Starting phenix.real_space_refine (version: 1.21rc1) on Fri Apr 28 07:21:26 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lbm_23255/04_2023/7lbm_23255_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lbm_23255/04_2023/7lbm_23255.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lbm_23255/04_2023/7lbm_23255.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lbm_23255/04_2023/7lbm_23255.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lbm_23255/04_2023/7lbm_23255_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lbm_23255/04_2023/7lbm_23255_updated.pdb" } resolution = 4.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.035 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 Fe 4 7.16 5 Zn 16 6.06 5 P 127 5.49 5 Mg 2 5.21 5 S 789 5.16 5 C 81738 2.51 5 N 22483 2.21 5 O 24118 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "0 ARG 60": "NH1" <-> "NH2" Residue "0 GLU 82": "OE1" <-> "OE2" Residue "0 GLU 177": "OE1" <-> "OE2" Residue "0 ARG 208": "NH1" <-> "NH2" Residue "0 ARG 212": "NH1" <-> "NH2" Residue "0 ARG 288": "NH1" <-> "NH2" Residue "0 GLU 307": "OE1" <-> "OE2" Residue "0 GLU 509": "OE1" <-> "OE2" Residue "0 GLU 510": "OE1" <-> "OE2" Residue "0 ARG 543": "NH1" <-> "NH2" Residue "0 GLU 602": "OE1" <-> "OE2" Residue "0 GLU 657": "OE1" <-> "OE2" Residue "0 ARG 701": "NH1" <-> "NH2" Residue "0 GLU 703": "OE1" <-> "OE2" Residue "0 GLU 711": "OE1" <-> "OE2" Residue "0 ARG 783": "NH1" <-> "NH2" Residue "0 ARG 784": "NH1" <-> "NH2" Residue "0 GLU 793": "OE1" <-> "OE2" Residue "0 ARG 800": "NH1" <-> "NH2" Residue "1 GLU 54": "OE1" <-> "OE2" Residue "1 GLU 143": "OE1" <-> "OE2" Residue "1 GLU 165": "OE1" <-> "OE2" Residue "1 GLU 313": "OE1" <-> "OE2" Residue "1 GLU 486": "OE1" <-> "OE2" Residue "1 GLU 606": "OE1" <-> "OE2" Residue "1 GLU 679": "OE1" <-> "OE2" Residue "1 GLU 751": "OE1" <-> "OE2" Residue "1 GLU 763": "OE1" <-> "OE2" Residue "1 GLU 812": "OE1" <-> "OE2" Residue "1 ARG 813": "NH1" <-> "NH2" Residue "1 GLU 833": "OE1" <-> "OE2" Residue "1 GLU 875": "OE1" <-> "OE2" Residue "1 GLU 910": "OE1" <-> "OE2" Residue "1 GLU 930": "OE1" <-> "OE2" Residue "1 GLU 939": "OE1" <-> "OE2" Residue "1 GLU 985": "OE1" <-> "OE2" Residue "1 GLU 1057": "OE1" <-> "OE2" Residue "1 GLU 1096": "OE1" <-> "OE2" Residue "1 GLU 1140": "OE1" <-> "OE2" Residue "1 GLU 1180": "OE1" <-> "OE2" Residue "1 TYR 1207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 GLU 1233": "OE1" <-> "OE2" Residue "1 GLU 1269": "OE1" <-> "OE2" Residue "2 ARG 90": "NH1" <-> "NH2" Residue "2 GLU 115": "OE1" <-> "OE2" Residue "2 GLU 147": "OE1" <-> "OE2" Residue "2 ARG 175": "NH1" <-> "NH2" Residue "2 GLU 193": "OE1" <-> "OE2" Residue "2 GLU 216": "OE1" <-> "OE2" Residue "2 GLU 234": "OE1" <-> "OE2" Residue "2 GLU 259": "OE1" <-> "OE2" Residue "2 GLU 284": "OE1" <-> "OE2" Residue "2 PHE 340": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ARG 354": "NH1" <-> "NH2" Residue "2 GLU 366": "OE1" <-> "OE2" Residue "2 ARG 385": "NH1" <-> "NH2" Residue "2 GLU 390": "OE1" <-> "OE2" Residue "2 GLU 414": "OE1" <-> "OE2" Residue "2 GLU 433": "OE1" <-> "OE2" Residue "2 ARG 466": "NH1" <-> "NH2" Residue "2 GLU 473": "OE1" <-> "OE2" Residue "2 GLU 480": "OE1" <-> "OE2" Residue "2 ARG 489": "NH1" <-> "NH2" Residue "2 ARG 517": "NH1" <-> "NH2" Residue "2 GLU 526": "OE1" <-> "OE2" Residue "2 GLU 555": "OE1" <-> "OE2" Residue "2 GLU 566": "OE1" <-> "OE2" Residue "2 GLU 587": "OE1" <-> "OE2" Residue "2 GLU 600": "OE1" <-> "OE2" Residue "2 GLU 637": "OE1" <-> "OE2" Residue "2 GLU 653": "OE1" <-> "OE2" Residue "2 GLU 661": "OE1" <-> "OE2" Residue "2 GLU 720": "OE1" <-> "OE2" Residue "2 ARG 915": "NH1" <-> "NH2" Residue "2 GLU 930": "OE1" <-> "OE2" Residue "2 GLU 936": "OE1" <-> "OE2" Residue "2 GLU 954": "OE1" <-> "OE2" Residue "2 ARG 979": "NH1" <-> "NH2" Residue "3 GLU 33": "OE1" <-> "OE2" Residue "3 GLU 45": "OE1" <-> "OE2" Residue "3 GLU 116": "OE1" <-> "OE2" Residue "3 ARG 132": "NH1" <-> "NH2" Residue "3 GLU 133": "OE1" <-> "OE2" Residue "3 GLU 167": "OE1" <-> "OE2" Residue "3 ARG 192": "NH1" <-> "NH2" Residue "A GLU 30": "OE1" <-> "OE2" Residue "A GLU 38": "OE1" <-> "OE2" Residue "A ARG 61": "NH1" <-> "NH2" Residue "A GLU 197": "OE1" <-> "OE2" Residue "A GLU 207": "OE1" <-> "OE2" Residue "A GLU 246": "OE1" <-> "OE2" Residue "A ARG 271": "NH1" <-> "NH2" Residue "A GLU 392": "OE1" <-> "OE2" Residue "A GLU 500": "OE1" <-> "OE2" Residue "A GLU 510": "OE1" <-> "OE2" Residue "A GLU 613": "OE1" <-> "OE2" Residue "A GLU 659": "OE1" <-> "OE2" Residue "A GLU 683": "OE1" <-> "OE2" Residue "A GLU 715": "OE1" <-> "OE2" Residue "A GLU 794": "OE1" <-> "OE2" Residue "A GLU 818": "OE1" <-> "OE2" Residue "A GLU 835": "OE1" <-> "OE2" Residue "A GLU 845": "OE1" <-> "OE2" Residue "A GLU 856": "OE1" <-> "OE2" Residue "A GLU 869": "OE1" <-> "OE2" Residue "A PHE 920": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 927": "OE1" <-> "OE2" Residue "A ARG 932": "NH1" <-> "NH2" Residue "A GLU 955": "OE1" <-> "OE2" Residue "A GLU 961": "OE1" <-> "OE2" Residue "A GLU 1011": "OE1" <-> "OE2" Residue "A GLU 1056": "OE1" <-> "OE2" Residue "A GLU 1071": "OE1" <-> "OE2" Residue "A GLU 1097": "OE1" <-> "OE2" Residue "A GLU 1126": "OE1" <-> "OE2" Residue "A ARG 1149": "NH1" <-> "NH2" Residue "A GLU 1152": "OE1" <-> "OE2" Residue "A GLU 1188": "OE1" <-> "OE2" Residue "A GLU 1191": "OE1" <-> "OE2" Residue "A GLU 1198": "OE1" <-> "OE2" Residue "A GLU 1215": "OE1" <-> "OE2" Residue "A GLU 1229": "OE1" <-> "OE2" Residue "A GLU 1233": "OE1" <-> "OE2" Residue "A GLU 1337": "OE1" <-> "OE2" Residue "A GLU 1372": "OE1" <-> "OE2" Residue "A GLU 1381": "OE1" <-> "OE2" Residue "A GLU 1434": "OE1" <-> "OE2" Residue "A GLU 1447": "OE1" <-> "OE2" Residue "A GLU 1478": "OE1" <-> "OE2" Residue "B GLU 16": "OE1" <-> "OE2" Residue "B GLU 60": "OE1" <-> "OE2" Residue "B GLU 79": "OE1" <-> "OE2" Residue "B GLU 89": "OE1" <-> "OE2" Residue "B GLU 173": "OE1" <-> "OE2" Residue "B ARG 255": "NH1" <-> "NH2" Residue "B GLU 266": "OE1" <-> "OE2" Residue "B GLU 293": "OE1" <-> "OE2" Residue "B GLU 307": "OE1" <-> "OE2" Residue "B GLU 313": "OE1" <-> "OE2" Residue "B GLU 358": "OE1" <-> "OE2" Residue "B GLU 381": "OE1" <-> "OE2" Residue "B ARG 491": "NH1" <-> "NH2" Residue "B GLU 543": "OE1" <-> "OE2" Residue "B GLU 547": "OE1" <-> "OE2" Residue "B GLU 555": "OE1" <-> "OE2" Residue "B GLU 609": "OE1" <-> "OE2" Residue "B GLU 611": "OE1" <-> "OE2" Residue "B GLU 629": "OE1" <-> "OE2" Residue "B ARG 721": "NH1" <-> "NH2" Residue "B PHE 740": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 791": "OE1" <-> "OE2" Residue "B GLU 816": "OE1" <-> "OE2" Residue "B GLU 827": "OE1" <-> "OE2" Residue "B GLU 830": "OE1" <-> "OE2" Residue "B GLU 875": "OE1" <-> "OE2" Residue "B GLU 900": "OE1" <-> "OE2" Residue "B GLU 914": "OE1" <-> "OE2" Residue "B GLU 952": "OE1" <-> "OE2" Residue "B GLU 1026": "OE1" <-> "OE2" Residue "B ARG 1078": "NH1" <-> "NH2" Residue "B GLU 1109": "OE1" <-> "OE2" Residue "B GLU 1136": "OE1" <-> "OE2" Residue "C GLU 24": "OE1" <-> "OE2" Residue "C GLU 92": "OE1" <-> "OE2" Residue "C GLU 144": "OE1" <-> "OE2" Residue "C PHE 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 201": "OE1" <-> "OE2" Residue "C GLU 227": "OE1" <-> "OE2" Residue "C GLU 266": "OE1" <-> "OE2" Residue "D GLU 25": "OE1" <-> "OE2" Residue "D GLU 36": "OE1" <-> "OE2" Residue "D GLU 42": "OE1" <-> "OE2" Residue "D GLU 49": "OE1" <-> "OE2" Residue "D GLU 52": "OE1" <-> "OE2" Residue "D ARG 77": "NH1" <-> "NH2" Residue "D GLU 78": "OE1" <-> "OE2" Residue "D GLU 96": "OE1" <-> "OE2" Residue "D GLU 106": "OE1" <-> "OE2" Residue "D GLU 119": "OE1" <-> "OE2" Residue "E GLU 4": "OE1" <-> "OE2" Residue "E GLU 6": "OE1" <-> "OE2" Residue "E GLU 38": "OE1" <-> "OE2" Residue "E GLU 39": "OE1" <-> "OE2" Residue "E ARG 52": "NH1" <-> "NH2" Residue "E ARG 54": "NH1" <-> "NH2" Residue "E ARG 55": "NH1" <-> "NH2" Residue "E GLU 78": "OE1" <-> "OE2" Residue "E GLU 128": "OE1" <-> "OE2" Residue "E GLU 154": "OE1" <-> "OE2" Residue "E GLU 158": "OE1" <-> "OE2" Residue "F GLU 86": "OE1" <-> "OE2" Residue "G ARG 16": "NH1" <-> "NH2" Residue "G GLU 33": "OE1" <-> "OE2" Residue "G ARG 110": "NH1" <-> "NH2" Residue "G GLU 142": "OE1" <-> "OE2" Residue "H GLU 7": "OE1" <-> "OE2" Residue "H GLU 18": "OE1" <-> "OE2" Residue "H GLU 31": "OE1" <-> "OE2" Residue "H GLU 33": "OE1" <-> "OE2" Residue "H GLU 66": "OE1" <-> "OE2" Residue "H GLU 74": "OE1" <-> "OE2" Residue "H GLU 89": "OE1" <-> "OE2" Residue "H GLU 100": "OE1" <-> "OE2" Residue "H GLU 103": "OE1" <-> "OE2" Residue "I GLU 31": "OE1" <-> "OE2" Residue "I GLU 64": "OE1" <-> "OE2" Residue "I GLU 82": "OE1" <-> "OE2" Residue "I GLU 93": "OE1" <-> "OE2" Residue "I PHE 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 28": "OE1" <-> "OE2" Residue "K GLU 14": "OE1" <-> "OE2" Residue "K GLU 38": "OE1" <-> "OE2" Residue "K GLU 85": "OE1" <-> "OE2" Residue "K GLU 103": "OE1" <-> "OE2" Residue "M GLU 19": "OE1" <-> "OE2" Residue "M GLU 41": "OE1" <-> "OE2" Residue "M GLU 310": "OE1" <-> "OE2" Residue "M GLU 317": "OE1" <-> "OE2" Residue "M GLU 323": "OE1" <-> "OE2" Residue "M ARG 363": "NH1" <-> "NH2" Residue "M GLU 375": "OE1" <-> "OE2" Residue "N GLU 17": "OE1" <-> "OE2" Residue "N GLU 21": "OE1" <-> "OE2" Residue "N ARG 51": "NH1" <-> "NH2" Residue "N ARG 53": "NH1" <-> "NH2" Residue "N GLU 80": "OE1" <-> "OE2" Residue "O ARG 28": "NH1" <-> "NH2" Residue "O GLU 36": "OE1" <-> "OE2" Residue "O ARG 44": "NH1" <-> "NH2" Residue "O ARG 105": "NH1" <-> "NH2" Residue "O ARG 112": "NH1" <-> "NH2" Residue "O ARG 127": "NH1" <-> "NH2" Residue "O GLU 147": "OE1" <-> "OE2" Residue "O GLU 179": "OE1" <-> "OE2" Residue "O ARG 248": "NH1" <-> "NH2" Residue "O GLU 273": "OE1" <-> "OE2" Residue "O ARG 290": "NH1" <-> "NH2" Residue "P ARG 203": "NH1" <-> "NH2" Residue "P GLU 206": "OE1" <-> "OE2" Residue "P ARG 208": "NH1" <-> "NH2" Residue "P ARG 235": "NH1" <-> "NH2" Residue "P ARG 269": "NH1" <-> "NH2" Residue "P GLU 271": "OE1" <-> "OE2" Residue "P ARG 294": "NH1" <-> "NH2" Residue "P ARG 318": "NH1" <-> "NH2" Residue "P GLU 320": "OE1" <-> "OE2" Residue "P GLU 323": "OE1" <-> "OE2" Residue "P GLU 326": "OE1" <-> "OE2" Residue "P ARG 336": "NH1" <-> "NH2" Residue "Q ARG 23": "NH1" <-> "NH2" Residue "Q GLU 29": "OE1" <-> "OE2" Residue "Q GLU 45": "OE1" <-> "OE2" Residue "Q ARG 88": "NH1" <-> "NH2" Residue "Q ARG 97": "NH1" <-> "NH2" Residue "Q ARG 113": "NH1" <-> "NH2" Residue "Q ARG 124": "NH1" <-> "NH2" Residue "Q PHE 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 162": "OE1" <-> "OE2" Residue "Q GLU 163": "OE1" <-> "OE2" Residue "Q GLU 185": "OE1" <-> "OE2" Residue "Q ARG 192": "NH1" <-> "NH2" Residue "R GLU 101": "OE1" <-> "OE2" Residue "R GLU 122": "OE1" <-> "OE2" Residue "R GLU 172": "OE1" <-> "OE2" Residue "R GLU 215": "OE1" <-> "OE2" Residue "R ARG 221": "NH1" <-> "NH2" Residue "R GLU 235": "OE1" <-> "OE2" Residue "S ARG 46": "NH1" <-> "NH2" Residue "S ARG 49": "NH1" <-> "NH2" Residue "S GLU 120": "OE1" <-> "OE2" Residue "S GLU 136": "OE1" <-> "OE2" Residue "S GLU 163": "OE1" <-> "OE2" Residue "S GLU 165": "OE1" <-> "OE2" Residue "S ARG 167": "NH1" <-> "NH2" Residue "S ARG 180": "NH1" <-> "NH2" Residue "T GLU 3": "OE1" <-> "OE2" Residue "T GLU 39": "OE1" <-> "OE2" Residue "T ARG 51": "NH1" <-> "NH2" Residue "T GLU 80": "OE1" <-> "OE2" Residue "T GLU 133": "OE1" <-> "OE2" Residue "T GLU 134": "OE1" <-> "OE2" Residue "T GLU 166": "OE1" <-> "OE2" Residue "T GLU 171": "OE1" <-> "OE2" Residue "T ARG 177": "NH1" <-> "NH2" Residue "T GLU 215": "OE1" <-> "OE2" Residue "T GLU 238": "OE1" <-> "OE2" Residue "W ARG 542": "NH1" <-> "NH2" Residue "W ARG 553": "NH1" <-> "NH2" Residue "W PHE 615": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d GLU 264": "OE1" <-> "OE2" Residue "d ARG 276": "NH1" <-> "NH2" Residue "e ARG 11": "NH1" <-> "NH2" Residue "e ARG 57": "NH1" <-> "NH2" Residue "e GLU 68": "OE1" <-> "OE2" Residue "e GLU 95": "OE1" <-> "OE2" Residue "e GLU 147": "OE1" <-> "OE2" Residue "e ARG 167": "NH1" <-> "NH2" Residue "e ARG 309": "NH1" <-> "NH2" Residue "f GLU 52": "OE1" <-> "OE2" Residue "f GLU 137": "OE1" <-> "OE2" Residue "f GLU 182": "OE1" <-> "OE2" Residue "f ARG 242": "NH1" <-> "NH2" Residue "g GLU 58": "OE1" <-> "OE2" Residue "g ARG 118": "NH1" <-> "NH2" Residue "g GLU 132": "OE1" <-> "OE2" Residue "h GLU 4": "OE1" <-> "OE2" Residue "h GLU 5": "OE1" <-> "OE2" Residue "h GLU 9": "OE1" <-> "OE2" Residue "h ARG 110": "NH1" <-> "NH2" Residue "h GLU 152": "OE1" <-> "OE2" Residue "h GLU 158": "OE1" <-> "OE2" Residue "h GLU 162": "OE1" <-> "OE2" Residue "i ARG 10": "NH1" <-> "NH2" Residue "i GLU 18": "OE1" <-> "OE2" Residue "i GLU 34": "OE1" <-> "OE2" Residue "i ARG 47": "NH1" <-> "NH2" Residue "i GLU 60": "OE1" <-> "OE2" Residue "i GLU 80": "OE1" <-> "OE2" Residue "i GLU 112": "OE1" <-> "OE2" Residue "i GLU 116": "OE1" <-> "OE2" Residue "j GLU 186": "OE1" <-> "OE2" Residue "j ARG 191": "NH1" <-> "NH2" Residue "j GLU 223": "OE1" <-> "OE2" Residue "j GLU 252": "OE1" <-> "OE2" Residue "j GLU 314": "OE1" <-> "OE2" Residue "j GLU 365": "OE1" <-> "OE2" Residue "j ARG 404": "NH1" <-> "NH2" Residue "j GLU 429": "OE1" <-> "OE2" Residue "j GLU 456": "OE1" <-> "OE2" Residue "j ARG 507": "NH1" <-> "NH2" Residue "j GLU 520": "OE1" <-> "OE2" Residue "j GLU 561": "OE1" <-> "OE2" Residue "j ARG 583": "NH1" <-> "NH2" Residue "k GLU 20": "OE1" <-> "OE2" Residue "k GLU 33": "OE1" <-> "OE2" Residue "k ARG 38": "NH1" <-> "NH2" Residue "k GLU 47": "OE1" <-> "OE2" Residue "k ARG 73": "NH1" <-> "NH2" Residue "k ARG 98": "NH1" <-> "NH2" Residue "k GLU 112": "OE1" <-> "OE2" Residue "k ARG 124": "NH1" <-> "NH2" Residue "k GLU 161": "OE1" <-> "OE2" Residue "k GLU 191": "OE1" <-> "OE2" Residue "l GLU 29": "OE1" <-> "OE2" Residue "l GLU 80": "OE1" <-> "OE2" Residue "l GLU 141": "OE1" <-> "OE2" Residue "l GLU 143": "OE1" <-> "OE2" Residue "l ARG 179": "NH1" <-> "NH2" Residue "m GLU 35": "OE1" <-> "OE2" Residue "m ARG 50": "NH1" <-> "NH2" Residue "m GLU 55": "OE1" <-> "OE2" Residue "m ARG 64": "NH1" <-> "NH2" Residue "m GLU 110": "OE1" <-> "OE2" Residue "m GLU 111": "OE1" <-> "OE2" Residue "m GLU 132": "OE1" <-> "OE2" Residue "n GLU 12": "OE1" <-> "OE2" Residue "n ARG 25": "NH1" <-> "NH2" Residue "n ARG 40": "NH1" <-> "NH2" Residue "n ARG 205": "NH1" <-> "NH2" Residue "n GLU 224": "OE1" <-> "OE2" Residue "n ARG 271": "NH1" <-> "NH2" Residue "n ARG 283": "NH1" <-> "NH2" Residue "o GLU 47": "OE1" <-> "OE2" Residue "o GLU 71": "OE1" <-> "OE2" Residue "o ARG 99": "NH1" <-> "NH2" Residue "o GLU 108": "OE1" <-> "OE2" Residue "q GLU 39": "OE1" <-> "OE2" Residue "q GLU 101": "OE1" <-> "OE2" Residue "q GLU 144": "OE1" <-> "OE2" Residue "r GLU 56": "OE1" <-> "OE2" Residue "r GLU 65": "OE1" <-> "OE2" Residue "r GLU 80": "OE1" <-> "OE2" Residue "r GLU 113": "OE1" <-> "OE2" Residue "r ARG 135": "NH1" <-> "NH2" Residue "r GLU 187": "OE1" <-> "OE2" Residue "r GLU 227": "OE1" <-> "OE2" Residue "r GLU 229": "OE1" <-> "OE2" Residue "r GLU 306": "OE1" <-> "OE2" Residue "r GLU 318": "OE1" <-> "OE2" Residue "r GLU 327": "OE1" <-> "OE2" Residue "r ARG 408": "NH1" <-> "NH2" Residue "r GLU 432": "OE1" <-> "OE2" Residue "r GLU 479": "OE1" <-> "OE2" Residue "r ARG 504": "NH1" <-> "NH2" Residue "r ARG 544": "NH1" <-> "NH2" Residue "r GLU 553": "OE1" <-> "OE2" Residue "r ARG 609": "NH1" <-> "NH2" Residue "r ARG 614": "NH1" <-> "NH2" Residue "r GLU 660": "OE1" <-> "OE2" Residue "r GLU 696": "OE1" <-> "OE2" Residue "r ARG 718": "NH1" <-> "NH2" Residue "r GLU 750": "OE1" <-> "OE2" Residue "r GLU 755": "OE1" <-> "OE2" Residue "r GLU 764": "OE1" <-> "OE2" Residue "r ARG 775": "NH1" <-> "NH2" Residue "r GLU 782": "OE1" <-> "OE2" Residue "r GLU 857": "OE1" <-> "OE2" Residue "r PHE 953": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r ARG 1209": "NH1" <-> "NH2" Residue "r ARG 1218": "NH1" <-> "NH2" Residue "r ARG 1222": "NH1" <-> "NH2" Residue "r GLU 1282": "OE1" <-> "OE2" Residue "r ARG 1288": "NH1" <-> "NH2" Residue "r GLU 1424": "OE1" <-> "OE2" Residue "s GLU 35": "OE1" <-> "OE2" Residue "s GLU 43": "OE1" <-> "OE2" Residue "s GLU 46": "OE1" <-> "OE2" Residue "s GLU 62": "OE1" <-> "OE2" Residue "s GLU 67": "OE1" <-> "OE2" Residue "s GLU 75": "OE1" <-> "OE2" Residue "s GLU 78": "OE1" <-> "OE2" Residue "s GLU 136": "OE1" <-> "OE2" Residue "s GLU 146": "OE1" <-> "OE2" Residue "t GLU 106": "OE1" <-> "OE2" Residue "t GLU 110": "OE1" <-> "OE2" Residue "t GLU 140": "OE1" <-> "OE2" Residue "u GLU 96": "OE1" <-> "OE2" Residue "u GLU 123": "OE1" <-> "OE2" Residue "v GLU 69": "OE1" <-> "OE2" Residue "v GLU 83": "OE1" <-> "OE2" Residue "w GLU 90": "OE1" <-> "OE2" Residue "w GLU 103": "OE1" <-> "OE2" Residue "x GLU 53": "OE1" <-> "OE2" Residue "x GLU 99": "OE1" <-> "OE2" Residue "x GLU 105": "OE1" <-> "OE2" Residue "y GLU 21": "OE1" <-> "OE2" Residue "y GLU 23": "OE1" <-> "OE2" Residue "y GLU 62": "OE1" <-> "OE2" Residue "y GLU 99": "OE1" <-> "OE2" Residue "y GLU 121": "OE1" <-> "OE2" Residue "z GLU 681": "OE1" <-> "OE2" Residue "z GLU 722": "OE1" <-> "OE2" Residue "z ARG 739": "NH1" <-> "NH2" Time to flip residues: 0.31s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 129277 Number of models: 1 Model: "" Number of chains: 68 Chain: "0" Number of atoms: 5864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 752, 5864 Classifications: {'peptide': 752} Link IDs: {'PTRANS': 36, 'TRANS': 715} Chain breaks: 5 Chain: "1" Number of atoms: 10636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1317, 10636 Classifications: {'peptide': 1317} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 68, 'TRANS': 1248} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "2" Number of atoms: 7007 Number of conformers: 1 Conformer: "" Number of residues, atoms: 897, 7007 Classifications: {'peptide': 897} Link IDs: {'PTRANS': 37, 'TRANS': 859} Chain breaks: 5 Chain: "3" Number of atoms: 1504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1504 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 13, 'TRANS': 181} Chain breaks: 2 Chain: "A" Number of atoms: 11519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1455, 11519 Classifications: {'peptide': 1455} Link IDs: {'PCIS': 2, 'PTRANS': 73, 'TRANS': 1379} Chain breaks: 5 Chain: "B" Number of atoms: 9129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1142, 9129 Classifications: {'peptide': 1142} Link IDs: {'PTRANS': 53, 'TRANS': 1088} Chain breaks: 3 Chain: "C" Number of atoms: 2147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2147 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 16, 'TRANS': 250} Chain breaks: 1 Chain: "D" Number of atoms: 1062 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1062 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 3, 'TRANS': 125} Chain: "E" Number of atoms: 1723 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1723 Classifications: {'peptide': 210} Link IDs: {'PTRANS': 11, 'TRANS': 198} Chain: "F" Number of atoms: 689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 689 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 6, 'TRANS': 79} Chain: "G" Number of atoms: 1351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1351 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 10, 'TRANS': 160} Chain: "H" Number of atoms: 1205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1205 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "I" Number of atoms: 942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 942 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 5, 'TRANS': 110} Chain: "J" Number of atoms: 533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 533 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 2, 'TRANS': 64} Chain: "K" Number of atoms: 928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 928 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 8, 'TRANS': 107} Chain: "L" Number of atoms: 388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 388 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 2, 'TRANS': 43} Chain: "M" Number of atoms: 930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 930 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 2, 'TRANS': 110} Chain breaks: 1 Chain: "N" Number of atoms: 806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 806 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 1, 'TRANS': 97} Chain: "O" Number of atoms: 2018 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2018 Classifications: {'peptide': 260} Link IDs: {'PTRANS': 14, 'TRANS': 245} Chain breaks: 1 Chain: "P" Number of atoms: 1462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1462 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 10, 'TRANS': 174} Chain: "Q" Number of atoms: 1520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1520 Classifications: {'peptide': 184} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 179} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "R" Number of atoms: 1357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1357 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 5, 'TRANS': 159} Chain: "S" Number of atoms: 1059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1059 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 5, 'TRANS': 121} Chain breaks: 1 Chain: "T" Number of atoms: 1788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1788 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 7, 'TRANS': 214} Chain breaks: 1 Chain: "U" Number of atoms: 1321 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 1321 Classifications: {'DNA': 64} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 63} Chain: "V" Number of atoms: 1300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 1300 Classifications: {'DNA': 64} Link IDs: {'rna3p': 63} Chain: "W" Number of atoms: 4645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 574, 4645 Classifications: {'peptide': 574} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 4, 'PTRANS': 22, 'TRANS': 547} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "X" Number of atoms: 6109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 760, 6109 Classifications: {'peptide': 760} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 727} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "Y" Number of atoms: 1631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1631 Classifications: {'peptide': 218} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 9, 'TRANS': 208} Chain breaks: 1 Unresolved non-hydrogen bonds: 142 Unresolved non-hydrogen angles: 181 Unresolved non-hydrogen dihedrals: 117 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 1, 'ASN:plan1': 3, 'TRP:plan': 1, 'ASP:plan': 2, 'PHE:plan': 2, 'GLU:plan': 6, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 89 Chain: "Z" Number of atoms: 3473 Number of conformers: 1 Conformer: "" Number of residues, atoms: 436, 3473 Classifications: {'peptide': 436} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 21, 'TRANS': 414} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2} Unresolved non-hydrogen planarities: 8 Chain: "a" Number of atoms: 2580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2580 Classifications: {'peptide': 331} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 312} Chain breaks: 1 Chain: "b" Number of atoms: 2065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 2065 Classifications: {'peptide': 263} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 253} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "c" Number of atoms: 522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 522 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 1, 'TRANS': 64} Chain: "d" Number of atoms: 2104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2104 Classifications: {'peptide': 275} Incomplete info: {'truncation_to_alanine': 42} Link IDs: {'PTRANS': 12, 'TRANS': 262} Chain breaks: 1 Unresolved non-hydrogen bonds: 148 Unresolved non-hydrogen angles: 185 Unresolved non-hydrogen dihedrals: 118 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 4, 'ASP:plan': 3, 'PHE:plan': 2, 'GLU:plan': 2, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 81 Chain: "e" Number of atoms: 2376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2376 Classifications: {'peptide': 298} Link IDs: {'PTRANS': 18, 'TRANS': 279} Chain breaks: 1 Chain: "f" Number of atoms: 2293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2293 Classifications: {'peptide': 281} Link IDs: {'PTRANS': 15, 'TRANS': 265} Chain breaks: 1 Chain: "g" Number of atoms: 1035 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1035 Classifications: {'peptide': 130} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 123} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "h" Number of atoms: 1230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1230 Classifications: {'peptide': 158} Link IDs: {'PTRANS': 8, 'TRANS': 149} Chain breaks: 2 Chain: "i" Number of atoms: 863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 863 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 1, 'TRANS': 108} Chain: "j" Number of atoms: 4005 Number of conformers: 1 Conformer: "" Number of residues, atoms: 504, 4005 Classifications: {'peptide': 504} Link IDs: {'PTRANS': 20, 'TRANS': 483} Chain breaks: 5 Chain: "k" Number of atoms: 1484 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1484 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 7, 'TRANS': 177} Chain breaks: 1 Chain: "l" Number of atoms: 1425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1425 Classifications: {'peptide': 184} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 174} Chain breaks: 2 Chain: "m" Number of atoms: 1024 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 1024 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 1, 'TRANS': 123} Chain breaks: 1 Chain: "n" Number of atoms: 2279 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2279 Classifications: {'peptide': 283} Link IDs: {'PTRANS': 11, 'TRANS': 271} Chain breaks: 2 Chain: "o" Number of atoms: 887 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 887 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 1, 'TRANS': 106} Chain: "p" Number of atoms: 893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 893 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 6, 'TRANS': 107} Chain breaks: 1 Chain: "q" Number of atoms: 1007 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 1007 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 4, 'TRANS': 117} Chain breaks: 2 Chain: "r" Number of atoms: 8174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1034, 8174 Classifications: {'peptide': 1034} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'CIS': 3, 'PTRANS': 56, 'TRANS': 974} Chain breaks: 14 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 114 Unresolved non-hydrogen angles: 148 Unresolved non-hydrogen dihedrals: 97 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 5, 'PHE:plan': 3, 'ASN:plan1': 1, 'TRP:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 57 Chain: "s" Number of atoms: 1084 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1084 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 1, 'TRANS': 133} Chain breaks: 2 Chain: "t" Number of atoms: 975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 975 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 7, 'TRANS': 108} Chain breaks: 2 Chain: "u" Number of atoms: 501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 501 Classifications: {'peptide': 60} Link IDs: {'PTRANS': 2, 'TRANS': 57} Chain breaks: 2 Chain: "v" Number of atoms: 1067 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1067 Classifications: {'peptide': 131} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 126} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "w" Number of atoms: 309 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 309 Classifications: {'peptide': 39} Link IDs: {'PTRANS': 1, 'TRANS': 37} Chain breaks: 3 Chain: "x" Number of atoms: 852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 852 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 2, 'TRANS': 108} Chain breaks: 1 Chain: "y" Number of atoms: 1003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 1003 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 3, 'TRANS': 112} Chain breaks: 1 Chain: "z" Number of atoms: 1168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1168 Classifications: {'peptide': 149} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 132} Chain breaks: 1 Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' MG': 2, ' ZN': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "O" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "Q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "X" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} Chain: "a" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "b" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "d" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 25483 SG CYS A 71 172.896 128.351 207.663 1.00 71.98 S ATOM 25505 SG CYS A 74 175.403 130.631 208.579 1.00 72.86 S ATOM 25552 SG CYS A 81 175.881 127.857 205.540 1.00 65.03 S ATOM 25787 SG CYS A 111 215.893 109.443 225.323 1.00 92.57 S ATOM 25815 SG CYS A 114 213.910 110.917 228.458 1.00 92.18 S ATOM 45229 SG CYS B1119 188.353 135.257 216.380 1.00 60.67 S ATOM 45251 SG CYS B1122 189.778 131.483 215.667 1.00 61.87 S ATOM 45366 SG CYS B1137 186.443 132.225 216.541 1.00 65.17 S ATOM 45387 SG CYS B1140 189.542 131.804 219.026 1.00 66.28 S ATOM 46362 SG CYS C 88 147.853 147.975 150.308 1.00 64.36 S ATOM 46375 SG CYS C 90 147.074 145.387 152.621 1.00 67.31 S ATOM 46410 SG CYS C 94 145.934 145.737 148.815 1.00 61.93 S ATOM 46432 SG CYS C 97 149.403 144.912 149.453 1.00 56.72 S ATOM 53898 SG CYS I 17 244.066 71.778 169.385 1.00 87.45 S ATOM 53922 SG CYS I 20 240.753 72.440 171.926 1.00 87.66 S ATOM 54108 SG CYS I 42 243.906 71.342 172.838 1.00 88.91 S ATOM 54460 SG CYS I 86 239.280 95.683 132.064 1.00 65.83 S ATOM 54484 SG CYS I 89 238.495 92.927 129.365 1.00 65.37 S ATOM 54688 SG CYS I 114 235.213 94.854 131.545 1.00 61.62 S ATOM 54723 SG CYS I 119 237.670 92.533 132.705 1.00 63.05 S ATOM 54833 SG CYS J 7 175.695 135.212 135.621 1.00 39.20 S ATOM 54857 SG CYS J 10 174.886 137.756 133.294 1.00 39.78 S ATOM 55121 SG CYS J 44 178.122 136.757 133.821 1.00 42.09 S ATOM 56297 SG CYS L 19 156.550 100.833 157.134 1.00 59.59 S ATOM 56316 SG CYS L 22 154.263 99.872 154.696 1.00 60.24 S ATOM 56433 SG CYS L 36 153.067 100.260 158.448 1.00 62.75 S ATOM 58430 SG CYS O 15 158.275 139.308 197.174 1.00 74.04 S ATOM 58577 SG CYS O 34 158.183 137.860 194.039 1.00 68.51 S ATOM 62786 SG CYS Q 129 161.995 124.958 218.138 1.00 97.06 S ATOM 62978 SG CYS Q 154 164.895 127.877 216.689 1.00 98.30 S ATOM 75765 SG CYS X 116 196.618 89.338 293.650 1.00 57.98 S ATOM 76074 SG CYS X 155 190.217 90.296 295.624 1.00 71.14 S ATOM 75905 SG CYS X 134 193.422 94.790 293.706 1.00 58.64 S ATOM 76363 SG CYS X 190 194.035 91.762 299.525 1.00 60.71 S ATOM 88304 SG CYS a 345 277.956 75.614 311.698 1.00 75.65 S ATOM 88326 SG CYS a 348 280.507 73.943 308.685 1.00 64.83 S ATOM 88483 SG CYS a 368 277.111 77.591 308.436 1.00 71.71 S ATOM 88504 SG CYS a 371 276.474 73.819 309.299 1.00 71.32 S ATOM 88424 SG CYS a 360 267.343 72.464 317.719 1.00 84.88 S ATOM 88442 SG CYS a 363 270.776 71.519 319.847 1.00 87.91 S ATOM 88591 SG CYS a 382 270.187 70.053 316.181 1.00 71.58 S ATOM 88608 SG CYS a 385 267.836 68.508 319.097 1.00 74.09 S ATOM 87868 SG CYS a 291 255.213 37.809 297.258 1.00 79.05 S ATOM 87890 SG CYS a 294 253.985 35.478 294.235 1.00 89.45 S ATOM 87979 SG CYS a 305 252.662 39.089 294.394 1.00 81.96 S ATOM 88002 SG CYS a 308 250.705 36.143 295.501 1.00 86.60 S ATOM 90512 SG CYS b 268 248.929 51.846 311.472 1.00 65.95 S ATOM 90531 SG CYS b 271 252.060 51.948 313.021 1.00 64.03 S ATOM 90616 SG CYS b 282 249.524 50.385 315.137 1.00 77.32 S ATOM 90636 SG CYS b 285 249.548 54.222 315.039 1.00 82.61 S ATOM 91243 SG CYS d 6 183.703 113.122 248.012 1.00200.73 S ATOM 91261 SG CYS d 9 183.187 115.185 244.795 1.00206.24 S ATOM 91379 SG CYS d 31 185.214 116.737 248.389 1.00212.05 S ATOM 91395 SG CYS d 34 181.713 115.779 248.359 1.00219.26 S ATOM 91349 SG CYS d 26 172.469 118.434 256.671 1.00197.12 S ATOM 91456 SG CYS d 46 172.659 116.851 253.699 1.00221.32 S ATOM 91474 SG CYS d 49 170.488 115.849 256.287 1.00223.19 S Time building chain proxies: 47.65, per 1000 atoms: 0.37 Number of scatterers: 129277 At special positions: 0 Unit cell: (337.821, 275.34, 389.712, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 16 29.99 Fe 4 26.01 S 789 16.00 P 127 15.00 Mg 2 11.99 O 24118 8.00 N 22483 7.00 C 81738 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS 0 798 " - pdb=" SG CYS 0 801 " distance=2.04 Simple disulfide: pdb=" SG CYS 0 801 " - pdb=" SG CYS 0 829 " distance=1.93 Simple disulfide: pdb=" SG CYS b 255 " - pdb=" SG CYS b 257 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 40.16 Conformation dependent library (CDL) restraints added in 13.7 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 X1000 " pdb="FE4 SF4 X1000 " - pdb=" SG CYS X 190 " pdb="FE1 SF4 X1000 " - pdb=" SG CYS X 116 " pdb="FE2 SF4 X1000 " - pdb=" SG CYS X 155 " pdb="FE3 SF4 X1000 " - pdb=" SG CYS X 134 " Number of angles added : 12 Zn2+ tetrahedral coordination pdb=" ZN A2002 " pdb="ZN ZN A2002 " - pdb=" NE2 HIS A 84 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 74 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 71 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 81 " pdb=" ZN A2003 " pdb="ZN ZN A2003 " - pdb=" SG CYS A 111 " pdb="ZN ZN A2003 " - pdb=" SG CYS A 114 " pdb=" ZN B1201 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1122 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1137 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1140 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1119 " pdb=" ZN C 301 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 94 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 90 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 88 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 97 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 17 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 20 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 42 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 119 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 89 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 86 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 114 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 10 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 44 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 7 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 22 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 36 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 19 " pdb=" ZN O 401 " pdb="ZN ZN O 401 " - pdb=" SG CYS O 34 " pdb="ZN ZN O 401 " - pdb=" SG CYS O 15 " pdb="ZN ZN O 401 " - pdb=" NE2 HIS O 18 " pdb=" ZN Q 501 " pdb="ZN ZN Q 501 " - pdb=" SG CYS Q 154 " pdb="ZN ZN Q 501 " - pdb=" SG CYS Q 129 " pdb=" ZN a 401 " pdb="ZN ZN a 401 " - pdb=" SG CYS a 345 " pdb="ZN ZN a 401 " - pdb=" SG CYS a 371 " pdb="ZN ZN a 401 " - pdb=" SG CYS a 368 " pdb="ZN ZN a 401 " - pdb=" SG CYS a 348 " pdb=" ZN a 402 " pdb="ZN ZN a 402 " - pdb=" SG CYS a 363 " pdb="ZN ZN a 402 " - pdb=" SG CYS a 385 " pdb="ZN ZN a 402 " - pdb=" SG CYS a 382 " pdb="ZN ZN a 402 " - pdb=" SG CYS a 360 " pdb=" ZN a 403 " pdb="ZN ZN a 403 " - pdb=" SG CYS a 308 " pdb="ZN ZN a 403 " - pdb=" SG CYS a 305 " pdb="ZN ZN a 403 " - pdb=" SG CYS a 294 " pdb="ZN ZN a 403 " - pdb=" SG CYS a 291 " pdb=" ZN b 401 " pdb="ZN ZN b 401 " - pdb=" SG CYS b 271 " pdb="ZN ZN b 401 " - pdb=" SG CYS b 268 " pdb="ZN ZN b 401 " - pdb=" SG CYS b 282 " pdb="ZN ZN b 401 " - pdb=" SG CYS b 285 " pdb=" ZN d 400 " pdb="ZN ZN d 400 " - pdb=" SG CYS d 34 " pdb="ZN ZN d 400 " - pdb=" SG CYS d 6 " pdb="ZN ZN d 400 " - pdb=" SG CYS d 9 " pdb="ZN ZN d 400 " - pdb=" SG CYS d 31 " pdb=" ZN d 401 " pdb="ZN ZN d 401 " - pdb=" ND1 HIS d 28 " pdb="ZN ZN d 401 " - pdb=" SG CYS d 46 " pdb="ZN ZN d 401 " - pdb=" SG CYS d 26 " pdb="ZN ZN d 401 " - pdb=" SG CYS d 49 " Number of angles added : 54 31246 Ramachandran restraints generated. 15623 Oldfield, 0 Emsley, 15623 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 30246 Finding SS restraints... Warning!!! ksdssp method is not applicable forstructures with more than 99999 atoms! Switching to from_ca. running find_ss_from_ca liberal... Secondary structure from input PDB file: 595 helices and 107 sheets defined 55.4% alpha, 10.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 40.01 Creating SS restraints... Processing helix chain '0' and resid 154 through 160 removed outlier: 3.800A pdb=" N SER 0 160 " --> pdb=" O GLY 0 156 " (cutoff:3.500A) Processing helix chain '0' and resid 267 through 272 removed outlier: 4.735A pdb=" N LEU 0 271 " --> pdb=" O CYS 0 267 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N ASN 0 272 " --> pdb=" O THR 0 268 " (cutoff:3.500A) No H-bonds generated for 'chain '0' and resid 267 through 272' Processing helix chain '0' and resid 364 through 375 Processing helix chain '0' and resid 466 through 485 Processing helix chain '0' and resid 488 through 496 removed outlier: 3.812A pdb=" N HIS 0 494 " --> pdb=" O ASP 0 490 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N GLN 0 496 " --> pdb=" O LEU 0 492 " (cutoff:3.500A) Processing helix chain '0' and resid 499 through 514 removed outlier: 4.505A pdb=" N GLN 0 514 " --> pdb=" O GLU 0 510 " (cutoff:3.500A) Processing helix chain '0' and resid 515 through 523 removed outlier: 6.487A pdb=" N GLN 0 519 " --> pdb=" O THR 0 515 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N GLN 0 520 " --> pdb=" O ALA 0 516 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N VAL 0 521 " --> pdb=" O ALA 0 517 " (cutoff:3.500A) Processing helix chain '0' and resid 524 through 537 removed outlier: 3.762A pdb=" N ALA 0 528 " --> pdb=" O THR 0 524 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N LEU 0 536 " --> pdb=" O SER 0 532 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N SER 0 537 " --> pdb=" O LEU 0 533 " (cutoff:3.500A) Processing helix chain '0' and resid 538 through 564 removed outlier: 5.662A pdb=" N THR 0 542 " --> pdb=" O PRO 0 538 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ARG 0 543 " --> pdb=" O CYS 0 539 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N VAL 0 544 " --> pdb=" O THR 0 540 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N CYS 0 545 " --> pdb=" O VAL 0 541 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N ASP 0 546 " --> pdb=" O THR 0 542 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N SER 0 562 " --> pdb=" O SER 0 558 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N LEU 0 563 " --> pdb=" O THR 0 559 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N LEU 0 564 " --> pdb=" O LEU 0 560 " (cutoff:3.500A) Processing helix chain '0' and resid 575 through 586 Processing helix chain '0' and resid 592 through 601 removed outlier: 4.156A pdb=" N MET 0 596 " --> pdb=" O ILE 0 592 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N ILE 0 597 " --> pdb=" O ASP 0 593 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ASN 0 598 " --> pdb=" O LYS 0 594 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N LYS 0 600 " --> pdb=" O MET 0 596 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N THR 0 601 " --> pdb=" O ILE 0 597 " (cutoff:3.500A) Processing helix chain '0' and resid 607 through 633 removed outlier: 3.635A pdb=" N LEU 0 611 " --> pdb=" O ASP 0 607 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLN 0 612 " --> pdb=" O MET 0 608 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLN 0 615 " --> pdb=" O LEU 0 611 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N GLN 0 616 " --> pdb=" O GLN 0 612 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N LEU 0 617 " --> pdb=" O ALA 0 613 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N TRP 0 620 " --> pdb=" O GLN 0 616 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU 0 632 " --> pdb=" O LEU 0 628 " (cutoff:3.500A) Proline residue: 0 633 - end of helix Processing helix chain '0' and resid 642 through 648 removed outlier: 3.952A pdb=" N LEU 0 646 " --> pdb=" O GLY 0 642 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N ARG 0 647 " --> pdb=" O HIS 0 643 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N ASP 0 648 " --> pdb=" O SER 0 644 " (cutoff:3.500A) No H-bonds generated for 'chain '0' and resid 642 through 648' Processing helix chain '0' and resid 649 through 669 removed outlier: 4.435A pdb=" N GLY 0 653 " --> pdb=" O GLY 0 649 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LEU 0 668 " --> pdb=" O ILE 0 664 " (cutoff:3.500A) Processing helix chain '0' and resid 684 through 701 Processing helix chain '0' and resid 710 through 724 removed outlier: 3.802A pdb=" N LEU 0 719 " --> pdb=" O ASP 0 715 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LEU 0 720 " --> pdb=" O GLU 0 716 " (cutoff:3.500A) Proline residue: 0 721 - end of helix Processing helix chain '0' and resid 737 through 742 removed outlier: 4.672A pdb=" N ARG 0 741 " --> pdb=" O GLY 0 737 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU 0 742 " --> pdb=" O LEU 0 738 " (cutoff:3.500A) No H-bonds generated for 'chain '0' and resid 737 through 742' Processing helix chain '0' and resid 816 through 824 removed outlier: 3.986A pdb=" N GLU 0 820 " --> pdb=" O VAL 0 816 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLN 0 821 " --> pdb=" O LYS 0 817 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ARG 0 822 " --> pdb=" O GLN 0 818 " (cutoff:3.500A) Processing helix chain '1' and resid 1 through 14 Processing helix chain '1' and resid 32 through 51 removed outlier: 3.606A pdb=" N PHE 1 47 " --> pdb=" O ALA 1 43 " (cutoff:3.500A) Processing helix chain '1' and resid 55 through 70 removed outlier: 3.686A pdb=" N GLN 1 70 " --> pdb=" O PHE 1 66 " (cutoff:3.500A) Processing helix chain '1' and resid 72 through 90 removed outlier: 4.058A pdb=" N GLY 1 90 " --> pdb=" O ALA 1 86 " (cutoff:3.500A) Processing helix chain '1' and resid 93 through 104 removed outlier: 3.611A pdb=" N SER 1 104 " --> pdb=" O SER 1 100 " (cutoff:3.500A) Processing helix chain '1' and resid 111 through 126 removed outlier: 3.558A pdb=" N LYS 1 124 " --> pdb=" O LYS 1 120 " (cutoff:3.500A) Processing helix chain '1' and resid 130 through 149 removed outlier: 3.787A pdb=" N THR 1 147 " --> pdb=" O GLU 1 143 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ILE 1 148 " --> pdb=" O LYS 1 144 " (cutoff:3.500A) Proline residue: 1 149 - end of helix Processing helix chain '1' and resid 153 through 172 removed outlier: 3.617A pdb=" N VAL 1 157 " --> pdb=" O SER 1 153 " (cutoff:3.500A) removed outlier: 5.074A pdb=" N GLN 1 158 " --> pdb=" O SER 1 154 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N GLN 1 159 " --> pdb=" O ALA 1 155 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N ALA 1 162 " --> pdb=" O GLN 1 158 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N ALA 1 163 " --> pdb=" O GLN 1 159 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N ARG 1 164 " --> pdb=" O LEU 1 160 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLU 1 165 " --> pdb=" O LEU 1 161 " (cutoff:3.500A) Processing helix chain '1' and resid 179 through 192 Proline residue: 1 192 - end of helix Processing helix chain '1' and resid 202 through 221 removed outlier: 3.977A pdb=" N PHE 1 212 " --> pdb=" O PHE 1 208 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ARG 1 213 " --> pdb=" O VAL 1 209 " (cutoff:3.500A) Proline residue: 1 214 - end of helix removed outlier: 4.299A pdb=" N ILE 1 218 " --> pdb=" O PRO 1 214 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N SER 1 220 " --> pdb=" O ALA 1 216 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N ILE 1 221 " --> pdb=" O ARG 1 217 " (cutoff:3.500A) Processing helix chain '1' and resid 238 through 243 removed outlier: 3.836A pdb=" N LYS 1 242 " --> pdb=" O CYS 1 238 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N LEU 1 243 " --> pdb=" O ASN 1 239 " (cutoff:3.500A) No H-bonds generated for 'chain '1' and resid 238 through 243' Processing helix chain '1' and resid 259 through 265 removed outlier: 4.137A pdb=" N PHE 1 263 " --> pdb=" O ASP 1 259 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N GLU 1 264 " --> pdb=" O LYS 1 260 " (cutoff:3.500A) Proline residue: 1 265 - end of helix No H-bonds generated for 'chain '1' and resid 259 through 265' Processing helix chain '1' and resid 266 through 276 Processing helix chain '1' and resid 279 through 288 Processing helix chain '1' and resid 297 through 317 removed outlier: 4.046A pdb=" N GLU 1 316 " --> pdb=" O MET 1 312 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N THR 1 317 " --> pdb=" O GLU 1 313 " (cutoff:3.500A) Processing helix chain '1' and resid 325 through 345 removed outlier: 6.739A pdb=" N LEU 1 329 " --> pdb=" O GLY 1 325 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N LEU 1 330 " --> pdb=" O THR 1 326 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N TRP 1 331 " --> pdb=" O SER 1 327 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N SER 1 336 " --> pdb=" O GLN 1 332 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLN 1 345 " --> pdb=" O PHE 1 341 " (cutoff:3.500A) Processing helix chain '1' and resid 348 through 363 removed outlier: 5.285A pdb=" N GLY 1 362 " --> pdb=" O GLN 1 358 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N ARG 1 363 " --> pdb=" O LYS 1 359 " (cutoff:3.500A) Processing helix chain '1' and resid 368 through 384 removed outlier: 4.012A pdb=" N PHE 1 379 " --> pdb=" O VAL 1 375 " (cutoff:3.500A) Processing helix chain '1' and resid 388 through 403 removed outlier: 4.670A pdb=" N PHE 1 392 " --> pdb=" O ALA 1 388 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N LEU 1 393 " --> pdb=" O LEU 1 389 " (cutoff:3.500A) Proline residue: 1 394 - end of helix removed outlier: 4.089A pdb=" N LYS 1 397 " --> pdb=" O LEU 1 393 " (cutoff:3.500A) Processing helix chain '1' and resid 422 through 439 removed outlier: 4.380A pdb=" N THR 1 426 " --> pdb=" O ALA 1 422 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N CYS 1 427 " --> pdb=" O PHE 1 423 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ILE 1 428 " --> pdb=" O ALA 1 424 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N TRP 1 429 " --> pdb=" O MET 1 425 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ARG 1 434 " --> pdb=" O ILE 1 430 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASN 1 438 " --> pdb=" O ARG 1 434 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ASP 1 439 " --> pdb=" O LYS 1 435 " (cutoff:3.500A) Processing helix chain '1' and resid 448 through 465 removed outlier: 4.950A pdb=" N LEU 1 453 " --> pdb=" O HIS 1 449 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N HIS 1 454 " --> pdb=" O SER 1 450 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N LYS 1 465 " --> pdb=" O SER 1 461 " (cutoff:3.500A) Processing helix chain '1' and resid 472 through 482 removed outlier: 4.373A pdb=" N SER 1 482 " --> pdb=" O CYS 1 478 " (cutoff:3.500A) Processing helix chain '1' and resid 486 through 500 removed outlier: 5.392A pdb=" N LEU 1 490 " --> pdb=" O GLU 1 486 " (cutoff:3.500A) Proline residue: 1 491 - end of helix Processing helix chain '1' and resid 524 through 532 removed outlier: 3.617A pdb=" N SER 1 530 " --> pdb=" O ASN 1 526 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N THR 1 532 " --> pdb=" O LEU 1 528 " (cutoff:3.500A) Processing helix chain '1' and resid 533 through 554 Processing helix chain '1' and resid 560 through 574 removed outlier: 4.157A pdb=" N TYR 1 573 " --> pdb=" O ARG 1 569 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N MET 1 574 " --> pdb=" O LEU 1 570 " (cutoff:3.500A) Processing helix chain '1' and resid 580 through 596 removed outlier: 3.850A pdb=" N LEU 1 588 " --> pdb=" O PHE 1 584 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N LEU 1 589 " --> pdb=" O ILE 1 585 " (cutoff:3.500A) Proline residue: 1 590 - end of helix removed outlier: 3.550A pdb=" N SER 1 595 " --> pdb=" O THR 1 591 " (cutoff:3.500A) Processing helix chain '1' and resid 597 through 611 removed outlier: 4.080A pdb=" N THR 1 603 " --> pdb=" O GLY 1 599 " (cutoff:3.500A) Processing helix chain '1' and resid 616 through 634 removed outlier: 3.760A pdb=" N VAL 1 633 " --> pdb=" O THR 1 629 " (cutoff:3.500A) Processing helix chain '1' and resid 638 through 656 removed outlier: 3.641A pdb=" N HIS 1 642 " --> pdb=" O GLN 1 638 " (cutoff:3.500A) Processing helix chain '1' and resid 657 through 670 removed outlier: 4.740A pdb=" N VAL 1 661 " --> pdb=" O GLY 1 657 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N GLN 1 662 " --> pdb=" O SER 1 658 " (cutoff:3.500A) Proline residue: 1 663 - end of helix removed outlier: 3.542A pdb=" N THR 1 666 " --> pdb=" O GLN 1 662 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N ARG 1 667 " --> pdb=" O PRO 1 663 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N PHE 1 668 " --> pdb=" O GLN 1 664 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N SER 1 670 " --> pdb=" O THR 1 666 " (cutoff:3.500A) Processing helix chain '1' and resid 680 through 699 Processing helix chain '1' and resid 710 through 723 removed outlier: 4.433A pdb=" N ASP 1 714 " --> pdb=" O THR 1 710 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ILE 1 715 " --> pdb=" O TRP 1 711 " (cutoff:3.500A) Processing helix chain '1' and resid 728 through 735 removed outlier: 3.685A pdb=" N SER 1 733 " --> pdb=" O SER 1 729 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N CYS 1 734 " --> pdb=" O HIS 1 730 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N PHE 1 735 " --> pdb=" O THR 1 731 " (cutoff:3.500A) Processing helix chain '1' and resid 736 through 747 removed outlier: 3.762A pdb=" N ASN 1 747 " --> pdb=" O PHE 1 743 " (cutoff:3.500A) Processing helix chain '1' and resid 752 through 770 removed outlier: 4.091A pdb=" N LEU 1 756 " --> pdb=" O SER 1 752 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LYS 1 757 " --> pdb=" O ARG 1 753 " (cutoff:3.500A) Processing helix chain '1' and resid 773 through 782 removed outlier: 5.097A pdb=" N ILE 1 777 " --> pdb=" O GLU 1 773 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N THR 1 778 " --> pdb=" O ASN 1 774 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N HIS 1 779 " --> pdb=" O ASP 1 775 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N PHE 1 780 " --> pdb=" O ILE 1 776 " (cutoff:3.500A) Processing helix chain '1' and resid 788 through 800 Processing helix chain '1' and resid 804 through 815 removed outlier: 4.454A pdb=" N TYR 1 808 " --> pdb=" O ASN 1 804 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ARG 1 809 " --> pdb=" O GLN 1 805 " (cutoff:3.500A) Processing helix chain '1' and resid 816 through 836 removed outlier: 4.519A pdb=" N VAL 1 820 " --> pdb=" O ALA 1 816 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N ALA 1 821 " --> pdb=" O ARG 1 817 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ASP 1 828 " --> pdb=" O ARG 1 824 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N THR 1 836 " --> pdb=" O TYR 1 832 " (cutoff:3.500A) Processing helix chain '1' and resid 839 through 855 removed outlier: 5.231A pdb=" N LEU 1 843 " --> pdb=" O GLY 1 839 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N LYS 1 845 " --> pdb=" O GLN 1 841 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL 1 854 " --> pdb=" O LEU 1 850 " (cutoff:3.500A) Processing helix chain '1' and resid 861 through 873 removed outlier: 5.260A pdb=" N SER 1 873 " --> pdb=" O LEU 1 869 " (cutoff:3.500A) Processing helix chain '1' and resid 876 through 891 removed outlier: 3.846A pdb=" N GLN 1 880 " --> pdb=" O GLY 1 876 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N VAL 1 881 " --> pdb=" O ASN 1 877 " (cutoff:3.500A) Processing helix chain '1' and resid 893 through 907 removed outlier: 4.943A pdb=" N ARG 1 897 " --> pdb=" O PRO 1 893 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ASN 1 898 " --> pdb=" O ASN 1 894 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LYS 1 905 " --> pdb=" O SER 1 901 " (cutoff:3.500A) Processing helix chain '1' and resid 910 through 915 removed outlier: 4.456A pdb=" N GLN 1 914 " --> pdb=" O GLU 1 910 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N ASN 1 915 " --> pdb=" O HIS 1 911 " (cutoff:3.500A) No H-bonds generated for 'chain '1' and resid 910 through 915' Processing helix chain '1' and resid 916 through 929 removed outlier: 4.261A pdb=" N LYS 1 920 " --> pdb=" O ASP 1 916 " (cutoff:3.500A) Proline residue: 1 929 - end of helix Processing helix chain '1' and resid 934 through 942 removed outlier: 3.748A pdb=" N ALA 1 938 " --> pdb=" O PHE 1 934 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLN 1 940 " --> pdb=" O GLY 1 936 " (cutoff:3.500A) removed outlier: 5.187A pdb=" N ASP 1 942 " --> pdb=" O ALA 1 938 " (cutoff:3.500A) Processing helix chain '1' and resid 958 through 978 Proline residue: 1 965 - end of helix removed outlier: 3.605A pdb=" N LEU 1 977 " --> pdb=" O ARG 1 973 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N LEU 1 978 " --> pdb=" O PHE 1 974 " (cutoff:3.500A) Processing helix chain '1' and resid 980 through 991 removed outlier: 5.446A pdb=" N LEU 1 984 " --> pdb=" O VAL 1 980 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLU 1 985 " --> pdb=" O SER 1 981 " (cutoff:3.500A) Processing helix chain '1' and resid 1000 through 1013 removed outlier: 3.763A pdb=" N GLU 11013 " --> pdb=" O LEU 11009 " (cutoff:3.500A) Processing helix chain '1' and resid 1019 through 1036 removed outlier: 4.088A pdb=" N LEU 11034 " --> pdb=" O ILE 11030 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LYS 11035 " --> pdb=" O ILE 11031 " (cutoff:3.500A) removed outlier: 5.015A pdb=" N ASP 11036 " --> pdb=" O GLY 11032 " (cutoff:3.500A) Processing helix chain '1' and resid 1045 through 1052 Processing helix chain '1' and resid 1064 through 1081 removed outlier: 3.791A pdb=" N TYR 11068 " --> pdb=" O ASP 11064 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N LEU 11075 " --> pdb=" O LEU 11071 " (cutoff:3.500A) Processing helix chain '1' and resid 1091 through 1096 removed outlier: 3.716A pdb=" N ASN 11095 " --> pdb=" O ASP 11091 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N GLU 11096 " --> pdb=" O TRP 11092 " (cutoff:3.500A) No H-bonds generated for 'chain '1' and resid 1091 through 1096' Processing helix chain '1' and resid 1099 through 1115 removed outlier: 3.503A pdb=" N LEU 11115 " --> pdb=" O GLU 11111 " (cutoff:3.500A) Processing helix chain '1' and resid 1119 through 1131 removed outlier: 3.604A pdb=" N VAL 11129 " --> pdb=" O ALA 11125 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N VAL 11130 " --> pdb=" O LEU 11126 " (cutoff:3.500A) Processing helix chain '1' and resid 1141 through 1157 removed outlier: 3.548A pdb=" N TRP 11145 " --> pdb=" O ASN 11141 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ALA 11155 " --> pdb=" O LEU 11151 " (cutoff:3.500A) Proline residue: 11157 - end of helix Processing helix chain '1' and resid 1158 through 1174 removed outlier: 4.878A pdb=" N VAL 11163 " --> pdb=" O PRO 11159 " (cutoff:3.500A) removed outlier: 5.368A pdb=" N LEU 11164 " --> pdb=" O TYR 11160 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N HIS 11165 " --> pdb=" O TRP 11161 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N ASP 11166 " --> pdb=" O ILE 11162 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N SER 11174 " --> pdb=" O SER 11170 " (cutoff:3.500A) Processing helix chain '1' and resid 1180 through 1185 removed outlier: 4.737A pdb=" N VAL 11184 " --> pdb=" O GLU 11180 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N GLY 11185 " --> pdb=" O THR 11181 " (cutoff:3.500A) No H-bonds generated for 'chain '1' and resid 1180 through 1185' Processing helix chain '1' and resid 1186 through 1193 removed outlier: 4.192A pdb=" N ASP 11192 " --> pdb=" O PHE 11188 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N PHE 11193 " --> pdb=" O ARG 11189 " (cutoff:3.500A) Processing helix chain '1' and resid 1194 through 1200 removed outlier: 4.057A pdb=" N GLN 11198 " --> pdb=" O THR 11194 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N SER 11199 " --> pdb=" O ALA 11195 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N TYR 11200 " --> pdb=" O CYS 11196 " (cutoff:3.500A) No H-bonds generated for 'chain '1' and resid 1194 through 1200' Processing helix chain '1' and resid 1203 through 1219 removed outlier: 3.700A pdb=" N TRP 11216 " --> pdb=" O ALA 11212 " (cutoff:3.500A) Processing helix chain '1' and resid 1220 through 1233 removed outlier: 3.976A pdb=" N LEU 11226 " --> pdb=" O GLY 11222 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N ILE 11227 " --> pdb=" O GLN 11223 " (cutoff:3.500A) Proline residue: 11228 - end of helix removed outlier: 3.530A pdb=" N THR 11232 " --> pdb=" O PRO 11228 " (cutoff:3.500A) Processing helix chain '1' and resid 1234 through 1239 removed outlier: 5.128A pdb=" N ILE 11238 " --> pdb=" O VAL 11234 " (cutoff:3.500A) Processing helix chain '1' and resid 1241 through 1263 Proline residue: 11254 - end of helix removed outlier: 4.908A pdb=" N GLN 11257 " --> pdb=" O GLY 11253 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N ARG 11258 " --> pdb=" O PRO 11254 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLN 11261 " --> pdb=" O GLN 11257 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLU 11262 " --> pdb=" O ARG 11258 " (cutoff:3.500A) Processing helix chain '1' and resid 1264 through 1285 removed outlier: 3.881A pdb=" N ILE 11268 " --> pdb=" O THR 11264 " (cutoff:3.500A) Processing helix chain '1' and resid 1290 through 1304 removed outlier: 3.552A pdb=" N ILE 11294 " --> pdb=" O TYR 11290 " (cutoff:3.500A) Processing helix chain '1' and resid 1311 through 1322 removed outlier: 4.018A pdb=" N LYS 11316 " --> pdb=" O GLU 11312 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ILE 11317 " --> pdb=" O GLN 11313 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ASN 11320 " --> pdb=" O LYS 11316 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LEU 11321 " --> pdb=" O ILE 11317 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N LYS 11322 " --> pdb=" O ILE 11318 " (cutoff:3.500A) Processing helix chain '1' and resid 1323 through 1334 removed outlier: 5.640A pdb=" N PHE 11331 " --> pdb=" O LEU 11327 " (cutoff:3.500A) removed outlier: 5.698A pdb=" N ILE 11332 " --> pdb=" O ARG 11328 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N THR 11333 " --> pdb=" O LEU 11329 " (cutoff:3.500A) Processing helix chain '1' and resid 416 through 421 removed outlier: 3.594A pdb=" N HIS 1 421 " --> pdb=" O GLN 1 418 " (cutoff:3.500A) Processing helix chain '1' and resid 992 through 997 Processing helix chain '2' and resid 4 through 16 removed outlier: 3.920A pdb=" N ILE 2 10 " --> pdb=" O LEU 2 6 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N LYS 2 15 " --> pdb=" O LEU 2 11 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N GLU 2 16 " --> pdb=" O GLN 2 12 " (cutoff:3.500A) Processing helix chain '2' and resid 19 through 31 Processing helix chain '2' and resid 41 through 52 removed outlier: 3.892A pdb=" N GLU 2 48 " --> pdb=" O ASP 2 44 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N GLN 2 49 " --> pdb=" O ALA 2 45 " (cutoff:3.500A) Processing helix chain '2' and resid 57 through 71 removed outlier: 3.786A pdb=" N GLN 2 71 " --> pdb=" O ALA 2 67 " (cutoff:3.500A) Processing helix chain '2' and resid 74 through 85 removed outlier: 6.406A pdb=" N VAL 2 78 " --> pdb=" O SER 2 74 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N LEU 2 79 " --> pdb=" O TYR 2 75 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N PHE 2 85 " --> pdb=" O ALA 2 81 " (cutoff:3.500A) Processing helix chain '2' and resid 92 through 105 removed outlier: 4.375A pdb=" N MET 2 103 " --> pdb=" O ASP 2 99 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N PHE 2 104 " --> pdb=" O ILE 2 100 " (cutoff:3.500A) Processing helix chain '2' and resid 115 through 148 removed outlier: 4.446A pdb=" N GLY 2 119 " --> pdb=" O GLU 2 115 " (cutoff:3.500A) Processing helix chain '2' and resid 155 through 166 removed outlier: 4.091A pdb=" N ALA 2 159 " --> pdb=" O GLU 2 155 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N MET 2 160 " --> pdb=" O LYS 2 156 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ARG 2 164 " --> pdb=" O MET 2 160 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N LEU 2 165 " --> pdb=" O CYS 2 161 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N GLU 2 166 " --> pdb=" O LEU 2 162 " (cutoff:3.500A) Processing helix chain '2' and resid 175 through 185 removed outlier: 4.413A pdb=" N GLU 2 184 " --> pdb=" O ILE 2 180 " (cutoff:3.500A) Processing helix chain '2' and resid 186 through 203 Processing helix chain '2' and resid 208 through 228 Proline residue: 2 226 - end of helix Processing helix chain '2' and resid 241 through 254 removed outlier: 4.008A pdb=" N HIS 2 245 " --> pdb=" O PHE 2 241 " (cutoff:3.500A) Processing helix chain '2' and resid 259 through 275 removed outlier: 3.592A pdb=" N LEU 2 263 " --> pdb=" O GLU 2 259 " (cutoff:3.500A) Processing helix chain '2' and resid 277 through 296 removed outlier: 3.652A pdb=" N VAL 2 282 " --> pdb=" O THR 2 278 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N SER 2 296 " --> pdb=" O GLY 2 292 " (cutoff:3.500A) Processing helix chain '2' and resid 299 through 324 removed outlier: 4.338A pdb=" N LEU 2 303 " --> pdb=" O GLY 2 299 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N LYS 2 304 " --> pdb=" O THR 2 300 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N ILE 2 313 " --> pdb=" O THR 2 309 " (cutoff:3.500A) Proline residue: 2 314 - end of helix Processing helix chain '2' and resid 329 through 345 removed outlier: 4.158A pdb=" N LEU 2 344 " --> pdb=" O PHE 2 340 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N THR 2 345 " --> pdb=" O LEU 2 341 " (cutoff:3.500A) Processing helix chain '2' and resid 346 through 356 Processing helix chain '2' and resid 358 through 371 removed outlier: 3.610A pdb=" N LEU 2 363 " --> pdb=" O CYS 2 359 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLN 2 370 " --> pdb=" O GLU 2 366 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N GLY 2 371 " --> pdb=" O CYS 2 367 " (cutoff:3.500A) Processing helix chain '2' and resid 374 through 393 removed outlier: 3.958A pdb=" N HIS 2 391 " --> pdb=" O ALA 2 387 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ALA 2 392 " --> pdb=" O ASP 2 388 " (cutoff:3.500A) Proline residue: 2 393 - end of helix Processing helix chain '2' and resid 405 through 421 Proline residue: 2 415 - end of helix Processing helix chain '2' and resid 432 through 444 removed outlier: 4.186A pdb=" N LEU 2 436 " --> pdb=" O PRO 2 432 " (cutoff:3.500A) Processing helix chain '2' and resid 446 through 459 removed outlier: 4.391A pdb=" N LEU 2 450 " --> pdb=" O LYS 2 446 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU 2 451 " --> pdb=" O SER 2 447 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N THR 2 458 " --> pdb=" O ALA 2 454 " (cutoff:3.500A) Processing helix chain '2' and resid 460 through 477 removed outlier: 5.024A pdb=" N TYR 2 477 " --> pdb=" O GLU 2 473 " (cutoff:3.500A) Processing helix chain '2' and resid 482 through 507 removed outlier: 3.542A pdb=" N TYR 2 507 " --> pdb=" O VAL 2 503 " (cutoff:3.500A) Processing helix chain '2' and resid 509 through 514 removed outlier: 5.975A pdb=" N LEU 2 513 " --> pdb=" O SER 2 509 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N SER 2 514 " --> pdb=" O GLU 2 510 " (cutoff:3.500A) No H-bonds generated for 'chain '2' and resid 509 through 514' Processing helix chain '2' and resid 523 through 532 Processing helix chain '2' and resid 544 through 549 removed outlier: 3.823A pdb=" N ARG 2 548 " --> pdb=" O HIS 2 544 " (cutoff:3.500A) Proline residue: 2 549 - end of helix No H-bonds generated for 'chain '2' and resid 544 through 549' Processing helix chain '2' and resid 552 through 562 removed outlier: 4.593A pdb=" N SER 2 556 " --> pdb=" O THR 2 552 " (cutoff:3.500A) Processing helix chain '2' and resid 574 through 595 removed outlier: 4.059A pdb=" N CYS 2 578 " --> pdb=" O TRP 2 574 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N LEU 2 579 " --> pdb=" O HIS 2 575 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N SER 2 582 " --> pdb=" O CYS 2 578 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N ALA 2 583 " --> pdb=" O LEU 2 579 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU 2 586 " --> pdb=" O SER 2 582 " (cutoff:3.500A) Processing helix chain '2' and resid 598 through 613 removed outlier: 3.994A pdb=" N LYS 2 612 " --> pdb=" O ASN 2 608 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N VAL 2 613 " --> pdb=" O ILE 2 609 " (cutoff:3.500A) Processing helix chain '2' and resid 614 through 632 removed outlier: 3.752A pdb=" N MET 2 630 " --> pdb=" O ALA 2 626 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N LEU 2 631 " --> pdb=" O HIS 2 627 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N GLY 2 632 " --> pdb=" O VAL 2 628 " (cutoff:3.500A) Processing helix chain '2' and resid 633 through 649 removed outlier: 5.167A pdb=" N GLU 2 637 " --> pdb=" O LEU 2 633 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N LYS 2 638 " --> pdb=" O ASP 2 634 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N SER 2 639 " --> pdb=" O GLU 2 635 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ILE 2 643 " --> pdb=" O SER 2 639 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLY 2 648 " --> pdb=" O ARG 2 644 " (cutoff:3.500A) Proline residue: 2 649 - end of helix Processing helix chain '2' and resid 658 through 675 removed outlier: 4.280A pdb=" N ARG 2 662 " --> pdb=" O PHE 2 658 " (cutoff:3.500A) Processing helix chain '2' and resid 676 through 682 removed outlier: 4.195A pdb=" N GLN 2 680 " --> pdb=" O ASP 2 676 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N THR 2 681 " --> pdb=" O VAL 2 677 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N ALA 2 682 " --> pdb=" O LEU 2 678 " (cutoff:3.500A) No H-bonds generated for 'chain '2' and resid 676 through 682' Processing helix chain '2' and resid 706 through 722 removed outlier: 3.711A pdb=" N VAL 2 710 " --> pdb=" O PRO 2 706 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N GLY 2 722 " --> pdb=" O VAL 2 718 " (cutoff:3.500A) Processing helix chain '2' and resid 725 through 740 removed outlier: 4.415A pdb=" N ILE 2 729 " --> pdb=" O ASP 2 725 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N HIS 2 730 " --> pdb=" O SER 2 726 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N GLY 2 739 " --> pdb=" O LEU 2 735 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLY 2 740 " --> pdb=" O LEU 2 736 " (cutoff:3.500A) Processing helix chain '2' and resid 741 through 755 removed outlier: 4.051A pdb=" N GLU 2 751 " --> pdb=" O ASN 2 747 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LYS 2 754 " --> pdb=" O LYS 2 750 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLU 2 755 " --> pdb=" O GLU 2 751 " (cutoff:3.500A) Processing helix chain '2' and resid 757 through 773 removed outlier: 4.028A pdb=" N SER 2 770 " --> pdb=" O GLU 2 766 " (cutoff:3.500A) Processing helix chain '2' and resid 775 through 794 Proline residue: 2 789 - end of helix removed outlier: 3.920A pdb=" N ASP 2 794 " --> pdb=" O GLY 2 790 " (cutoff:3.500A) Processing helix chain '2' and resid 795 through 802 removed outlier: 5.668A pdb=" N HIS 2 799 " --> pdb=" O SER 2 795 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N SER 2 800 " --> pdb=" O SER 2 796 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N LEU 2 801 " --> pdb=" O LYS 2 797 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N MET 2 802 " --> pdb=" O TRP 2 798 " (cutoff:3.500A) No H-bonds generated for 'chain '2' and resid 795 through 802' Processing helix chain '2' and resid 803 through 824 removed outlier: 4.213A pdb=" N ALA 2 808 " --> pdb=" O PRO 2 804 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N HIS 2 824 " --> pdb=" O SER 2 820 " (cutoff:3.500A) Processing helix chain '2' and resid 895 through 914 removed outlier: 3.663A pdb=" N SER 2 914 " --> pdb=" O SER 2 910 " (cutoff:3.500A) Processing helix chain '2' and resid 918 through 935 removed outlier: 3.521A pdb=" N LEU 2 935 " --> pdb=" O CYS 2 931 " (cutoff:3.500A) Processing helix chain '2' and resid 940 through 945 removed outlier: 6.831A pdb=" N LEU 2 944 " --> pdb=" O ARG 2 940 " (cutoff:3.500A) Processing helix chain '2' and resid 949 through 960 removed outlier: 6.652A pdb=" N SER 2 953 " --> pdb=" O PHE 2 949 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N GLU 2 954 " --> pdb=" O THR 2 950 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N LEU 2 955 " --> pdb=" O THR 2 951 " (cutoff:3.500A) Processing helix chain '2' and resid 965 through 972 removed outlier: 3.749A pdb=" N ALA 2 969 " --> pdb=" O LYS 2 965 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N ASP 2 972 " --> pdb=" O LEU 2 968 " (cutoff:3.500A) Processing helix chain '2' and resid 975 through 989 removed outlier: 3.872A pdb=" N GLN 2 980 " --> pdb=" O PRO 2 976 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ALA 2 988 " --> pdb=" O LYS 2 984 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LEU 2 989 " --> pdb=" O ALA 2 985 " (cutoff:3.500A) Processing helix chain '3' and resid 27 through 39 removed outlier: 4.509A pdb=" N TYR 3 31 " --> pdb=" O ASN 3 27 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N GLU 3 33 " --> pdb=" O GLY 3 29 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N GLY 3 34 " --> pdb=" O PRO 3 30 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N LYS 3 37 " --> pdb=" O GLU 3 33 " (cutoff:3.500A) Processing helix chain '3' and resid 40 through 48 Processing helix chain '3' and resid 90 through 101 removed outlier: 4.706A pdb=" N GLY 3 100 " --> pdb=" O THR 3 96 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ILE 3 101 " --> pdb=" O TRP 3 97 " (cutoff:3.500A) Processing helix chain '3' and resid 113 through 133 removed outlier: 3.643A pdb=" N GLY 3 117 " --> pdb=" O LEU 3 113 " (cutoff:3.500A) Processing helix chain '3' and resid 165 through 177 removed outlier: 4.282A pdb=" N GLY 3 177 " --> pdb=" O ILE 3 173 " (cutoff:3.500A) Processing helix chain '3' and resid 188 through 199 removed outlier: 3.946A pdb=" N LEU 3 194 " --> pdb=" O ALA 3 190 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ALA 3 198 " --> pdb=" O LEU 3 194 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N ALA 3 199 " --> pdb=" O PHE 3 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 27 through 35 Processing helix chain 'A' and resid 77 through 82 Proline residue: A 82 - end of helix Processing helix chain 'A' and resid 96 through 110 removed outlier: 5.274A pdb=" N VAL A 101 " --> pdb=" O VAL A 97 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N LYS A 102 " --> pdb=" O GLY A 98 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N CYS A 109 " --> pdb=" O LYS A 105 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL A 110 " --> pdb=" O VAL A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 134 removed outlier: 4.703A pdb=" N SER A 133 " --> pdb=" O ILE A 129 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N LYS A 134 " --> pdb=" O LEU A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 149 removed outlier: 3.620A pdb=" N ARG A 140 " --> pdb=" O GLN A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 229 removed outlier: 3.812A pdb=" N ARG A 227 " --> pdb=" O GLU A 223 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ILE A 228 " --> pdb=" O ILE A 224 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N SER A 229 " --> pdb=" O PHE A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 237 Processing helix chain 'A' and resid 244 through 249 removed outlier: 4.212A pdb=" N MET A 248 " --> pdb=" O ARG A 244 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N ILE A 249 " --> pdb=" O PRO A 245 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 244 through 249' Processing helix chain 'A' and resid 257 through 262 removed outlier: 3.544A pdb=" N ARG A 261 " --> pdb=" O PRO A 257 " (cutoff:3.500A) Proline residue: A 262 - end of helix No H-bonds generated for 'chain 'A' and resid 257 through 262' Processing helix chain 'A' and resid 274 through 296 Processing helix chain 'A' and resid 299 through 319 removed outlier: 3.942A pdb=" N ALA A 304 " --> pdb=" O ALA A 300 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N GLU A 305 " --> pdb=" O HIS A 301 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N VAL A 318 " --> pdb=" O VAL A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 344 removed outlier: 3.942A pdb=" N ARG A 342 " --> pdb=" O SER A 338 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N LYS A 344 " --> pdb=" O LYS A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 389 removed outlier: 5.341A pdb=" N THR A 389 " --> pdb=" O ALA A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 409 removed outlier: 5.812A pdb=" N ASP A 400 " --> pdb=" O PRO A 396 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N ARG A 401 " --> pdb=" O PHE A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 485 through 493 removed outlier: 4.050A pdb=" N THR A 489 " --> pdb=" O ASN A 485 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N THR A 490 " --> pdb=" O LEU A 486 " (cutoff:3.500A) Proline residue: A 491 - end of helix No H-bonds generated for 'chain 'A' and resid 485 through 493' Processing helix chain 'A' and resid 508 through 518 Processing helix chain 'A' and resid 520 through 525 removed outlier: 3.877A pdb=" N ILE A 525 " --> pdb=" O VAL A 521 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 550 removed outlier: 3.689A pdb=" N LYS A 550 " --> pdb=" O ARG A 546 " (cutoff:3.500A) Processing helix chain 'A' and resid 556 through 568 removed outlier: 4.057A pdb=" N PHE A 566 " --> pdb=" O ASN A 562 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LEU A 567 " --> pdb=" O LEU A 563 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N SER A 568 " --> pdb=" O LEU A 564 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 597 removed outlier: 3.624A pdb=" N ILE A 591 " --> pdb=" O THR A 587 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ILE A 595 " --> pdb=" O ILE A 591 " (cutoff:3.500A) Proline residue: A 597 - end of helix Processing helix chain 'A' and resid 612 through 617 removed outlier: 3.661A pdb=" N GLY A 616 " --> pdb=" O ASP A 612 " (cutoff:3.500A) Proline residue: A 617 - end of helix No H-bonds generated for 'chain 'A' and resid 612 through 617' Processing helix chain 'A' and resid 651 through 660 Processing helix chain 'A' and resid 661 through 684 removed outlier: 3.692A pdb=" N SER A 670 " --> pdb=" O ARG A 666 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ILE A 672 " --> pdb=" O PHE A 668 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N THR A 674 " --> pdb=" O SER A 670 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N LEU A 681 " --> pdb=" O ASN A 677 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ILE A 682 " --> pdb=" O ASN A 678 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 694 removed outlier: 3.624A pdb=" N SER A 692 " --> pdb=" O GLY A 688 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N ALA A 694 " --> pdb=" O GLY A 690 " (cutoff:3.500A) Processing helix chain 'A' and resid 695 through 723 Processing helix chain 'A' and resid 732 through 760 removed outlier: 3.870A pdb=" N LEU A 760 " --> pdb=" O ALA A 756 " (cutoff:3.500A) Processing helix chain 'A' and resid 764 through 773 Processing helix chain 'A' and resid 777 through 786 Processing helix chain 'A' and resid 816 through 821 Processing helix chain 'A' and resid 832 through 869 removed outlier: 3.991A pdb=" N GLU A 845 " --> pdb=" O MET A 841 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLY A 846 " --> pdb=" O GLY A 842 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N GLY A 858 " --> pdb=" O THR A 854 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N TYR A 859 " --> pdb=" O ALA A 855 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N ILE A 860 " --> pdb=" O GLU A 856 " (cutoff:3.500A) removed outlier: 5.289A pdb=" N GLN A 861 " --> pdb=" O THR A 857 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N SER A 867 " --> pdb=" O ARG A 863 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N MET A 868 " --> pdb=" O LEU A 864 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 902 removed outlier: 4.107A pdb=" N VAL A 901 " --> pdb=" O ALA A 897 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N GLU A 902 " --> pdb=" O GLY A 898 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 897 through 902' Processing helix chain 'A' and resid 912 through 920 Processing helix chain 'A' and resid 926 through 934 removed outlier: 4.450A pdb=" N ARG A 932 " --> pdb=" O ARG A 928 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N THR A 933 " --> pdb=" O ALA A 929 " (cutoff:3.500A) Processing helix chain 'A' and resid 935 through 945 removed outlier: 6.618A pdb=" N LYS A 940 " --> pdb=" O GLU A 936 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N ASP A 941 " --> pdb=" O ASP A 937 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N SER A 944 " --> pdb=" O LYS A 940 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ASN A 945 " --> pdb=" O ASP A 941 " (cutoff:3.500A) Processing helix chain 'A' and resid 946 through 971 removed outlier: 3.633A pdb=" N PHE A 956 " --> pdb=" O LEU A 952 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLU A 957 " --> pdb=" O GLU A 953 " (cutoff:3.500A) Proline residue: A 971 - end of helix Processing helix chain 'A' and resid 982 through 995 Processing helix chain 'A' and resid 1005 through 1021 removed outlier: 3.681A pdb=" N LYS A1019 " --> pdb=" O GLU A1015 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N VAL A1021 " --> pdb=" O SER A1017 " (cutoff:3.500A) Processing helix chain 'A' and resid 1027 through 1039 removed outlier: 3.619A pdb=" N LEU A1039 " --> pdb=" O GLU A1035 " (cutoff:3.500A) Processing helix chain 'A' and resid 1040 through 1050 removed outlier: 3.825A pdb=" N CYS A1050 " --> pdb=" O ARG A1046 " (cutoff:3.500A) Processing helix chain 'A' and resid 1051 through 1057 removed outlier: 4.058A pdb=" N ALA A1055 " --> pdb=" O SER A1051 " (cutoff:3.500A) Processing helix chain 'A' and resid 1061 through 1081 removed outlier: 3.690A pdb=" N GLY A1070 " --> pdb=" O ASP A1066 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLU A1073 " --> pdb=" O LEU A1069 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N ALA A1081 " --> pdb=" O ASN A1077 " (cutoff:3.500A) Processing helix chain 'A' and resid 1086 through 1100 removed outlier: 3.673A pdb=" N LEU A1090 " --> pdb=" O MET A1086 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N GLU A1097 " --> pdb=" O GLN A1093 " (cutoff:3.500A) Proline residue: A1098 - end of helix Processing helix chain 'A' and resid 1120 through 1130 removed outlier: 3.925A pdb=" N ILE A1130 " --> pdb=" O GLU A1126 " (cutoff:3.500A) Processing helix chain 'A' and resid 1146 through 1151 removed outlier: 5.406A pdb=" N ALA A1151 " --> pdb=" O SER A1147 " (cutoff:3.500A) Processing helix chain 'A' and resid 1152 through 1159 Processing helix chain 'A' and resid 1165 through 1170 removed outlier: 3.717A pdb=" N VAL A1169 " --> pdb=" O THR A1165 " (cutoff:3.500A) Processing helix chain 'A' and resid 1189 through 1197 removed outlier: 4.713A pdb=" N VAL A1193 " --> pdb=" O ASP A1189 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ASN A1194 " --> pdb=" O GLN A1190 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N VAL A1195 " --> pdb=" O GLU A1191 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N TYR A1196 " --> pdb=" O TRP A1192 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N TYR A1197 " --> pdb=" O VAL A1193 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1189 through 1197' Processing helix chain 'A' and resid 1217 through 1225 removed outlier: 3.632A pdb=" N ASP A1223 " --> pdb=" O LYS A1219 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ARG A1224 " --> pdb=" O HIS A1220 " (cutoff:3.500A) Processing helix chain 'A' and resid 1227 through 1240 removed outlier: 3.644A pdb=" N PHE A1239 " --> pdb=" O ILE A1235 " (cutoff:3.500A) Processing helix chain 'A' and resid 1264 through 1269 removed outlier: 5.571A pdb=" N LYS A1268 " --> pdb=" O SER A1264 " (cutoff:3.500A) Processing helix chain 'A' and resid 1280 through 1295 removed outlier: 3.528A pdb=" N ILE A1288 " --> pdb=" O PHE A1284 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N SER A1290 " --> pdb=" O ARG A1286 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N MET A1292 " --> pdb=" O ILE A1288 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N LEU A1293 " --> pdb=" O GLU A1289 " (cutoff:3.500A) Processing helix chain 'A' and resid 1342 through 1349 removed outlier: 3.532A pdb=" N VAL A1346 " --> pdb=" O SER A1342 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N SER A1348 " --> pdb=" O MET A1344 " (cutoff:3.500A) Processing helix chain 'A' and resid 1361 through 1369 Processing helix chain 'A' and resid 1370 through 1390 removed outlier: 5.354A pdb=" N ASP A1389 " --> pdb=" O VAL A1385 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N GLY A1390 " --> pdb=" O ILE A1386 " (cutoff:3.500A) Processing helix chain 'A' and resid 1394 through 1407 removed outlier: 3.880A pdb=" N LEU A1398 " --> pdb=" O ASN A1394 " (cutoff:3.500A) Processing helix chain 'A' and resid 1415 through 1423 removed outlier: 3.687A pdb=" N ARG A1421 " --> pdb=" O HIS A1417 " (cutoff:3.500A) removed outlier: 5.379A pdb=" N ASP A1423 " --> pdb=" O VAL A1419 " (cutoff:3.500A) Processing helix chain 'A' and resid 1425 through 1433 removed outlier: 3.672A pdb=" N SER A1431 " --> pdb=" O LEU A1427 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N PHE A1432 " --> pdb=" O MET A1428 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N GLU A1433 " --> pdb=" O LYS A1429 " (cutoff:3.500A) Processing helix chain 'A' and resid 1434 through 1446 removed outlier: 3.610A pdb=" N VAL A1438 " --> pdb=" O GLU A1434 " (cutoff:3.500A) Processing helix chain 'A' and resid 1453 through 1461 removed outlier: 3.939A pdb=" N ASN A1457 " --> pdb=" O GLY A1453 " (cutoff:3.500A) Processing helix chain 'A' and resid 1476 through 1484 removed outlier: 3.515A pdb=" N CYS A1480 " --> pdb=" O ASP A1476 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N TYR A1482 " --> pdb=" O GLU A1478 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N GLY A1483 " --> pdb=" O LYS A1479 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N MET A1484 " --> pdb=" O CYS A1480 " (cutoff:3.500A) Processing helix chain 'A' and resid 348 through 353 Processing helix chain 'B' and resid 21 through 38 Processing helix chain 'B' and resid 40 through 62 removed outlier: 3.792A pdb=" N SER B 46 " --> pdb=" O GLN B 42 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N VAL B 55 " --> pdb=" O ILE B 51 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N GLN B 56 " --> pdb=" O GLN B 52 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ARG B 57 " --> pdb=" O MET B 53 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ALA B 62 " --> pdb=" O ILE B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 117 Processing helix chain 'B' and resid 167 through 175 Processing helix chain 'B' and resid 268 through 277 removed outlier: 3.625A pdb=" N GLY B 277 " --> pdb=" O PHE B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 289 removed outlier: 3.790A pdb=" N HIS B 287 " --> pdb=" O ASP B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 309 removed outlier: 3.671A pdb=" N MET B 298 " --> pdb=" O ASP B 294 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LYS B 302 " --> pdb=" O MET B 298 " (cutoff:3.500A) Proline residue: B 303 - end of helix removed outlier: 4.096A pdb=" N ALA B 308 " --> pdb=" O SER B 304 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N PHE B 309 " --> pdb=" O LEU B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 313 through 326 removed outlier: 3.907A pdb=" N ARG B 324 " --> pdb=" O PHE B 320 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N GLY B 325 " --> pdb=" O ILE B 321 " (cutoff:3.500A) removed outlier: 5.892A pdb=" N ALA B 326 " --> pdb=" O GLY B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 345 removed outlier: 3.834A pdb=" N LYS B 337 " --> pdb=" O GLU B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 357 through 378 Processing helix chain 'B' and resid 387 through 392 removed outlier: 3.913A pdb=" N LYS B 391 " --> pdb=" O HIS B 387 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N ARG B 392 " --> pdb=" O TYR B 388 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 387 through 392' Processing helix chain 'B' and resid 398 through 424 removed outlier: 3.505A pdb=" N LEU B 403 " --> pdb=" O LEU B 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 451 removed outlier: 3.529A pdb=" N ALA B 434 " --> pdb=" O ASN B 430 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ILE B 435 " --> pdb=" O LEU B 431 " (cutoff:3.500A) removed outlier: 5.749A pdb=" N LYS B 436 " --> pdb=" O GLU B 432 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N THR B 437 " --> pdb=" O LEU B 433 " (cutoff:3.500A) removed outlier: 8.290A pdb=" N ARG B 438 " --> pdb=" O ALA B 434 " (cutoff:3.500A) removed outlier: 7.456A pdb=" N ILE B 439 " --> pdb=" O ILE B 435 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N ILE B 440 " --> pdb=" O LYS B 436 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N SER B 441 " --> pdb=" O THR B 437 " (cutoff:3.500A) Processing helix chain 'B' and resid 459 through 464 removed outlier: 4.716A pdb=" N ARG B 463 " --> pdb=" O ALA B 459 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N ALA B 464 " --> pdb=" O HIS B 460 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 459 through 464' Processing helix chain 'B' and resid 474 through 484 removed outlier: 3.977A pdb=" N ARG B 483 " --> pdb=" O LEU B 479 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ARG B 484 " --> pdb=" O SER B 480 " (cutoff:3.500A) Processing helix chain 'B' and resid 538 through 549 removed outlier: 3.835A pdb=" N SER B 549 " --> pdb=" O LEU B 545 " (cutoff:3.500A) Processing helix chain 'B' and resid 552 through 557 removed outlier: 6.219A pdb=" N SER B 557 " --> pdb=" O LEU B 553 " (cutoff:3.500A) Processing helix chain 'B' and resid 560 through 565 removed outlier: 4.570A pdb=" N ALA B 564 " --> pdb=" O ALA B 560 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N THR B 565 " --> pdb=" O ILE B 561 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 560 through 565' Processing helix chain 'B' and resid 579 through 594 removed outlier: 4.002A pdb=" N THR B 586 " --> pdb=" O GLN B 582 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LYS B 589 " --> pdb=" O ASN B 585 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLN B 593 " --> pdb=" O LYS B 589 " (cutoff:3.500A) Processing helix chain 'B' and resid 636 through 646 removed outlier: 4.108A pdb=" N ARG B 646 " --> pdb=" O GLN B 642 " (cutoff:3.500A) Processing helix chain 'B' and resid 652 through 660 removed outlier: 3.592A pdb=" N GLY B 660 " --> pdb=" O LEU B 656 " (cutoff:3.500A) Processing helix chain 'B' and resid 666 through 674 removed outlier: 4.521A pdb=" N THR B 672 " --> pdb=" O LEU B 668 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N VAL B 673 " --> pdb=" O GLU B 669 " (cutoff:3.500A) removed outlier: 5.599A pdb=" N MET B 674 " --> pdb=" O GLU B 670 " (cutoff:3.500A) Processing helix chain 'B' and resid 705 through 711 removed outlier: 3.766A pdb=" N ILE B 710 " --> pdb=" O VAL B 706 " (cutoff:3.500A) removed outlier: 5.015A pdb=" N ILE B 711 " --> pdb=" O CYS B 707 " (cutoff:3.500A) Processing helix chain 'B' and resid 713 through 718 removed outlier: 3.927A pdb=" N ASN B 717 " --> pdb=" O PHE B 713 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N GLN B 718 " --> pdb=" O PRO B 714 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 713 through 718' Processing helix chain 'B' and resid 719 through 732 removed outlier: 4.181A pdb=" N LYS B 730 " --> pdb=" O SER B 726 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N GLN B 731 " --> pdb=" O ALA B 727 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA B 732 " --> pdb=" O MET B 728 " (cutoff:3.500A) Processing helix chain 'B' and resid 739 through 744 removed outlier: 5.575A pdb=" N MET B 744 " --> pdb=" O PHE B 740 " (cutoff:3.500A) Processing helix chain 'B' and resid 763 through 768 removed outlier: 3.989A pdb=" N LEU B 767 " --> pdb=" O SER B 763 " (cutoff:3.500A) Processing helix chain 'B' and resid 797 through 804 Processing helix chain 'B' and resid 968 through 976 removed outlier: 4.771A pdb=" N ILE B 972 " --> pdb=" O ASN B 968 " (cutoff:3.500A) Proline residue: B 973 - end of helix Processing helix chain 'B' and resid 977 through 994 removed outlier: 4.230A pdb=" N LEU B 981 " --> pdb=" O THR B 977 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ILE B 982 " --> pdb=" O ILE B 978 " (cutoff:3.500A) Processing helix chain 'B' and resid 1007 through 1019 removed outlier: 3.801A pdb=" N TYR B1018 " --> pdb=" O LEU B1014 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLY B1019 " --> pdb=" O LEU B1015 " (cutoff:3.500A) Processing helix chain 'B' and resid 1054 through 1059 removed outlier: 4.103A pdb=" N LYS B1058 " --> pdb=" O MET B1054 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILE B1059 " --> pdb=" O VAL B1055 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1054 through 1059' Processing helix chain 'B' and resid 1087 through 1098 Processing helix chain 'B' and resid 1099 through 1108 Processing helix chain 'B' and resid 1152 through 1166 removed outlier: 3.830A pdb=" N MET B1165 " --> pdb=" O GLU B1161 " (cutoff:3.500A) Processing helix chain 'B' and resid 699 through 704 removed outlier: 3.762A pdb=" N LEU B 704 " --> pdb=" O SER B 701 " (cutoff:3.500A) Processing helix chain 'C' and resid 27 through 40 Processing helix chain 'C' and resid 60 through 71 removed outlier: 3.905A pdb=" N ILE C 71 " --> pdb=" O ARG C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 77 through 83 removed outlier: 4.850A pdb=" N LYS C 81 " --> pdb=" O ASP C 77 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N LEU C 82 " --> pdb=" O ILE C 78 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N GLN C 83 " --> pdb=" O VAL C 79 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 77 through 83' Processing helix chain 'C' and resid 116 through 121 removed outlier: 4.007A pdb=" N LEU C 120 " --> pdb=" O THR C 116 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N ILE C 121 " --> pdb=" O SER C 117 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 116 through 121' Processing helix chain 'C' and resid 169 through 174 removed outlier: 3.915A pdb=" N HIS C 173 " --> pdb=" O PHE C 169 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N ALA C 174 " --> pdb=" O GLY C 170 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 169 through 174' Processing helix chain 'C' and resid 240 through 271 removed outlier: 4.682A pdb=" N VAL C 271 " --> pdb=" O ILE C 267 " (cutoff:3.500A) Processing helix chain 'D' and resid 25 through 30 removed outlier: 3.632A pdb=" N ALA D 29 " --> pdb=" O GLU D 25 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N GLU D 30 " --> pdb=" O PHE D 26 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 25 through 30' Processing helix chain 'D' and resid 33 through 52 removed outlier: 3.745A pdb=" N ARG D 44 " --> pdb=" O LEU D 40 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N GLU D 49 " --> pdb=" O LYS D 45 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ALA D 51 " --> pdb=" O GLN D 47 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N GLU D 52 " --> pdb=" O ASN D 48 " (cutoff:3.500A) Processing helix chain 'D' and resid 58 through 72 removed outlier: 3.895A pdb=" N ARG D 70 " --> pdb=" O ASN D 66 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N PHE D 71 " --> pdb=" O TYR D 67 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N SER D 72 " --> pdb=" O THR D 68 " (cutoff:3.500A) Processing helix chain 'D' and resid 76 through 91 removed outlier: 4.630A pdb=" N ILE D 80 " --> pdb=" O ASN D 76 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ARG D 84 " --> pdb=" O ILE D 80 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N GLN D 89 " --> pdb=" O SER D 85 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LYS D 90 " --> pdb=" O LEU D 86 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N LYS D 91 " --> pdb=" O LEU D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 93 through 104 removed outlier: 3.846A pdb=" N CYS D 104 " --> pdb=" O LEU D 100 " (cutoff:3.500A) Processing helix chain 'D' and resid 107 through 116 removed outlier: 3.526A pdb=" N ILE D 115 " --> pdb=" O SER D 111 " (cutoff:3.500A) Proline residue: D 116 - end of helix Processing helix chain 'D' and resid 124 through 139 removed outlier: 4.882A pdb=" N GLN D 128 " --> pdb=" O ASP D 124 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N GLN D 129 " --> pdb=" O GLU D 125 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 25 removed outlier: 4.175A pdb=" N LEU E 10 " --> pdb=" O GLU E 6 " (cutoff:3.500A) Processing helix chain 'E' and resid 29 through 35 removed outlier: 3.518A pdb=" N GLN E 35 " --> pdb=" O ASP E 31 " (cutoff:3.500A) Processing helix chain 'E' and resid 36 through 45 Processing helix chain 'E' and resid 48 through 53 Proline residue: E 53 - end of helix Processing helix chain 'E' and resid 83 through 98 removed outlier: 3.833A pdb=" N GLU E 96 " --> pdb=" O GLN E 92 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N GLU E 97 " --> pdb=" O ARG E 93 " (cutoff:3.500A) Processing helix chain 'E' and resid 111 through 123 removed outlier: 4.081A pdb=" N GLN E 116 " --> pdb=" O PRO E 112 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N SER E 117 " --> pdb=" O SER E 113 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N VAL E 119 " --> pdb=" O LYS E 115 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N MET E 121 " --> pdb=" O SER E 117 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N ALA E 122 " --> pdb=" O LEU E 118 " (cutoff:3.500A) Proline residue: E 123 - end of helix Processing helix chain 'E' and resid 131 through 137 removed outlier: 3.541A pdb=" N LEU E 135 " --> pdb=" O LEU E 131 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU E 136 " --> pdb=" O GLN E 132 " (cutoff:3.500A) removed outlier: 5.363A pdb=" N ILE E 137 " --> pdb=" O GLN E 133 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 131 through 137' Processing helix chain 'E' and resid 152 through 164 removed outlier: 3.545A pdb=" N LYS E 164 " --> pdb=" O LEU E 160 " (cutoff:3.500A) Processing helix chain 'E' and resid 177 through 184 Processing helix chain 'F' and resid 58 through 76 removed outlier: 3.528A pdb=" N CYS F 76 " --> pdb=" O GLN F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 88 through 100 Processing helix chain 'F' and resid 119 through 124 removed outlier: 6.211A pdb=" N ILE F 124 " --> pdb=" O VAL F 120 " (cutoff:3.500A) Processing helix chain 'G' and resid 21 through 34 removed outlier: 3.915A pdb=" N THR G 25 " --> pdb=" O ASN G 21 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N THR G 32 " --> pdb=" O GLN G 28 " (cutoff:3.500A) Processing helix chain 'H' and resid 84 through 89 removed outlier: 4.977A pdb=" N PHE H 88 " --> pdb=" O ARG H 84 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N GLU H 89 " --> pdb=" O ALA H 85 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 84 through 89' Processing helix chain 'H' and resid 128 through 133 removed outlier: 3.776A pdb=" N LEU H 132 " --> pdb=" O ASP H 128 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N HIS H 133 " --> pdb=" O ALA H 129 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 128 through 133' Processing helix chain 'H' and resid 44 through 49 Proline residue: H 49 - end of helix No H-bonds generated for 'chain 'H' and resid 44 through 49' Processing helix chain 'I' and resid 62 through 68 removed outlier: 4.960A pdb=" N THR I 66 " --> pdb=" O VAL I 62 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N GLN I 67 " --> pdb=" O ASP I 63 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N ILE I 68 " --> pdb=" O GLU I 64 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 62 through 68' Processing helix chain 'I' and resid 69 through 75 removed outlier: 3.693A pdb=" N VAL I 72 " --> pdb=" O ILE I 69 " (cutoff:3.500A) Processing helix chain 'J' and resid 17 through 28 removed outlier: 3.713A pdb=" N GLU J 28 " --> pdb=" O LEU J 24 " (cutoff:3.500A) Processing helix chain 'J' and resid 30 through 39 Processing helix chain 'J' and resid 42 through 51 removed outlier: 4.796A pdb=" N LEU J 49 " --> pdb=" O CYS J 45 " (cutoff:3.500A) Processing helix chain 'J' and resid 54 through 62 removed outlier: 4.530A pdb=" N LYS J 58 " --> pdb=" O ASP J 54 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ASN J 61 " --> pdb=" O GLU J 57 " (cutoff:3.500A) removed outlier: 5.360A pdb=" N TYR J 62 " --> pdb=" O LYS J 58 " (cutoff:3.500A) Processing helix chain 'K' and resid 39 through 53 removed outlier: 4.867A pdb=" N ILE K 45 " --> pdb=" O THR K 41 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ILE K 46 " --> pdb=" O LEU K 42 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N LYS K 52 " --> pdb=" O SER K 48 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N ASP K 53 " --> pdb=" O GLN K 49 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 114 Processing helix chain 'K' and resid 5 through 10 removed outlier: 3.743A pdb=" N SER K 9 " --> pdb=" O ALA K 6 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N PHE K 10 " --> pdb=" O PHE K 7 " (cutoff:3.500A) Processing helix chain 'M' and resid 12 through 27 removed outlier: 4.863A pdb=" N SER M 16 " --> pdb=" O LYS M 12 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ILE M 18 " --> pdb=" O TYR M 14 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N GLU M 19 " --> pdb=" O ARG M 15 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ASP M 20 " --> pdb=" O SER M 16 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASP M 24 " --> pdb=" O ASP M 20 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N ASP M 27 " --> pdb=" O ASN M 23 " (cutoff:3.500A) Processing helix chain 'M' and resid 35 through 51 removed outlier: 4.315A pdb=" N LEU M 42 " --> pdb=" O VAL M 38 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N GLU M 47 " --> pdb=" O LYS M 43 " (cutoff:3.500A) Processing helix chain 'N' and resid 9 through 26 removed outlier: 3.623A pdb=" N GLU N 21 " --> pdb=" O GLU N 17 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N SER N 25 " --> pdb=" O GLU N 21 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLN N 26 " --> pdb=" O LEU N 22 " (cutoff:3.500A) Processing helix chain 'N' and resid 31 through 50 removed outlier: 4.339A pdb=" N GLN N 35 " --> pdb=" O GLN N 31 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N LEU N 37 " --> pdb=" O ALA N 33 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N LYS N 42 " --> pdb=" O LEU N 38 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ALA N 43 " --> pdb=" O GLN N 39 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ALA N 47 " --> pdb=" O ALA N 43 " (cutoff:3.500A) Processing helix chain 'O' and resid 47 through 52 removed outlier: 3.720A pdb=" N TRP O 52 " --> pdb=" O VAL O 48 " (cutoff:3.500A) Processing helix chain 'O' and resid 108 through 129 removed outlier: 4.057A pdb=" N ARG O 112 " --> pdb=" O SER O 108 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ARG O 127 " --> pdb=" O THR O 123 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N ILE O 128 " --> pdb=" O MET O 124 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ASN O 129 " --> pdb=" O ALA O 125 " (cutoff:3.500A) Processing helix chain 'O' and resid 131 through 149 removed outlier: 3.712A pdb=" N VAL O 135 " --> pdb=" O PRO O 131 " (cutoff:3.500A) Processing helix chain 'O' and resid 155 through 172 removed outlier: 3.932A pdb=" N ALA O 160 " --> pdb=" O ASN O 156 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N GLY O 172 " --> pdb=" O CYS O 168 " (cutoff:3.500A) Processing helix chain 'O' and resid 176 through 184 removed outlier: 3.701A pdb=" N VAL O 183 " --> pdb=" O GLU O 179 " (cutoff:3.500A) Processing helix chain 'O' and resid 187 through 203 removed outlier: 4.792A pdb=" N ARG O 193 " --> pdb=" O LYS O 189 " (cutoff:3.500A) Processing helix chain 'O' and resid 210 through 223 removed outlier: 4.095A pdb=" N PHE O 214 " --> pdb=" O THR O 210 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N MET O 215 " --> pdb=" O THR O 211 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N SER O 216 " --> pdb=" O GLY O 212 " (cutoff:3.500A) removed outlier: 5.806A pdb=" N ARG O 217 " --> pdb=" O ASP O 213 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N PHE O 218 " --> pdb=" O PHE O 214 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N CYS O 219 " --> pdb=" O MET O 215 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N SER O 220 " --> pdb=" O SER O 216 " (cutoff:3.500A) Processing helix chain 'O' and resid 225 through 243 Processing helix chain 'O' and resid 249 through 265 removed outlier: 3.748A pdb=" N SER O 265 " --> pdb=" O ALA O 261 " (cutoff:3.500A) Processing helix chain 'O' and resid 270 through 279 removed outlier: 3.857A pdb=" N GLY O 279 " --> pdb=" O GLY O 275 " (cutoff:3.500A) Processing helix chain 'O' and resid 281 through 294 Proline residue: O 294 - end of helix Processing helix chain 'O' and resid 295 through 300 removed outlier: 3.530A pdb=" N LEU O 299 " --> pdb=" O ARG O 295 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N PHE O 300 " --> pdb=" O ALA O 296 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 295 through 300' Processing helix chain 'P' and resid 179 through 187 removed outlier: 4.088A pdb=" N ILE P 183 " --> pdb=" O ASP P 179 " (cutoff:3.500A) Processing helix chain 'P' and resid 226 through 245 removed outlier: 4.267A pdb=" N GLY P 245 " --> pdb=" O VAL P 241 " (cutoff:3.500A) Processing helix chain 'P' and resid 269 through 277 removed outlier: 4.280A pdb=" N LEU P 273 " --> pdb=" O ARG P 269 " (cutoff:3.500A) Processing helix chain 'P' and resid 317 through 332 removed outlier: 3.514A pdb=" N ALA P 324 " --> pdb=" O GLU P 320 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N PHE P 325 " --> pdb=" O ILE P 321 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N GLU P 326 " --> pdb=" O TYR P 322 " (cutoff:3.500A) Proline residue: P 330 - end of helix Processing helix chain 'Q' and resid 12 through 27 removed outlier: 4.622A pdb=" N GLY Q 24 " --> pdb=" O TYR Q 20 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N PHE Q 25 " --> pdb=" O VAL Q 21 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N TYR Q 26 " --> pdb=" O ILE Q 22 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N GLY Q 27 " --> pdb=" O ARG Q 23 " (cutoff:3.500A) Processing helix chain 'Q' and resid 28 through 39 removed outlier: 3.722A pdb=" N ALA Q 33 " --> pdb=" O GLU Q 29 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LEU Q 37 " --> pdb=" O ALA Q 33 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N ILE Q 38 " --> pdb=" O LEU Q 34 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N ARG Q 39 " --> pdb=" O ASP Q 35 " (cutoff:3.500A) Processing helix chain 'Q' and resid 44 through 52 Processing helix chain 'Q' and resid 55 through 70 removed outlier: 3.817A pdb=" N ASP Q 69 " --> pdb=" O ASN Q 65 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N LYS Q 70 " --> pdb=" O LEU Q 66 " (cutoff:3.500A) Processing helix chain 'Q' and resid 96 through 124 removed outlier: 4.101A pdb=" N ASN Q 101 " --> pdb=" O ARG Q 97 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ARG Q 124 " --> pdb=" O ASP Q 120 " (cutoff:3.500A) Processing helix chain 'Q' and resid 140 through 145 Processing helix chain 'Q' and resid 174 through 195 removed outlier: 3.687A pdb=" N ALA Q 178 " --> pdb=" O ARG Q 174 " (cutoff:3.500A) Proline residue: Q 186 - end of helix Processing helix chain 'R' and resid 75 through 92 Processing helix chain 'R' and resid 98 through 107 removed outlier: 3.916A pdb=" N ILE R 102 " --> pdb=" O THR R 98 " (cutoff:3.500A) Processing helix chain 'R' and resid 111 through 128 Proline residue: R 128 - end of helix Processing helix chain 'R' and resid 147 through 162 Processing helix chain 'R' and resid 166 through 174 removed outlier: 4.280A pdb=" N ASP R 170 " --> pdb=" O ILE R 166 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N ILE R 171 " --> pdb=" O LEU R 167 " (cutoff:3.500A) Processing helix chain 'R' and resid 177 through 188 removed outlier: 5.627A pdb=" N ALA R 181 " --> pdb=" O ASN R 177 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N VAL R 182 " --> pdb=" O SER R 178 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ASP R 187 " --> pdb=" O LYS R 183 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N GLN R 188 " --> pdb=" O ALA R 184 " (cutoff:3.500A) Processing helix chain 'R' and resid 213 through 222 removed outlier: 4.811A pdb=" N ARG R 221 " --> pdb=" O GLN R 217 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N SER R 222 " --> pdb=" O LYS R 218 " (cutoff:3.500A) Processing helix chain 'R' and resid 227 through 239 Processing helix chain 'S' and resid 172 through 183 removed outlier: 4.588A pdb=" N ILE S 176 " --> pdb=" O ASN S 172 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N MET S 177 " --> pdb=" O HIS S 173 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N GLN S 178 " --> pdb=" O PHE S 174 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N GLN S 179 " --> pdb=" O SER S 175 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ARG S 180 " --> pdb=" O ILE S 176 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N LEU S 182 " --> pdb=" O GLN S 178 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N LYS S 183 " --> pdb=" O GLN S 179 " (cutoff:3.500A) Processing helix chain 'T' and resid 24 through 34 removed outlier: 3.880A pdb=" N GLN T 29 " --> pdb=" O LYS T 25 " (cutoff:3.500A) Processing helix chain 'T' and resid 122 through 136 removed outlier: 3.581A pdb=" N ARG T 126 " --> pdb=" O GLU T 122 " (cutoff:3.500A) Processing helix chain 'T' and resid 158 through 172 removed outlier: 4.415A pdb=" N LYS T 170 " --> pdb=" O GLU T 166 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N GLU T 171 " --> pdb=" O ARG T 167 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N ASP T 172 " --> pdb=" O LYS T 168 " (cutoff:3.500A) Processing helix chain 'T' and resid 181 through 191 removed outlier: 4.311A pdb=" N ASP T 185 " --> pdb=" O GLN T 181 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N MET T 186 " --> pdb=" O HIS T 182 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU T 187 " --> pdb=" O VAL T 183 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N SER T 189 " --> pdb=" O ASP T 185 " (cutoff:3.500A) Processing helix chain 'T' and resid 198 through 207 removed outlier: 4.008A pdb=" N ASP T 204 " --> pdb=" O LYS T 200 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ILE T 205 " --> pdb=" O ASP T 201 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N LYS T 207 " --> pdb=" O VAL T 203 " (cutoff:3.500A) Processing helix chain 'T' and resid 209 through 221 removed outlier: 3.817A pdb=" N GLU T 219 " --> pdb=" O GLU T 215 " (cutoff:3.500A) Processing helix chain 'W' and resid 92 through 104 Processing helix chain 'W' and resid 119 through 130 removed outlier: 3.657A pdb=" N GLY W 130 " --> pdb=" O ALA W 126 " (cutoff:3.500A) Processing helix chain 'W' and resid 132 through 144 Processing helix chain 'W' and resid 149 through 160 removed outlier: 3.676A pdb=" N MET W 153 " --> pdb=" O PRO W 149 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N CYS W 159 " --> pdb=" O PHE W 155 " (cutoff:3.500A) Processing helix chain 'W' and resid 182 through 191 removed outlier: 4.381A pdb=" N ASP W 191 " --> pdb=" O HIS W 187 " (cutoff:3.500A) Processing helix chain 'W' and resid 192 through 198 Processing helix chain 'W' and resid 276 through 288 Processing helix chain 'W' and resid 317 through 329 Processing helix chain 'W' and resid 345 through 358 removed outlier: 4.131A pdb=" N VAL W 349 " --> pdb=" O GLY W 345 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N GLY W 350 " --> pdb=" O LYS W 346 " (cutoff:3.500A) Processing helix chain 'W' and resid 367 through 382 Processing helix chain 'W' and resid 409 through 415 removed outlier: 4.942A pdb=" N HIS W 415 " --> pdb=" O SER W 411 " (cutoff:3.500A) Processing helix chain 'W' and resid 420 through 433 removed outlier: 4.548A pdb=" N THR W 432 " --> pdb=" O GLU W 428 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N GLN W 433 " --> pdb=" O TRP W 429 " (cutoff:3.500A) Processing helix chain 'W' and resid 447 through 459 removed outlier: 4.127A pdb=" N GLN W 459 " --> pdb=" O LEU W 455 " (cutoff:3.500A) Processing helix chain 'W' and resid 480 through 485 removed outlier: 4.473A pdb=" N ILE W 484 " --> pdb=" O LEU W 480 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLY W 485 " --> pdb=" O ASN W 481 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 480 through 485' Processing helix chain 'W' and resid 492 through 498 removed outlier: 4.390A pdb=" N ASN W 498 " --> pdb=" O MET W 494 " (cutoff:3.500A) Processing helix chain 'W' and resid 515 through 526 removed outlier: 5.282A pdb=" N LYS W 526 " --> pdb=" O TYR W 522 " (cutoff:3.500A) Processing helix chain 'W' and resid 527 through 537 removed outlier: 4.910A pdb=" N ILE W 531 " --> pdb=" O THR W 527 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N LEU W 532 " --> pdb=" O LYS W 528 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LEU W 533 " --> pdb=" O LYS W 529 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N ASN W 537 " --> pdb=" O LEU W 533 " (cutoff:3.500A) Processing helix chain 'W' and resid 538 through 555 Processing helix chain 'W' and resid 564 through 576 removed outlier: 3.744A pdb=" N LEU W 568 " --> pdb=" O ASN W 564 " (cutoff:3.500A) Processing helix chain 'W' and resid 585 through 598 removed outlier: 4.036A pdb=" N HIS W 598 " --> pdb=" O GLN W 594 " (cutoff:3.500A) Processing helix chain 'W' and resid 609 through 614 removed outlier: 3.824A pdb=" N THR W 613 " --> pdb=" O LYS W 609 " (cutoff:3.500A) Processing helix chain 'W' and resid 632 through 644 removed outlier: 3.661A pdb=" N GLU W 636 " --> pdb=" O SER W 632 " (cutoff:3.500A) Processing helix chain 'W' and resid 668 through 684 removed outlier: 4.410A pdb=" N TYR W 672 " --> pdb=" O GLN W 668 " (cutoff:3.500A) Processing helix chain 'W' and resid 695 through 700 removed outlier: 3.949A pdb=" N GLU W 699 " --> pdb=" O GLY W 695 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N ASP W 700 " --> pdb=" O MET W 696 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 695 through 700' Processing helix chain 'W' and resid 705 through 718 removed outlier: 4.670A pdb=" N GLN W 709 " --> pdb=" O THR W 705 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLN W 710 " --> pdb=" O LYS W 706 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA W 718 " --> pdb=" O GLN W 714 " (cutoff:3.500A) Processing helix chain 'X' and resid 18 through 35 removed outlier: 3.740A pdb=" N PHE X 22 " --> pdb=" O TYR X 18 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA X 34 " --> pdb=" O ARG X 30 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N LYS X 35 " --> pdb=" O THR X 31 " (cutoff:3.500A) Processing helix chain 'X' and resid 47 through 63 Processing helix chain 'X' and resid 76 through 99 removed outlier: 3.652A pdb=" N GLU X 98 " --> pdb=" O TYR X 94 " (cutoff:3.500A) Processing helix chain 'X' and resid 111 through 116 removed outlier: 3.792A pdb=" N CYS X 116 " --> pdb=" O ARG X 112 " (cutoff:3.500A) Processing helix chain 'X' and resid 118 through 124 Proline residue: X 123 - end of helix Processing helix chain 'X' and resid 126 through 138 Processing helix chain 'X' and resid 139 through 149 removed outlier: 4.160A pdb=" N ARG X 143 " --> pdb=" O ALA X 139 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ALA X 144 " --> pdb=" O SER X 140 " (cutoff:3.500A) Processing helix chain 'X' and resid 155 through 164 removed outlier: 6.487A pdb=" N GLU X 159 " --> pdb=" O CYS X 155 " (cutoff:3.500A) Processing helix chain 'X' and resid 176 through 188 removed outlier: 3.533A pdb=" N GLN X 187 " --> pdb=" O LEU X 183 " (cutoff:3.500A) Processing helix chain 'X' and resid 190 through 199 Processing helix chain 'X' and resid 208 through 214 removed outlier: 3.760A pdb=" N LEU X 212 " --> pdb=" O SER X 208 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ASP X 214 " --> pdb=" O HIS X 210 " (cutoff:3.500A) Processing helix chain 'X' and resid 222 through 229 removed outlier: 4.423A pdb=" N LYS X 228 " --> pdb=" O GLU X 224 " (cutoff:3.500A) Processing helix chain 'X' and resid 238 through 248 Processing helix chain 'X' and resid 252 through 277 Processing helix chain 'X' and resid 278 through 290 Processing helix chain 'X' and resid 325 through 346 removed outlier: 4.376A pdb=" N VAL X 346 " --> pdb=" O TRP X 342 " (cutoff:3.500A) Processing helix chain 'X' and resid 353 through 364 Processing helix chain 'X' and resid 368 through 387 removed outlier: 3.698A pdb=" N LEU X 372 " --> pdb=" O GLN X 368 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N CYS X 375 " --> pdb=" O PRO X 371 " (cutoff:3.500A) removed outlier: 5.641A pdb=" N ALA X 376 " --> pdb=" O LEU X 372 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N GLU X 377 " --> pdb=" O ARG X 373 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N GLU X 387 " --> pdb=" O LEU X 383 " (cutoff:3.500A) Processing helix chain 'X' and resid 390 through 410 removed outlier: 4.219A pdb=" N PHE X 394 " --> pdb=" O ASP X 390 " (cutoff:3.500A) Proline residue: X 396 - end of helix Processing helix chain 'X' and resid 439 through 451 removed outlier: 4.881A pdb=" N ALA X 443 " --> pdb=" O ASP X 439 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ILE X 444 " --> pdb=" O ALA X 440 " (cutoff:3.500A) Proline residue: X 446 - end of helix Processing helix chain 'X' and resid 463 through 472 removed outlier: 4.579A pdb=" N TYR X 467 " --> pdb=" O PRO X 463 " (cutoff:3.500A) Proline residue: X 468 - end of helix removed outlier: 3.897A pdb=" N ASP X 472 " --> pdb=" O PRO X 468 " (cutoff:3.500A) Processing helix chain 'X' and resid 513 through 531 Processing helix chain 'X' and resid 541 through 556 removed outlier: 3.760A pdb=" N TYR X 553 " --> pdb=" O VAL X 549 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLN X 555 " --> pdb=" O SER X 551 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N GLY X 556 " --> pdb=" O TRP X 552 " (cutoff:3.500A) Processing helix chain 'X' and resid 557 through 565 Processing helix chain 'X' and resid 573 through 591 removed outlier: 3.609A pdb=" N THR X 577 " --> pdb=" O ASP X 573 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N SER X 578 " --> pdb=" O GLY X 574 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N GLU X 589 " --> pdb=" O GLN X 585 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ASN X 590 " --> pdb=" O GLU X 586 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N GLY X 591 " --> pdb=" O ALA X 587 " (cutoff:3.500A) Processing helix chain 'X' and resid 602 through 607 removed outlier: 3.940A pdb=" N GLU X 606 " --> pdb=" O GLY X 602 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLY X 607 " --> pdb=" O LYS X 603 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 602 through 607' Processing helix chain 'X' and resid 630 through 643 removed outlier: 4.133A pdb=" N LYS X 634 " --> pdb=" O SER X 630 " (cutoff:3.500A) Processing helix chain 'X' and resid 647 through 666 removed outlier: 3.646A pdb=" N THR X 653 " --> pdb=" O ASN X 649 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N ARG X 666 " --> pdb=" O GLN X 662 " (cutoff:3.500A) Processing helix chain 'X' and resid 682 through 687 removed outlier: 4.395A pdb=" N ARG X 686 " --> pdb=" O LYS X 682 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N GLY X 687 " --> pdb=" O ARG X 683 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 682 through 687' Processing helix chain 'X' and resid 688 through 694 removed outlier: 3.814A pdb=" N LEU X 693 " --> pdb=" O LYS X 689 " (cutoff:3.500A) Proline residue: X 694 - end of helix Processing helix chain 'X' and resid 695 through 702 removed outlier: 4.977A pdb=" N HIS X 700 " --> pdb=" O TRP X 696 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N THR X 702 " --> pdb=" O GLN X 698 " (cutoff:3.500A) Processing helix chain 'X' and resid 709 through 726 removed outlier: 4.810A pdb=" N GLN X 726 " --> pdb=" O ARG X 722 " (cutoff:3.500A) Processing helix chain 'X' and resid 729 through 735 removed outlier: 4.170A pdb=" N GLN X 733 " --> pdb=" O HIS X 729 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LEU X 734 " --> pdb=" O ARG X 730 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N GLY X 735 " --> pdb=" O GLU X 731 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 729 through 735' Processing helix chain 'X' and resid 740 through 746 removed outlier: 4.233A pdb=" N LEU X 744 " --> pdb=" O SER X 740 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N GLU X 745 " --> pdb=" O LEU X 741 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N SER X 746 " --> pdb=" O GLU X 742 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 740 through 746' Processing helix chain 'X' and resid 747 through 757 removed outlier: 3.726A pdb=" N ALA X 757 " --> pdb=" O ILE X 753 " (cutoff:3.500A) Processing helix chain 'Y' and resid 108 through 122 removed outlier: 3.521A pdb=" N GLU Y 112 " --> pdb=" O ASN Y 108 " (cutoff:3.500A) Proline residue: Y 122 - end of helix Processing helix chain 'Y' and resid 123 through 132 Processing helix chain 'Y' and resid 138 through 147 removed outlier: 3.726A pdb=" N ARG Y 146 " --> pdb=" O PHE Y 142 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N LEU Y 147 " --> pdb=" O TRP Y 143 " (cutoff:3.500A) Processing helix chain 'Y' and resid 378 through 385 removed outlier: 4.456A pdb=" N TYR Y 382 " --> pdb=" O LYS Y 378 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N GLY Y 385 " --> pdb=" O ARG Y 381 " (cutoff:3.500A) Processing helix chain 'Y' and resid 396 through 413 removed outlier: 4.207A pdb=" N ILE Y 400 " --> pdb=" O THR Y 396 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ILE Y 401 " --> pdb=" O SER Y 397 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N GLU Y 412 " --> pdb=" O ARG Y 408 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N ALA Y 413 " --> pdb=" O GLN Y 409 " (cutoff:3.500A) Processing helix chain 'Y' and resid 423 through 435 Processing helix chain 'Y' and resid 455 through 480 Proline residue: Y 480 - end of helix Processing helix chain 'Y' and resid 485 through 516 removed outlier: 3.513A pdb=" N LYS Y 489 " --> pdb=" O PHE Y 485 " (cutoff:3.500A) Proline residue: Y 507 - end of helix removed outlier: 3.820A pdb=" N GLN Y 515 " --> pdb=" O LYS Y 511 " (cutoff:3.500A) removed outlier: 5.886A pdb=" N TYR Y 516 " --> pdb=" O ILE Y 512 " (cutoff:3.500A) Processing helix chain 'Y' and resid 522 through 548 removed outlier: 3.755A pdb=" N GLU Y 526 " --> pdb=" O VAL Y 522 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N THR Y 548 " --> pdb=" O LEU Y 544 " (cutoff:3.500A) Processing helix chain 'Z' and resid 18 through 26 removed outlier: 6.316A pdb=" N PHE Z 22 " --> pdb=" O ASN Z 18 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N GLY Z 25 " --> pdb=" O GLU Z 21 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N LEU Z 26 " --> pdb=" O PHE Z 22 " (cutoff:3.500A) Processing helix chain 'Z' and resid 27 through 37 removed outlier: 4.499A pdb=" N GLY Z 36 " --> pdb=" O ASP Z 32 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N HIS Z 37 " --> pdb=" O ARG Z 33 " (cutoff:3.500A) Processing helix chain 'Z' and resid 38 through 48 removed outlier: 3.768A pdb=" N GLU Z 47 " --> pdb=" O ALA Z 43 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU Z 48 " --> pdb=" O VAL Z 44 " (cutoff:3.500A) Processing helix chain 'Z' and resid 49 through 61 removed outlier: 5.253A pdb=" N PHE Z 61 " --> pdb=" O MET Z 57 " (cutoff:3.500A) Processing helix chain 'Z' and resid 67 through 75 removed outlier: 3.796A pdb=" N VAL Z 71 " --> pdb=" O PRO Z 67 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N VAL Z 75 " --> pdb=" O VAL Z 71 " (cutoff:3.500A) Processing helix chain 'Z' and resid 79 through 94 removed outlier: 3.589A pdb=" N GLU Z 84 " --> pdb=" O SER Z 80 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N GLU Z 85 " --> pdb=" O LYS Z 81 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N SER Z 86 " --> pdb=" O ALA Z 82 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ARG Z 94 " --> pdb=" O LEU Z 90 " (cutoff:3.500A) Processing helix chain 'Z' and resid 111 through 123 Processing helix chain 'Z' and resid 144 through 165 Processing helix chain 'Z' and resid 172 through 183 removed outlier: 5.863A pdb=" N ALA Z 176 " --> pdb=" O SER Z 172 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLN Z 177 " --> pdb=" O GLN Z 173 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N GLY Z 183 " --> pdb=" O LEU Z 179 " (cutoff:3.500A) Processing helix chain 'Z' and resid 197 through 207 removed outlier: 4.120A pdb=" N LEU Z 206 " --> pdb=" O GLN Z 202 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N ASP Z 207 " --> pdb=" O PHE Z 203 " (cutoff:3.500A) Processing helix chain 'Z' and resid 208 through 224 removed outlier: 4.041A pdb=" N THR Z 222 " --> pdb=" O GLN Z 218 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ALA Z 223 " --> pdb=" O TYR Z 219 " (cutoff:3.500A) removed outlier: 5.479A pdb=" N GLN Z 224 " --> pdb=" O LEU Z 220 " (cutoff:3.500A) Processing helix chain 'Z' and resid 229 through 243 removed outlier: 3.536A pdb=" N ILE Z 233 " --> pdb=" O ASP Z 229 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N PHE Z 242 " --> pdb=" O PHE Z 238 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N SER Z 243 " --> pdb=" O GLN Z 239 " (cutoff:3.500A) Processing helix chain 'Z' and resid 255 through 269 Processing helix chain 'Z' and resid 284 through 290 removed outlier: 3.668A pdb=" N ASN Z 289 " --> pdb=" O ARG Z 285 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU Z 290 " --> pdb=" O LEU Z 286 " (cutoff:3.500A) Processing helix chain 'Z' and resid 321 through 332 Processing helix chain 'Z' and resid 347 through 358 removed outlier: 3.718A pdb=" N GLY Z 358 " --> pdb=" O ALA Z 354 " (cutoff:3.500A) Processing helix chain 'Z' and resid 360 through 372 removed outlier: 4.387A pdb=" N ILE Z 364 " --> pdb=" O THR Z 360 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N ILE Z 365 " --> pdb=" O ALA Z 361 " (cutoff:3.500A) Processing helix chain 'Z' and resid 373 through 378 removed outlier: 5.574A pdb=" N LYS Z 378 " --> pdb=" O PRO Z 374 " (cutoff:3.500A) Processing helix chain 'Z' and resid 384 through 397 removed outlier: 5.223A pdb=" N GLU Z 397 " --> pdb=" O LEU Z 393 " (cutoff:3.500A) Processing helix chain 'Z' and resid 414 through 429 removed outlier: 4.751A pdb=" N PHE Z 418 " --> pdb=" O SER Z 414 " (cutoff:3.500A) Processing helix chain 'Z' and resid 447 through 458 removed outlier: 4.317A pdb=" N VAL Z 451 " --> pdb=" O GLY Z 447 " (cutoff:3.500A) Processing helix chain 'a' and resid 68 through 74 removed outlier: 4.609A pdb=" N GLU a 72 " --> pdb=" O SER a 68 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ASP a 73 " --> pdb=" O ARG a 69 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N GLN a 74 " --> pdb=" O THR a 70 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 68 through 74' Processing helix chain 'a' and resid 79 through 99 Processing helix chain 'a' and resid 123 through 138 removed outlier: 4.140A pdb=" N HIS a 127 " --> pdb=" O ASN a 123 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N ASP a 136 " --> pdb=" O LYS a 132 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N MET a 137 " --> pdb=" O LYS a 133 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N THR a 138 " --> pdb=" O ALA a 134 " (cutoff:3.500A) Processing helix chain 'a' and resid 144 through 159 removed outlier: 3.512A pdb=" N SER a 148 " --> pdb=" O SER a 144 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N HIS a 158 " --> pdb=" O GLN a 154 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N MET a 159 " --> pdb=" O THR a 155 " (cutoff:3.500A) Processing helix chain 'a' and resid 181 through 193 removed outlier: 4.155A pdb=" N LEU a 185 " --> pdb=" O ASN a 181 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ILE a 186 " --> pdb=" O ILE a 182 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LYS a 193 " --> pdb=" O LEU a 189 " (cutoff:3.500A) Processing helix chain 'a' and resid 205 through 216 Processing helix chain 'a' and resid 224 through 237 removed outlier: 3.590A pdb=" N TYR a 228 " --> pdb=" O ASP a 224 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N SER a 237 " --> pdb=" O THR a 233 " (cutoff:3.500A) Processing helix chain 'a' and resid 314 through 327 removed outlier: 6.796A pdb=" N LEU a 318 " --> pdb=" O SER a 314 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N ALA a 319 " --> pdb=" O ALA a 315 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N SER a 321 " --> pdb=" O HIS a 317 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N TYR a 322 " --> pdb=" O LEU a 318 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N HIS a 323 " --> pdb=" O ALA a 319 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N HIS a 324 " --> pdb=" O ARG a 320 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N LEU a 325 " --> pdb=" O SER a 321 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N PHE a 326 " --> pdb=" O TYR a 322 " (cutoff:3.500A) Proline residue: a 327 - end of helix Processing helix chain 'a' and resid 368 through 377 Processing helix chain 'a' and resid 382 through 387 removed outlier: 3.729A pdb=" N ILE a 386 " --> pdb=" O CYS a 382 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N HIS a 387 " --> pdb=" O PRO a 383 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 382 through 387' Processing helix chain 'b' and resid 18 through 29 removed outlier: 3.788A pdb=" N GLU b 29 " --> pdb=" O GLN b 25 " (cutoff:3.500A) Processing helix chain 'b' and resid 33 through 53 removed outlier: 4.092A pdb=" N ASN b 52 " --> pdb=" O HIS b 48 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N ARG b 53 " --> pdb=" O LEU b 49 " (cutoff:3.500A) Processing helix chain 'b' and resid 101 through 120 removed outlier: 3.609A pdb=" N THR b 120 " --> pdb=" O LYS b 116 " (cutoff:3.500A) Processing helix chain 'b' and resid 132 through 152 removed outlier: 5.793A pdb=" N SER b 136 " --> pdb=" O LEU b 132 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N VAL b 151 " --> pdb=" O MET b 147 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N LYS b 152 " --> pdb=" O ASN b 148 " (cutoff:3.500A) Processing helix chain 'b' and resid 173 through 188 removed outlier: 4.239A pdb=" N ASN b 179 " --> pdb=" O MET b 175 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL b 180 " --> pdb=" O ASN b 176 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASN b 188 " --> pdb=" O ALA b 184 " (cutoff:3.500A) Processing helix chain 'b' and resid 200 through 211 removed outlier: 3.991A pdb=" N GLY b 211 " --> pdb=" O CYS b 207 " (cutoff:3.500A) Processing helix chain 'b' and resid 222 through 230 removed outlier: 3.892A pdb=" N TRP b 229 " --> pdb=" O GLN b 225 " (cutoff:3.500A) Processing helix chain 'b' and resid 234 through 241 removed outlier: 4.175A pdb=" N SER b 239 " --> pdb=" O GLN b 235 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N GLN b 240 " --> pdb=" O ASP b 236 " (cutoff:3.500A) Processing helix chain 'c' and resid 13 through 27 Processing helix chain 'c' and resid 46 through 67 removed outlier: 3.926A pdb=" N VAL c 50 " --> pdb=" O ILE c 46 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N ASN c 51 " --> pdb=" O ALA c 47 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N VAL c 52 " --> pdb=" O GLU c 48 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N GLY c 58 " --> pdb=" O GLN c 54 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ALA c 65 " --> pdb=" O MET c 61 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N PHE c 66 " --> pdb=" O ASP c 62 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N SER c 67 " --> pdb=" O GLN c 63 " (cutoff:3.500A) Processing helix chain 'd' and resid 31 through 42 removed outlier: 3.810A pdb=" N ARG d 41 " --> pdb=" O LEU d 37 " (cutoff:3.500A) Processing helix chain 'd' and resid 65 through 83 removed outlier: 4.547A pdb=" N ILE d 81 " --> pdb=" O LYS d 77 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N TYR d 82 " --> pdb=" O VAL d 78 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N ASN d 83 " --> pdb=" O LEU d 79 " (cutoff:3.500A) Processing helix chain 'd' and resid 85 through 90 removed outlier: 3.603A pdb=" N PHE d 89 " --> pdb=" O ARG d 85 " (cutoff:3.500A) Proline residue: d 90 - end of helix No H-bonds generated for 'chain 'd' and resid 85 through 90' Processing helix chain 'd' and resid 91 through 112 removed outlier: 3.730A pdb=" N TYR d 95 " --> pdb=" O SER d 91 " (cutoff:3.500A) Processing helix chain 'd' and resid 113 through 132 removed outlier: 4.198A pdb=" N ASN d 117 " --> pdb=" O VAL d 113 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N ASP d 131 " --> pdb=" O LYS d 127 " (cutoff:3.500A) Processing helix chain 'd' and resid 133 through 187 Processing helix chain 'd' and resid 193 through 210 removed outlier: 3.592A pdb=" N LEU d 197 " --> pdb=" O PRO d 193 " (cutoff:3.500A) Processing helix chain 'd' and resid 262 through 270 removed outlier: 4.829A pdb=" N GLY d 267 " --> pdb=" O LEU d 263 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N ARG d 268 " --> pdb=" O GLU d 264 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N LEU d 269 " --> pdb=" O MET d 265 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N GLY d 270 " --> pdb=" O LEU d 266 " (cutoff:3.500A) Processing helix chain 'd' and resid 271 through 276 removed outlier: 3.810A pdb=" N VAL d 275 " --> pdb=" O TYR d 271 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N ARG d 276 " --> pdb=" O LEU d 272 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 271 through 276' Processing helix chain 'd' and resid 279 through 286 removed outlier: 3.570A pdb=" N GLY d 285 " --> pdb=" O GLN d 281 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N GLY d 286 " --> pdb=" O ASP d 282 " (cutoff:3.500A) Processing helix chain 'd' and resid 288 through 302 removed outlier: 6.649A pdb=" N ALA d 292 " --> pdb=" O THR d 288 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N CYS d 293 " --> pdb=" O SER d 289 " (cutoff:3.500A) Processing helix chain 'd' and resid 12 through 17 Proline residue: d 17 - end of helix No H-bonds generated for 'chain 'd' and resid 12 through 17' Processing helix chain 'e' and resid 56 through 70 removed outlier: 4.084A pdb=" N GLU e 68 " --> pdb=" O LYS e 64 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LEU e 69 " --> pdb=" O LEU e 65 " (cutoff:3.500A) removed outlier: 5.743A pdb=" N SER e 70 " --> pdb=" O LEU e 66 " (cutoff:3.500A) Processing helix chain 'e' and resid 97 through 104 removed outlier: 3.662A pdb=" N ILE e 101 " --> pdb=" O ASP e 97 " (cutoff:3.500A) Processing helix chain 'e' and resid 110 through 132 Processing helix chain 'e' and resid 139 through 144 removed outlier: 3.583A pdb=" N LEU e 143 " --> pdb=" O LYS e 139 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N LEU e 144 " --> pdb=" O PRO e 140 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 139 through 144' Processing helix chain 'e' and resid 180 through 186 Processing helix chain 'e' and resid 192 through 209 Processing helix chain 'e' and resid 217 through 230 Processing helix chain 'e' and resid 233 through 238 removed outlier: 6.000A pdb=" N TRP e 237 " --> pdb=" O THR e 233 " (cutoff:3.500A) Proline residue: e 238 - end of helix No H-bonds generated for 'chain 'e' and resid 233 through 238' Processing helix chain 'e' and resid 256 through 262 removed outlier: 4.344A pdb=" N SER e 262 " --> pdb=" O HIS e 258 " (cutoff:3.500A) Processing helix chain 'e' and resid 265 through 277 Processing helix chain 'e' and resid 279 through 284 removed outlier: 6.580A pdb=" N ILE e 284 " --> pdb=" O PRO e 280 " (cutoff:3.500A) Processing helix chain 'e' and resid 285 through 292 removed outlier: 3.568A pdb=" N MET e 292 " --> pdb=" O GLN e 288 " (cutoff:3.500A) Processing helix chain 'e' and resid 303 through 308 Proline residue: e 308 - end of helix Processing helix chain 'f' and resid 5 through 10 Processing helix chain 'f' and resid 15 through 38 removed outlier: 4.507A pdb=" N GLY f 38 " --> pdb=" O ALA f 34 " (cutoff:3.500A) Processing helix chain 'f' and resid 49 through 71 Processing helix chain 'f' and resid 76 through 94 Processing helix chain 'f' and resid 95 through 100 removed outlier: 3.929A pdb=" N HIS f 100 " --> pdb=" O VAL f 96 " (cutoff:3.500A) Processing helix chain 'f' and resid 101 through 117 removed outlier: 4.454A pdb=" N GLU f 117 " --> pdb=" O CYS f 113 " (cutoff:3.500A) Processing helix chain 'f' and resid 121 through 130 removed outlier: 4.283A pdb=" N LEU f 129 " --> pdb=" O PHE f 125 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N ARG f 130 " --> pdb=" O VAL f 126 " (cutoff:3.500A) Processing helix chain 'f' and resid 132 through 150 removed outlier: 4.525A pdb=" N LEU f 148 " --> pdb=" O LEU f 144 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N LEU f 149 " --> pdb=" O GLU f 145 " (cutoff:3.500A) Processing helix chain 'f' and resid 163 through 177 Processing helix chain 'f' and resid 185 through 202 removed outlier: 3.711A pdb=" N THR f 201 " --> pdb=" O ARG f 197 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N ASP f 202 " --> pdb=" O ILE f 198 " (cutoff:3.500A) Processing helix chain 'f' and resid 208 through 225 Processing helix chain 'f' and resid 228 through 234 removed outlier: 3.517A pdb=" N LEU f 232 " --> pdb=" O MET f 228 " (cutoff:3.500A) Processing helix chain 'f' and resid 237 through 242 removed outlier: 4.596A pdb=" N ASN f 241 " --> pdb=" O MET f 237 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N ARG f 242 " --> pdb=" O LEU f 238 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 237 through 242' Processing helix chain 'f' and resid 243 through 262 Processing helix chain 'f' and resid 266 through 284 removed outlier: 4.168A pdb=" N VAL f 270 " --> pdb=" O ARG f 266 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N GLU f 284 " --> pdb=" O CYS f 280 " (cutoff:3.500A) Processing helix chain 'g' and resid 9 through 14 removed outlier: 4.159A pdb=" N ILE g 13 " --> pdb=" O ASN g 9 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N SER g 14 " --> pdb=" O LEU g 10 " (cutoff:3.500A) No H-bonds generated for 'chain 'g' and resid 9 through 14' Processing helix chain 'g' and resid 25 through 35 removed outlier: 3.883A pdb=" N LEU g 30 " --> pdb=" O SER g 26 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N SER g 34 " --> pdb=" O LEU g 30 " (cutoff:3.500A) Processing helix chain 'g' and resid 45 through 54 removed outlier: 4.166A pdb=" N VAL g 49 " --> pdb=" O CYS g 45 " (cutoff:3.500A) Processing helix chain 'g' and resid 56 through 63 removed outlier: 3.536A pdb=" N MET g 63 " --> pdb=" O HIS g 59 " (cutoff:3.500A) Processing helix chain 'g' and resid 110 through 137 removed outlier: 4.089A pdb=" N VAL g 114 " --> pdb=" O ASP g 110 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N ILE g 115 " --> pdb=" O LEU g 111 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ASN g 116 " --> pdb=" O GLY g 112 " (cutoff:3.500A) Processing helix chain 'h' and resid 4 through 36 removed outlier: 3.711A pdb=" N LEU h 8 " --> pdb=" O GLU h 4 " (cutoff:3.500A) Processing helix chain 'h' and resid 42 through 67 removed outlier: 5.366A pdb=" N GLU h 66 " --> pdb=" O VAL h 62 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N LYS h 67 " --> pdb=" O LEU h 63 " (cutoff:3.500A) Processing helix chain 'h' and resid 69 through 74 removed outlier: 4.627A pdb=" N GLN h 74 " --> pdb=" O LEU h 70 " (cutoff:3.500A) Processing helix chain 'h' and resid 102 through 110 Proline residue: h 106 - end of helix Processing helix chain 'h' and resid 114 through 132 removed outlier: 4.209A pdb=" N GLY h 132 " --> pdb=" O ALA h 128 " (cutoff:3.500A) Processing helix chain 'h' and resid 134 through 161 removed outlier: 3.592A pdb=" N LYS h 138 " --> pdb=" O ASP h 134 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N SER h 161 " --> pdb=" O GLU h 157 " (cutoff:3.500A) Processing helix chain 'h' and resid 174 through 187 Processing helix chain 'i' and resid 7 through 37 removed outlier: 3.696A pdb=" N LEU i 35 " --> pdb=" O VAL i 31 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N SER i 36 " --> pdb=" O ILE i 32 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N LYS i 37 " --> pdb=" O LEU i 33 " (cutoff:3.500A) Processing helix chain 'i' and resid 41 through 74 removed outlier: 3.686A pdb=" N THR i 53 " --> pdb=" O ALA i 49 " (cutoff:3.500A) Processing helix chain 'i' and resid 83 through 116 removed outlier: 3.612A pdb=" N GLU i 116 " --> pdb=" O GLU i 112 " (cutoff:3.500A) Processing helix chain 'j' and resid 35 through 47 removed outlier: 3.598A pdb=" N ASN j 39 " --> pdb=" O SER j 35 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N LEU j 40 " --> pdb=" O MET j 36 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ALA j 41 " --> pdb=" O SER j 37 " (cutoff:3.500A) Processing helix chain 'j' and resid 95 through 119 Processing helix chain 'j' and resid 140 through 178 removed outlier: 6.565A pdb=" N GLU j 173 " --> pdb=" O LYS j 169 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N ASN j 174 " --> pdb=" O SER j 170 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N GLN j 175 " --> pdb=" O VAL j 171 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N GLU j 176 " --> pdb=" O THR j 172 " (cutoff:3.500A) Processing helix chain 'j' and resid 182 through 194 removed outlier: 6.226A pdb=" N GLU j 186 " --> pdb=" O ASP j 182 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU j 187 " --> pdb=" O PHE j 183 " (cutoff:3.500A) Processing helix chain 'j' and resid 289 through 318 removed outlier: 3.531A pdb=" N THR j 293 " --> pdb=" O PRO j 289 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL j 316 " --> pdb=" O SER j 312 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ILE j 318 " --> pdb=" O GLU j 314 " (cutoff:3.500A) Processing helix chain 'j' and resid 366 through 393 removed outlier: 3.509A pdb=" N LEU j 377 " --> pdb=" O HIS j 373 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N SER j 388 " --> pdb=" O LYS j 384 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N SER j 389 " --> pdb=" O GLN j 385 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N ILE j 390 " --> pdb=" O THR j 386 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N MET j 391 " --> pdb=" O LEU j 387 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N MET j 392 " --> pdb=" O SER j 388 " (cutoff:3.500A) Proline residue: j 393 - end of helix Processing helix chain 'j' and resid 402 through 411 removed outlier: 6.401A pdb=" N ARG j 406 " --> pdb=" O HIS j 402 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N LEU j 407 " --> pdb=" O LYS j 403 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLY j 409 " --> pdb=" O MET j 405 " (cutoff:3.500A) Proline residue: j 410 - end of helix Processing helix chain 'j' and resid 415 through 424 removed outlier: 4.206A pdb=" N GLN j 422 " --> pdb=" O ILE j 418 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N SER j 423 " --> pdb=" O ASN j 419 " (cutoff:3.500A) removed outlier: 5.751A pdb=" N SER j 424 " --> pdb=" O SER j 420 " (cutoff:3.500A) Processing helix chain 'j' and resid 426 through 456 removed outlier: 4.428A pdb=" N LYS j 430 " --> pdb=" O GLY j 426 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ILE j 455 " --> pdb=" O LEU j 451 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N GLU j 456 " --> pdb=" O ALA j 452 " (cutoff:3.500A) Processing helix chain 'j' and resid 517 through 545 removed outlier: 4.579A pdb=" N LEU j 521 " --> pdb=" O GLN j 517 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N GLN j 538 " --> pdb=" O VAL j 534 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N MET j 544 " --> pdb=" O LEU j 540 " (cutoff:3.500A) Processing helix chain 'j' and resid 597 through 602 removed outlier: 3.964A pdb=" N CYS j 601 " --> pdb=" O PRO j 597 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N LYS j 602 " --> pdb=" O ARG j 598 " (cutoff:3.500A) No H-bonds generated for 'chain 'j' and resid 597 through 602' Processing helix chain 'j' and resid 612 through 617 removed outlier: 5.071A pdb=" N SER j 616 " --> pdb=" O ASP j 612 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N HIS j 617 " --> pdb=" O ASN j 613 " (cutoff:3.500A) No H-bonds generated for 'chain 'j' and resid 612 through 617' Processing helix chain 'j' and resid 634 through 648 removed outlier: 4.181A pdb=" N SER j 647 " --> pdb=" O MET j 643 " (cutoff:3.500A) Proline residue: j 648 - end of helix Processing helix chain 'k' and resid 29 through 43 removed outlier: 3.870A pdb=" N GLY k 41 " --> pdb=" O HIS k 37 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU k 42 " --> pdb=" O ARG k 38 " (cutoff:3.500A) Processing helix chain 'k' and resid 113 through 122 Processing helix chain 'k' and resid 181 through 194 removed outlier: 3.672A pdb=" N ASP k 185 " --> pdb=" O MET k 181 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N LEU k 193 " --> pdb=" O PHE k 189 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LYS k 194 " --> pdb=" O ALA k 190 " (cutoff:3.500A) Processing helix chain 'l' and resid 16 through 32 removed outlier: 3.725A pdb=" N GLY l 32 " --> pdb=" O LEU l 28 " (cutoff:3.500A) Processing helix chain 'l' and resid 90 through 99 removed outlier: 4.393A pdb=" N LEU l 94 " --> pdb=" O ASN l 90 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N LYS l 99 " --> pdb=" O MET l 95 " (cutoff:3.500A) Processing helix chain 'l' and resid 149 through 165 removed outlier: 4.149A pdb=" N CYS l 153 " --> pdb=" O VAL l 149 " (cutoff:3.500A) removed outlier: 5.886A pdb=" N SER l 155 " --> pdb=" O SER l 151 " (cutoff:3.500A) removed outlier: 5.697A pdb=" N LEU l 156 " --> pdb=" O ASP l 152 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N SER l 163 " --> pdb=" O GLU l 159 " (cutoff:3.500A) Processing helix chain 'l' and resid 173 through 179 removed outlier: 4.313A pdb=" N GLY l 177 " --> pdb=" O PRO l 173 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ARG l 179 " --> pdb=" O VAL l 175 " (cutoff:3.500A) Processing helix chain 'l' and resid 186 through 204 removed outlier: 3.836A pdb=" N MET l 190 " --> pdb=" O PRO l 186 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LYS l 202 " --> pdb=" O ASN l 198 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N GLN l 203 " --> pdb=" O LYS l 199 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N GLN l 204 " --> pdb=" O ILE l 200 " (cutoff:3.500A) Processing helix chain 'm' and resid 11 through 39 Processing helix chain 'm' and resid 49 through 89 Processing helix chain 'm' and resid 90 through 132 Processing helix chain 'n' and resid 7 through 38 removed outlier: 3.789A pdb=" N ASP n 37 " --> pdb=" O ASP n 33 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N GLY n 38 " --> pdb=" O CYS n 34 " (cutoff:3.500A) Processing helix chain 'n' and resid 44 through 77 removed outlier: 4.336A pdb=" N ARG n 48 " --> pdb=" O THR n 44 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLU n 49 " --> pdb=" O LEU n 45 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU n 76 " --> pdb=" O ARG n 72 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N VAL n 77 " --> pdb=" O LEU n 73 " (cutoff:3.500A) Processing helix chain 'n' and resid 87 through 95 removed outlier: 3.625A pdb=" N SER n 93 " --> pdb=" O SER n 89 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU n 94 " --> pdb=" O GLY n 90 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ASP n 95 " --> pdb=" O LEU n 91 " (cutoff:3.500A) Processing helix chain 'n' and resid 96 through 102 removed outlier: 5.915A pdb=" N LYS n 100 " --> pdb=" O PRO n 96 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N THR n 101 " --> pdb=" O VAL n 97 " (cutoff:3.500A) Proline residue: n 102 - end of helix No H-bonds generated for 'chain 'n' and resid 96 through 102' Processing helix chain 'n' and resid 103 through 132 removed outlier: 5.946A pdb=" N LEU n 107 " --> pdb=" O LEU n 103 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LEU n 108 " --> pdb=" O TYR n 104 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N SER n 132 " --> pdb=" O LEU n 128 " (cutoff:3.500A) Processing helix chain 'n' and resid 158 through 174 removed outlier: 3.806A pdb=" N PHE n 173 " --> pdb=" O ILE n 169 " (cutoff:3.500A) Proline residue: n 174 - end of helix Processing helix chain 'n' and resid 236 through 254 removed outlier: 4.089A pdb=" N GLN n 254 " --> pdb=" O LEU n 250 " (cutoff:3.500A) Processing helix chain 'n' and resid 259 through 274 removed outlier: 4.639A pdb=" N VAL n 263 " --> pdb=" O PRO n 259 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ARG n 264 " --> pdb=" O ASP n 260 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ILE n 274 " --> pdb=" O LEU n 270 " (cutoff:3.500A) Processing helix chain 'n' and resid 306 through 311 Processing helix chain 'o' and resid 43 through 61 removed outlier: 5.870A pdb=" N GLU o 47 " --> pdb=" O THR o 43 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N LEU o 59 " --> pdb=" O CYS o 55 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N VAL o 60 " --> pdb=" O PHE o 56 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N SER o 61 " --> pdb=" O ALA o 57 " (cutoff:3.500A) Processing helix chain 'o' and resid 69 through 106 removed outlier: 4.303A pdb=" N ILE o 73 " --> pdb=" O ASP o 69 " (cutoff:3.500A) Processing helix chain 'o' and resid 107 through 149 Processing helix chain 'p' and resid 57 through 91 Proline residue: p 65 - end of helix Processing helix chain 'p' and resid 101 through 137 removed outlier: 4.065A pdb=" N CYS p 105 " --> pdb=" O ARG p 101 " (cutoff:3.500A) Processing helix chain 'p' and resid 156 through 185 removed outlier: 3.512A pdb=" N VAL p 185 " --> pdb=" O CYS p 181 " (cutoff:3.500A) Processing helix chain 'q' and resid 30 through 58 Processing helix chain 'q' and resid 72 through 101 removed outlier: 3.559A pdb=" N THR q 76 " --> pdb=" O GLN q 72 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N GLN q 84 " --> pdb=" O ASP q 80 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU q 85 " --> pdb=" O ASN q 81 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ARG q 90 " --> pdb=" O SER q 86 " (cutoff:3.500A) Processing helix chain 'q' and resid 110 through 115 removed outlier: 3.685A pdb=" N LEU q 114 " --> pdb=" O PRO q 110 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N ILE q 115 " --> pdb=" O VAL q 111 " (cutoff:3.500A) No H-bonds generated for 'chain 'q' and resid 110 through 115' Processing helix chain 'q' and resid 139 through 175 Processing helix chain 'r' and resid 51 through 76 removed outlier: 3.636A pdb=" N ILE r 55 " --> pdb=" O LEU r 51 " (cutoff:3.500A) Proline residue: r 74 - end of helix Processing helix chain 'r' and resid 77 through 106 Processing helix chain 'r' and resid 109 through 149 removed outlier: 3.536A pdb=" N GLN r 125 " --> pdb=" O PHE r 121 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA r 126 " --> pdb=" O LEU r 122 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N LEU r 149 " --> pdb=" O VAL r 145 " (cutoff:3.500A) Processing helix chain 'r' and resid 153 through 163 removed outlier: 3.677A pdb=" N ALA r 157 " --> pdb=" O ALA r 153 " (cutoff:3.500A) Processing helix chain 'r' and resid 173 through 180 Proline residue: r 179 - end of helix Processing helix chain 'r' and resid 184 through 206 removed outlier: 4.677A pdb=" N LYS r 188 " --> pdb=" O THR r 184 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N GLN r 189 " --> pdb=" O LYS r 185 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N ALA r 190 " --> pdb=" O ILE r 186 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N THR r 191 " --> pdb=" O GLU r 187 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N LEU r 192 " --> pdb=" O LYS r 188 " (cutoff:3.500A) Processing helix chain 'r' and resid 269 through 283 removed outlier: 3.544A pdb=" N ARG r 281 " --> pdb=" O LEU r 277 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N LEU r 282 " --> pdb=" O VAL r 278 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N PHE r 283 " --> pdb=" O GLN r 279 " (cutoff:3.500A) Processing helix chain 'r' and resid 287 through 319 removed outlier: 3.503A pdb=" N PHE r 299 " --> pdb=" O CYS r 295 " (cutoff:3.500A) Processing helix chain 'r' and resid 396 through 424 removed outlier: 3.757A pdb=" N LEU r 400 " --> pdb=" O SER r 396 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLN r 414 " --> pdb=" O HIS r 410 " (cutoff:3.500A) Processing helix chain 'r' and resid 471 through 485 removed outlier: 5.848A pdb=" N LEU r 475 " --> pdb=" O ASP r 471 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ASP r 476 " --> pdb=" O GLN r 472 " (cutoff:3.500A) Processing helix chain 'r' and resid 490 through 511 removed outlier: 3.883A pdb=" N PHE r 498 " --> pdb=" O GLN r 494 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N HIS r 511 " --> pdb=" O GLN r 507 " (cutoff:3.500A) Processing helix chain 'r' and resid 528 through 534 removed outlier: 4.670A pdb=" N ASN r 532 " --> pdb=" O HIS r 528 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N SER r 534 " --> pdb=" O ILE r 530 " (cutoff:3.500A) Processing helix chain 'r' and resid 638 through 665 removed outlier: 3.507A pdb=" N ASN r 651 " --> pdb=" O MET r 647 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N MET r 652 " --> pdb=" O CYS r 648 " (cutoff:3.500A) Proline residue: r 653 - end of helix removed outlier: 3.696A pdb=" N LEU r 664 " --> pdb=" O GLU r 660 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N GLU r 665 " --> pdb=" O LEU r 661 " (cutoff:3.500A) Processing helix chain 'r' and resid 694 through 706 removed outlier: 5.928A pdb=" N LEU r 706 " --> pdb=" O ASP r 702 " (cutoff:3.500A) Processing helix chain 'r' and resid 735 through 740 removed outlier: 6.501A pdb=" N GLN r 739 " --> pdb=" O SER r 735 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N GLY r 740 " --> pdb=" O THR r 736 " (cutoff:3.500A) No H-bonds generated for 'chain 'r' and resid 735 through 740' Processing helix chain 'r' and resid 759 through 788 removed outlier: 4.195A pdb=" N VAL r 763 " --> pdb=" O GLY r 759 " (cutoff:3.500A) Proline residue: r 788 - end of helix Processing helix chain 'r' and resid 791 through 798 removed outlier: 3.822A pdb=" N SER r 798 " --> pdb=" O LEU r 794 " (cutoff:3.500A) Processing helix chain 'r' and resid 848 through 863 removed outlier: 3.526A pdb=" N LEU r 852 " --> pdb=" O HIS r 848 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N HIS r 853 " --> pdb=" O ASN r 849 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N GLN r 854 " --> pdb=" O THR r 850 " (cutoff:3.500A) Proline residue: r 863 - end of helix Processing helix chain 'r' and resid 864 through 885 removed outlier: 4.293A pdb=" N THR r 875 " --> pdb=" O VAL r 871 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLN r 876 " --> pdb=" O LEU r 872 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N ALA r 877 " --> pdb=" O PHE r 873 " (cutoff:3.500A) Proline residue: r 878 - end of helix removed outlier: 4.192A pdb=" N LYS r 884 " --> pdb=" O ASN r 880 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N LEU r 885 " --> pdb=" O ALA r 881 " (cutoff:3.500A) Processing helix chain 'r' and resid 958 through 967 removed outlier: 3.505A pdb=" N PHE r 962 " --> pdb=" O GLY r 958 " (cutoff:3.500A) Processing helix chain 'r' and resid 1178 through 1187 removed outlier: 5.600A pdb=" N LEU r1182 " --> pdb=" O THR r1178 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N ASN r1183 " --> pdb=" O HIS r1179 " (cutoff:3.500A) Processing helix chain 'r' and resid 1205 through 1227 removed outlier: 4.132A pdb=" N PHE r1210 " --> pdb=" O PRO r1206 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N GLU r1227 " --> pdb=" O ILE r1223 " (cutoff:3.500A) Processing helix chain 'r' and resid 1274 through 1288 removed outlier: 3.830A pdb=" N LEU r1278 " --> pdb=" O LYS r1274 " (cutoff:3.500A) removed outlier: 5.467A pdb=" N GLN r1279 " --> pdb=" O PRO r1275 " (cutoff:3.500A) Processing helix chain 'r' and resid 1295 through 1308 removed outlier: 4.429A pdb=" N LEU r1299 " --> pdb=" O LYS r1295 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N ILE r1300 " --> pdb=" O ALA r1296 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA r1301 " --> pdb=" O ASN r1297 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N ALA r1308 " --> pdb=" O LYS r1304 " (cutoff:3.500A) Processing helix chain 'r' and resid 1309 through 1325 Processing helix chain 'r' and resid 1411 through 1427 removed outlier: 3.511A pdb=" N VAL r1415 " --> pdb=" O ALA r1411 " (cutoff:3.500A) Proline residue: r1427 - end of helix Processing helix chain 'r' and resid 1434 through 1444 removed outlier: 3.588A pdb=" N ALA r1444 " --> pdb=" O ARG r1440 " (cutoff:3.500A) Processing helix chain 'r' and resid 1169 through 1174 removed outlier: 3.506A pdb=" N ILE r1173 " --> pdb=" O ALA r1170 " (cutoff:3.500A) Proline residue: r1174 - end of helix Processing helix chain 's' and resid 29 through 50 removed outlier: 4.051A pdb=" N ALA s 33 " --> pdb=" O ARG s 29 " (cutoff:3.500A) Processing helix chain 's' and resid 62 through 70 Processing helix chain 's' and resid 76 through 123 removed outlier: 3.805A pdb=" N LYS s 88 " --> pdb=" O LEU s 84 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N HIS s 91 " --> pdb=" O GLY s 87 " (cutoff:3.500A) Processing helix chain 's' and resid 139 through 156 removed outlier: 5.419A pdb=" N ILE s 143 " --> pdb=" O ARG s 139 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N SER s 144 " --> pdb=" O LYS s 140 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N SER s 145 " --> pdb=" O GLY s 141 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N GLU s 146 " --> pdb=" O ALA s 142 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N GLU s 147 " --> pdb=" O ILE s 143 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N ILE s 148 " --> pdb=" O SER s 144 " (cutoff:3.500A) Processing helix chain 's' and resid 179 through 186 removed outlier: 3.628A pdb=" N GLY s 185 " --> pdb=" O GLU s 181 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N LEU s 186 " --> pdb=" O MET s 182 " (cutoff:3.500A) Processing helix chain 's' and resid 187 through 194 Proline residue: s 193 - end of helix Processing helix chain 't' and resid 15 through 21 removed outlier: 5.762A pdb=" N LYS t 19 " --> pdb=" O MET t 15 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N GLU t 20 " --> pdb=" O GLN t 16 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N TYR t 21 " --> pdb=" O TYR t 17 " (cutoff:3.500A) No H-bonds generated for 'chain 't' and resid 15 through 21' Processing helix chain 't' and resid 22 through 30 removed outlier: 4.280A pdb=" N ILE t 26 " --> pdb=" O THR t 22 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N GLN t 27 " --> pdb=" O ASP t 23 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N GLU t 28 " --> pdb=" O GLU t 24 " (cutoff:3.500A) Processing helix chain 't' and resid 74 through 96 removed outlier: 3.745A pdb=" N LEU t 78 " --> pdb=" O HIS t 74 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N LEU t 96 " --> pdb=" O LEU t 92 " (cutoff:3.500A) Processing helix chain 't' and resid 105 through 172 Proline residue: t 128 - end of helix removed outlier: 3.589A pdb=" N LEU t 171 " --> pdb=" O CYS t 167 " (cutoff:3.500A) Proline residue: t 172 - end of helix Processing helix chain 'u' and resid 66 through 76 removed outlier: 4.039A pdb=" N CYS u 75 " --> pdb=" O ASN u 71 " (cutoff:3.500A) Processing helix chain 'u' and resid 84 through 104 removed outlier: 4.347A pdb=" N ASN u 88 " --> pdb=" O HIS u 84 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N MET u 104 " --> pdb=" O LEU u 100 " (cutoff:3.500A) Processing helix chain 'u' and resid 111 through 137 removed outlier: 4.860A pdb=" N GLN u 115 " --> pdb=" O PRO u 111 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N GLN u 116 " --> pdb=" O GLU u 112 " (cutoff:3.500A) Processing helix chain 'v' and resid 1 through 29 removed outlier: 4.731A pdb=" N PHE v 5 " --> pdb=" O MET v 1 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N ASP v 28 " --> pdb=" O ILE v 24 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N PHE v 29 " --> pdb=" O ILE v 25 " (cutoff:3.500A) Processing helix chain 'v' and resid 32 through 59 removed outlier: 4.266A pdb=" N GLY v 36 " --> pdb=" O SER v 32 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N GLN v 57 " --> pdb=" O LYS v 53 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N LEU v 58 " --> pdb=" O CYS v 54 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N HIS v 59 " --> pdb=" O ARG v 55 " (cutoff:3.500A) Processing helix chain 'v' and resid 64 through 73 Processing helix chain 'v' and resid 76 through 117 removed outlier: 4.331A pdb=" N TYR v 80 " --> pdb=" O ASN v 76 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N THR v 81 " --> pdb=" O PRO v 77 " (cutoff:3.500A) Processing helix chain 'v' and resid 122 through 128 removed outlier: 4.229A pdb=" N SER v 126 " --> pdb=" O ALA v 122 " (cutoff:3.500A) Processing helix chain 'w' and resid 82 through 88 removed outlier: 4.194A pdb=" N HIS w 86 " --> pdb=" O ASN w 82 " (cutoff:3.500A) Processing helix chain 'w' and resid 89 through 96 Processing helix chain 'w' and resid 104 through 109 removed outlier: 4.019A pdb=" N LEU w 109 " --> pdb=" O LEU w 105 " (cutoff:3.500A) Processing helix chain 'w' and resid 126 through 133 Processing helix chain 'w' and resid 146 through 151 Processing helix chain 'x' and resid 3 through 29 removed outlier: 3.829A pdb=" N GLN x 7 " --> pdb=" O ASP x 3 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU x 8 " --> pdb=" O ARG x 4 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N ILE x 23 " --> pdb=" O PHE x 19 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N VAL x 25 " --> pdb=" O ASN x 21 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N LEU x 26 " --> pdb=" O ALA x 22 " (cutoff:3.500A) Processing helix chain 'x' and resid 51 through 78 removed outlier: 3.597A pdb=" N ALA x 55 " --> pdb=" O THR x 51 " (cutoff:3.500A) Proline residue: x 77 - end of helix Processing helix chain 'x' and resid 82 through 133 removed outlier: 4.642A pdb=" N GLN x 86 " --> pdb=" O THR x 82 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N ALA x 87 " --> pdb=" O ALA x 83 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N ALA x 88 " --> pdb=" O ALA x 84 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LYS x 117 " --> pdb=" O MET x 113 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ILE x 118 " --> pdb=" O LEU x 114 " (cutoff:3.500A) Processing helix chain 'y' and resid 14 through 31 removed outlier: 4.180A pdb=" N PHE y 18 " --> pdb=" O ASN y 14 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLN y 19 " --> pdb=" O ARG y 15 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N ASN y 30 " --> pdb=" O GLN y 26 " (cutoff:3.500A) Proline residue: y 31 - end of helix Processing helix chain 'y' and resid 32 through 41 Processing helix chain 'y' and resid 45 through 59 removed outlier: 4.214A pdb=" N TRP y 58 " --> pdb=" O TYR y 54 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N LYS y 59 " --> pdb=" O LEU y 55 " (cutoff:3.500A) Processing helix chain 'y' and resid 60 through 66 removed outlier: 4.300A pdb=" N LYS y 65 " --> pdb=" O PRO y 61 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N TYR y 66 " --> pdb=" O GLU y 62 " (cutoff:3.500A) Processing helix chain 'y' and resid 69 through 82 removed outlier: 4.673A pdb=" N LEU y 73 " --> pdb=" O TYR y 69 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N HIS y 74 " --> pdb=" O PRO y 70 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N GLU y 82 " --> pdb=" O LEU y 78 " (cutoff:3.500A) Processing helix chain 'y' and resid 83 through 89 removed outlier: 4.363A pdb=" N VAL y 89 " --> pdb=" O ARG y 85 " (cutoff:3.500A) Processing helix chain 'y' and resid 90 through 105 removed outlier: 3.911A pdb=" N ALA y 94 " --> pdb=" O ASN y 90 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLN y 101 " --> pdb=" O ILE y 97 " (cutoff:3.500A) Processing helix chain 'y' and resid 109 through 131 Processing helix chain 'z' and resid 618 through 629 removed outlier: 3.898A pdb=" N ASN z 628 " --> pdb=" O ALA z 624 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ILE z 629 " --> pdb=" O VAL z 625 " (cutoff:3.500A) Processing helix chain 'z' and resid 633 through 650 removed outlier: 3.507A pdb=" N PHE z 642 " --> pdb=" O LEU z 638 " (cutoff:3.500A) Proline residue: z 644 - end of helix Processing helix chain 'z' and resid 675 through 685 removed outlier: 5.889A pdb=" N GLN z 679 " --> pdb=" O PRO z 675 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N GLY z 680 " --> pdb=" O SER z 676 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU z 685 " --> pdb=" O GLU z 681 " (cutoff:3.500A) Processing helix chain 'z' and resid 739 through 744 removed outlier: 3.544A pdb=" N ASP z 744 " --> pdb=" O GLN z 740 " (cutoff:3.500A) Processing helix chain 'z' and resid 746 through 764 removed outlier: 3.789A pdb=" N GLN z 750 " --> pdb=" O ASN z 746 " (cutoff:3.500A) Proline residue: z 764 - end of helix Processing helix chain 'z' and resid 768 through 785 Processing sheet with id= 1, first strand: chain '0' and resid 36 through 39 removed outlier: 6.680A pdb=" N ALA 0 36 " --> pdb=" O THR 0 48 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain '0' and resid 86 through 90 removed outlier: 5.895A pdb=" N ARG 0 95 " --> pdb=" O ASP 0 90 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ALA 0 111 " --> pdb=" O SER 0 117 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N SER 0 117 " --> pdb=" O ALA 0 111 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain '0' and resid 134 through 137 removed outlier: 5.670A pdb=" N GLY 0 178 " --> pdb=" O LEU 0 137 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain '0' and resid 187 through 194 removed outlier: 3.649A pdb=" N VAL 0 190 " --> pdb=" O SER 0 202 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N SER 0 202 " --> pdb=" O VAL 0 190 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N GLN 0 198 " --> pdb=" O LYS 0 194 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain '0' and resid 215 through 221 removed outlier: 3.632A pdb=" N LEU 0 215 " --> pdb=" O ASP 0 232 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N THR 0 221 " --> pdb=" O ILE 0 226 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ILE 0 226 " --> pdb=" O THR 0 221 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N TYR 0 242 " --> pdb=" O ALA 0 229 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALA 0 231 " --> pdb=" O GLN 0 240 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N GLN 0 240 " --> pdb=" O ALA 0 231 " (cutoff:3.500A) removed outlier: 5.024A pdb=" N PHE 0 241 " --> pdb=" O LEU 0 260 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU 0 260 " --> pdb=" O PHE 0 241 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASP 0 256 " --> pdb=" O CYS 0 245 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ARG 0 254 " --> pdb=" O SER 0 247 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain '0' and resid 278 through 281 removed outlier: 6.723A pdb=" N CYS 0 297 " --> pdb=" O THR 0 281 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain '0' and resid 337 through 341 removed outlier: 4.743A pdb=" N VAL 0 306 " --> pdb=" O THR 0 345 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N SER 0 343 " --> pdb=" O CYS 0 308 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain '0' and resid 353 through 357 removed outlier: 7.789A pdb=" N GLY 0 381 " --> pdb=" O PRO 0 357 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N SER 0 390 " --> pdb=" O PHE 0 386 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N VAL 0 391 " --> pdb=" O PHE 0 405 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ALA 0 403 " --> pdb=" O ILE 0 393 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain '0' and resid 433 through 437 removed outlier: 3.708A pdb=" N ALA 0 433 " --> pdb=" O ILE 0 446 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N ALA 0 442 " --> pdb=" O SER 0 437 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N LEU 0 441 " --> pdb=" O LEU 0 457 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU 0 455 " --> pdb=" O LEU 0 443 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LYS 0 451 " --> pdb=" O ASP 0 447 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N LEU 0 452 " --> pdb=" O CYS 0 19 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N TYR 0 17 " --> pdb=" O VAL 0 454 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N LEU 0 748 " --> pdb=" O ALA 0 16 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain '0' and resid 794 through 798 removed outlier: 8.091A pdb=" N GLU 0 794 " --> pdb=" O LEU 0 807 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N CYS 0 803 " --> pdb=" O CYS 0 798 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain '0' and resid 103 through 106 removed outlier: 3.947A pdb=" N GLY 0 103 " --> pdb=" O VAL 0 126 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain '0' and resid 292 through 300 removed outlier: 6.949A pdb=" N GLU 0 292 " --> pdb=" O LEU 0 311 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU 0 311 " --> pdb=" O GLU 0 292 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N SER 0 303 " --> pdb=" O SER 0 300 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain '1' and resid 505 through 509 removed outlier: 7.228A pdb=" N MET 1 505 " --> pdb=" O GLY 1 518 " (cutoff:3.500A) removed outlier: 5.113A pdb=" N GLY 1 518 " --> pdb=" O MET 1 505 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N CYS 1 514 " --> pdb=" O LEU 1 509 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain '3' and resid 81 through 89 removed outlier: 7.403A pdb=" N TYR 3 81 " --> pdb=" O ASN 3 72 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N LEU 3 68 " --> pdb=" O HIS 3 85 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N TYR 3 66 " --> pdb=" O PRO 3 87 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N SER 3 89 " --> pdb=" O THR 3 64 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N THR 3 64 " --> pdb=" O SER 3 89 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N ALA 3 16 " --> pdb=" O GLY 3 63 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLN 3 65 " --> pdb=" O ALA 3 16 " (cutoff:3.500A) removed outlier: 5.203A pdb=" N HIS 3 139 " --> pdb=" O VAL 3 15 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N ASP 3 17 " --> pdb=" O HIS 3 139 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N VAL 3 141 " --> pdb=" O ASP 3 17 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N CYS 3 142 " --> pdb=" O HIS 3 179 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N CYS 3 146 " --> pdb=" O VAL 3 183 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE 3 182 " --> pdb=" O LEU 3 222 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LEU 3 222 " --> pdb=" O ILE 3 182 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'A' and resid 20 through 23 removed outlier: 3.579A pdb=" N VAL A 21 " --> pdb=" O ASP A1449 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ASP A1449 " --> pdb=" O VAL A 21 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N GLU A1447 " --> pdb=" O PHE A 23 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'A' and resid 85 through 90 removed outlier: 7.245A pdb=" N THR A 251 " --> pdb=" O LEU A 90 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'A' and resid 199 through 203 removed outlier: 5.237A pdb=" N TRP A 202 " --> pdb=" O LYS A 212 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N LYS A 212 " --> pdb=" O TRP A 202 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'A' and resid 361 through 366 removed outlier: 6.021A pdb=" N PHE A 361 " --> pdb=" O LEU A 505 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N THR A 365 " --> pdb=" O MET A 501 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N ASP A 454 " --> pdb=" O VAL A 474 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N MET A 470 " --> pdb=" O PHE A 458 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N ASP A 376 " --> pdb=" O GLY A 471 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL A 380 " --> pdb=" O ARG A 475 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'A' and resid 390 through 394 removed outlier: 5.128A pdb=" N TYR A 444 " --> pdb=" O VAL A 394 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'A' and resid 602 through 605 No H-bonds generated for sheet with id= 20 Processing sheet with id= 21, first strand: chain 'A' and resid 1171 through 1178 removed outlier: 6.425A pdb=" N TRP A1210 " --> pdb=" O ILE A1261 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N ILE A1261 " --> pdb=" O TRP A1210 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N LEU A1216 " --> pdb=" O LEU A1255 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N LEU A1255 " --> pdb=" O LEU A1216 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ARG A1258 " --> pdb=" O ILE A1246 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ARG A1260 " --> pdb=" O ASN A1244 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N ASP A1242 " --> pdb=" O MET A1262 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'A' and resid 1309 through 1312 removed outlier: 4.298A pdb=" N MET A1309 " --> pdb=" O GLU A1337 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N LEU A1139 " --> pdb=" O THR A1338 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N SER A1138 " --> pdb=" O ASN A1360 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ASN A1360 " --> pdb=" O SER A1138 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'A' and resid 1318 through 1323 removed outlier: 4.797A pdb=" N LYS A1319 " --> pdb=" O LEU A1331 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N GLU A1327 " --> pdb=" O THR A1323 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'B' and resid 82 through 89 removed outlier: 4.372A pdb=" N ASP B 127 " --> pdb=" O GLU B 89 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N GLN B 90 " --> pdb=" O ASP B 127 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'B' and resid 96 through 100 removed outlier: 4.468A pdb=" N ALA B 104 " --> pdb=" O GLU B 100 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'B' and resid 191 through 195 removed outlier: 6.502A pdb=" N GLU B 191 " --> pdb=" O LEU B 470 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N VAL B 466 " --> pdb=" O ILE B 195 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'B' and resid 203 through 209 removed outlier: 4.867A pdb=" N THR B 204 " --> pdb=" O ARG B 222 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N ARG B 222 " --> pdb=" O THR B 204 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ILE B 235 " --> pdb=" O CYS B 221 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N SER B 233 " --> pdb=" O SER B 223 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N ARG B 255 " --> pdb=" O LEU B 240 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'B' and resid 530 through 533 Processing sheet with id= 29, first strand: chain 'B' and resid 601 through 606 Processing sheet with id= 30, first strand: chain 'B' and resid 746 through 752 removed outlier: 4.844A pdb=" N THR B 746 " --> pdb=" O SER B 813 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N TYR B 811 " --> pdb=" O ALA B 748 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N ARG B 807 " --> pdb=" O TYR B 752 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N LYS B 917 " --> pdb=" O GLU B 818 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLN B 906 " --> pdb=" O ARG B 922 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'B' and resid 758 through 761 Processing sheet with id= 32, first strand: chain 'B' and resid 775 through 783 No H-bonds generated for sheet with id= 32 Processing sheet with id= 33, first strand: chain 'B' and resid 826 through 830 removed outlier: 4.675A pdb=" N GLU B 826 " --> pdb=" O THR B 872 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N VAL B 828 " --> pdb=" O THR B 870 " (cutoff:3.500A) removed outlier: 5.207A pdb=" N GLY B 868 " --> pdb=" O GLU B 830 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ILE B 867 " --> pdb=" O THR B 894 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS B 869 " --> pdb=" O CYS B 892 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N VAL B 871 " --> pdb=" O ARG B 890 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N THR B 888 " --> pdb=" O LEU B 873 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'B' and resid 933 through 936 removed outlier: 4.857A pdb=" N ASP B 933 " --> pdb=" O CYS B 945 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'B' and resid 1114 through 1120 removed outlier: 3.597A pdb=" N TYR B1114 " --> pdb=" O MET B1151 " (cutoff:3.500A) removed outlier: 8.515A pdb=" N GLN B1145 " --> pdb=" O ASN B1120 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'B' and resid 1127 through 1130 removed outlier: 3.876A pdb=" N GLU B1136 " --> pdb=" O ALA B1128 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N THR B1130 " --> pdb=" O THR B1134 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N THR B1134 " --> pdb=" O THR B1130 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'B' and resid 127 through 133 removed outlier: 6.827A pdb=" N ILE B 128 " --> pdb=" O HIS B 144 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LYS B 130 " --> pdb=" O THR B 142 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N THR B 142 " --> pdb=" O LYS B 130 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'B' and resid 120 through 125 No H-bonds generated for sheet with id= 38 Processing sheet with id= 39, first strand: chain 'C' and resid 8 through 12 removed outlier: 6.137A pdb=" N LYS C 20 " --> pdb=" O THR C 12 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL C 19 " --> pdb=" O VAL C 233 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N PHE C 21 " --> pdb=" O TYR C 231 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLU C 234 " --> pdb=" O GLY C 181 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N GLY C 181 " --> pdb=" O GLU C 234 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'C' and resid 48 through 53 removed outlier: 6.325A pdb=" N ARG C 160 " --> pdb=" O ASP C 53 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N GLU C 158 " --> pdb=" O SER C 56 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'C' and resid 98 through 106 Processing sheet with id= 42, first strand: chain 'E' and resid 59 through 63 removed outlier: 3.923A pdb=" N VAL E 60 " --> pdb=" O VAL E 74 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N ARG E 101 " --> pdb=" O GLN E 71 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'E' and resid 146 through 151 removed outlier: 5.123A pdb=" N VAL E 190 " --> pdb=" O MET E 151 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N GLN E 189 " --> pdb=" O VAL E 209 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ARG E 195 " --> pdb=" O TYR E 203 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'F' and resid 105 through 111 removed outlier: 6.531A pdb=" N ILE F 106 " --> pdb=" O ASP F 117 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ASP F 117 " --> pdb=" O ILE F 106 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ARG F 108 " --> pdb=" O TYR F 115 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N TYR F 115 " --> pdb=" O ARG F 108 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N LEU F 110 " --> pdb=" O GLY F 113 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'G' and resid 6 through 13 removed outlier: 3.568A pdb=" N TYR G 72 " --> pdb=" O LEU G 7 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'G' and resid 36 through 39 removed outlier: 3.840A pdb=" N THR G 37 " --> pdb=" O VAL G 45 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'G' and resid 96 through 100 removed outlier: 6.256A pdb=" N LEU G 97 " --> pdb=" O ILE G 108 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N SER G 105 " --> pdb=" O ILE G 157 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N PHE G 107 " --> pdb=" O ALA G 159 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N SER G 109 " --> pdb=" O GLY G 161 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N GLY G 149 " --> pdb=" O ILE G 160 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'H' and resid 6 through 11 removed outlier: 3.629A pdb=" N LYS H 146 " --> pdb=" O ARG H 57 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'H' and resid 26 through 32 removed outlier: 3.809A pdb=" N SER H 32 " --> pdb=" O MET H 37 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N MET H 37 " --> pdb=" O SER H 32 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE H 40 " --> pdb=" O ARG H 124 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ARG H 124 " --> pdb=" O ILE H 40 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N LEU H 122 " --> pdb=" O ASP H 42 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'I' and resid 26 through 30 removed outlier: 3.568A pdb=" N ASP I 29 " --> pdb=" O ILE I 34 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ILE I 34 " --> pdb=" O ASP I 29 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'I' and resid 79 through 82 removed outlier: 5.488A pdb=" N HIS I 121 " --> pdb=" O CYS I 114 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'K' and resid 18 through 23 removed outlier: 5.808A pdb=" N LYS K 18 " --> pdb=" O ASN K 36 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N ASN K 29 " --> pdb=" O THR K 77 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'L' and resid 16 through 19 removed outlier: 6.011A pdb=" N TYR L 17 " --> pdb=" O ASN L 26 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N THR L 24 " --> pdb=" O CYS L 19 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'M' and resid 335 through 338 removed outlier: 3.670A pdb=" N ILE M 357 " --> pdb=" O VAL M 336 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N GLN M 338 " --> pdb=" O ASP M 355 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N ASP M 355 " --> pdb=" O GLN M 338 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'M' and resid 341 through 345 removed outlier: 4.036A pdb=" N LYS M 341 " --> pdb=" O HIS M 352 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N LYS M 348 " --> pdb=" O SER M 345 " (cutoff:3.500A) removed outlier: 8.237A pdb=" N ASN M 347 " --> pdb=" O TRP M 376 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N PHE M 351 " --> pdb=" O GLY M 372 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N GLY M 372 " --> pdb=" O PHE M 351 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA M 370 " --> pdb=" O LEU M 353 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'N' and resid 56 through 60 No H-bonds generated for sheet with id= 56 Processing sheet with id= 57, first strand: chain 'N' and resid 64 through 67 removed outlier: 3.758A pdb=" N THR N 64 " --> pdb=" O VAL N 75 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'O' and resid 23 through 27 removed outlier: 4.297A pdb=" N ASP O 31 " --> pdb=" O ASP O 26 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'P' and resid 163 through 166 removed outlier: 6.666A pdb=" N VAL P 259 " --> pdb=" O GLN P 166 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N CYS P 262 " --> pdb=" O VAL P 310 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N VAL P 310 " --> pdb=" O CYS P 262 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N LYS P 309 " --> pdb=" O PHE P 305 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N PHE P 280 " --> pdb=" O ARG P 294 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'P' and resid 169 through 173 removed outlier: 4.747A pdb=" N LYS P 218 " --> pdb=" O PHE P 214 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N PHE P 214 " --> pdb=" O LYS P 218 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'Q' and resid 126 through 130 No H-bonds generated for sheet with id= 61 Processing sheet with id= 62, first strand: chain 'S' and resid 45 through 49 removed outlier: 4.949A pdb=" N VAL S 102 " --> pdb=" O ARG S 108 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N ARG S 108 " --> pdb=" O VAL S 102 " (cutoff:3.500A) removed outlier: 5.667A pdb=" N TRP S 143 " --> pdb=" O LYS S 115 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'S' and resid 125 through 128 removed outlier: 4.305A pdb=" N GLU S 136 " --> pdb=" O THR S 128 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'T' and resid 19 through 23 removed outlier: 4.458A pdb=" N VAL T 84 " --> pdb=" O GLU T 115 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'T' and resid 222 through 225 removed outlier: 3.583A pdb=" N THR T 232 " --> pdb=" O ASN T 224 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'W' and resid 75 through 78 removed outlier: 5.713A pdb=" N GLY W 82 " --> pdb=" O LEU W 118 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'W' and resid 166 through 170 removed outlier: 4.498A pdb=" N TYR W 175 " --> pdb=" O VAL W 272 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'W' and resid 388 through 392 removed outlier: 4.652A pdb=" N VAL W 405 " --> pdb=" O GLN W 388 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N CYS W 390 " --> pdb=" O VAL W 405 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N CYS W 361 " --> pdb=" O SER W 404 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLY W 365 " --> pdb=" O SER W 408 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N LEU W 437 " --> pdb=" O ARG W 360 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N CYS W 462 " --> pdb=" O GLY W 436 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N TYR W 489 " --> pdb=" O VAL W 337 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain 'W' and resid 578 through 581 removed outlier: 4.444A pdb=" N SER W 686 " --> pdb=" O VAL W 505 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LYS W 688 " --> pdb=" O CYS W 507 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain 'X' and resid 1 through 4 Processing sheet with id= 71, first strand: chain 'X' and resid 38 through 41 Processing sheet with id= 72, first strand: chain 'X' and resid 172 through 175 removed outlier: 3.897A pdb=" N VAL X 204 " --> pdb=" O LEU X 105 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU X 109 " --> pdb=" O VAL X 206 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N VAL X 231 " --> pdb=" O SER X 453 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N THR X 457 " --> pdb=" O PHE X 233 " (cutoff:3.500A) Processing sheet with id= 73, first strand: chain 'X' and resid 348 through 352 removed outlier: 7.350A pdb=" N HIS X 348 " --> pdb=" O PRO X 420 " (cutoff:3.500A) Processing sheet with id= 74, first strand: chain 'X' and resid 489 through 496 removed outlier: 3.533A pdb=" N GLY X 675 " --> pdb=" O CYS X 489 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N CYS X 491 " --> pdb=" O GLY X 675 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N MET X 493 " --> pdb=" O MET X 677 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ASP X 681 " --> pdb=" O ILE X 495 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N ARG X 616 " --> pdb=" O TYR X 674 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N ALA X 617 " --> pdb=" O GLY X 534 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL X 536 " --> pdb=" O ALA X 617 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N ALA X 594 " --> pdb=" O ASP X 533 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU X 597 " --> pdb=" O PHE X 568 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N VAL X 599 " --> pdb=" O GLU X 570 " (cutoff:3.500A) Processing sheet with id= 75, first strand: chain 'Z' and resid 96 through 100 Processing sheet with id= 76, first strand: chain 'Z' and resid 306 through 310 removed outlier: 7.154A pdb=" N PHE Z 306 " --> pdb=" O TYR Z 318 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N TYR Z 313 " --> pdb=" O VAL Z 346 " (cutoff:3.500A) Processing sheet with id= 77, first strand: chain 'a' and resid 102 through 109 removed outlier: 3.586A pdb=" N GLN a 103 " --> pdb=" O ARG a 59 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N HIS a 60 " --> pdb=" O SER a 164 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N SER a 172 " --> pdb=" O ASP a 66 " (cutoff:3.500A) Processing sheet with id= 78, first strand: chain 'a' and resid 255 through 259 removed outlier: 6.116A pdb=" N GLN a 256 " --> pdb=" O PHE a 290 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N PHE a 290 " --> pdb=" O GLN a 256 " (cutoff:3.500A) Processing sheet with id= 79, first strand: chain 'a' and resid 331 through 335 Processing sheet with id= 80, first strand: chain 'b' and resid 54 through 62 removed outlier: 4.555A pdb=" N ASN b 9 " --> pdb=" O SER b 54 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU b 11 " --> pdb=" O LYS b 56 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LYS b 158 " --> pdb=" O LEU b 8 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N ALA b 166 " --> pdb=" O ASP b 16 " (cutoff:3.500A) Processing sheet with id= 81, first strand: chain 'b' and resid 265 through 269 removed outlier: 4.265A pdb=" N SER b 273 " --> pdb=" O CYS b 268 " (cutoff:3.500A) Processing sheet with id= 82, first strand: chain 'c' and resid 8 through 11 Processing sheet with id= 83, first strand: chain 'd' and resid 20 through 23 Processing sheet with id= 84, first strand: chain 'e' and resid 24 through 29 removed outlier: 4.441A pdb=" N ILE e 87 " --> pdb=" O ILE e 43 " (cutoff:3.500A) Processing sheet with id= 85, first strand: chain 'g' and resid 65 through 70 removed outlier: 3.518A pdb=" N ILE g 69 " --> pdb=" O ARG g 82 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N HIS g 72 " --> pdb=" O ILE g 80 " (cutoff:3.500A) Processing sheet with id= 86, first strand: chain 'g' and resid 104 through 108 removed outlier: 4.183A pdb=" N ALA g 108 " --> pdb=" O ASP g 97 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ASP g 97 " --> pdb=" O ALA g 108 " (cutoff:3.500A) Processing sheet with id= 87, first strand: chain 'g' and resid 78 through 83 removed outlier: 3.663A pdb=" N ALA g 96 " --> pdb=" O LYS g 83 " (cutoff:3.500A) Processing sheet with id= 88, first strand: chain 'j' and resid 222 through 225 Processing sheet with id= 89, first strand: chain 'j' and resid 253 through 262 removed outlier: 5.129A pdb=" N SER j 254 " --> pdb=" O SER j 348 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N SER j 348 " --> pdb=" O SER j 254 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N TYR j 256 " --> pdb=" O CYS j 346 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N CYS j 346 " --> pdb=" O TYR j 256 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N GLN j 340 " --> pdb=" O GLN j 262 " (cutoff:3.500A) Processing sheet with id= 90, first strand: chain 'j' and resid 458 through 465 removed outlier: 6.885A pdb=" N SER j 474 " --> pdb=" O SER j 465 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ARG j 510 " --> pdb=" O HIS j 506 " (cutoff:3.500A) Processing sheet with id= 91, first strand: chain 'j' and resid 546 through 549 removed outlier: 4.254A pdb=" N VAL j 571 " --> pdb=" O LEU j 549 " (cutoff:3.500A) Processing sheet with id= 92, first strand: chain 'j' and resid 578 through 584 removed outlier: 4.128A pdb=" N ALA j 579 " --> pdb=" O GLN j 595 " (cutoff:3.500A) removed outlier: 5.203A pdb=" N ILE j 592 " --> pdb=" O VAL j 625 " (cutoff:3.500A) Processing sheet with id= 93, first strand: chain 'k' and resid 123 through 126 removed outlier: 3.813A pdb=" N ARG k 124 " --> pdb=" O LEU k 59 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N VAL k 57 " --> pdb=" O ASP k 126 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N LEU k 52 " --> pdb=" O MET k 76 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N PHE k 68 " --> pdb=" O LEU k 60 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N VAL k 69 " --> pdb=" O LEU k 88 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N LEU k 88 " --> pdb=" O VAL k 69 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N SER k 75 " --> pdb=" O PRO k 82 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N ASN k 104 " --> pdb=" O GLY k 89 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N MET k 18 " --> pdb=" O CYS k 105 " (cutoff:3.500A) removed outlier: 8.239A pdb=" N SER k 166 " --> pdb=" O ILE k 148 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N ILE k 148 " --> pdb=" O SER k 166 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU k 168 " --> pdb=" O TYR k 146 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LYS k 132 " --> pdb=" O LYS k 147 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL k 130 " --> pdb=" O PHE k 149 " (cutoff:3.500A) Processing sheet with id= 94, first strand: chain 'k' and resid 50 through 57 removed outlier: 3.787A pdb=" N ALA k 131 " --> pdb=" O ASP k 53 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N HIS k 127 " --> pdb=" O VAL k 57 " (cutoff:3.500A) Processing sheet with id= 95, first strand: chain 'l' and resid 3 through 9 removed outlier: 3.993A pdb=" N VAL l 3 " --> pdb=" O TYR l 144 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N TYR l 144 " --> pdb=" O VAL l 3 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ILE l 138 " --> pdb=" O MET l 9 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N GLY l 137 " --> pdb=" O VAL l 129 " (cutoff:3.500A) Processing sheet with id= 96, first strand: chain 'l' and resid 40 through 47 removed outlier: 6.682A pdb=" N CYS l 40 " --> pdb=" O SER l 69 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N ASN l 68 " --> pdb=" O SER l 74 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N SER l 74 " --> pdb=" O ASN l 68 " (cutoff:3.500A) Processing sheet with id= 97, first strand: chain 'n' and resid 176 through 182 removed outlier: 3.884A pdb=" N THR n 193 " --> pdb=" O SER n 177 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LEU n 191 " --> pdb=" O HIS n 179 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N ALA n 188 " --> pdb=" O MET n 204 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N MET n 204 " --> pdb=" O ALA n 188 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N VAL n 202 " --> pdb=" O LEU n 190 " (cutoff:3.500A) Processing sheet with id= 98, first strand: chain 'r' and resid 229 through 232 removed outlier: 4.688A pdb=" N GLU r 229 " --> pdb=" O LEU r 253 " (cutoff:3.500A) Processing sheet with id= 99, first strand: chain 'r' and resid 323 through 329 removed outlier: 8.346A pdb=" N LEU r 323 " --> pdb=" O TRP r 340 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LEU r 335 " --> pdb=" O ILE r 359 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N THR r 358 " --> pdb=" O PHE r 373 " (cutoff:3.500A) Processing sheet with id=100, first strand: chain 'r' and resid 428 through 431 removed outlier: 4.193A pdb=" N LEU r 438 " --> pdb=" O ILE r 454 " (cutoff:3.500A) Processing sheet with id=101, first strand: chain 'r' and resid 514 through 518 removed outlier: 3.605A pdb=" N LYS r 541 " --> pdb=" O ILE r 515 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ASN r 536 " --> pdb=" O MET r 554 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N LEU r 538 " --> pdb=" O VAL r 552 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LEU r 542 " --> pdb=" O TYR r 548 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N TYR r 548 " --> pdb=" O LEU r 542 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N GLN r 547 " --> pdb=" O VAL r 573 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N LYS r 567 " --> pdb=" O GLU r 553 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N TYR r 568 " --> pdb=" O ARG r 614 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N ARG r 614 " --> pdb=" O TYR r 568 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N PHE r 570 " --> pdb=" O ALA r 612 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ALA r 612 " --> pdb=" O PHE r 570 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N SER r 572 " --> pdb=" O THR r 610 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N ASN r 574 " --> pdb=" O THR r 608 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N THR r 608 " --> pdb=" O ASN r 574 " (cutoff:3.500A) Processing sheet with id=102, first strand: chain 'r' and resid 671 through 674 removed outlier: 3.978A pdb=" N GLN r 672 " --> pdb=" O ALA r 681 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N SER r 679 " --> pdb=" O GLU r 674 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N HIS r 680 " --> pdb=" O LEU r 712 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N LEU r 712 " --> pdb=" O HIS r 680 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N CYS r 708 " --> pdb=" O LEU r 684 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ASP r 707 " --> pdb=" O VAL r 725 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N THR r 719 " --> pdb=" O GLN r 713 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N PHE r 726 " --> pdb=" O ARG r 743 " (cutoff:3.500A) Processing sheet with id=103, first strand: chain 'r' and resid 807 through 812 removed outlier: 5.407A pdb=" N SER r 818 " --> pdb=" O TYR r 812 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N GLY r 817 " --> pdb=" O VAL r 838 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLN r 823 " --> pdb=" O HIS r 832 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LYS r 830 " --> pdb=" O ASN r 825 " (cutoff:3.500A) Processing sheet with id=104, first strand: chain 'r' and resid 904 through 909 removed outlier: 4.204A pdb=" N HIS r 913 " --> pdb=" O GLN r 909 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N THR r 912 " --> pdb=" O CYS r 928 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N TYR r 922 " --> pdb=" O PHE r 918 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ARG r 929 " --> pdb=" O VAL r 933 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N VAL r 933 " --> pdb=" O ARG r 929 " (cutoff:3.500A) Processing sheet with id=105, first strand: chain 'r' and resid 1247 through 1253 removed outlier: 4.498A pdb=" N LYS r1248 " --> pdb=" O THR r1266 " (cutoff:3.500A) Processing sheet with id=106, first strand: chain 'r' and resid 1362 through 1369 removed outlier: 4.470A pdb=" N MET r1363 " --> pdb=" O ILE r1388 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N PHE r1365 " --> pdb=" O PRO r1386 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU r1367 " --> pdb=" O ILE r1384 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N LEU r1369 " --> pdb=" O SER r1382 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N SER r1382 " --> pdb=" O LEU r1369 " (cutoff:3.500A) Processing sheet with id=107, first strand: chain 'z' and resid 689 through 694 removed outlier: 3.944A pdb=" N LEU z 690 " --> pdb=" O LYS z 709 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ASN z 692 " --> pdb=" O ILE z 707 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASP z 694 " --> pdb=" O HIS z 705 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N HIS z 705 " --> pdb=" O ASP z 694 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N VAL z 704 " --> pdb=" O VAL z 725 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VAL z 725 " --> pdb=" O VAL z 704 " (cutoff:3.500A) 6170 hydrogen bonds defined for protein. 18369 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: 64.71 Time building geometry restraints manager: 44.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.38: 48626 1.38 - 1.60: 82060 1.60 - 1.83: 1343 1.83 - 2.05: 2 2.05 - 2.28: 12 Bond restraints: 132043 Sorted by residual: bond pdb=" CA PRO z 719 " pdb=" C PRO z 719 " ideal model delta sigma weight residual 1.517 1.416 0.101 6.70e-03 2.23e+04 2.29e+02 bond pdb=" C TRP r 245 " pdb=" N ARG r 246 " ideal model delta sigma weight residual 1.329 1.533 -0.203 1.43e-02 4.89e+03 2.02e+02 bond pdb=" CA LEU j 440 " pdb=" C LEU j 440 " ideal model delta sigma weight residual 1.524 1.390 0.134 1.27e-02 6.20e+03 1.11e+02 bond pdb=" CA LEU z 721 " pdb=" C LEU z 721 " ideal model delta sigma weight residual 1.521 1.415 0.106 1.17e-02 7.31e+03 8.26e+01 bond pdb=" CA ILE j 497 " pdb=" C ILE j 497 " ideal model delta sigma weight residual 1.524 1.429 0.095 1.16e-02 7.43e+03 6.75e+01 ... (remaining 132038 not shown) Histogram of bond angle deviations from ideal: 73.20 - 88.36: 12 88.36 - 103.52: 2097 103.52 - 118.68: 105961 118.68 - 133.84: 70876 133.84 - 149.00: 141 Bond angle restraints: 179087 Sorted by residual: angle pdb=" C LEU z 715 " pdb=" N PRO z 716 " pdb=" CA PRO z 716 " ideal model delta sigma weight residual 119.84 149.00 -29.16 1.25e+00 6.40e-01 5.44e+02 angle pdb=" C SER A1623 " pdb=" N PRO A1624 " pdb=" CA PRO A1624 " ideal model delta sigma weight residual 119.85 139.04 -19.19 1.01e+00 9.80e-01 3.61e+02 angle pdb=" C TRP r 245 " pdb=" N ARG r 246 " pdb=" CA ARG r 246 " ideal model delta sigma weight residual 122.65 102.58 20.07 1.49e+00 4.50e-01 1.81e+02 angle pdb=" N TRP j 194 " pdb=" CA TRP j 194 " pdb=" C TRP j 194 " ideal model delta sigma weight residual 109.11 127.58 -18.47 1.42e+00 4.96e-01 1.69e+02 angle pdb=" C VAL r 243 " pdb=" N PRO r 244 " pdb=" CA PRO r 244 " ideal model delta sigma weight residual 120.03 132.43 -12.40 9.90e-01 1.02e+00 1.57e+02 ... (remaining 179082 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 70540 17.99 - 35.99: 7323 35.99 - 53.98: 1840 53.98 - 71.97: 352 71.97 - 89.97: 147 Dihedral angle restraints: 80202 sinusoidal: 33718 harmonic: 46484 Sorted by residual: dihedral pdb=" CA ARG r 148 " pdb=" C ARG r 148 " pdb=" N LEU r 149 " pdb=" CA LEU r 149 " ideal model delta harmonic sigma weight residual -180.00 -121.73 -58.27 0 5.00e+00 4.00e-02 1.36e+02 dihedral pdb=" CA LYS I 57 " pdb=" C LYS I 57 " pdb=" N ILE I 58 " pdb=" CA ILE I 58 " ideal model delta harmonic sigma weight residual 180.00 123.48 56.52 0 5.00e+00 4.00e-02 1.28e+02 dihedral pdb=" CA LEU X 102 " pdb=" C LEU X 102 " pdb=" N PRO X 103 " pdb=" CA PRO X 103 " ideal model delta harmonic sigma weight residual -180.00 -123.72 -56.28 0 5.00e+00 4.00e-02 1.27e+02 ... (remaining 80199 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.145: 19903 0.145 - 0.290: 320 0.290 - 0.435: 33 0.435 - 0.579: 16 0.579 - 0.724: 3 Chirality restraints: 20275 Sorted by residual: chirality pdb=" CA SER r 798 " pdb=" N SER r 798 " pdb=" C SER r 798 " pdb=" CB SER r 798 " both_signs ideal model delta sigma weight residual False 2.51 1.79 0.72 2.00e-01 2.50e+01 1.31e+01 chirality pdb=" CA THR 0 48 " pdb=" N THR 0 48 " pdb=" C THR 0 48 " pdb=" CB THR 0 48 " both_signs ideal model delta sigma weight residual False 2.53 1.85 0.68 2.00e-01 2.50e+01 1.15e+01 chirality pdb=" CA SER j 35 " pdb=" N SER j 35 " pdb=" C SER j 35 " pdb=" CB SER j 35 " both_signs ideal model delta sigma weight residual False 2.51 1.92 0.59 2.00e-01 2.50e+01 8.57e+00 ... (remaining 20272 not shown) Planarity restraints: 22522 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN x 7 " 0.043 2.00e-02 2.50e+03 8.10e-02 6.57e+01 pdb=" C GLN x 7 " -0.140 2.00e-02 2.50e+03 pdb=" O GLN x 7 " 0.051 2.00e-02 2.50e+03 pdb=" N LEU x 8 " 0.046 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR 3 46 " 0.037 2.00e-02 2.50e+03 7.36e-02 5.42e+01 pdb=" C TYR 3 46 " -0.127 2.00e-02 2.50e+03 pdb=" O TYR 3 46 " 0.048 2.00e-02 2.50e+03 pdb=" N PHE 3 47 " 0.043 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE Y 479 " -0.124 5.00e-02 4.00e+02 1.72e-01 4.76e+01 pdb=" N PRO Y 480 " 0.297 5.00e-02 4.00e+02 pdb=" CA PRO Y 480 " -0.099 5.00e-02 4.00e+02 pdb=" CD PRO Y 480 " -0.074 5.00e-02 4.00e+02 ... (remaining 22519 not shown) Histogram of nonbonded interaction distances: 1.02 - 1.79: 160 1.79 - 2.57: 2393 2.57 - 3.35: 174928 3.35 - 4.12: 315999 4.12 - 4.90: 564627 Nonbonded interactions: 1058107 Sorted by model distance: nonbonded pdb=" OE1 GLN W 274 " pdb=" CD GLN W 459 " model vdw 1.016 3.270 nonbonded pdb=" C SER j 388 " pdb=" CE MET k 46 " model vdw 1.019 3.690 nonbonded pdb=" O GLU r 231 " pdb=" CD2 LEU r 250 " model vdw 1.027 3.460 nonbonded pdb=" CB PRO W 110 " pdb=" ND2 ASN Z 312 " model vdw 1.043 3.520 nonbonded pdb=" NZ LYS m 115 " pdb=" N LEU o 143 " model vdw 1.073 3.200 ... (remaining 1058102 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.42 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.110 Extract box with map and model: 23.070 Check model and map are aligned: 1.420 Set scattering table: 0.860 Process input model: 336.360 Find NCS groups from input model: 4.630 Set up NCS constraints: 0.440 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 373.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4734 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 : 0.009 0.203 132043 Z= 0.594 Angle : 1.082 29.157 179087 Z= 0.633 Chirality : 0.058 0.724 20275 Planarity : 0.007 0.172 22522 Dihedral : 16.062 89.968 49947 Min Nonbonded Distance : 1.016 Molprobity Statistics. All-atom Clashscore : 31.82 Ramachandran Plot: Outliers : 0.68 % Allowed : 11.32 % Favored : 88.00 % Rotamer Outliers : 1.26 % Cbeta Deviations : 0.15 % Peptide Plane: Cis-proline : 0.84 % Cis-general : 0.05 % Twisted Proline : 1.96 % Twisted General : 0.47 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.89 (0.06), residues: 15623 helix: -1.84 (0.05), residues: 7265 sheet: -2.53 (0.12), residues: 1648 loop : -3.41 (0.06), residues: 6710 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 31246 Ramachandran restraints generated. 15623 Oldfield, 0 Emsley, 15623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 31246 Ramachandran restraints generated. 15623 Oldfield, 0 Emsley, 15623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 4544 residues out of total 14130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 177 poor density : 4367 time to evaluate : 10.198 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET b 157 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 177 outliers final: 60 residues processed: 4491 average time/residue: 1.1470 time to fit residues: 8934.4046 Evaluate side-chains 3741 residues out of total 14130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 3681 time to evaluate : 10.739 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET b 157 " (corrupted residue). Skipping it. revert: symmetry clash outliers start: 60 outliers final: 4 residues processed: 60 average time/residue: 1.0898 time to fit residues: 131.2545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1577 random chunks: chunk 1331 optimal weight: 3.9990 chunk 1195 optimal weight: 9.9990 chunk 663 optimal weight: 3.9990 chunk 408 optimal weight: 0.7980 chunk 806 optimal weight: 20.0000 chunk 638 optimal weight: 0.9980 chunk 1236 optimal weight: 0.9990 chunk 478 optimal weight: 5.9990 chunk 751 optimal weight: 9.9990 chunk 919 optimal weight: 9.9990 chunk 1432 optimal weight: 2.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 508 HIS 0 514 GLN ** 0 567 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 598 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 612 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 619 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 643 HIS ** 0 683 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 743 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 821 GLN 1 46 GLN 1 113 GLN ** 1 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 303 GLN 1 332 GLN ** 1 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 415 ASN 1 433 ASN 1 460 GLN ** 1 526 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 541 HIS ** 1 662 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 759 ASN 1 805 GLN 1 898 ASN 1 907 ASN ** 11103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 11198 GLN 11250 HIS 11300 HIS 2 217 GLN ** 2 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 266 GLN ** 2 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 353 GLN 2 406 ASN 2 408 GLN ** 2 530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 541 ASN 2 645 GLN 2 699 ASN 2 799 HIS ** 2 945 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 48 ASN 3 72 ASN ** 3 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 171 GLN ** 3 179 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 62 GLN A 122 ASN A 330 GLN A 372 ASN A 387 ASN ** A 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 461 GLN ** A 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 502 ASN A 504 HIS A 531 ASN A 539 GLN A 576 GLN A 606 HIS ** A 620 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 654 HIS ** A 677 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 685 HIS ** A 757 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 783 GLN ** A 791 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 792 ASN A 825 ASN ** A 861 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 989 ASN A 997 ASN A1044 HIS A1230 GLN A1384 HIS A1422 GLN A1445 HIS ** A1457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 98 HIS B 117 ASN B 139 GLN ** B 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 245 GLN B 314 GLN B 315 ASN ** B 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 481 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 503 ASN B 518 HIS B 654 GLN ** B 718 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 825 GLN B 876 ASN B 913 GLN ** B 941 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1013 ASN B1053 HIS B1117 HIS B1133 HIS C 32 ASN C 217 GLN C 260 GLN C 265 HIS D 93 HIS E 148 HIS F 46 GLN G 14 HIS ** G 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 93 ASN ** G 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 29 HIS ** H 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 41 ASN I 60 HIS ** I 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 2 ASN K 89 ASN ** M 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 8 ASN N 50 GLN ** O 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 315 GLN P 164 GLN P 173 ASN ** P 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 90 GLN R 117 GLN R 158 HIS ** S 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 112 HIS W 187 HIS ** W 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 545 GLN W 683 GLN ** X 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 250 ASN ** X 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 384 HIS X 452 GLN X 555 GLN X 564 ASN X 659 HIS X 729 HIS Y 384 HIS Y 442 GLN Y 520 ASN Y 524 HIS ** Z 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 64 GLN ** Z 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 117 ASN Z 161 HIS Z 181 GLN ** Z 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 424 HIS a 235 HIS ** a 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 340 ASN ** a 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 46 ASN ** b 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 28 HIS ** d 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 130 GLN e 258 HIS e 288 GLN f 18 GLN ** g 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 91 GLN g 116 ASN h 35 ASN h 139 GLN h 179 ASN ** i 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 58 HIS j 38 GLN j 227 ASN ** j 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 299 GLN j 329 ASN ** j 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 492 GLN j 517 GLN j 528 GLN ** j 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 547 GLN j 565 ASN ** k 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 19 GLN l 90 ASN ** m 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 58 ASN ** m 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 84 GLN m 102 ASN ** m 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 59 ASN n 109 GLN n 220 ASN n 245 HIS n 252 HIS ** o 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 109 GLN p 84 GLN p 92 GLN p 124 HIS q 53 GLN q 84 GLN q 171 ASN ** r 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 276 GLN r 304 GLN ** r 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 410 HIS r 411 GLN ** r 453 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 495 GLN ** r 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 532 ASN ** r 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 607 GLN r 638 ASN r 698 GLN r 717 ASN r 751 ASN r 828 HIS r 832 HIS ** r 849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 856 GLN r 898 ASN r 902 GLN r 920 ASN r1426 ASN s 109 GLN s 127 GLN ** t 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 129 ASN ** v 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 94 GLN x 9 GLN ** x 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 100 GLN ** y 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** y 127 ASN z 628 ASN z 636 HIS z 705 HIS ** z 732 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 753 HIS Total number of N/Q/H flips: 182 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4965 moved from start: 0.3246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.104 132043 Z= 0.305 Angle : 0.862 16.745 179087 Z= 0.446 Chirality : 0.049 0.375 20275 Planarity : 0.007 0.125 22522 Dihedral : 10.945 88.806 18410 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 22.56 Ramachandran Plot: Outliers : 0.28 % Allowed : 9.41 % Favored : 90.31 % Rotamer Outliers : 0.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.84 % Cis-general : 0.05 % Twisted Proline : 1.68 % Twisted General : 0.30 % 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: -2.59 (0.06), residues: 15623 helix: -0.58 (0.06), residues: 7413 sheet: -2.06 (0.12), residues: 1759 loop : -2.99 (0.07), residues: 6451 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 31246 Ramachandran restraints generated. 15623 Oldfield, 0 Emsley, 15623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 31246 Ramachandran restraints generated. 15623 Oldfield, 0 Emsley, 15623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 4043 residues out of total 14130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 3993 time to evaluate : 10.965 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET b 157 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 50 outliers final: 18 residues processed: 4028 average time/residue: 1.1521 time to fit residues: 7992.7848 Evaluate side-chains 3588 residues out of total 14130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 3570 time to evaluate : 10.805 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "MET b 157 " (corrupted residue). Skipping it. outliers start: 18 outliers final: 1 residues processed: 18 average time/residue: 0.9054 time to fit residues: 46.6043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1577 random chunks: chunk 795 optimal weight: 0.9980 chunk 444 optimal weight: 6.9990 chunk 1191 optimal weight: 6.9990 chunk 975 optimal weight: 30.0000 chunk 395 optimal weight: 0.7980 chunk 1434 optimal weight: 5.9990 chunk 1549 optimal weight: 5.9990 chunk 1277 optimal weight: 0.9980 chunk 1422 optimal weight: 6.9990 chunk 489 optimal weight: 0.6980 chunk 1150 optimal weight: 3.9990 overall best weight: 1.4982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 514 GLN 0 567 HIS ** 0 598 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 612 GLN ** 0 619 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 743 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 68 HIS ** 1 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 351 HIS ** 1 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 526 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 628 HIS ** 1 662 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 746 ASN 2 22 GLN 2 194 HIS ** 2 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 603 GLN 2 645 GLN 2 680 GLN 2 737 HIS ** 2 747 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 171 GLN ** 3 179 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 372 ASN ** A 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 432 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 620 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 677 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 704 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 757 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 765 ASN ** A 791 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 804 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 861 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1032 GLN B 145 GLN ** B 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 481 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 503 ASN ** B 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 912 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1049 GLN ** C 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 19 GLN G 4 HIS ** G 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 76 ASN ** H 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 48 ASN N 8 ASN O 271 GLN ** S 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 30 GLN T 131 GLN ** T 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 159 HIS W 415 HIS ** W 459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 498 ASN ** X 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 659 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 726 GLN ** Z 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 312 ASN ** Z 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 257 HIS ** a 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 187 GLN b 248 HIS ** d 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 288 GLN ** g 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 528 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 539 GLN ** k 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 47 GLN ** m 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 55 HIS n 130 GLN o 66 ASN ** o 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 141 GLN ** o 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 81 ASN p 115 GLN p 175 HIS q 171 ASN ** r 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 453 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** r 494 GLN ** r 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 507 GLN ** r 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 607 GLN ** r 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 828 HIS ** r 832 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** s 109 GLN ** t 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 116 GLN ** z 635 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** z 700 ASN ** z 732 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 742 GLN z 753 HIS ** z 778 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 56 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4987 moved from start: 0.4106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.088 132043 Z= 0.265 Angle : 0.801 19.892 179087 Z= 0.411 Chirality : 0.047 0.380 20275 Planarity : 0.006 0.146 22522 Dihedral : 10.756 85.599 18410 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 21.51 Ramachandran Plot: Outliers : 0.24 % Allowed : 9.26 % Favored : 90.49 % Rotamer Outliers : 0.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.84 % Cis-general : 0.05 % Twisted Proline : 1.40 % Twisted General : 0.24 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.99 (0.06), residues: 15623 helix: -0.03 (0.06), residues: 7466 sheet: -1.80 (0.12), residues: 1755 loop : -2.76 (0.07), residues: 6402 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 31246 Ramachandran restraints generated. 15623 Oldfield, 0 Emsley, 15623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 31246 Ramachandran restraints generated. 15623 Oldfield, 0 Emsley, 15623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 3885 residues out of total 14130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 3859 time to evaluate : 10.830 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET b 157 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 8 residues processed: 3874 average time/residue: 1.1484 time to fit residues: 7641.5352 Evaluate side-chains 3531 residues out of total 14130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 3523 time to evaluate : 10.737 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "MET b 157 " (corrupted residue). Skipping it. outliers start: 8 outliers final: 2 residues processed: 8 average time/residue: 0.8717 time to fit residues: 29.0108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1577 random chunks: chunk 1417 optimal weight: 4.9990 chunk 1078 optimal weight: 40.0000 chunk 744 optimal weight: 0.9980 chunk 158 optimal weight: 8.9990 chunk 684 optimal weight: 6.9990 chunk 963 optimal weight: 20.0000 chunk 1439 optimal weight: 7.9990 chunk 1524 optimal weight: 0.9980 chunk 752 optimal weight: 20.0000 chunk 1364 optimal weight: 3.9990 chunk 410 optimal weight: 0.7980 overall best weight: 2.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 104 GLN 0 473 HIS ** 0 619 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 723 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 743 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 292 GLN ** 1 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 526 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 639 ASN ** 11124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 11320 ASN ** 2 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 261 GLN ** 2 530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 680 GLN ** 2 730 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 747 ASN ** 3 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 168 ASN 3 171 GLN ** 3 179 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 22 GLN ** A 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 143 HIS A 288 ASN A 341 GLN ** A 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 432 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 504 HIS ** A 620 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 678 ASN ** A 704 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 757 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 783 GLN A 791 GLN A 809 HIS ** A 861 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 997 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1299 GLN B 42 GLN ** B 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 245 GLN ** B 481 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 695 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 699 HIS B 741 HIS ** B 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 912 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1049 GLN ** B1120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 95 GLN G 60 GLN ** G 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 76 ASN ** H 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 551 HIS W 595 ASN ** X 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 176 ASN ** X 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 430 ASN X 452 GLN X 519 ASN ** X 659 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 662 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 698 GLN Y 442 GLN ** Z 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 365 ASN ** b 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 179 ASN ** d 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 96 ASN ** d 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 288 GLN ** f 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 161 HIS g 59 HIS ** h 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 149 ASN ** i 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 376 HIS j 463 HIS ** j 506 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** j 522 GLN ** j 528 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 538 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 595 GLN ** k 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 16 GLN m 47 GLN ** m 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 75 ASN ** n 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 130 GLN o 140 GLN ** o 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 171 ASN ** r 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 330 HIS ** r 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 453 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** r 507 GLN r 607 GLN ** r 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 698 GLN ** r 832 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 109 GLN ** s 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** v 18 ASN v 21 GLN ** x 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 86 GLN y 30 ASN y 50 ASN ** y 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** y 104 HIS y 127 ASN z 700 ASN ** z 732 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 742 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 66 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5082 moved from start: 0.4841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.115 132043 Z= 0.291 Angle : 0.808 13.276 179087 Z= 0.419 Chirality : 0.048 0.298 20275 Planarity : 0.006 0.201 22522 Dihedral : 10.702 83.337 18410 Min Nonbonded Distance : 1.766 Molprobity Statistics. All-atom Clashscore : 23.20 Ramachandran Plot: Outliers : 0.20 % Allowed : 9.49 % Favored : 90.32 % Rotamer Outliers : 0.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.84 % Cis-general : 0.05 % Twisted Proline : 1.12 % Twisted General : 0.23 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.79 (0.06), residues: 15623 helix: 0.08 (0.06), residues: 7508 sheet: -1.59 (0.12), residues: 1696 loop : -2.65 (0.07), residues: 6419 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 31246 Ramachandran restraints generated. 15623 Oldfield, 0 Emsley, 15623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 31246 Ramachandran restraints generated. 15623 Oldfield, 0 Emsley, 15623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 3854 residues out of total 14130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 3839 time to evaluate : 10.966 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET b 157 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 4 residues processed: 3852 average time/residue: 1.1627 time to fit residues: 7695.1140 Evaluate side-chains 3551 residues out of total 14130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 3547 time to evaluate : 10.845 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.8869 time to fit residues: 22.6203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1577 random chunks: chunk 1269 optimal weight: 4.9990 chunk 865 optimal weight: 0.4980 chunk 22 optimal weight: 1.9990 chunk 1134 optimal weight: 20.0000 chunk 628 optimal weight: 0.7980 chunk 1300 optimal weight: 0.7980 chunk 1053 optimal weight: 10.0000 chunk 1 optimal weight: 9.9990 chunk 778 optimal weight: 0.0170 chunk 1368 optimal weight: 5.9990 chunk 384 optimal weight: 0.8980 overall best weight: 0.6018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 43 ASN 0 225 ASN ** 0 598 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 619 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 723 GLN 1 68 HIS ** 1 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 526 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 353 GLN ** 2 530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 680 GLN 2 699 ASN 2 737 HIS ** 3 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 171 GLN ** 3 179 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 341 GLN ** A 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 432 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 620 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 704 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 757 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1397 HIS A1410 HIS ** B 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 111 ASN B 145 GLN B 481 HIS ** B 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 699 HIS ** B 912 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 930 GLN B 941 GLN ** B1073 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 260 GLN ** D 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 139 GLN H 76 ASN ** H 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 45 ASN ** S 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 158 ASN W 625 GLN ** X 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 176 ASN ** X 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 659 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 662 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 698 GLN ** Z 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 448 HIS a 227 HIS ** a 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 96 ASN ** d 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 288 GLN ** f 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 142 GLN g 116 ASN h 55 GLN h 141 GLN ** i 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 57 GLN j 192 GLN ** j 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 383 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 463 HIS j 535 HIS j 553 ASN ** k 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 237 GLN ** o 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 130 GLN ** o 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 147 ASN ** p 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 175 HIS ** q 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 171 ASN ** r 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** r 279 GLN ** r 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 330 HIS ** r 453 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 607 GLN ** r 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 698 GLN ** r 832 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** r 883 ASN ** r 964 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 109 GLN ** s 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** y 50 ASN ** y 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 700 ASN ** z 732 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 742 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 778 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 52 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4982 moved from start: 0.5206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.069 132043 Z= 0.217 Angle : 0.769 13.568 179087 Z= 0.391 Chirality : 0.046 0.328 20275 Planarity : 0.006 0.147 22522 Dihedral : 10.552 83.005 18410 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 19.99 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.73 % Favored : 91.09 % Rotamer Outliers : 0.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.84 % Cis-general : 0.05 % Twisted Proline : 0.98 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.07), residues: 15623 helix: 0.32 (0.06), residues: 7499 sheet: -1.40 (0.12), residues: 1648 loop : -2.50 (0.07), residues: 6476 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 31246 Ramachandran restraints generated. 15623 Oldfield, 0 Emsley, 15623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 31246 Ramachandran restraints generated. 15623 Oldfield, 0 Emsley, 15623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 3782 residues out of total 14130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 3773 time to evaluate : 9.832 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET b 157 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 1 residues processed: 3777 average time/residue: 1.1706 time to fit residues: 7584.2419 Evaluate side-chains 3512 residues out of total 14130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 3511 time to evaluate : 9.602 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.9676 time to fit residues: 15.7717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1577 random chunks: chunk 512 optimal weight: 0.0270 chunk 1372 optimal weight: 10.0000 chunk 301 optimal weight: 10.0000 chunk 894 optimal weight: 30.0000 chunk 376 optimal weight: 0.8980 chunk 1525 optimal weight: 0.0970 chunk 1266 optimal weight: 0.8980 chunk 706 optimal weight: 10.0000 chunk 126 optimal weight: 40.0000 chunk 504 optimal weight: 2.9990 chunk 801 optimal weight: 0.8980 overall best weight: 0.5636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 375 GLN 0 392 HIS ** 0 619 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 723 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 526 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 730 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 11015 HIS ** 11103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 237 HIS ** 2 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 261 GLN ** 2 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 171 GLN ** 3 179 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 341 GLN A 372 ASN ** A 432 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 620 HIS ** A 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 704 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 757 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1397 HIS B 111 ASN B 145 GLN B 481 HIS ** B 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 639 HIS B 699 HIS B 906 GLN ** B 912 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 930 GLN ** B1073 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1094 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 217 GLN D 66 ASN D 93 HIS ** D 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 95 GLN G 4 HIS G 139 GLN H 76 ASN ** H 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 21 ASN ** I 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 13 GLN M 308 GLN ** M 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 709 GLN ** X 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 176 ASN ** X 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 402 ASN X 434 HIS ** X 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 662 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 698 GLN ** Z 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 390 GLN Z 448 HIS ** a 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 376 HIS ** b 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 288 GLN ** f 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 108 HIS ** h 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 218 HIS ** j 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 383 HIS ** j 463 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 16 GLN ** m 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 57 GLN ** n 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 140 GLN ** o 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 171 ASN ** r 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 453 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 607 GLN ** r 823 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 108 GLN s 109 GLN ** t 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** y 50 ASN ** y 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 700 ASN ** z 732 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 742 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 778 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 48 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4982 moved from start: 0.5496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.119 132043 Z= 0.221 Angle : 0.766 13.353 179087 Z= 0.389 Chirality : 0.046 0.360 20275 Planarity : 0.006 0.131 22522 Dihedral : 10.461 83.225 18410 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 20.48 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.89 % Favored : 90.93 % Rotamer Outliers : 0.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.84 % Cis-general : 0.05 % Twisted Proline : 0.84 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.37 (0.07), residues: 15623 helix: 0.41 (0.06), residues: 7523 sheet: -1.26 (0.12), residues: 1697 loop : -2.45 (0.07), residues: 6403 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 31246 Ramachandran restraints generated. 15623 Oldfield, 0 Emsley, 15623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 31246 Ramachandran restraints generated. 15623 Oldfield, 0 Emsley, 15623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 3720 residues out of total 14130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 3716 time to evaluate : 10.940 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET b 157 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 3719 average time/residue: 1.1883 time to fit residues: 7602.3975 Evaluate side-chains 3486 residues out of total 14130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 3485 time to evaluate : 10.795 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 1.0186 time to fit residues: 17.6282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1577 random chunks: chunk 1471 optimal weight: 10.0000 chunk 171 optimal weight: 30.0000 chunk 869 optimal weight: 9.9990 chunk 1114 optimal weight: 8.9990 chunk 863 optimal weight: 6.9990 chunk 1284 optimal weight: 5.9990 chunk 852 optimal weight: 4.9990 chunk 1519 optimal weight: 8.9990 chunk 951 optimal weight: 5.9990 chunk 926 optimal weight: 0.4980 chunk 701 optimal weight: 2.9990 overall best weight: 4.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 598 ASN 0 616 GLN ** 0 619 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 723 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 743 GLN ** 1 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 526 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 730 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 1 779 HIS ** 11124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 730 HIS ** 3 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 179 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 222 HIS A 288 ASN A 372 ASN A 403 GLN A 441 GLN ** A 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 704 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 757 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 780 ASN ** A 997 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1299 GLN A1384 HIS ** B 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 639 HIS ** B 649 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 722 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 912 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 930 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1021 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1073 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1120 ASN B1133 HIS ** C 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 55 GLN D 93 HIS ** D 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 30 GLN ** E 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 21 ASN ** I 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 352 HIS R 209 GLN ** S 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 14 GLN ** T 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 195 GLN W 83 HIS W 665 GLN W 709 GLN ** X 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 176 ASN ** X 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 555 GLN ** X 662 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 698 GLN X 726 GLN ** Y 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 448 HIS ** a 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 63 HIS ** d 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 73 ASN ** e 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 61 ASN ** g 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 383 HIS ** j 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 463 HIS ** j 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 528 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 565 ASN ** k 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 109 GLN o 140 GLN ** o 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 58 GLN ** p 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 453 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** r 511 HIS ** r 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 651 ASN r 698 GLN ** r 823 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 832 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** s 109 GLN ** t 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** y 19 GLN ** y 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 636 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** z 700 ASN ** z 732 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 47 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5249 moved from start: 0.6223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.221 132043 Z= 0.420 Angle : 0.928 16.709 179087 Z= 0.492 Chirality : 0.052 0.324 20275 Planarity : 0.007 0.216 22522 Dihedral : 10.810 81.564 18410 Min Nonbonded Distance : 1.796 Molprobity Statistics. All-atom Clashscore : 28.53 Ramachandran Plot: Outliers : 0.22 % Allowed : 10.30 % Favored : 89.48 % Rotamer Outliers : 0.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.84 % Cis-general : 0.05 % Twisted Proline : 0.84 % Twisted General : 0.20 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.83 (0.06), residues: 15623 helix: -0.03 (0.06), residues: 7504 sheet: -1.45 (0.12), residues: 1668 loop : -2.61 (0.07), residues: 6451 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 31246 Ramachandran restraints generated. 15623 Oldfield, 0 Emsley, 15623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 31246 Ramachandran restraints generated. 15623 Oldfield, 0 Emsley, 15623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 3762 residues out of total 14130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 3761 time to evaluate : 10.838 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET b 157 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 3761 average time/residue: 1.1814 time to fit residues: 7645.5271 Evaluate side-chains 3489 residues out of total 14130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 3488 time to evaluate : 10.220 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 2.1787 time to fit residues: 18.1796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1577 random chunks: chunk 940 optimal weight: 0.0050 chunk 606 optimal weight: 3.9990 chunk 907 optimal weight: 30.0000 chunk 457 optimal weight: 0.8980 chunk 298 optimal weight: 9.9990 chunk 294 optimal weight: 2.9990 chunk 966 optimal weight: 2.9990 chunk 1035 optimal weight: 0.9990 chunk 751 optimal weight: 0.5980 chunk 141 optimal weight: 6.9990 chunk 1194 optimal weight: 2.9990 overall best weight: 1.0998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 392 HIS ** 0 619 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 781 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 444 GLN ** 1 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 526 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 684 ASN ** 1 730 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 1 898 ASN 11124 ASN ** 2 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 730 HIS 3 171 GLN ** 3 179 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 372 ASN ** A 432 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 704 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 742 ASN ** A 757 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1042 ASN A1299 GLN ** A1397 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1462 GLN B 111 ASN B 145 GLN B 518 HIS B 649 ASN ** B 695 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 912 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 930 GLN ** B1021 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1073 GLN ** D 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 210 GLN G 139 GLN H 76 ASN ** H 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 21 ASN M 352 HIS ** Q 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 95 HIS ** S 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 144 GLN T 160 GLN W 665 GLN X 176 ASN ** X 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 348 HIS ** X 662 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 698 GLN ** Z 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 116 GLN ** Z 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 176 ASN ** d 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 258 HIS e 288 GLN ** f 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 72 HIS h 18 GLN j 38 GLN j 193 HIS ** j 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 492 GLN ** j 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 531 GLN ** j 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 16 GLN ** m 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** m 104 GLN ** n 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 88 ASN ** n 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 140 GLN ** o 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 58 GLN ** p 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 175 HIS ** q 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 84 GLN ** q 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 171 ASN ** r 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 374 HIS ** r 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 453 HIS ** r 511 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** r 651 ASN r 698 GLN ** r 832 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** r 883 ASN ** r 964 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 109 GLN ** t 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** y 50 ASN ** y 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 700 ASN ** z 732 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 742 GLN ** z 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 778 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 57 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5088 moved from start: 0.6385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.121 132043 Z= 0.240 Angle : 0.814 16.546 179087 Z= 0.413 Chirality : 0.047 0.399 20275 Planarity : 0.006 0.132 22522 Dihedral : 10.572 82.165 18410 Min Nonbonded Distance : 1.815 Molprobity Statistics. All-atom Clashscore : 22.53 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.95 % Favored : 90.91 % Rotamer Outliers : 0.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.84 % Cis-general : 0.05 % Twisted Proline : 0.84 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.45 (0.07), residues: 15623 helix: 0.31 (0.06), residues: 7522 sheet: -1.33 (0.12), residues: 1698 loop : -2.44 (0.07), residues: 6403 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 31246 Ramachandran restraints generated. 15623 Oldfield, 0 Emsley, 15623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 31246 Ramachandran restraints generated. 15623 Oldfield, 0 Emsley, 15623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 3764 residues out of total 14130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 3759 time to evaluate : 10.885 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET b 157 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 3762 average time/residue: 1.1892 time to fit residues: 7694.2661 Evaluate side-chains 3529 residues out of total 14130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 3527 time to evaluate : 9.875 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.9411 time to fit residues: 17.7460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1577 random chunks: chunk 1382 optimal weight: 4.9990 chunk 1456 optimal weight: 0.9980 chunk 1328 optimal weight: 5.9990 chunk 1416 optimal weight: 2.9990 chunk 1455 optimal weight: 0.8980 chunk 852 optimal weight: 10.0000 chunk 617 optimal weight: 5.9990 chunk 1112 optimal weight: 0.1980 chunk 434 optimal weight: 0.4980 chunk 1279 optimal weight: 0.8980 chunk 1339 optimal weight: 0.1980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 63 HIS 0 104 GLN ** 0 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 598 ASN ** 0 619 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 526 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 730 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 1 998 HIS ** 2 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 544 HIS ** 3 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 179 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 222 HIS ** A 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 432 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 601 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 704 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 780 ASN ** A 989 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 HIS A1042 ASN A1093 GLN B 111 ASN B 420 GLN ** B 912 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1021 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 93 HIS ** D 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 43 GLN ** E 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 139 GLN H 76 ASN J 26 GLN ** Q 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 144 GLN W 366 ASN ** W 638 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 176 ASN ** X 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 363 GLN ** X 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 662 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 698 GLN ** Z 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 25 GLN ** d 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 258 HIS e 288 GLN ** f 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 281 HIS ** g 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 554 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 53 GLN ** m 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 57 GLN n 59 ASN ** n 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 58 GLN ** p 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 171 ASN ** r 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 651 ASN r 823 GLN ** r 832 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** r 867 GLN ** r 909 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 913 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 964 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 109 GLN ** t 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** y 50 ASN ** y 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 700 ASN ** z 732 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 778 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5040 moved from start: 0.6585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.121 132043 Z= 0.223 Angle : 0.812 18.438 179087 Z= 0.410 Chirality : 0.047 0.366 20275 Planarity : 0.006 0.119 22522 Dihedral : 10.437 84.427 18410 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 21.01 Ramachandran Plot: Outliers : 0.14 % Allowed : 9.23 % Favored : 90.63 % Rotamer Outliers : 0.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.84 % Cis-general : 0.05 % Twisted Proline : 0.84 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.07), residues: 15623 helix: 0.49 (0.06), residues: 7519 sheet: -1.24 (0.12), residues: 1748 loop : -2.38 (0.08), residues: 6356 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 31246 Ramachandran restraints generated. 15623 Oldfield, 0 Emsley, 15623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 31246 Ramachandran restraints generated. 15623 Oldfield, 0 Emsley, 15623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 3680 residues out of total 14130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 3675 time to evaluate : 10.863 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET b 157 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 0 residues processed: 3679 average time/residue: 1.1834 time to fit residues: 7496.2908 Evaluate side-chains 3454 residues out of total 14130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 3454 time to evaluate : 10.803 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 15.8235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1577 random chunks: chunk 1411 optimal weight: 0.9990 chunk 930 optimal weight: 1.9990 chunk 1497 optimal weight: 50.0000 chunk 914 optimal weight: 5.9990 chunk 710 optimal weight: 0.0070 chunk 1041 optimal weight: 9.9990 chunk 1571 optimal weight: 6.9990 chunk 1446 optimal weight: 3.9990 chunk 1251 optimal weight: 0.2980 chunk 129 optimal weight: 40.0000 chunk 966 optimal weight: 8.9990 overall best weight: 1.4604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 375 GLN 0 392 HIS 0 609 ASN ** 0 615 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 619 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 723 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 454 HIS ** 1 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 526 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 730 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 11015 HIS ** 11103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 544 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 179 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 432 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 704 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 757 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 809 HIS A1397 HIS ** A1457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 111 ASN ** B 912 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 930 GLN ** B1021 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1049 GLN ** C 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 93 HIS ** D 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 43 GLN ** E 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 139 GLN ** I 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 26 GLN ** Q 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 144 GLN T 229 HIS ** W 638 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 176 ASN ** X 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 662 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 698 GLN ** Z 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 258 HIS e 288 GLN ** f 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 218 HIS ** j 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 383 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 506 HIS ** j 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 554 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 57 GLN n 59 ASN ** n 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 66 ASN ** o 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 58 GLN ** p 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 57 ASN ** q 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 171 ASN ** r 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 374 HIS ** r 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 651 ASN ** r 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 832 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 848 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 867 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 883 ASN ** r 964 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r1183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r1259 GLN s 109 GLN ** t 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** y 50 ASN ** y 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 700 ASN ** z 732 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 778 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5091 moved from start: 0.6774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.098 132043 Z= 0.243 Angle : 0.804 13.288 179087 Z= 0.410 Chirality : 0.047 0.390 20275 Planarity : 0.006 0.122 22522 Dihedral : 10.412 85.158 18410 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 22.42 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.36 % Favored : 90.51 % Rotamer Outliers : 0.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.84 % Cis-general : 0.05 % Twisted Proline : 0.84 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.07), residues: 15623 helix: 0.51 (0.06), residues: 7518 sheet: -1.26 (0.12), residues: 1762 loop : -2.36 (0.08), residues: 6343 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 31246 Ramachandran restraints generated. 15623 Oldfield, 0 Emsley, 15623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 31246 Ramachandran restraints generated. 15623 Oldfield, 0 Emsley, 15623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 3636 residues out of total 14130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 3634 time to evaluate : 11.020 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET b 157 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 3634 average time/residue: 1.1987 time to fit residues: 7498.4574 Evaluate side-chains 3437 residues out of total 14130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 3437 time to evaluate : 10.890 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 15.7908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1577 random chunks: chunk 767 optimal weight: 7.9990 chunk 993 optimal weight: 9.9990 chunk 1332 optimal weight: 1.9990 chunk 383 optimal weight: 0.9990 chunk 1153 optimal weight: 5.9990 chunk 184 optimal weight: 7.9990 chunk 347 optimal weight: 0.6980 chunk 1253 optimal weight: 0.9990 chunk 524 optimal weight: 0.0170 chunk 1286 optimal weight: 0.0870 chunk 158 optimal weight: 40.0000 overall best weight: 0.5600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 598 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 609 ASN ** 0 615 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 619 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 292 GLN ** 1 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 431 HIS 1 454 HIS ** 1 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 526 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 725 HIS 1 822 HIS ** 2 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 353 GLN ** 2 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 544 HIS ** 2 920 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 179 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 432 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 601 ASN ** A 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 704 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 888 GLN A 989 ASN A1397 HIS A1410 HIS ** B 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 111 ASN B 642 GLN B 683 GLN ** B 912 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 930 GLN B1021 HIS ** C 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 93 HIS ** D 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 139 GLN H 76 ASN J 26 GLN ** M 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 65 ASN R 95 HIS ** S 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 595 ASN W 638 GLN ** X 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 176 ASN ** X 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 662 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 698 GLN ** Z 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 65 GLN ** d 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 258 HIS e 288 GLN ** f 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 55 GLN j 218 HIS j 292 GLN j 299 GLN j 317 GLN ** j 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 517 GLN ** j 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 554 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 59 ASN ** o 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 109 GLN ** o 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 58 GLN p 81 ASN ** p 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 171 ASN ** r 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 464 GLN r 472 GLN ** r 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 832 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** r 853 HIS ** r 867 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 964 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r1258 ASN ** r1259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 109 GLN ** t 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** y 50 ASN ** y 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 700 ASN ** z 732 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 778 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 49 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4641 r_free = 0.4641 target = 0.215298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.169430 restraints weight = 307203.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.175904 restraints weight = 168960.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.179156 restraints weight = 97994.277| |-----------------------------------------------------------------------------| r_work (final): 0.4159 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4161 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4161 r_free = 0.4161 target_work(ls_wunit_k1) = 0.163 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4161 r_free = 0.4161 target_work(ls_wunit_k1) = 0.163 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.4161 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6079 moved from start: 0.6917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.093 132043 Z= 0.216 Angle : 0.794 19.118 179087 Z= 0.401 Chirality : 0.046 0.331 20275 Planarity : 0.006 0.122 22522 Dihedral : 10.333 86.185 18410 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 20.39 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.85 % Favored : 91.03 % Rotamer Outliers : 0.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.84 % Cis-general : 0.05 % Twisted Proline : 0.84 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.07), residues: 15623 helix: 0.59 (0.06), residues: 7515 sheet: -1.23 (0.12), residues: 1750 loop : -2.31 (0.08), residues: 6358 =============================================================================== Job complete usr+sys time: 86772.56 seconds wall clock time: 1485 minutes 46.69 seconds (89146.69 seconds total)