REVERT: h 478 ASP cc_start: 0.7669 (t70) cc_final: 0.7406 (t0) REVERT: q 20 LYS cc_start: 0.8517 (mttt) cc_final: 0.8194 (mtmt) REVERT: q 34 GLN cc_start: 0.7689 (tp-100) cc_final: 0.6900 (tp-100) REVERT: q 175 ASN cc_start: 0.8999 (OUTLIER) cc_final: 0.8766 (p0) REVERT: q 181 LYS cc_start: 0.7733 (mmmt) cc_final: 0.7480 (tppt) REVERT: q 254 LYS cc_start: 0.8220 (tttm) cc_final: 0.7824 (tttt) REVERT: q 281 LYS cc_start: 0.7951 (ttmt) cc_final: 0.7523 (tttm) REVERT: q 357 ASP cc_start: 0.8203 (OUTLIER) cc_final: 0.7794 (t0) REVERT: q 382 ASP cc_start: 0.7709 (m-30) cc_final: 0.7456 (m-30) REVERT: q 522 ASP cc_start: 0.7132 (t70) cc_final: 0.6894 (t0) REVERT: q 534 LYS cc_start: 0.3042 (OUTLIER) cc_final: 0.1367 (tttp) REVERT: z 127 LYS cc_start: 0.6705 (OUTLIER) cc_final: 0.6337 (tttt) REVERT: z 181 LYS cc_start: 0.7194 (mttt) cc_final: 0.6725 (mtpt) REVERT: z 240 GLU cc_start: 0.7786 (mm-30) cc_final: 0.7321 (pt0) REVERT: z 241 LYS cc_start: 0.8541 (ttmt) cc_final: 0.7797 (pttp) REVERT: z 258 LYS cc_start: 0.8031 (mttt) cc_final: 0.7717 (mtmt) REVERT: z 264 ARG cc_start: 0.7401 (mtp85) cc_final: 0.6826 (mtp85) REVERT: z 295 LYS cc_start: 0.8241 (OUTLIER) cc_final: 0.7980 (mttm) REVERT: z 338 ASP cc_start: 0.7836 (OUTLIER) cc_final: 0.7450 (m-30) REVERT: z 358 GLU cc_start: 0.8062 (tt0) cc_final: 0.7611 (mp0) REVERT: z 359 LYS cc_start: 0.8179 (mttt) cc_final: 0.7864 (mtmt) REVERT: z 432 ARG cc_start: 0.7777 (OUTLIER) cc_final: 0.7015 (ptm160) REVERT: K 101 HIS cc_start: 0.7335 (m-70) cc_final: 0.7104 (m170) REVERT: K 132 MET cc_start: 0.8192 (ttp) cc_final: 0.7984 (ptm) outliers start: 262 outliers final: 198 residues processed: 1092 average time/residue: 0.6749 time to fit residues: 1258.0883 Evaluate side-chains 1088 residues out of total 7685 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 219 poor density : 869 time to evaluate : 6.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 GLU Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 284 ASN Chi-restraints excluded: chain A residue 337 GLU Chi-restraints excluded: chain A residue 359 ASP Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 505 GLU Chi-restraints excluded: chain A residue 532 LYS Chi-restraints excluded: chain B residue 416 LEU Chi-restraints excluded: chain B residue 422 THR Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 230 THR Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 267 SER Chi-restraints excluded: chain D residue 296 ASN Chi-restraints excluded: chain D residue 332 ASP Chi-restraints excluded: chain D residue 374 LEU Chi-restraints excluded: chain D residue 377 THR Chi-restraints excluded: chain D residue 404 SER Chi-restraints excluded: chain D residue 422 ILE Chi-restraints excluded: chain D residue 437 THR Chi-restraints excluded: chain D residue 490 THR Chi-restraints excluded: chain D residue 519 LEU Chi-restraints excluded: chain D residue 533 ASP Chi-restraints excluded: chain E residue 23 ASP Chi-restraints excluded: chain E residue 47 THR Chi-restraints excluded: chain E residue 65 ASP Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 122 GLN Chi-restraints excluded: chain E residue 220 GLU Chi-restraints excluded: chain E residue 230 VAL Chi-restraints excluded: chain E residue 298 ASN Chi-restraints excluded: chain E residue 372 LEU Chi-restraints excluded: chain E residue 408 VAL Chi-restraints excluded: chain E residue 418 VAL Chi-restraints excluded: chain E residue 511 ILE Chi-restraints excluded: chain E residue 529 LYS Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 59 MET Chi-restraints excluded: chain G residue 146 ILE Chi-restraints excluded: chain G residue 161 THR Chi-restraints excluded: chain G residue 192 GLU Chi-restraints excluded: chain G residue 209 ILE Chi-restraints excluded: chain G residue 252 SER Chi-restraints excluded: chain G residue 255 ASP Chi-restraints excluded: chain G residue 341 ASP Chi-restraints excluded: chain G residue 373 THR Chi-restraints excluded: chain G residue 458 SER Chi-restraints excluded: chain G residue 460 ILE Chi-restraints excluded: chain H residue 9 LEU Chi-restraints excluded: chain H residue 22 LEU Chi-restraints excluded: chain H residue 37 ARG Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 130 GLN Chi-restraints excluded: chain H residue 185 MET Chi-restraints excluded: chain H residue 239 LEU Chi-restraints excluded: chain H residue 297 ASP Chi-restraints excluded: chain H residue 351 THR Chi-restraints excluded: chain H residue 362 THR Chi-restraints excluded: chain H residue 400 ILE Chi-restraints excluded: chain H residue 404 SER Chi-restraints excluded: chain H residue 405 VAL Chi-restraints excluded: chain H residue 427 ILE Chi-restraints excluded: chain H residue 456 ASP Chi-restraints excluded: chain N residue 115 VAL Chi-restraints excluded: chain Q residue 3 LEU Chi-restraints excluded: chain Q residue 23 SER Chi-restraints excluded: chain Q residue 45 THR Chi-restraints excluded: chain Q residue 90 SER Chi-restraints excluded: chain Q residue 105 LEU Chi-restraints excluded: chain Q residue 170 SER Chi-restraints excluded: chain Q residue 175 ASN Chi-restraints excluded: chain Q residue 212 ILE Chi-restraints excluded: chain Q residue 253 THR Chi-restraints excluded: chain Q residue 289 ASN Chi-restraints excluded: chain Q residue 296 LYS Chi-restraints excluded: chain Q residue 393 ASP Chi-restraints excluded: chain Q residue 480 LEU Chi-restraints excluded: chain Z residue 4 VAL Chi-restraints excluded: chain Z residue 57 THR Chi-restraints excluded: chain Z residue 108 LEU Chi-restraints excluded: chain Z residue 149 ILE Chi-restraints excluded: chain Z residue 176 ILE Chi-restraints excluded: chain Z residue 257 GLU Chi-restraints excluded: chain Z residue 281 VAL Chi-restraints excluded: chain Z residue 408 VAL Chi-restraints excluded: chain Z residue 414 VAL Chi-restraints excluded: chain Z residue 429 VAL Chi-restraints excluded: chain Z residue 488 VAL Chi-restraints excluded: chain Z residue 522 MET Chi-restraints excluded: chain Z residue 526 MET Chi-restraints excluded: chain a residue 55 THR Chi-restraints excluded: chain a residue 56 ASN Chi-restraints excluded: chain a residue 101 LEU Chi-restraints excluded: chain a residue 106 GLU Chi-restraints excluded: chain a residue 167 PHE Chi-restraints excluded: chain a residue 329 SER Chi-restraints excluded: chain a residue 358 ASP Chi-restraints excluded: chain a residue 391 SER Chi-restraints excluded: chain a residue 486 ILE Chi-restraints excluded: chain b residue 30 ILE Chi-restraints excluded: chain b residue 184 VAL Chi-restraints excluded: chain b residue 212 SER Chi-restraints excluded: chain b residue 261 THR Chi-restraints excluded: chain b residue 363 SER Chi-restraints excluded: chain b residue 434 VAL Chi-restraints excluded: chain b residue 446 LEU Chi-restraints excluded: chain b residue 513 VAL Chi-restraints excluded: chain d residue 26 ASP Chi-restraints excluded: chain d residue 50 THR Chi-restraints excluded: chain d residue 94 LEU Chi-restraints excluded: chain d residue 260 MET Chi-restraints excluded: chain d residue 265 VAL Chi-restraints excluded: chain d residue 311 ASP Chi-restraints excluded: chain d residue 324 VAL Chi-restraints excluded: chain d residue 374 LEU Chi-restraints excluded: chain d residue 377 THR Chi-restraints excluded: chain d residue 385 THR Chi-restraints excluded: chain d residue 411 VAL Chi-restraints excluded: chain d residue 468 ASN Chi-restraints excluded: chain d residue 472 ASN Chi-restraints excluded: chain d residue 478 THR Chi-restraints excluded: chain d residue 483 ARG Chi-restraints excluded: chain e residue 6 THR Chi-restraints excluded: chain e residue 205 ASP Chi-restraints excluded: chain e residue 215 VAL Chi-restraints excluded: chain e residue 228 VAL Chi-restraints excluded: chain e residue 298 ASN Chi-restraints excluded: chain e residue 381 ARG Chi-restraints excluded: chain e residue 418 VAL Chi-restraints excluded: chain e residue 526 MET Chi-restraints excluded: chain g residue 61 ASN Chi-restraints excluded: chain g residue 73 GLN Chi-restraints excluded: chain g residue 153 LEU Chi-restraints excluded: chain g residue 161 THR Chi-restraints excluded: chain g residue 192 GLU Chi-restraints excluded: chain g residue 195 ILE Chi-restraints excluded: chain g residue 242 ASP Chi-restraints excluded: chain g residue 284 GLN Chi-restraints excluded: chain g residue 288 ASP Chi-restraints excluded: chain g residue 341 ASP Chi-restraints excluded: chain g residue 365 ASP Chi-restraints excluded: chain g residue 373 THR Chi-restraints excluded: chain g residue 460 ILE Chi-restraints excluded: chain g residue 471 THR Chi-restraints excluded: chain g residue 508 THR Chi-restraints excluded: chain g residue 528 LYS Chi-restraints excluded: chain h residue 4 THR Chi-restraints excluded: chain h residue 7 ILE Chi-restraints excluded: chain h residue 9 LEU Chi-restraints excluded: chain h residue 34 GLU Chi-restraints excluded: chain h residue 38 THR Chi-restraints excluded: chain h residue 85 SER Chi-restraints excluded: chain h residue 142 THR Chi-restraints excluded: chain h residue 211 VAL Chi-restraints excluded: chain h residue 251 ASP Chi-restraints excluded: chain h residue 322 THR Chi-restraints excluded: chain h residue 362 THR Chi-restraints excluded: chain h residue 382 MET Chi-restraints excluded: chain h residue 400 ILE Chi-restraints excluded: chain h residue 404 SER Chi-restraints excluded: chain h residue 427 ILE Chi-restraints excluded: chain n residue 92 VAL Chi-restraints excluded: chain q residue 113 GLU Chi-restraints excluded: chain q residue 125 VAL Chi-restraints excluded: chain q residue 130 GLU Chi-restraints excluded: chain q residue 170 SER Chi-restraints excluded: chain q residue 175 ASN Chi-restraints excluded: chain q residue 212 ILE Chi-restraints excluded: chain q residue 218 LEU Chi-restraints excluded: chain q residue 253 THR Chi-restraints excluded: chain q residue 355 VAL Chi-restraints excluded: chain q residue 357 ASP Chi-restraints excluded: chain q residue 385 MET Chi-restraints excluded: chain q residue 386 ASP Chi-restraints excluded: chain q residue 475 ASN Chi-restraints excluded: chain q residue 480 LEU Chi-restraints excluded: chain q residue 534 LYS Chi-restraints excluded: chain z residue 38 LEU Chi-restraints excluded: chain z residue 127 LYS Chi-restraints excluded: chain z residue 149 ILE Chi-restraints excluded: chain z residue 159 LYS Chi-restraints excluded: chain z residue 163 GLU Chi-restraints excluded: chain z residue 170 GLU Chi-restraints excluded: chain z residue 175 SER Chi-restraints excluded: chain z residue 213 ASP Chi-restraints excluded: chain z residue 235 VAL Chi-restraints excluded: chain z residue 280 LYS Chi-restraints excluded: chain z residue 281 VAL Chi-restraints excluded: chain z residue 286 ASP Chi-restraints excluded: chain z residue 295 LYS Chi-restraints excluded: chain z residue 338 ASP Chi-restraints excluded: chain z residue 340 SER Chi-restraints excluded: chain z residue 408 VAL Chi-restraints excluded: chain z residue 432 ARG Chi-restraints excluded: chain z residue 526 MET Chi-restraints excluded: chain K residue 67 LEU Chi-restraints excluded: chain K residue 82 MET Chi-restraints excluded: chain K residue 115 ASN Chi-restraints excluded: chain K residue 141 SER Chi-restraints excluded: chain K residue 147 ARG Chi-restraints excluded: chain K residue 179 ASP Chi-restraints excluded: chain K residue 267 LEU Chi-restraints excluded: chain K residue 272 CYS Chi-restraints excluded: chain K residue 299 LEU Chi-restraints excluded: chain K residue 309 ILE Chi-restraints excluded: chain K residue 318 THR Chi-restraints excluded: chain K residue 336 LYS Chi-restraints excluded: chain K residue 340 TRP Chi-restraints excluded: chain P residue 53 LEU Chi-restraints excluded: chain P residue 91 PHE Chi-restraints excluded: chain P residue 95 LEU Chi-restraints excluded: chain P residue 130 ILE Chi-restraints excluded: chain P residue 139 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 912 random chunks: chunk 543 optimal weight: 1.9990 chunk 351 optimal weight: 5.9990 chunk 524 optimal weight: 2.9990 chunk 264 optimal weight: 0.8980 chunk 172 optimal weight: 6.9990 chunk 170 optimal weight: 0.9990 chunk 558 optimal weight: 2.9990 chunk 598 optimal weight: 0.9990 chunk 434 optimal weight: 0.9990 chunk 81 optimal weight: 0.7980 chunk 690 optimal weight: 0.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 138 GLN G 61 ASN ** H 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 234 ASN Q 365 HIS Q 475 ASN ** Z 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 56 ASN d 366 ASN d 510 GLN ** h 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** z 161 HIS ** P 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7264 moved from start: 0.2657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 71861 Z= 0.166 Angle : 0.547 13.057 97066 Z= 0.272 Chirality : 0.041 0.177 11504 Planarity : 0.004 0.052 12403 Dihedral : 6.700 150.355 10017 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.25 % Favored : 96.74 % Rotamer: Outliers : 2.52 % Allowed : 18.62 % Favored : 78.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.37 % 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: 0.33 (0.09), residues: 9177 helix: 1.29 (0.08), residues: 4611 sheet: -0.54 (0.14), residues: 1307 loop : -0.93 (0.11), residues: 3259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP b 130 HIS 0.005 0.001 HIS z 161 PHE 0.012 0.001 PHE a 167 TYR 0.022 0.001 TYR P 120 ARG 0.014 0.000 ARG B 481 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18354 Ramachandran restraints generated. 9177 Oldfield, 0 Emsley, 9177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18354 Ramachandran restraints generated. 9177 Oldfield, 0 Emsley, 9177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1133 residues out of total 7685 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 193 poor density : 940 time to evaluate : 6.460 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 GLU cc_start: 0.4890 (OUTLIER) cc_final: 0.3726 (tm-30) REVERT: A 80 ASP cc_start: 0.7610 (t70) cc_final: 0.6944 (m-30) REVERT: A 81 LEU cc_start: 0.8558 (tp) cc_final: 0.8278 (tp) REVERT: A 84 LYS cc_start: 0.8069 (mtmm) cc_final: 0.7712 (mmmt) REVERT: A 171 MET cc_start: 0.6874 (mtp) cc_final: 0.6672 (mtp) REVERT: A 206 MET cc_start: 0.7057 (mmm) cc_final: 0.6512 (mmm) REVERT: A 207 GLU cc_start: 0.8647 (OUTLIER) cc_final: 0.7467 (mp0) REVERT: A 245 LYS cc_start: 0.8088 (tttt) cc_final: 0.7785 (tttm) REVERT: A 251 GLN cc_start: 0.8031 (mt0) cc_final: 0.7643 (tt0) REVERT: A 337 GLU cc_start: 0.7389 (OUTLIER) cc_final: 0.6734 (tm-30) REVERT: A 344 MET cc_start: 0.7525 (mmt) cc_final: 0.7235 (mmm) REVERT: B 273 GLU cc_start: 0.7597 (tp30) cc_final: 0.7175 (mt-10) REVERT: D 193 LYS cc_start: 0.7937 (mttt) cc_final: 0.7439 (tttp) REVERT: D 232 LYS cc_start: 0.8044 (tppt) cc_final: 0.7632 (ptmt) REVERT: D 302 LYS cc_start: 0.8363 (ttmm) cc_final: 0.7875 (tttm) REVERT: D 374 LEU cc_start: 0.8725 (OUTLIER) cc_final: 0.8387 (tm) REVERT: E 20 LYS cc_start: 0.7887 (tttp) cc_final: 0.7606 (tttm) REVERT: E 149 ASP cc_start: 0.7657 (m-30) cc_final: 0.7151 (m-30) REVERT: E 199 MET cc_start: 0.7787 (mmm) cc_final: 0.7324 (mmm) REVERT: E 220 GLU cc_start: 0.7546 (OUTLIER) cc_final: 0.7158 (pm20) REVERT: E 368 LYS cc_start: 0.8033 (ttpp) cc_final: 0.7492 (tptt) REVERT: E 468 MET cc_start: 0.7645 (mpp) cc_final: 0.7396 (mpp) REVERT: E 501 MET cc_start: 0.7401 (mmt) cc_final: 0.6880 (mmm) REVERT: E 509 THR cc_start: 0.8935 (m) cc_final: 0.8689 (m) REVERT: E 535 LYS cc_start: 0.8304 (pttp) cc_final: 0.7886 (pttm) REVERT: G 47 MET cc_start: 0.8743 (mmm) cc_final: 0.6924 (mmm) REVERT: G 133 MET cc_start: 0.7739 (mtt) cc_final: 0.7144 (mtt) REVERT: G 152 MET cc_start: 0.7880 (mmm) cc_final: 0.7223 (mmt) REVERT: G 200 ARG cc_start: 0.7676 (tpt170) cc_final: 0.7438 (tpt170) REVERT: G 277 GLN cc_start: 0.6959 (tp-100) cc_final: 0.6525 (tt0) REVERT: G 284 GLN cc_start: 0.7881 (tp40) cc_final: 0.7629 (mt0) REVERT: H 10 LYS cc_start: 0.7672 (ttpp) cc_final: 0.7272 (ttpt) REVERT: H 22 LEU cc_start: 0.7863 (OUTLIER) cc_final: 0.7570 (tt) REVERT: H 34 GLU cc_start: 0.8242 (tm-30) cc_final: 0.7997 (tm-30) REVERT: H 344 ARG cc_start: 0.7649 (ttm110) cc_final: 0.7107 (mtt-85) REVERT: H 404 SER cc_start: 0.8641 (OUTLIER) cc_final: 0.8324 (p) REVERT: H 440 LYS cc_start: 0.8641 (tptt) cc_final: 0.8239 (tttp) REVERT: N 82 MET cc_start: 0.2112 (mmm) cc_final: 0.1865 (mmp) REVERT: Q 31 ARG cc_start: 0.7280 (mmp-170) cc_final: 0.6945 (mmt90) REVERT: Q 52 MET cc_start: 0.8756 (mmm) cc_final: 0.8342 (mmp) REVERT: Q 55 MET cc_start: 0.7864 (mtm) cc_final: 0.7468 (mtm) REVERT: Q 238 LYS cc_start: 0.7362 (mmtp) cc_final: 0.6479 (mptt) REVERT: Q 299 ASP cc_start: 0.7741 (m-30) cc_final: 0.7226 (m-30) REVERT: Q 344 MET cc_start: 0.8452 (tpp) cc_final: 0.8076 (tpp) REVERT: Q 357 ASP cc_start: 0.7042 (t0) cc_final: 0.6654 (p0) REVERT: Z 49 SER cc_start: 0.8293 (m) cc_final: 0.8084 (t) REVERT: Z 195 GLU cc_start: 0.8156 (pt0) cc_final: 0.7660 (mt-10) REVERT: Z 258 LYS cc_start: 0.7878 (mttt) cc_final: 0.7644 (mttm) REVERT: Z 264 ARG cc_start: 0.7567 (mtp85) cc_final: 0.6480 (mtp85) REVERT: Z 522 MET cc_start: 0.8279 (OUTLIER) cc_final: 0.8070 (mtp) REVERT: a 47 ASP cc_start: 0.6919 (t0) cc_final: 0.6692 (t0) REVERT: a 63 LYS cc_start: 0.7565 (mtpt) cc_final: 0.7196 (ptpt) REVERT: a 189 ARG cc_start: 0.6585 (ttm-80) cc_final: 0.6137 (ttm-80) REVERT: a 247 LYS cc_start: 0.7369 (pttm) cc_final: 0.6979 (pttp) REVERT: a 382 ASP cc_start: 0.7362 (m-30) cc_final: 0.7100 (m-30) REVERT: a 505 GLU cc_start: 0.7282 (mt-10) cc_final: 0.6922 (mt-10) REVERT: a 532 LYS cc_start: 0.8481 (tttt) cc_final: 0.8102 (tttm) REVERT: b 347 LYS cc_start: 0.8224 (mmtm) cc_final: 0.7595 (mtmm) REVERT: d 27 ARG cc_start: 0.6469 (mmm-85) cc_final: 0.6233 (mpp80) REVERT: d 104 ASP cc_start: 0.8837 (p0) cc_final: 0.8618 (p0) REVERT: d 196 ASP cc_start: 0.7982 (t0) cc_final: 0.7385 (p0) REVERT: d 277 ARG cc_start: 0.7236 (ttm-80) cc_final: 0.6937 (ttm-80) REVERT: d 363 GLU cc_start: 0.7628 (tt0) cc_final: 0.7228 (pt0) REVERT: d 414 CYS cc_start: 0.7341 (m) cc_final: 0.6857 (m) REVERT: d 429 GLU cc_start: 0.7943 (mp0) cc_final: 0.7435 (mp0) REVERT: d 431 GLU cc_start: 0.7695 (tp30) cc_final: 0.7462 (tp30) REVERT: d 505 GLU cc_start: 0.7407 (pp20) cc_final: 0.7028 (tp30) REVERT: d 524 GLU cc_start: 0.7667 (tp30) cc_final: 0.7449 (tp30) REVERT: e 67 ASP cc_start: 0.7297 (m-30) cc_final: 0.6916 (t70) REVERT: e 210 LYS cc_start: 0.8300 (tttp) cc_final: 0.8025 (tttt) REVERT: e 263 LYS cc_start: 0.7981 (ttmt) cc_final: 0.7666 (mtmt) REVERT: e 381 ARG cc_start: 0.7524 (OUTLIER) cc_final: 0.7206 (ttt-90) REVERT: e 448 MET cc_start: 0.7983 (mtp) cc_final: 0.7477 (mtp) REVERT: e 503 GLN cc_start: 0.7637 (tt0) cc_final: 0.7019 (mt0) REVERT: g 21 LYS cc_start: 0.7450 (mmtm) cc_final: 0.6802 (mtmm) REVERT: g 31 LYS cc_start: 0.7159 (mtpt) cc_final: 0.6927 (mtmt) REVERT: g 84 SER cc_start: 0.8211 (t) cc_final: 0.7659 (p) REVERT: g 117 MET cc_start: 0.8187 (ttp) cc_final: 0.7885 (ttp) REVERT: g 133 MET cc_start: 0.7194 (mtt) cc_final: 0.6896 (mtp) REVERT: g 152 MET cc_start: 0.7953 (mmm) cc_final: 0.7733 (mmm) REVERT: g 156 ILE cc_start: 0.8103 (OUTLIER) cc_final: 0.7871 (mp) REVERT: g 200 ARG cc_start: 0.7831 (tpt170) cc_final: 0.7411 (tpt-90) REVERT: g 242 ASP cc_start: 0.7774 (OUTLIER) cc_final: 0.7414 (m-30) REVERT: g 393 ASP cc_start: 0.7565 (t0) cc_final: 0.7308 (t0) REVERT: h 81 ASP cc_start: 0.6391 (m-30) cc_final: 0.6011 (m-30) REVERT: h 106 LYS cc_start: 0.7990 (tttt) cc_final: 0.7411 (ttmt) REVERT: h 153 LYS cc_start: 0.7729 (mmtt) cc_final: 0.7279 (mtmt) REVERT: h 156 GLU cc_start: 0.7298 (mt-10) cc_final: 0.6689 (pt0) REVERT: h 239 LEU cc_start: 0.8739 (OUTLIER) cc_final: 0.8526 (mt) REVERT: h 240 LEU cc_start: 0.8281 (OUTLIER) cc_final: 0.7970 (mt) REVERT: h 320 LYS cc_start: 0.8425 (mtpp) cc_final: 0.8190 (mmmt) REVERT: h 338 SER cc_start: 0.8274 (m) cc_final: 0.7941 (t) REVERT: h 368 LYS cc_start: 0.8244 (mttt) cc_final: 0.7845 (mmmt) REVERT: h 459 ASN cc_start: 0.7711 (m-40) cc_final: 0.7300 (t0) REVERT: h 482 GLU cc_start: 0.7495 (mt-10) cc_final: 0.7281 (mt-10) REVERT: q 20 LYS cc_start: 0.8478 (mttt) cc_final: 0.8196 (mtmt) REVERT: q 34 GLN cc_start: 0.7626 (tp-100) cc_final: 0.6519 (tt0) REVERT: q 130 GLU cc_start: 0.7149 (OUTLIER) cc_final: 0.6904 (pt0) REVERT: q 175 ASN cc_start: 0.8775 (OUTLIER) cc_final: 0.8556 (p0) REVERT: q 254 LYS cc_start: 0.8047 (tttm) cc_final: 0.7629 (tptt) REVERT: q 281 LYS cc_start: 0.7863 (ttmt) cc_final: 0.7498 (tttm) REVERT: q 357 ASP cc_start: 0.8012 (t0) cc_final: 0.7750 (t70) REVERT: q 382 ASP cc_start: 0.7663 (m-30) cc_final: 0.7430 (m-30) REVERT: q 522 ASP cc_start: 0.7123 (t70) cc_final: 0.6889 (t0) REVERT: q 534 LYS cc_start: 0.2874 (OUTLIER) cc_final: 0.1258 (tttp) REVERT: z 44 MET cc_start: 0.7525 (tpp) cc_final: 0.7110 (tpp) REVERT: z 127 LYS cc_start: 0.6604 (OUTLIER) cc_final: 0.6270 (tttt) REVERT: z 149 ILE cc_start: 0.7103 (OUTLIER) cc_final: 0.6829 (mm) REVERT: z 181 LYS cc_start: 0.7063 (mttt) cc_final: 0.6650 (mtpt) REVERT: z 226 GLU cc_start: 0.7856 (mm-30) cc_final: 0.7610 (mm-30) REVERT: z 240 GLU cc_start: 0.7693 (mm-30) cc_final: 0.7263 (pt0) REVERT: z 241 LYS cc_start: 0.8461 (ttmt) cc_final: 0.7696 (pttp) REVERT: z 258 LYS cc_start: 0.7960 (mttt) cc_final: 0.7694 (mtmt) REVERT: z 264 ARG cc_start: 0.7311 (mtp85) cc_final: 0.6785 (mtp85) REVERT: z 295 LYS cc_start: 0.8242 (OUTLIER) cc_final: 0.7938 (mttm) REVERT: z 338 ASP cc_start: 0.7875 (OUTLIER) cc_final: 0.7458 (m-30) REVERT: z 358 GLU cc_start: 0.8044 (tt0) cc_final: 0.7673 (mp0) REVERT: z 359 LYS cc_start: 0.8099 (mttt) cc_final: 0.7808 (mtmt) REVERT: z 432 ARG cc_start: 0.7653 (OUTLIER) cc_final: 0.7053 (ptm160) REVERT: K 82 MET cc_start: 0.7696 (OUTLIER) cc_final: 0.7424 (tpt) REVERT: K 132 MET cc_start: 0.8047 (ttp) cc_final: 0.7802 (ptm) REVERT: P 139 ARG cc_start: 0.6065 (OUTLIER) cc_final: 0.5060 (mtp-110) outliers start: 193 outliers final: 140 residues processed: 1081 average time/residue: 0.7002 time to fit residues: 1288.1260 Evaluate side-chains 1056 residues out of total 7685 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 163 poor density : 893 time to evaluate : 6.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 GLU Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 284 ASN Chi-restraints excluded: chain A residue 337 GLU Chi-restraints excluded: chain A residue 359 ASP Chi-restraints excluded: chain A residue 532 LYS Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 199 THR Chi-restraints excluded: chain D residue 296 ASN Chi-restraints excluded: chain D residue 332 ASP Chi-restraints excluded: chain D residue 374 LEU Chi-restraints excluded: chain D residue 377 THR Chi-restraints excluded: chain D residue 404 SER Chi-restraints excluded: chain E residue 65 ASP Chi-restraints excluded: chain E residue 220 GLU Chi-restraints excluded: chain E residue 230 VAL Chi-restraints excluded: chain E residue 298 ASN Chi-restraints excluded: chain E residue 372 LEU Chi-restraints excluded: chain E residue 408 VAL Chi-restraints excluded: chain E residue 418 VAL Chi-restraints excluded: chain G residue 146 ILE Chi-restraints excluded: chain G residue 161 THR Chi-restraints excluded: chain G residue 192 GLU Chi-restraints excluded: chain G residue 252 SER Chi-restraints excluded: chain G residue 255 ASP Chi-restraints excluded: chain G residue 341 ASP Chi-restraints excluded: chain G residue 350 LEU Chi-restraints excluded: chain G residue 458 SER Chi-restraints excluded: chain G residue 460 ILE Chi-restraints excluded: chain H residue 9 LEU Chi-restraints excluded: chain H residue 22 LEU Chi-restraints excluded: chain H residue 37 ARG Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 130 GLN Chi-restraints excluded: chain H residue 234 ASN Chi-restraints excluded: chain H residue 297 ASP Chi-restraints excluded: chain H residue 351 THR Chi-restraints excluded: chain H residue 400 ILE Chi-restraints excluded: chain H residue 404 SER Chi-restraints excluded: chain H residue 405 VAL Chi-restraints excluded: chain H residue 427 ILE Chi-restraints excluded: chain H residue 456 ASP Chi-restraints excluded: chain N residue 115 VAL Chi-restraints excluded: chain Q residue 23 SER Chi-restraints excluded: chain Q residue 45 THR Chi-restraints excluded: chain Q residue 90 SER Chi-restraints excluded: chain Q residue 105 LEU Chi-restraints excluded: chain Q residue 175 ASN Chi-restraints excluded: chain Q residue 212 ILE Chi-restraints excluded: chain Q residue 253 THR Chi-restraints excluded: chain Q residue 289 ASN Chi-restraints excluded: chain Q residue 296 LYS Chi-restraints excluded: chain Q residue 480 LEU Chi-restraints excluded: chain Z residue 4 VAL Chi-restraints excluded: chain Z residue 108 LEU Chi-restraints excluded: chain Z residue 149 ILE Chi-restraints excluded: chain Z residue 176 ILE Chi-restraints excluded: chain Z residue 257 GLU Chi-restraints excluded: chain Z residue 414 VAL Chi-restraints excluded: chain Z residue 488 VAL Chi-restraints excluded: chain Z residue 522 MET Chi-restraints excluded: chain Z residue 526 MET Chi-restraints excluded: chain a residue 55 THR Chi-restraints excluded: chain a residue 101 LEU Chi-restraints excluded: chain a residue 106 GLU Chi-restraints excluded: chain a residue 166 ASP Chi-restraints excluded: chain a residue 167 PHE Chi-restraints excluded: chain a residue 358 ASP Chi-restraints excluded: chain a residue 486 ILE Chi-restraints excluded: chain b residue 212 SER Chi-restraints excluded: chain b residue 363 SER Chi-restraints excluded: chain b residue 434 VAL Chi-restraints excluded: chain b residue 485 ILE Chi-restraints excluded: chain b residue 513 VAL Chi-restraints excluded: chain d residue 50 THR Chi-restraints excluded: chain d residue 94 LEU Chi-restraints excluded: chain d residue 265 VAL Chi-restraints excluded: chain d residue 311 ASP Chi-restraints excluded: chain d residue 324 VAL Chi-restraints excluded: chain d residue 374 LEU Chi-restraints excluded: chain d residue 377 THR Chi-restraints excluded: chain d residue 385 THR Chi-restraints excluded: chain d residue 411 VAL Chi-restraints excluded: chain d residue 468 ASN Chi-restraints excluded: chain e residue 6 THR Chi-restraints excluded: chain e residue 205 ASP Chi-restraints excluded: chain e residue 228 VAL Chi-restraints excluded: chain e residue 298 ASN Chi-restraints excluded: chain e residue 372 LEU Chi-restraints excluded: chain e residue 381 ARG Chi-restraints excluded: chain e residue 418 VAL Chi-restraints excluded: chain e residue 468 MET Chi-restraints excluded: chain g residue 73 GLN Chi-restraints excluded: chain g residue 153 LEU Chi-restraints excluded: chain g residue 156 ILE Chi-restraints excluded: chain g residue 161 THR Chi-restraints excluded: chain g residue 192 GLU Chi-restraints excluded: chain g residue 242 ASP Chi-restraints excluded: chain g residue 284 GLN Chi-restraints excluded: chain g residue 288 ASP Chi-restraints excluded: chain g residue 341 ASP Chi-restraints excluded: chain g residue 407 LEU Chi-restraints excluded: chain g residue 460 ILE Chi-restraints excluded: chain g residue 471 THR Chi-restraints excluded: chain g residue 528 LYS Chi-restraints excluded: chain h residue 7 ILE Chi-restraints excluded: chain h residue 9 LEU Chi-restraints excluded: chain h residue 34 GLU Chi-restraints excluded: chain h residue 37 ARG Chi-restraints excluded: chain h residue 85 SER Chi-restraints excluded: chain h residue 142 THR Chi-restraints excluded: chain h residue 211 VAL Chi-restraints excluded: chain h residue 239 LEU Chi-restraints excluded: chain h residue 240 LEU Chi-restraints excluded: chain h residue 246 LEU Chi-restraints excluded: chain h residue 251 ASP Chi-restraints excluded: chain h residue 308 MET Chi-restraints excluded: chain h residue 322 THR Chi-restraints excluded: chain h residue 362 THR Chi-restraints excluded: chain h residue 382 MET Chi-restraints excluded: chain h residue 400 ILE Chi-restraints excluded: chain h residue 404 SER Chi-restraints excluded: chain h residue 427 ILE Chi-restraints excluded: chain n residue 27 THR Chi-restraints excluded: chain n residue 76 ASN Chi-restraints excluded: chain q residue 125 VAL Chi-restraints excluded: chain q residue 130 GLU Chi-restraints excluded: chain q residue 146 LEU Chi-restraints excluded: chain q residue 175 ASN Chi-restraints excluded: chain q residue 212 ILE Chi-restraints excluded: chain q residue 253 THR Chi-restraints excluded: chain q residue 355 VAL Chi-restraints excluded: chain q residue 385 MET Chi-restraints excluded: chain q residue 480 LEU Chi-restraints excluded: chain q residue 534 LYS Chi-restraints excluded: chain z residue 127 LYS Chi-restraints excluded: chain z residue 135 GLU Chi-restraints excluded: chain z residue 149 ILE Chi-restraints excluded: chain z residue 159 LYS Chi-restraints excluded: chain z residue 170 GLU Chi-restraints excluded: chain z residue 235 VAL Chi-restraints excluded: chain z residue 295 LYS Chi-restraints excluded: chain z residue 338 ASP Chi-restraints excluded: chain z residue 340 SER Chi-restraints excluded: chain z residue 408 VAL Chi-restraints excluded: chain z residue 432 ARG Chi-restraints excluded: chain z residue 526 MET Chi-restraints excluded: chain K residue 11 ASP Chi-restraints excluded: chain K residue 67 LEU Chi-restraints excluded: chain K residue 82 MET Chi-restraints excluded: chain K residue 141 SER Chi-restraints excluded: chain K residue 179 ASP Chi-restraints excluded: chain K residue 267 LEU Chi-restraints excluded: chain K residue 272 CYS Chi-restraints excluded: chain K residue 299 LEU Chi-restraints excluded: chain K residue 309 ILE Chi-restraints excluded: chain K residue 336 LYS Chi-restraints excluded: chain K residue 340 TRP Chi-restraints excluded: chain P residue 47 THR Chi-restraints excluded: chain P residue 53 LEU Chi-restraints excluded: chain P residue 95 LEU Chi-restraints excluded: chain P residue 139 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 912 random chunks: chunk 799 optimal weight: 9.9990 chunk 842 optimal weight: 0.8980 chunk 768 optimal weight: 2.9990 chunk 819 optimal weight: 2.9990 chunk 841 optimal weight: 6.9990 chunk 493 optimal weight: 0.9980 chunk 356 optimal weight: 5.9990 chunk 643 optimal weight: 9.9990 chunk 251 optimal weight: 10.0000 chunk 740 optimal weight: 6.9990 chunk 774 optimal weight: 4.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 61 ASN ** H 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 234 ASN ** Q 365 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 56 ASN a 170 ASN a 425 ASN ** b 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 30 GLN ** h 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7297 moved from start: 0.2685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 71861 Z= 0.282 Angle : 0.591 13.283 97066 Z= 0.292 Chirality : 0.043 0.181 11504 Planarity : 0.004 0.065 12403 Dihedral : 6.708 152.715 10015 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.73 % Favored : 96.26 % Rotamer: Outliers : 2.48 % Allowed : 18.84 % Favored : 78.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.37 % 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: 0.27 (0.09), residues: 9177 helix: 1.20 (0.08), residues: 4621 sheet: -0.48 (0.14), residues: 1284 loop : -0.96 (0.10), residues: 3272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.001 TRP b 130 HIS 0.004 0.001 HIS G 226 PHE 0.013 0.001 PHE H 220 TYR 0.032 0.002 TYR P 120 ARG 0.014 0.000 ARG B 481 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18354 Ramachandran restraints generated. 9177 Oldfield, 0 Emsley, 9177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18354 Ramachandran restraints generated. 9177 Oldfield, 0 Emsley, 9177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1079 residues out of total 7685 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 190 poor density : 889 time to evaluate : 6.523 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 GLU cc_start: 0.4925 (OUTLIER) cc_final: 0.3715 (tm-30) REVERT: A 80 ASP cc_start: 0.7578 (t70) cc_final: 0.6983 (m-30) REVERT: A 81 LEU cc_start: 0.8543 (tp) cc_final: 0.8256 (tp) REVERT: A 84 LYS cc_start: 0.8093 (mtmm) cc_final: 0.7671 (mmmt) REVERT: A 171 MET cc_start: 0.6960 (mtp) cc_final: 0.6732 (mtp) REVERT: A 207 GLU cc_start: 0.8642 (OUTLIER) cc_final: 0.7406 (mp0) REVERT: A 245 LYS cc_start: 0.8104 (tttt) cc_final: 0.7787 (tttm) REVERT: A 251 GLN cc_start: 0.8048 (mt0) cc_final: 0.7641 (tt0) REVERT: A 337 GLU cc_start: 0.7465 (OUTLIER) cc_final: 0.6797 (tm-30) REVERT: A 344 MET cc_start: 0.7534 (mmt) cc_final: 0.7232 (mmm) REVERT: B 273 GLU cc_start: 0.7605 (tp30) cc_final: 0.7185 (mt-10) REVERT: D 193 LYS cc_start: 0.7973 (mttt) cc_final: 0.7417 (tttp) REVERT: D 232 LYS cc_start: 0.8079 (tppt) cc_final: 0.7670 (ptmt) REVERT: D 302 LYS cc_start: 0.8377 (ttmm) cc_final: 0.7890 (tttm) REVERT: D 374 LEU cc_start: 0.8740 (OUTLIER) cc_final: 0.8385 (tm) REVERT: E 20 LYS cc_start: 0.7887 (tttp) cc_final: 0.7597 (tttm) REVERT: E 149 ASP cc_start: 0.7705 (m-30) cc_final: 0.7258 (m-30) REVERT: E 368 LYS cc_start: 0.8070 (ttpp) cc_final: 0.7518 (tptt) REVERT: E 468 MET cc_start: 0.7773 (mpp) cc_final: 0.7263 (mpp) REVERT: E 501 MET cc_start: 0.7382 (mmt) cc_final: 0.6845 (mmm) REVERT: E 535 LYS cc_start: 0.8345 (pttp) cc_final: 0.7942 (pttm) REVERT: G 152 MET cc_start: 0.7861 (mmm) cc_final: 0.7269 (mmt) REVERT: G 200 ARG cc_start: 0.7704 (tpt170) cc_final: 0.7366 (tpt170) REVERT: G 277 GLN cc_start: 0.7010 (tp-100) cc_final: 0.6520 (tt0) REVERT: G 284 GLN cc_start: 0.7918 (tp40) cc_final: 0.7604 (mt0) REVERT: H 10 LYS cc_start: 0.7700 (ttpp) cc_final: 0.7295 (ttpt) REVERT: H 22 LEU cc_start: 0.7894 (OUTLIER) cc_final: 0.7621 (tt) REVERT: H 34 GLU cc_start: 0.8250 (tm-30) cc_final: 0.7992 (tm-30) REVERT: H 404 SER cc_start: 0.8764 (OUTLIER) cc_final: 0.8407 (p) REVERT: H 440 LYS cc_start: 0.8673 (tptt) cc_final: 0.8255 (tttp) REVERT: N 82 MET cc_start: 0.2021 (mmm) cc_final: 0.1759 (mmp) REVERT: Q 31 ARG cc_start: 0.7374 (mmp-170) cc_final: 0.7004 (mmt90) REVERT: Q 52 MET cc_start: 0.8754 (mmm) cc_final: 0.8342 (mmp) REVERT: Q 55 MET cc_start: 0.7868 (mtm) cc_final: 0.7453 (mtm) REVERT: Q 238 LYS cc_start: 0.7319 (mmtp) cc_final: 0.6915 (mptt) REVERT: Q 299 ASP cc_start: 0.7823 (m-30) cc_final: 0.7279 (m-30) REVERT: Q 357 ASP cc_start: 0.7170 (t0) cc_final: 0.6611 (p0) REVERT: Q 494 GLU cc_start: 0.8088 (mp0) cc_final: 0.7500 (mp0) REVERT: Z 195 GLU cc_start: 0.8177 (pt0) cc_final: 0.7696 (mt-10) REVERT: Z 258 LYS cc_start: 0.7902 (mttt) cc_final: 0.7669 (mttm) REVERT: Z 264 ARG cc_start: 0.7567 (mtp85) cc_final: 0.6531 (mtp85) REVERT: a 47 ASP cc_start: 0.7107 (t0) cc_final: 0.6835 (t0) REVERT: a 63 LYS cc_start: 0.7763 (mtpt) cc_final: 0.7374 (ptpt) REVERT: a 189 ARG cc_start: 0.6541 (ttm-80) cc_final: 0.6077 (ttm-80) REVERT: a 247 LYS cc_start: 0.7406 (pttm) cc_final: 0.6989 (pttp) REVERT: a 382 ASP cc_start: 0.7399 (m-30) cc_final: 0.7135 (m-30) REVERT: a 532 LYS cc_start: 0.8489 (tttt) cc_final: 0.8112 (tttm) REVERT: b 130 TRP cc_start: 0.8064 (m-10) cc_final: 0.7863 (m100) REVERT: b 347 LYS cc_start: 0.8221 (mmtm) cc_final: 0.7591 (mtmm) REVERT: d 104 ASP cc_start: 0.8904 (p0) cc_final: 0.8685 (p0) REVERT: d 196 ASP cc_start: 0.8035 (t0) cc_final: 0.7429 (p0) REVERT: d 277 ARG cc_start: 0.7230 (ttm-80) cc_final: 0.6921 (ttm-80) REVERT: d 363 GLU cc_start: 0.7706 (tt0) cc_final: 0.7239 (pt0) REVERT: d 429 GLU cc_start: 0.7986 (mp0) cc_final: 0.7463 (mp0) REVERT: d 431 GLU cc_start: 0.7786 (tp30) cc_final: 0.7517 (tp30) REVERT: d 505 GLU cc_start: 0.7441 (pp20) cc_final: 0.7030 (tp30) REVERT: d 524 GLU cc_start: 0.7694 (tp30) cc_final: 0.7460 (tp30) REVERT: e 67 ASP cc_start: 0.7274 (m-30) cc_final: 0.6901 (t70) REVERT: e 210 LYS cc_start: 0.8329 (tttp) cc_final: 0.8038 (tttt) REVERT: e 263 LYS cc_start: 0.8031 (ttmt) cc_final: 0.7722 (mtmt) REVERT: e 381 ARG cc_start: 0.7613 (OUTLIER) cc_final: 0.7220 (ttt-90) REVERT: e 448 MET cc_start: 0.7971 (mtp) cc_final: 0.7478 (mtp) REVERT: e 503 GLN cc_start: 0.7682 (tt0) cc_final: 0.7022 (mt0) REVERT: g 21 LYS cc_start: 0.7499 (mmtm) cc_final: 0.6808 (mtmm) REVERT: g 31 LYS cc_start: 0.7167 (mtpt) cc_final: 0.6923 (mtmt) REVERT: g 84 SER cc_start: 0.8553 (t) cc_final: 0.8009 (p) REVERT: g 117 MET cc_start: 0.8256 (ttp) cc_final: 0.7903 (ttp) REVERT: g 133 MET cc_start: 0.7309 (mtt) cc_final: 0.6956 (mtp) REVERT: g 200 ARG cc_start: 0.7829 (tpt170) cc_final: 0.7392 (tpt-90) REVERT: g 242 ASP cc_start: 0.7897 (OUTLIER) cc_final: 0.7456 (m-30) REVERT: g 393 ASP cc_start: 0.7643 (t0) cc_final: 0.7394 (t0) REVERT: h 30 GLN cc_start: 0.8317 (mm-40) cc_final: 0.8108 (mm-40) REVERT: h 81 ASP cc_start: 0.6526 (m-30) cc_final: 0.6150 (m-30) REVERT: h 153 LYS cc_start: 0.7728 (mmtt) cc_final: 0.7267 (mtmt) REVERT: h 156 GLU cc_start: 0.7310 (mt-10) cc_final: 0.6695 (pt0) REVERT: h 239 LEU cc_start: 0.8765 (OUTLIER) cc_final: 0.8547 (mt) REVERT: h 320 LYS cc_start: 0.8497 (mtpp) cc_final: 0.8142 (mmmt) REVERT: h 338 SER cc_start: 0.8307 (m) cc_final: 0.7906 (t) REVERT: h 368 LYS cc_start: 0.8275 (mttt) cc_final: 0.7896 (mmmt) REVERT: h 459 ASN cc_start: 0.7709 (m-40) cc_final: 0.7302 (t0) REVERT: h 482 GLU cc_start: 0.7510 (mt-10) cc_final: 0.7281 (mt-10) REVERT: q 20 LYS cc_start: 0.8490 (mttt) cc_final: 0.8197 (mtmt) REVERT: q 34 GLN cc_start: 0.7601 (tp-100) cc_final: 0.6795 (tp-100) REVERT: q 175 ASN cc_start: 0.8883 (OUTLIER) cc_final: 0.8621 (p0) REVERT: q 254 LYS cc_start: 0.8143 (tttm) cc_final: 0.7734 (tptt) REVERT: q 281 LYS cc_start: 0.7901 (ttmt) cc_final: 0.7530 (tttm) REVERT: q 357 ASP cc_start: 0.8070 (t0) cc_final: 0.7814 (t70) REVERT: q 382 ASP cc_start: 0.7692 (m-30) cc_final: 0.7453 (m-30) REVERT: q 534 LYS cc_start: 0.2996 (OUTLIER) cc_final: 0.1382 (tttp) REVERT: z 44 MET cc_start: 0.7534 (tpp) cc_final: 0.7126 (tpp) REVERT: z 127 LYS cc_start: 0.6667 (OUTLIER) cc_final: 0.6327 (tttt) REVERT: z 181 LYS cc_start: 0.7095 (mttt) cc_final: 0.6674 (mtpt) REVERT: z 226 GLU cc_start: 0.7858 (mm-30) cc_final: 0.7532 (mm-30) REVERT: z 240 GLU cc_start: 0.7714 (mm-30) cc_final: 0.7275 (pt0) REVERT: z 241 LYS cc_start: 0.8525 (ttmt) cc_final: 0.7776 (pttp) REVERT: z 258 LYS cc_start: 0.7987 (mttt) cc_final: 0.7710 (mtmt) REVERT: z 264 ARG cc_start: 0.7333 (mtp85) cc_final: 0.6771 (mtp85) REVERT: z 295 LYS cc_start: 0.8249 (OUTLIER) cc_final: 0.7964 (mttm) REVERT: z 338 ASP cc_start: 0.7905 (OUTLIER) cc_final: 0.7511 (m-30) REVERT: z 358 GLU cc_start: 0.8047 (tt0) cc_final: 0.7652 (mp0) REVERT: z 359 LYS cc_start: 0.8080 (mttt) cc_final: 0.7787 (mtmt) REVERT: z 432 ARG cc_start: 0.7677 (OUTLIER) cc_final: 0.6974 (ptm160) REVERT: K 82 MET cc_start: 0.7754 (OUTLIER) cc_final: 0.7486 (tpt) outliers start: 190 outliers final: 156 residues processed: 1029 average time/residue: 0.6844 time to fit residues: 1201.5276 Evaluate side-chains 1042 residues out of total 7685 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 172 poor density : 870 time to evaluate : 6.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 GLU Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 284 ASN Chi-restraints excluded: chain A residue 337 GLU Chi-restraints excluded: chain A residue 359 ASP Chi-restraints excluded: chain A residue 532 LYS Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 186 MET Chi-restraints excluded: chain D residue 199 THR Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 296 ASN Chi-restraints excluded: chain D residue 332 ASP Chi-restraints excluded: chain D residue 374 LEU Chi-restraints excluded: chain D residue 377 THR Chi-restraints excluded: chain D residue 404 SER Chi-restraints excluded: chain E residue 65 ASP Chi-restraints excluded: chain E residue 122 GLN Chi-restraints excluded: chain E residue 220 GLU Chi-restraints excluded: chain E residue 230 VAL Chi-restraints excluded: chain E residue 287 GLU Chi-restraints excluded: chain E residue 298 ASN Chi-restraints excluded: chain E residue 372 LEU Chi-restraints excluded: chain E residue 408 VAL Chi-restraints excluded: chain E residue 418 VAL Chi-restraints excluded: chain E residue 494 LEU Chi-restraints excluded: chain G residue 144 VAL Chi-restraints excluded: chain G residue 146 ILE Chi-restraints excluded: chain G residue 161 THR Chi-restraints excluded: chain G residue 192 GLU Chi-restraints excluded: chain G residue 252 SER Chi-restraints excluded: chain G residue 255 ASP Chi-restraints excluded: chain G residue 341 ASP Chi-restraints excluded: chain G residue 422 LEU Chi-restraints excluded: chain G residue 458 SER Chi-restraints excluded: chain G residue 460 ILE Chi-restraints excluded: chain H residue 9 LEU Chi-restraints excluded: chain H residue 22 LEU Chi-restraints excluded: chain H residue 37 ARG Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 130 GLN Chi-restraints excluded: chain H residue 239 LEU Chi-restraints excluded: chain H residue 297 ASP Chi-restraints excluded: chain H residue 351 THR Chi-restraints excluded: chain H residue 400 ILE Chi-restraints excluded: chain H residue 404 SER Chi-restraints excluded: chain H residue 405 VAL Chi-restraints excluded: chain H residue 427 ILE Chi-restraints excluded: chain H residue 456 ASP Chi-restraints excluded: chain N residue 115 VAL Chi-restraints excluded: chain Q residue 23 SER Chi-restraints excluded: chain Q residue 45 THR Chi-restraints excluded: chain Q residue 90 SER Chi-restraints excluded: chain Q residue 105 LEU Chi-restraints excluded: chain Q residue 175 ASN Chi-restraints excluded: chain Q residue 212 ILE Chi-restraints excluded: chain Q residue 253 THR Chi-restraints excluded: chain Q residue 289 ASN Chi-restraints excluded: chain Q residue 296 LYS Chi-restraints excluded: chain Q residue 480 LEU Chi-restraints excluded: chain Z residue 4 VAL Chi-restraints excluded: chain Z residue 108 LEU Chi-restraints excluded: chain Z residue 149 ILE Chi-restraints excluded: chain Z residue 176 ILE Chi-restraints excluded: chain Z residue 257 GLU Chi-restraints excluded: chain Z residue 414 VAL Chi-restraints excluded: chain Z residue 488 VAL Chi-restraints excluded: chain Z residue 522 MET Chi-restraints excluded: chain Z residue 526 MET Chi-restraints excluded: chain a residue 55 THR Chi-restraints excluded: chain a residue 101 LEU Chi-restraints excluded: chain a residue 167 PHE Chi-restraints excluded: chain a residue 358 ASP Chi-restraints excluded: chain a residue 486 ILE Chi-restraints excluded: chain b residue 184 VAL Chi-restraints excluded: chain b residue 212 SER Chi-restraints excluded: chain b residue 261 THR Chi-restraints excluded: chain b residue 363 SER Chi-restraints excluded: chain b residue 434 VAL Chi-restraints excluded: chain b residue 446 LEU Chi-restraints excluded: chain b residue 513 VAL Chi-restraints excluded: chain d residue 50 THR Chi-restraints excluded: chain d residue 94 LEU Chi-restraints excluded: chain d residue 149 THR Chi-restraints excluded: chain d residue 265 VAL Chi-restraints excluded: chain d residue 311 ASP Chi-restraints excluded: chain d residue 324 VAL Chi-restraints excluded: chain d residue 374 LEU Chi-restraints excluded: chain d residue 377 THR Chi-restraints excluded: chain d residue 385 THR Chi-restraints excluded: chain d residue 411 VAL Chi-restraints excluded: chain d residue 468 ASN Chi-restraints excluded: chain e residue 6 THR Chi-restraints excluded: chain e residue 205 ASP Chi-restraints excluded: chain e residue 215 VAL Chi-restraints excluded: chain e residue 228 VAL Chi-restraints excluded: chain e residue 298 ASN Chi-restraints excluded: chain e residue 372 LEU Chi-restraints excluded: chain e residue 381 ARG Chi-restraints excluded: chain e residue 418 VAL Chi-restraints excluded: chain e residue 468 MET Chi-restraints excluded: chain g residue 73 GLN Chi-restraints excluded: chain g residue 153 LEU Chi-restraints excluded: chain g residue 161 THR Chi-restraints excluded: chain g residue 192 GLU Chi-restraints excluded: chain g residue 242 ASP Chi-restraints excluded: chain g residue 284 GLN Chi-restraints excluded: chain g residue 288 ASP Chi-restraints excluded: chain g residue 341 ASP Chi-restraints excluded: chain g residue 373 THR Chi-restraints excluded: chain g residue 460 ILE Chi-restraints excluded: chain g residue 471 THR Chi-restraints excluded: chain g residue 528 LYS Chi-restraints excluded: chain h residue 4 THR Chi-restraints excluded: chain h residue 9 LEU Chi-restraints excluded: chain h residue 34 GLU Chi-restraints excluded: chain h residue 37 ARG Chi-restraints excluded: chain h residue 38 THR Chi-restraints excluded: chain h residue 85 SER Chi-restraints excluded: chain h residue 142 THR Chi-restraints excluded: chain h residue 211 VAL Chi-restraints excluded: chain h residue 239 LEU Chi-restraints excluded: chain h residue 251 ASP Chi-restraints excluded: chain h residue 308 MET Chi-restraints excluded: chain h residue 322 THR Chi-restraints excluded: chain h residue 362 THR Chi-restraints excluded: chain h residue 382 MET Chi-restraints excluded: chain h residue 400 ILE Chi-restraints excluded: chain h residue 404 SER Chi-restraints excluded: chain h residue 427 ILE Chi-restraints excluded: chain n residue 27 THR Chi-restraints excluded: chain q residue 125 VAL Chi-restraints excluded: chain q residue 130 GLU Chi-restraints excluded: chain q residue 146 LEU Chi-restraints excluded: chain q residue 175 ASN Chi-restraints excluded: chain q residue 212 ILE Chi-restraints excluded: chain q residue 253 THR Chi-restraints excluded: chain q residue 355 VAL Chi-restraints excluded: chain q residue 385 MET Chi-restraints excluded: chain q residue 480 LEU Chi-restraints excluded: chain q residue 534 LYS Chi-restraints excluded: chain z residue 127 LYS Chi-restraints excluded: chain z residue 135 GLU Chi-restraints excluded: chain z residue 149 ILE Chi-restraints excluded: chain z residue 159 LYS Chi-restraints excluded: chain z residue 170 GLU Chi-restraints excluded: chain z residue 213 ASP Chi-restraints excluded: chain z residue 235 VAL Chi-restraints excluded: chain z residue 295 LYS Chi-restraints excluded: chain z residue 338 ASP Chi-restraints excluded: chain z residue 340 SER Chi-restraints excluded: chain z residue 408 VAL Chi-restraints excluded: chain z residue 432 ARG Chi-restraints excluded: chain z residue 526 MET Chi-restraints excluded: chain K residue 11 ASP Chi-restraints excluded: chain K residue 67 LEU Chi-restraints excluded: chain K residue 82 MET Chi-restraints excluded: chain K residue 115 ASN Chi-restraints excluded: chain K residue 141 SER Chi-restraints excluded: chain K residue 179 ASP Chi-restraints excluded: chain K residue 267 LEU Chi-restraints excluded: chain K residue 269 MET Chi-restraints excluded: chain K residue 272 CYS Chi-restraints excluded: chain K residue 299 LEU Chi-restraints excluded: chain K residue 309 ILE Chi-restraints excluded: chain K residue 336 LYS Chi-restraints excluded: chain K residue 340 TRP Chi-restraints excluded: chain K residue 350 SER Chi-restraints excluded: chain P residue 47 THR Chi-restraints excluded: chain P residue 53 LEU Chi-restraints excluded: chain P residue 95 LEU Chi-restraints excluded: chain P residue 139 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 912 random chunks: chunk 816 optimal weight: 0.9990 chunk 537 optimal weight: 0.9990 chunk 866 optimal weight: 0.5980 chunk 528 optimal weight: 5.9990 chunk 410 optimal weight: 6.9990 chunk 602 optimal weight: 5.9990 chunk 908 optimal weight: 0.0040 chunk 836 optimal weight: 5.9990 chunk 723 optimal weight: 7.9990 chunk 75 optimal weight: 3.9990 chunk 558 optimal weight: 2.9990 overall best weight: 1.1198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 61 ASN H 60 ASN H 234 ASN ** Q 365 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 56 ASN ** h 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 80 HIS ** P 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7259 moved from start: 0.2789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 71861 Z= 0.175 Angle : 0.544 12.971 97066 Z= 0.269 Chirality : 0.041 0.172 11504 Planarity : 0.004 0.059 12403 Dihedral : 6.417 143.470 10015 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.26 % Favored : 96.73 % Rotamer: Outliers : 2.36 % Allowed : 19.01 % Favored : 78.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.37 % 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: 0.50 (0.09), residues: 9177 helix: 1.41 (0.08), residues: 4619 sheet: -0.45 (0.14), residues: 1299 loop : -0.84 (0.11), residues: 3259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP b 130 HIS 0.005 0.001 HIS G 226 PHE 0.013 0.001 PHE a 167 TYR 0.030 0.001 TYR P 120 ARG 0.015 0.000 ARG B 481 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18354 Ramachandran restraints generated. 9177 Oldfield, 0 Emsley, 9177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18354 Ramachandran restraints generated. 9177 Oldfield, 0 Emsley, 9177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1106 residues out of total 7685 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 181 poor density : 925 time to evaluate : 6.560 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 GLU cc_start: 0.4978 (OUTLIER) cc_final: 0.3836 (tm-30) REVERT: A 80 ASP cc_start: 0.7610 (t70) cc_final: 0.6942 (m-30) REVERT: A 81 LEU cc_start: 0.8545 (tp) cc_final: 0.8267 (tp) REVERT: A 84 LYS cc_start: 0.8074 (mtmm) cc_final: 0.7710 (mmmt) REVERT: A 206 MET cc_start: 0.7054 (mmm) cc_final: 0.6486 (mmm) REVERT: A 207 GLU cc_start: 0.8640 (OUTLIER) cc_final: 0.7430 (mp0) REVERT: A 245 LYS cc_start: 0.8075 (tttt) cc_final: 0.7753 (tttm) REVERT: A 251 GLN cc_start: 0.7962 (mt0) cc_final: 0.7620 (tt0) REVERT: A 337 GLU cc_start: 0.7405 (OUTLIER) cc_final: 0.6744 (tm-30) REVERT: A 344 MET cc_start: 0.7545 (mmt) cc_final: 0.7250 (mmm) REVERT: A 416 GLU cc_start: 0.8290 (mp0) cc_final: 0.8079 (mp0) REVERT: B 273 GLU cc_start: 0.7594 (tp30) cc_final: 0.7153 (mt-10) REVERT: D 193 LYS cc_start: 0.7925 (mttt) cc_final: 0.7262 (tptt) REVERT: D 232 LYS cc_start: 0.8004 (tppt) cc_final: 0.7613 (ptmt) REVERT: D 302 LYS cc_start: 0.8305 (ttmm) cc_final: 0.7768 (tttm) REVERT: D 374 LEU cc_start: 0.8717 (OUTLIER) cc_final: 0.8380 (tm) REVERT: E 149 ASP cc_start: 0.7649 (m-30) cc_final: 0.7154 (m-30) REVERT: E 220 GLU cc_start: 0.7580 (OUTLIER) cc_final: 0.7142 (pm20) REVERT: E 468 MET cc_start: 0.7639 (mpp) cc_final: 0.7382 (mpp) REVERT: E 501 MET cc_start: 0.7449 (mmt) cc_final: 0.6926 (mmm) REVERT: E 535 LYS cc_start: 0.8319 (pttp) cc_final: 0.7900 (pttm) REVERT: G 133 MET cc_start: 0.7715 (mtt) cc_final: 0.7135 (mtt) REVERT: G 152 MET cc_start: 0.7913 (mmm) cc_final: 0.7652 (mmt) REVERT: G 200 ARG cc_start: 0.7733 (tpt170) cc_final: 0.7390 (tpt170) REVERT: G 277 GLN cc_start: 0.6983 (tp-100) cc_final: 0.6539 (tt0) REVERT: G 284 GLN cc_start: 0.7860 (tp40) cc_final: 0.7620 (mt0) REVERT: H 10 LYS cc_start: 0.7701 (ttpp) cc_final: 0.7294 (ttpt) REVERT: H 22 LEU cc_start: 0.7835 (OUTLIER) cc_final: 0.7591 (tt) REVERT: H 34 GLU cc_start: 0.8241 (tm-30) cc_final: 0.8002 (tm-30) REVERT: H 184 MET cc_start: 0.8091 (mmm) cc_final: 0.7629 (mmt) REVERT: H 362 THR cc_start: 0.8515 (m) cc_final: 0.8188 (p) REVERT: H 440 LYS cc_start: 0.8614 (tptt) cc_final: 0.8249 (tttp) REVERT: N 82 MET cc_start: 0.2087 (mmm) cc_final: 0.1827 (mmp) REVERT: Q 31 ARG cc_start: 0.7299 (mmp-170) cc_final: 0.6959 (mmt90) REVERT: Q 52 MET cc_start: 0.8754 (mmm) cc_final: 0.8347 (mmp) REVERT: Q 55 MET cc_start: 0.7821 (mtm) cc_final: 0.7423 (mtm) REVERT: Q 238 LYS cc_start: 0.7504 (mmtp) cc_final: 0.6797 (mptt) REVERT: Q 299 ASP cc_start: 0.7747 (m-30) cc_final: 0.7235 (m-30) REVERT: Q 357 ASP cc_start: 0.7130 (t0) cc_final: 0.6630 (p0) REVERT: Q 386 ASP cc_start: 0.8134 (m-30) cc_final: 0.7790 (m-30) REVERT: Q 494 GLU cc_start: 0.7993 (mp0) cc_final: 0.7429 (mp0) REVERT: Z 49 SER cc_start: 0.8303 (m) cc_final: 0.8099 (t) REVERT: Z 195 GLU cc_start: 0.8134 (pt0) cc_final: 0.7726 (mt-10) REVERT: Z 258 LYS cc_start: 0.7879 (mttt) cc_final: 0.7653 (mttm) REVERT: Z 264 ARG cc_start: 0.7553 (mtp85) cc_final: 0.6513 (mtp85) REVERT: a 47 ASP cc_start: 0.7120 (t0) cc_final: 0.6867 (t0) REVERT: a 63 LYS cc_start: 0.7744 (mtpt) cc_final: 0.7445 (ptpt) REVERT: a 106 GLU cc_start: 0.6737 (OUTLIER) cc_final: 0.6515 (pt0) REVERT: a 189 ARG cc_start: 0.6599 (ttm-80) cc_final: 0.6132 (ttm-80) REVERT: a 247 LYS cc_start: 0.7398 (pttm) cc_final: 0.6977 (pttp) REVERT: a 382 ASP cc_start: 0.7372 (m-30) cc_final: 0.7111 (m-30) REVERT: a 505 GLU cc_start: 0.7314 (mt-10) cc_final: 0.6969 (mt-10) REVERT: a 532 LYS cc_start: 0.8474 (tttt) cc_final: 0.8125 (tttm) REVERT: b 18 GLU cc_start: 0.7794 (tm-30) cc_final: 0.7449 (tm-30) REVERT: b 130 TRP cc_start: 0.7972 (m-10) cc_final: 0.7752 (m100) REVERT: b 157 GLN cc_start: 0.7281 (tp40) cc_final: 0.6484 (mm110) REVERT: b 347 LYS cc_start: 0.8209 (mmtm) cc_final: 0.7580 (mtmm) REVERT: d 69 THR cc_start: 0.8611 (m) cc_final: 0.8328 (p) REVERT: d 196 ASP cc_start: 0.8023 (t0) cc_final: 0.7493 (p0) REVERT: d 277 ARG cc_start: 0.7239 (ttm-80) cc_final: 0.6937 (ttm-80) REVERT: d 363 GLU cc_start: 0.7714 (tt0) cc_final: 0.7264 (pt0) REVERT: d 429 GLU cc_start: 0.7991 (mp0) cc_final: 0.7486 (mp0) REVERT: d 505 GLU cc_start: 0.7387 (pp20) cc_final: 0.6977 (tp30) REVERT: d 524 GLU cc_start: 0.7702 (tp30) cc_final: 0.7478 (tp30) REVERT: e 67 ASP cc_start: 0.7269 (m-30) cc_final: 0.6903 (t70) REVERT: e 210 LYS cc_start: 0.8346 (tttp) cc_final: 0.8065 (tttp) REVERT: e 263 LYS cc_start: 0.8002 (ttmt) cc_final: 0.7714 (mtmt) REVERT: e 381 ARG cc_start: 0.7459 (OUTLIER) cc_final: 0.7128 (ttt-90) REVERT: e 448 MET cc_start: 0.7994 (mtp) cc_final: 0.7508 (mtp) REVERT: e 503 GLN cc_start: 0.7636 (tt0) cc_final: 0.7030 (mt0) REVERT: g 21 LYS cc_start: 0.7416 (mmtm) cc_final: 0.6781 (mtmm) REVERT: g 31 LYS cc_start: 0.7142 (mtpt) cc_final: 0.6810 (mtmt) REVERT: g 117 MET cc_start: 0.8239 (ttp) cc_final: 0.7957 (ttp) REVERT: g 133 MET cc_start: 0.7194 (mtt) cc_final: 0.6889 (mtp) REVERT: g 200 ARG cc_start: 0.7820 (tpt170) cc_final: 0.7386 (tpt-90) REVERT: g 242 ASP cc_start: 0.7778 (OUTLIER) cc_final: 0.7424 (m-30) REVERT: g 393 ASP cc_start: 0.7576 (t0) cc_final: 0.7344 (t0) REVERT: h 81 ASP cc_start: 0.6432 (m-30) cc_final: 0.6068 (m-30) REVERT: h 153 LYS cc_start: 0.7799 (mmtt) cc_final: 0.7350 (mtmt) REVERT: h 156 GLU cc_start: 0.7250 (mt-10) cc_final: 0.6671 (pt0) REVERT: h 239 LEU cc_start: 0.8753 (OUTLIER) cc_final: 0.8531 (mt) REVERT: h 320 LYS cc_start: 0.8464 (mtpp) cc_final: 0.8176 (mmmt) REVERT: h 338 SER cc_start: 0.8281 (m) cc_final: 0.7908 (t) REVERT: h 365 PRO cc_start: 0.6955 (Cg_endo) cc_final: 0.6728 (Cg_exo) REVERT: h 368 LYS cc_start: 0.8258 (mttt) cc_final: 0.7818 (mmmt) REVERT: h 459 ASN cc_start: 0.7698 (m-40) cc_final: 0.7296 (t0) REVERT: h 482 GLU cc_start: 0.7414 (mt-10) cc_final: 0.7207 (mt-10) REVERT: q 20 LYS cc_start: 0.8503 (mttt) cc_final: 0.8222 (mtmt) REVERT: q 34 GLN cc_start: 0.7658 (tp-100) cc_final: 0.6553 (tt0) REVERT: q 130 GLU cc_start: 0.7147 (OUTLIER) cc_final: 0.6909 (pt0) REVERT: q 175 ASN cc_start: 0.8783 (OUTLIER) cc_final: 0.8524 (p0) REVERT: q 254 LYS cc_start: 0.8006 (tttm) cc_final: 0.7594 (tptt) REVERT: q 281 LYS cc_start: 0.7849 (ttmt) cc_final: 0.7502 (ttpp) REVERT: q 357 ASP cc_start: 0.7916 (t0) cc_final: 0.7677 (t0) REVERT: q 382 ASP cc_start: 0.7655 (m-30) cc_final: 0.7441 (m-30) REVERT: q 534 LYS cc_start: 0.3024 (OUTLIER) cc_final: 0.1447 (tttp) REVERT: z 44 MET cc_start: 0.7536 (tpp) cc_final: 0.7076 (tpp) REVERT: z 127 LYS cc_start: 0.6555 (OUTLIER) cc_final: 0.6277 (tttt) REVERT: z 149 ILE cc_start: 0.7093 (OUTLIER) cc_final: 0.6794 (mm) REVERT: z 181 LYS cc_start: 0.7103 (mttt) cc_final: 0.6704 (mtpt) REVERT: z 226 GLU cc_start: 0.7868 (mm-30) cc_final: 0.7624 (mm-30) REVERT: z 240 GLU cc_start: 0.7642 (mm-30) cc_final: 0.7250 (pt0) REVERT: z 241 LYS cc_start: 0.8434 (ttmt) cc_final: 0.7658 (pttp) REVERT: z 258 LYS cc_start: 0.7945 (mttt) cc_final: 0.7687 (mtmt) REVERT: z 264 ARG cc_start: 0.7334 (mtp85) cc_final: 0.6783 (mtp85) REVERT: z 295 LYS cc_start: 0.8234 (OUTLIER) cc_final: 0.7956 (mttm) REVERT: z 338 ASP cc_start: 0.7890 (OUTLIER) cc_final: 0.7479 (m-30) REVERT: z 358 GLU cc_start: 0.8022 (tt0) cc_final: 0.7664 (mp0) REVERT: z 359 LYS cc_start: 0.8081 (mttt) cc_final: 0.7799 (mtmt) REVERT: z 432 ARG cc_start: 0.7649 (OUTLIER) cc_final: 0.7142 (ptm160) REVERT: K 82 MET cc_start: 0.7735 (OUTLIER) cc_final: 0.7453 (tpp) REVERT: P 187 MET cc_start: 0.6151 (OUTLIER) cc_final: 0.3269 (mtm) outliers start: 181 outliers final: 142 residues processed: 1056 average time/residue: 0.7188 time to fit residues: 1293.9855 Evaluate side-chains 1062 residues out of total 7685 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 162 poor density : 900 time to evaluate : 6.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 GLU Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 284 ASN Chi-restraints excluded: chain A residue 337 GLU Chi-restraints excluded: chain A residue 359 ASP Chi-restraints excluded: chain A residue 532 LYS Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 199 THR Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 296 ASN Chi-restraints excluded: chain D residue 332 ASP Chi-restraints excluded: chain D residue 374 LEU Chi-restraints excluded: chain D residue 377 THR Chi-restraints excluded: chain D residue 404 SER Chi-restraints excluded: chain E residue 65 ASP Chi-restraints excluded: chain E residue 220 GLU Chi-restraints excluded: chain E residue 230 VAL Chi-restraints excluded: chain E residue 287 GLU Chi-restraints excluded: chain E residue 298 ASN Chi-restraints excluded: chain E residue 408 VAL Chi-restraints excluded: chain E residue 418 VAL Chi-restraints excluded: chain G residue 96 THR Chi-restraints excluded: chain G residue 144 VAL Chi-restraints excluded: chain G residue 146 ILE Chi-restraints excluded: chain G residue 161 THR Chi-restraints excluded: chain G residue 192 GLU Chi-restraints excluded: chain G residue 252 SER Chi-restraints excluded: chain G residue 255 ASP Chi-restraints excluded: chain G residue 422 LEU Chi-restraints excluded: chain G residue 458 SER Chi-restraints excluded: chain G residue 460 ILE Chi-restraints excluded: chain H residue 9 LEU Chi-restraints excluded: chain H residue 22 LEU Chi-restraints excluded: chain H residue 37 ARG Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 130 GLN Chi-restraints excluded: chain H residue 234 ASN Chi-restraints excluded: chain H residue 297 ASP Chi-restraints excluded: chain H residue 351 THR Chi-restraints excluded: chain H residue 400 ILE Chi-restraints excluded: chain H residue 405 VAL Chi-restraints excluded: chain H residue 427 ILE Chi-restraints excluded: chain H residue 456 ASP Chi-restraints excluded: chain N residue 115 VAL Chi-restraints excluded: chain Q residue 23 SER Chi-restraints excluded: chain Q residue 45 THR Chi-restraints excluded: chain Q residue 90 SER Chi-restraints excluded: chain Q residue 105 LEU Chi-restraints excluded: chain Q residue 175 ASN Chi-restraints excluded: chain Q residue 212 ILE Chi-restraints excluded: chain Q residue 253 THR Chi-restraints excluded: chain Q residue 289 ASN Chi-restraints excluded: chain Q residue 480 LEU Chi-restraints excluded: chain Z residue 4 VAL Chi-restraints excluded: chain Z residue 108 LEU Chi-restraints excluded: chain Z residue 149 ILE Chi-restraints excluded: chain Z residue 176 ILE Chi-restraints excluded: chain Z residue 257 GLU Chi-restraints excluded: chain Z residue 414 VAL Chi-restraints excluded: chain Z residue 488 VAL Chi-restraints excluded: chain Z residue 522 MET Chi-restraints excluded: chain Z residue 526 MET Chi-restraints excluded: chain a residue 55 THR Chi-restraints excluded: chain a residue 101 LEU Chi-restraints excluded: chain a residue 106 GLU Chi-restraints excluded: chain a residue 166 ASP Chi-restraints excluded: chain a residue 167 PHE Chi-restraints excluded: chain a residue 329 SER Chi-restraints excluded: chain a residue 358 ASP Chi-restraints excluded: chain a residue 486 ILE Chi-restraints excluded: chain b residue 184 VAL Chi-restraints excluded: chain b residue 212 SER Chi-restraints excluded: chain b residue 261 THR Chi-restraints excluded: chain b residue 363 SER Chi-restraints excluded: chain b residue 434 VAL Chi-restraints excluded: chain b residue 446 LEU Chi-restraints excluded: chain b residue 513 VAL Chi-restraints excluded: chain d residue 50 THR Chi-restraints excluded: chain d residue 94 LEU Chi-restraints excluded: chain d residue 265 VAL Chi-restraints excluded: chain d residue 311 ASP Chi-restraints excluded: chain d residue 324 VAL Chi-restraints excluded: chain d residue 374 LEU Chi-restraints excluded: chain d residue 377 THR Chi-restraints excluded: chain d residue 385 THR Chi-restraints excluded: chain d residue 411 VAL Chi-restraints excluded: chain d residue 468 ASN Chi-restraints excluded: chain e residue 6 THR Chi-restraints excluded: chain e residue 215 VAL Chi-restraints excluded: chain e residue 228 VAL Chi-restraints excluded: chain e residue 298 ASN Chi-restraints excluded: chain e residue 372 LEU Chi-restraints excluded: chain e residue 381 ARG Chi-restraints excluded: chain e residue 418 VAL Chi-restraints excluded: chain g residue 73 GLN Chi-restraints excluded: chain g residue 153 LEU Chi-restraints excluded: chain g residue 161 THR Chi-restraints excluded: chain g residue 192 GLU Chi-restraints excluded: chain g residue 195 ILE Chi-restraints excluded: chain g residue 242 ASP Chi-restraints excluded: chain g residue 284 GLN Chi-restraints excluded: chain g residue 288 ASP Chi-restraints excluded: chain g residue 341 ASP Chi-restraints excluded: chain g residue 373 THR Chi-restraints excluded: chain g residue 460 ILE Chi-restraints excluded: chain g residue 471 THR Chi-restraints excluded: chain g residue 508 THR Chi-restraints excluded: chain g residue 528 LYS Chi-restraints excluded: chain h residue 4 THR Chi-restraints excluded: chain h residue 9 LEU Chi-restraints excluded: chain h residue 34 GLU Chi-restraints excluded: chain h residue 37 ARG Chi-restraints excluded: chain h residue 38 THR Chi-restraints excluded: chain h residue 85 SER Chi-restraints excluded: chain h residue 142 THR Chi-restraints excluded: chain h residue 211 VAL Chi-restraints excluded: chain h residue 239 LEU Chi-restraints excluded: chain h residue 251 ASP Chi-restraints excluded: chain h residue 308 MET Chi-restraints excluded: chain h residue 362 THR Chi-restraints excluded: chain h residue 382 MET Chi-restraints excluded: chain h residue 400 ILE Chi-restraints excluded: chain h residue 427 ILE Chi-restraints excluded: chain q residue 125 VAL Chi-restraints excluded: chain q residue 130 GLU Chi-restraints excluded: chain q residue 146 LEU Chi-restraints excluded: chain q residue 175 ASN Chi-restraints excluded: chain q residue 212 ILE Chi-restraints excluded: chain q residue 253 THR Chi-restraints excluded: chain q residue 355 VAL Chi-restraints excluded: chain q residue 385 MET Chi-restraints excluded: chain q residue 480 LEU Chi-restraints excluded: chain q residue 534 LYS Chi-restraints excluded: chain z residue 127 LYS Chi-restraints excluded: chain z residue 135 GLU Chi-restraints excluded: chain z residue 149 ILE Chi-restraints excluded: chain z residue 159 LYS Chi-restraints excluded: chain z residue 170 GLU Chi-restraints excluded: chain z residue 235 VAL Chi-restraints excluded: chain z residue 295 LYS Chi-restraints excluded: chain z residue 338 ASP Chi-restraints excluded: chain z residue 340 SER Chi-restraints excluded: chain z residue 408 VAL Chi-restraints excluded: chain z residue 432 ARG Chi-restraints excluded: chain K residue 11 ASP Chi-restraints excluded: chain K residue 67 LEU Chi-restraints excluded: chain K residue 82 MET Chi-restraints excluded: chain K residue 179 ASP Chi-restraints excluded: chain K residue 267 LEU Chi-restraints excluded: chain K residue 269 MET Chi-restraints excluded: chain K residue 272 CYS Chi-restraints excluded: chain K residue 299 LEU Chi-restraints excluded: chain K residue 309 ILE Chi-restraints excluded: chain K residue 318 THR Chi-restraints excluded: chain K residue 336 LYS Chi-restraints excluded: chain K residue 340 TRP Chi-restraints excluded: chain K residue 350 SER Chi-restraints excluded: chain P residue 53 LEU Chi-restraints excluded: chain P residue 95 LEU Chi-restraints excluded: chain P residue 139 ARG Chi-restraints excluded: chain P residue 187 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 912 random chunks: chunk 443 optimal weight: 0.8980 chunk 574 optimal weight: 0.0980 chunk 770 optimal weight: 4.9990 chunk 221 optimal weight: 0.1980 chunk 667 optimal weight: 2.9990 chunk 106 optimal weight: 1.9990 chunk 201 optimal weight: 2.9990 chunk 724 optimal weight: 4.9990 chunk 303 optimal weight: 5.9990 chunk 744 optimal weight: 5.9990 chunk 91 optimal weight: 2.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 314 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 61 ASN H 234 ASN ** Q 365 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 56 ASN a 425 ASN b 381 GLN e 522 GLN h 30 GLN ** h 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.139232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.119909 restraints weight = 95976.506| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 1.61 r_work: 0.3265 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3147 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3101 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3101 r_free = 0.3101 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3100 r_free = 0.3100 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.3100 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.2803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.197 71861 Z= 0.207 Angle : 0.603 59.196 97066 Z= 0.312 Chirality : 0.041 0.159 11504 Planarity : 0.004 0.056 12403 Dihedral : 6.409 143.441 10012 Min Nonbonded Distance : 1.617 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.26 % Favored : 96.73 % Rotamer: Outliers : 2.31 % Allowed : 19.26 % Favored : 78.43 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 0.37 % 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: 0.51 (0.09), residues: 9177 helix: 1.42 (0.08), residues: 4620 sheet: -0.44 (0.14), residues: 1299 loop : -0.84 (0.11), residues: 3258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP b 130 HIS 0.008 0.001 HIS B 314 PHE 0.013 0.001 PHE a 167 TYR 0.039 0.001 TYR P 169 ARG 0.013 0.000 ARG B 481 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 21169.83 seconds wall clock time: 370 minutes 40.26 seconds (22240.26 seconds total)