Starting phenix.real_space_refine (version: dev) on Mon Dec 19 03:13:53 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eto_31301/12_2022/7eto_31301.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eto_31301/12_2022/7eto_31301.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eto_31301/12_2022/7eto_31301.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eto_31301/12_2022/7eto_31301.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eto_31301/12_2022/7eto_31301.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eto_31301/12_2022/7eto_31301.pdb" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.009 sd= 0.019 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "x ARG 10": "NH1" <-> "NH2" Residue "x ASP 28": "OD1" <-> "OD2" Residue "x GLU 32": "OE1" <-> "OE2" Residue "x GLU 43": "OE1" <-> "OE2" Residue "x GLU 65": "OE1" <-> "OE2" Residue "x GLU 78": "OE1" <-> "OE2" Residue "x GLU 79": "OE1" <-> "OE2" Residue "x PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x ASP 98": "OD1" <-> "OD2" Residue "x ASP 104": "OD1" <-> "OD2" Residue "x PHE 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x ASP 121": "OD1" <-> "OD2" Residue "x GLU 123": "OE1" <-> "OE2" Residue "x GLU 142": "OE1" <-> "OE2" Residue "x PHE 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x GLU 163": "OE1" <-> "OE2" Residue "x GLU 168": "OE1" <-> "OE2" Residue "x GLU 169": "OE1" <-> "OE2" Residue "x GLU 172": "OE1" <-> "OE2" Residue "x ARG 176": "NH1" <-> "NH2" Residue "x ARG 190": "NH1" <-> "NH2" Residue "x GLU 218": "OE1" <-> "OE2" Residue "x GLU 219": "OE1" <-> "OE2" Residue "x GLU 221": "OE1" <-> "OE2" Residue "x GLU 230": "OE1" <-> "OE2" Residue "x GLU 238": "OE1" <-> "OE2" Residue "x GLU 259": "OE1" <-> "OE2" Residue "x GLU 269": "OE1" <-> "OE2" Residue "x GLU 273": "OE1" <-> "OE2" Residue "x ASP 274": "OD1" <-> "OD2" Residue "x ASP 280": "OD1" <-> "OD2" Residue "h ASP 20": "OD1" <-> "OD2" Residue "h TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h ASP 106": "OD1" <-> "OD2" Residue "h GLU 145": "OE1" <-> "OE2" Residue "h ASP 190": "OD1" <-> "OD2" Residue "h GLU 225": "OE1" <-> "OE2" Residue "h GLU 236": "OE1" <-> "OE2" Residue "h GLU 244": "OE1" <-> "OE2" Residue "h GLU 249": "OE1" <-> "OE2" Residue "h ARG 251": "NH1" <-> "NH2" Residue "h ASP 262": "OD1" <-> "OD2" Residue "h ARG 276": "NH1" <-> "NH2" Residue "h ASP 279": "OD1" <-> "OD2" Residue "h ASP 280": "OD1" <-> "OD2" Residue "I ASP 20": "OD1" <-> "OD2" Residue "I ARG 60": "NH1" <-> "NH2" Residue "I ARG 74": "NH1" <-> "NH2" Residue "I ARG 75": "NH1" <-> "NH2" Residue "I GLU 131": "OE1" <-> "OE2" Residue "I ARG 160": "NH1" <-> "NH2" Residue "I GLU 163": "OE1" <-> "OE2" Residue "I ARG 178": "NH1" <-> "NH2" Residue "I GLU 213": "OE1" <-> "OE2" Residue "I ARG 220": "NH1" <-> "NH2" Residue "I ARG 243": "NH1" <-> "NH2" Residue "I GLU 244": "OE1" <-> "OE2" Residue "I ARG 245": "NH1" <-> "NH2" Residue "I GLU 249": "OE1" <-> "OE2" Residue "I ASP 263": "OD1" <-> "OD2" Residue "I GLU 264": "OE1" <-> "OE2" Residue "H ASP 2230": "OD1" <-> "OD2" Residue "H PHE 2237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n GLU 5": "OE1" <-> "OE2" Residue "n ASP 20": "OD1" <-> "OD2" Residue "n ARG 56": "NH1" <-> "NH2" Residue "n GLU 163": "OE1" <-> "OE2" Residue "n GLU 213": "OE1" <-> "OE2" Residue "n ASP 263": "OD1" <-> "OD2" Residue "n GLU 264": "OE1" <-> "OE2" Residue "n ASP 280": "OD1" <-> "OD2" Residue "o ARG 74": "NH1" <-> "NH2" Residue "o ARG 75": "NH1" <-> "NH2" Residue "o GLU 131": "OE1" <-> "OE2" Residue "o GLU 145": "OE1" <-> "OE2" Residue "o ARG 160": "NH1" <-> "NH2" Residue "o GLU 163": "OE1" <-> "OE2" Residue "o ARG 178": "NH1" <-> "NH2" Residue "o ARG 220": "NH1" <-> "NH2" Residue "o ARG 243": "NH1" <-> "NH2" Residue "o ASP 262": "OD1" <-> "OD2" Residue "o ASP 263": "OD1" <-> "OD2" Residue "o ASP 280": "OD1" <-> "OD2" Residue "o ASP 292": "OD1" <-> "OD2" Residue "o ASP 296": "OD1" <-> "OD2" Residue "g GLU 177": "OE1" <-> "OE2" Residue "g ARG 179": "NH1" <-> "NH2" Residue "g ASP 217": "OD1" <-> "OD2" Residue "g ARG 237": "NH1" <-> "NH2" Residue "m GLU 54": "OE1" <-> "OE2" Residue "m GLU 60": "OE1" <-> "OE2" Residue "m ARG 78": "NH1" <-> "NH2" Residue "m ARG 112": "NH1" <-> "NH2" Residue "m GLU 177": "OE1" <-> "OE2" Residue "m TYR 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m TYR 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m PHE 263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m ASP 277": "OD1" <-> "OD2" Residue "M GLU 12": "OE1" <-> "OE2" Residue "M GLU 19": "OE1" <-> "OE2" Residue "M GLU 35": "OE1" <-> "OE2" Residue "M ARG 41": "NH1" <-> "NH2" Residue "M TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 46": "NH1" <-> "NH2" Residue "M ARG 53": "NH1" <-> "NH2" Residue "M ARG 57": "NH1" <-> "NH2" Residue "M ARG 80": "NH1" <-> "NH2" Residue "M GLU 85": "OE1" <-> "OE2" Residue "M ARG 91": "NH1" <-> "NH2" Residue "M GLU 119": "OE1" <-> "OE2" Residue "M ARG 123": "NH1" <-> "NH2" Residue "M ARG 135": "NH1" <-> "NH2" Residue "M PHE 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 171": "OE1" <-> "OE2" Residue "M ARG 302": "NH1" <-> "NH2" Residue "M GLU 305": "OE1" <-> "OE2" Residue "M ASP 319": "OD1" <-> "OD2" Residue "M ARG 325": "NH1" <-> "NH2" Residue "M ARG 337": "NH1" <-> "NH2" Residue "M GLU 340": "OE1" <-> "OE2" Residue "M GLU 349": "OE1" <-> "OE2" Residue "M ASP 355": "OD1" <-> "OD2" Residue "M ARG 369": "NH1" <-> "NH2" Residue "M ARG 372": "NH1" <-> "NH2" Residue "M ASP 373": "OD1" <-> "OD2" Residue "M GLU 374": "OE1" <-> "OE2" Residue "M ARG 380": "NH1" <-> "NH2" Residue "M PHE 390": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 396": "NH1" <-> "NH2" Residue "M ARG 401": "NH1" <-> "NH2" Residue "M GLU 405": "OE1" <-> "OE2" Residue "M ARG 408": "NH1" <-> "NH2" Residue "M ASP 416": "OD1" <-> "OD2" Residue "M ARG 434": "NH1" <-> "NH2" Residue "M ARG 447": "NH1" <-> "NH2" Residue "M ARG 449": "NH1" <-> "NH2" Residue "M GLU 456": "OE1" <-> "OE2" Residue "M ARG 462": "NH1" <-> "NH2" Residue "M ARG 492": "NH1" <-> "NH2" Residue "M ARG 498": "NH1" <-> "NH2" Residue "M ARG 507": "NH1" <-> "NH2" Residue "M ARG 508": "NH1" <-> "NH2" Residue "M ARG 513": "NH1" <-> "NH2" Residue "M ASP 530": "OD1" <-> "OD2" Residue "M ARG 544": "NH1" <-> "NH2" Residue "M PHE 559": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 578": "OE1" <-> "OE2" Residue "M ARG 587": "NH1" <-> "NH2" Residue "M ARG 588": "NH1" <-> "NH2" Residue "N GLU 17": "OE1" <-> "OE2" Residue "N GLU 20": "OE1" <-> "OE2" Residue "N GLU 21": "OE1" <-> "OE2" Residue "N ARG 25": "NH1" <-> "NH2" Residue "N ARG 29": "NH1" <-> "NH2" Residue "N ARG 32": "NH1" <-> "NH2" Residue "N GLU 36": "OE1" <-> "OE2" Residue "N ASP 37": "OD1" <-> "OD2" Residue "N ARG 43": "NH1" <-> "NH2" Residue "N ARG 48": "NH1" <-> "NH2" Residue "N GLU 64": "OE1" <-> "OE2" Residue "O PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 20": "OE1" <-> "OE2" Residue "O ARG 55": "NH1" <-> "NH2" Residue "O GLU 80": "OE1" <-> "OE2" Residue "1 ASP 28": "OD1" <-> "OD2" Residue "1 GLU 43": "OE1" <-> "OE2" Residue "1 GLU 55": "OE1" <-> "OE2" Residue "1 TYR 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 GLU 65": "OE1" <-> "OE2" Residue "1 GLU 113": "OE1" <-> "OE2" Residue "1 ASP 121": "OD1" <-> "OD2" Residue "1 GLU 123": "OE1" <-> "OE2" Residue "1 GLU 163": "OE1" <-> "OE2" Residue "1 GLU 169": "OE1" <-> "OE2" Residue "1 GLU 172": "OE1" <-> "OE2" Residue "1 ARG 190": "NH1" <-> "NH2" Residue "1 GLU 218": "OE1" <-> "OE2" Residue "1 GLU 219": "OE1" <-> "OE2" Residue "1 GLU 230": "OE1" <-> "OE2" Residue "1 GLU 238": "OE1" <-> "OE2" Residue "1 GLU 269": "OE1" <-> "OE2" Residue "1 GLU 273": "OE1" <-> "OE2" Residue "1 ASP 274": "OD1" <-> "OD2" Residue "1 TYR 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 27": "OE1" <-> "OE2" Residue "Q GLU 31": "OE1" <-> "OE2" Residue "Q ASP 56": "OD1" <-> "OD2" Residue "Q ASP 63": "OD1" <-> "OD2" Residue "R GLU 31": "OE1" <-> "OE2" Residue "R GLU 34": "OE1" <-> "OE2" Residue "R ASP 56": "OD1" <-> "OD2" Residue "S GLU 34": "OE1" <-> "OE2" Residue "T GLU 27": "OE1" <-> "OE2" Residue "T GLU 34": "OE1" <-> "OE2" Residue "T PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 63": "OD1" <-> "OD2" Residue "i ASP 15": "OD1" <-> "OD2" Residue "i GLU 27": "OE1" <-> "OE2" Residue "i ASP 56": "OD1" <-> "OD2" Residue "i ARG 74": "NH1" <-> "NH2" Residue "j GLU 27": "OE1" <-> "OE2" Residue "j GLU 34": "OE1" <-> "OE2" Residue "j ARG 72": "NH1" <-> "NH2" Residue "a ARG 110": "NH1" <-> "NH2" Residue "a ARG 162": "NH1" <-> "NH2" Residue "a ARG 173": "NH1" <-> "NH2" Residue "a ARG 212": "NH1" <-> "NH2" Residue "a ARG 234": "NH1" <-> "NH2" Residue "a GLU 403": "OE1" <-> "OE2" Residue "a ARG 405": "NH1" <-> "NH2" Residue "a ARG 433": "NH1" <-> "NH2" Residue "a ASP 434": "OD1" <-> "OD2" Residue "a GLU 456": "OE1" <-> "OE2" Residue "a GLU 511": "OE1" <-> "OE2" Residue "a ASP 520": "OD1" <-> "OD2" Residue "a ARG 555": "NH1" <-> "NH2" Residue "a GLU 572": "OE1" <-> "OE2" Residue "a ARG 574": "NH1" <-> "NH2" Residue "a GLU 577": "OE1" <-> "OE2" Residue "a PHE 597": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ARG 642": "NH1" <-> "NH2" Residue "a ASP 663": "OD1" <-> "OD2" Residue "a GLU 700": "OE1" <-> "OE2" Residue "a GLU 701": "OE1" <-> "OE2" Residue "a GLU 764": "OE1" <-> "OE2" Residue "a GLU 777": "OE1" <-> "OE2" Residue "a PHE 784": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ASP 844": "OD1" <-> "OD2" Residue "a GLU 855": "OE1" <-> "OE2" Residue "a GLU 859": "OE1" <-> "OE2" Residue "a ASP 867": "OD1" <-> "OD2" Residue "a GLU 894": "OE1" <-> "OE2" Residue "a ARG 904": "NH1" <-> "NH2" Residue "a GLU 932": "OE1" <-> "OE2" Residue "a PHE 939": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ARG 941": "NH1" <-> "NH2" Residue "a GLU 982": "OE1" <-> "OE2" Residue "a GLU 1067": "OE1" <-> "OE2" Residue "a GLU 1068": "OE1" <-> "OE2" Residue "a GLU 1126": "OE1" <-> "OE2" Residue "a ARG 1132": "NH1" <-> "NH2" Residue "a PHE 1153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 1250": "OE1" <-> "OE2" Residue "a ASP 1283": "OD1" <-> "OD2" Residue "a GLU 1284": "OE1" <-> "OE2" Residue "a GLU 1312": "OE1" <-> "OE2" Residue "a GLU 1320": "OE1" <-> "OE2" Residue "A GLU 2": "OE1" <-> "OE2" Residue "A GLU 30": "OE1" <-> "OE2" Residue "A GLU 44": "OE1" <-> "OE2" Residue "A PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 99": "NH1" <-> "NH2" Residue "A GLU 155": "OE1" <-> "OE2" Residue "A ASP 169": "OD1" <-> "OD2" Residue "A GLU 172": "OE1" <-> "OE2" Residue "A PHE 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 234": "NH1" <-> "NH2" Residue "A GLU 370": "OE1" <-> "OE2" Residue "A ASP 390": "OD1" <-> "OD2" Residue "A PHE 395": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 433": "NH1" <-> "NH2" Residue "A ASP 444": "OD1" <-> "OD2" Residue "A GLU 456": "OE1" <-> "OE2" Residue "A GLU 466": "OE1" <-> "OE2" Residue "A PHE 516": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 532": "OE1" <-> "OE2" Residue "A PHE 539": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 547": "OE1" <-> "OE2" Residue "A ARG 555": "NH1" <-> "NH2" Residue "A ASP 563": "OD1" <-> "OD2" Residue "A ARG 574": "NH1" <-> "NH2" Residue "A GLU 591": "OE1" <-> "OE2" Residue "A ASP 614": "OD1" <-> "OD2" Residue "A ARG 642": "NH1" <-> "NH2" Residue "A GLU 659": "OE1" <-> "OE2" Residue "A GLU 700": "OE1" <-> "OE2" Residue "A TYR 706": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 712": "OD1" <-> "OD2" Residue "A GLU 728": "OE1" <-> "OE2" Residue "A ASP 763": "OD1" <-> "OD2" Residue "A GLU 764": "OE1" <-> "OE2" Residue "A ASP 769": "OD1" <-> "OD2" Residue "A ASP 810": "OD1" <-> "OD2" Residue "A GLU 855": "OE1" <-> "OE2" Residue "A GLU 862": "OE1" <-> "OE2" Residue "A ASP 867": "OD1" <-> "OD2" Residue "A ARG 877": "NH1" <-> "NH2" Residue "A GLU 878": "OE1" <-> "OE2" Residue "A ARG 904": "NH1" <-> "NH2" Residue "A ARG 941": "NH1" <-> "NH2" Residue "A ASP 955": "OD1" <-> "OD2" Residue "A ASP 1040": "OD1" <-> "OD2" Residue "A PHE 1042": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1043": "OE1" <-> "OE2" Residue "A ASP 1112": "OD1" <-> "OD2" Residue "A ASP 1125": "OD1" <-> "OD2" Residue "A ARG 1132": "NH1" <-> "NH2" Residue "A ASP 1203": "OD1" <-> "OD2" Residue "A TYR 1205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1208": "OE1" <-> "OE2" Residue "A GLU 1270": "OE1" <-> "OE2" Residue "A ASP 1283": "OD1" <-> "OD2" Residue "A GLU 1312": "OE1" <-> "OE2" Residue "A ARG 1316": "NH1" <-> "NH2" Residue "A GLU 1348": "OE1" <-> "OE2" Residue "A TYR 1354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 62": "OE1" <-> "OE2" Residue "B ARG 162": "NH1" <-> "NH2" Residue "B ARG 173": "NH1" <-> "NH2" Residue "B ARG 209": "NH1" <-> "NH2" Residue "B ARG 212": "NH1" <-> "NH2" Residue "B ARG 234": "NH1" <-> "NH2" Residue "B PHE 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 310": "OE1" <-> "OE2" Residue "B GLU 364": "OE1" <-> "OE2" Residue "B GLU 386": "OE1" <-> "OE2" Residue "B ASP 390": "OD1" <-> "OD2" Residue "B ARG 405": "NH1" <-> "NH2" Residue "B ARG 433": "NH1" <-> "NH2" Residue "B PHE 442": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 466": "OE1" <-> "OE2" Residue "B GLU 511": "OE1" <-> "OE2" Residue "B ASP 520": "OD1" <-> "OD2" Residue "B GLU 547": "OE1" <-> "OE2" Residue "B ARG 574": "NH1" <-> "NH2" Residue "B GLU 577": "OE1" <-> "OE2" Residue "B ASP 589": "OD1" <-> "OD2" Residue "B ARG 642": "NH1" <-> "NH2" Residue "B PHE 672": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 686": "NH1" <-> "NH2" Residue "B PHE 719": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 725": "NH1" <-> "NH2" Residue "B GLU 728": "OE1" <-> "OE2" Residue "B ASP 735": "OD1" <-> "OD2" Residue "B ASP 753": "OD1" <-> "OD2" Residue "B TYR 771": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 772": "NH1" <-> "NH2" Residue "B ASP 775": "OD1" <-> "OD2" Residue "B GLU 777": "OE1" <-> "OE2" Residue "B PHE 784": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 812": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 844": "OD1" <-> "OD2" Residue "B GLU 855": "OE1" <-> "OE2" Residue "B GLU 859": "OE1" <-> "OE2" Residue "B GLU 862": "OE1" <-> "OE2" Residue "B GLU 888": "OE1" <-> "OE2" Residue "B ARG 904": "NH1" <-> "NH2" Residue "B GLU 932": "OE1" <-> "OE2" Residue "B ARG 941": "NH1" <-> "NH2" Residue "B GLU 962": "OE1" <-> "OE2" Residue "B ASP 1040": "OD1" <-> "OD2" Residue "B ASP 1112": "OD1" <-> "OD2" Residue "B PHE 1117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 1132": "NH1" <-> "NH2" Residue "B ASP 1216": "OD1" <-> "OD2" Residue "B GLU 1250": "OE1" <-> "OE2" Residue "B PHE 1279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1305": "OE1" <-> "OE2" Residue "B GLU 1312": "OE1" <-> "OE2" Residue "B GLU 1320": "OE1" <-> "OE2" Residue "B TYR 1354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 2": "OE1" <-> "OE2" Residue "C GLU 44": "OE1" <-> "OE2" Residue "C PHE 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 141": "OE1" <-> "OE2" Residue "C GLU 155": "OE1" <-> "OE2" Residue "C ARG 162": "NH1" <-> "NH2" Residue "C ARG 173": "NH1" <-> "NH2" Residue "C ARG 212": "NH1" <-> "NH2" Residue "C ARG 234": "NH1" <-> "NH2" Residue "C ASP 342": "OD1" <-> "OD2" Residue "C GLU 370": "OE1" <-> "OE2" Residue "C ARG 405": "NH1" <-> "NH2" Residue "C ASP 418": "OD1" <-> "OD2" Residue "C ARG 433": "NH1" <-> "NH2" Residue "C GLU 456": "OE1" <-> "OE2" Residue "C GLU 466": "OE1" <-> "OE2" Residue "C ARG 477": "NH1" <-> "NH2" Residue "C GLU 486": "OE1" <-> "OE2" Residue "C ARG 493": "NH1" <-> "NH2" Residue "C PHE 498": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 539": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 563": "OD1" <-> "OD2" Residue "C GLU 572": "OE1" <-> "OE2" Residue "C ARG 574": "NH1" <-> "NH2" Residue "C GLU 577": "OE1" <-> "OE2" Residue "C ASP 614": "OD1" <-> "OD2" Residue "C ARG 642": "NH1" <-> "NH2" Residue "C GLU 700": "OE1" <-> "OE2" Residue "C ASP 735": "OD1" <-> "OD2" Residue "C ASP 753": "OD1" <-> "OD2" Residue "C ASP 769": "OD1" <-> "OD2" Residue "C GLU 777": "OE1" <-> "OE2" Residue "C GLU 855": "OE1" <-> "OE2" Residue "C GLU 859": "OE1" <-> "OE2" Residue "C ASP 863": "OD1" <-> "OD2" Residue "C GLU 878": "OE1" <-> "OE2" Residue "C GLU 894": "OE1" <-> "OE2" Residue "C ARG 904": "NH1" <-> "NH2" Residue "C GLU 932": "OE1" <-> "OE2" Residue "C ARG 941": "NH1" <-> "NH2" Residue "C GLU 962": "OE1" <-> "OE2" Residue "C ARG 968": "NH1" <-> "NH2" Residue "C GLU 982": "OE1" <-> "OE2" Residue "C PHE 991": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 1040": "OD1" <-> "OD2" Residue "C GLU 1067": "OE1" <-> "OE2" Residue "C GLU 1126": "OE1" <-> "OE2" Residue "C ARG 1132": "NH1" <-> "NH2" Residue "C GLU 1138": "OE1" <-> "OE2" Residue "C ASP 1216": "OD1" <-> "OD2" Residue "C ARG 1247": "NH1" <-> "NH2" Residue "C GLU 1250": "OE1" <-> "OE2" Residue "C GLU 1305": "OE1" <-> "OE2" Residue "C GLU 1312": "OE1" <-> "OE2" Residue "D ARG 110": "NH1" <-> "NH2" Residue "D GLU 141": "OE1" <-> "OE2" Residue "D ASP 149": "OD1" <-> "OD2" Residue "D ARG 162": "NH1" <-> "NH2" Residue "D ARG 173": "NH1" <-> "NH2" Residue "D ARG 212": "NH1" <-> "NH2" Residue "D ARG 234": "NH1" <-> "NH2" Residue "D TYR 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 370": "OE1" <-> "OE2" Residue "D GLU 386": "OE1" <-> "OE2" Residue "D ASP 390": "OD1" <-> "OD2" Residue "D ARG 405": "NH1" <-> "NH2" Residue "D TYR 407": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 433": "NH1" <-> "NH2" Residue "D GLU 466": "OE1" <-> "OE2" Residue "D ARG 477": "NH1" <-> "NH2" Residue "D PHE 483": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 511": "OE1" <-> "OE2" Residue "D ASP 520": "OD1" <-> "OD2" Residue "D ARG 555": "NH1" <-> "NH2" Residue "D ARG 574": "NH1" <-> "NH2" Residue "D GLU 577": "OE1" <-> "OE2" Residue "D GLU 580": "OE1" <-> "OE2" Residue "D TYR 606": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 608": "OE1" <-> "OE2" Residue "D ARG 642": "NH1" <-> "NH2" Residue "D GLU 659": "OE1" <-> "OE2" Residue "D PHE 719": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 745": "OE1" <-> "OE2" Residue "D ASP 761": "OD1" <-> "OD2" Residue "D GLU 764": "OE1" <-> "OE2" Residue "D ASP 810": "OD1" <-> "OD2" Residue "D GLU 855": "OE1" <-> "OE2" Residue "D GLU 859": "OE1" <-> "OE2" Residue "D GLU 888": "OE1" <-> "OE2" Residue "D ARG 904": "NH1" <-> "NH2" Residue "D TYR 933": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 941": "NH1" <-> "NH2" Residue "D GLU 982": "OE1" <-> "OE2" Residue "D ASP 1040": "OD1" <-> "OD2" Residue "D ASP 1070": "OD1" <-> "OD2" Residue "D ASP 1112": "OD1" <-> "OD2" Residue "D ARG 1132": "NH1" <-> "NH2" Residue "D GLU 1138": "OE1" <-> "OE2" Residue "D ASP 1206": "OD1" <-> "OD2" Residue "D GLU 1219": "OE1" <-> "OE2" Residue "D GLU 1305": "OE1" <-> "OE2" Residue "D GLU 1312": "OE1" <-> "OE2" Residue "D PHE 1368": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 30": "OE1" <-> "OE2" Residue "Y ARG 110": "NH1" <-> "NH2" Residue "Y GLU 141": "OE1" <-> "OE2" Residue "Y ARG 162": "NH1" <-> "NH2" Residue "Y ARG 173": "NH1" <-> "NH2" Residue "Y ARG 212": "NH1" <-> "NH2" Residue "Y ARG 234": "NH1" <-> "NH2" Residue "Y PHE 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y TYR 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 373": "NH1" <-> "NH2" Residue "Y GLU 386": "OE1" <-> "OE2" Residue "Y ARG 405": "NH1" <-> "NH2" Residue "Y GLU 411": "OE1" <-> "OE2" Residue "Y ASP 418": "OD1" <-> "OD2" Residue "Y ARG 433": "NH1" <-> "NH2" Residue "Y ASP 444": "OD1" <-> "OD2" Residue "Y GLU 466": "OE1" <-> "OE2" Residue "Y GLU 486": "OE1" <-> "OE2" Residue "Y ASP 520": "OD1" <-> "OD2" Residue "Y GLU 532": "OE1" <-> "OE2" Residue "Y GLU 544": "OE1" <-> "OE2" Residue "Y ARG 555": "NH1" <-> "NH2" Residue "Y ARG 574": "NH1" <-> "NH2" Residue "Y GLU 577": "OE1" <-> "OE2" Residue "Y GLU 580": "OE1" <-> "OE2" Residue "Y ASP 589": "OD1" <-> "OD2" Residue "Y GLU 591": "OE1" <-> "OE2" Residue "Y ARG 642": "NH1" <-> "NH2" Residue "Y GLU 728": "OE1" <-> "OE2" Residue "Y ASP 753": "OD1" <-> "OD2" Residue "Y ASP 761": "OD1" <-> "OD2" Residue "Y GLU 764": "OE1" <-> "OE2" Residue "Y ASP 770": "OD1" <-> "OD2" Residue "Y ARG 772": "NH1" <-> "NH2" Residue "Y GLU 777": "OE1" <-> "OE2" Residue "Y ASP 810": "OD1" <-> "OD2" Residue "Y GLU 859": "OE1" <-> "OE2" Residue "Y ASP 867": "OD1" <-> "OD2" Residue "Y ARG 904": "NH1" <-> "NH2" Residue "Y GLU 932": "OE1" <-> "OE2" Residue "Y TYR 933": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 941": "NH1" <-> "NH2" Residue "Y GLU 962": "OE1" <-> "OE2" Residue "Y TYR 1013": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ASP 1040": "OD1" <-> "OD2" Residue "Y PHE 1042": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 1068": "OE1" <-> "OE2" Residue "Y ASP 1112": "OD1" <-> "OD2" Residue "Y ARG 1132": "NH1" <-> "NH2" Residue "Y GLU 1173": "OE1" <-> "OE2" Residue "Y TYR 1205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 1348": "OE1" <-> "OE2" Residue "Z GLU 33": "OE1" <-> "OE2" Residue "Z GLU 51": "OE1" <-> "OE2" Residue "Z PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 110": "NH1" <-> "NH2" Residue "Z GLU 141": "OE1" <-> "OE2" Residue "Z PHE 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 162": "NH1" <-> "NH2" Residue "Z ARG 173": "NH1" <-> "NH2" Residue "Z ARG 212": "NH1" <-> "NH2" Residue "Z ARG 234": "NH1" <-> "NH2" Residue "Z ARG 361": "NH1" <-> "NH2" Residue "Z ASP 404": "OD1" <-> "OD2" Residue "Z ARG 405": "NH1" <-> "NH2" Residue "Z TYR 407": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 433": "NH1" <-> "NH2" Residue "Z ASP 441": "OD1" <-> "OD2" Residue "Z GLU 511": "OE1" <-> "OE2" Residue "Z PHE 539": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 544": "OE1" <-> "OE2" Residue "Z ARG 555": "NH1" <-> "NH2" Residue "Z GLU 572": "OE1" <-> "OE2" Residue "Z ARG 574": "NH1" <-> "NH2" Residue "Z GLU 580": "OE1" <-> "OE2" Residue "Z GLU 591": "OE1" <-> "OE2" Residue "Z GLU 608": "OE1" <-> "OE2" Residue "Z ARG 642": "NH1" <-> "NH2" Residue "Z ASP 810": "OD1" <-> "OD2" Residue "Z GLU 855": "OE1" <-> "OE2" Residue "Z GLU 859": "OE1" <-> "OE2" Residue "Z ASP 863": "OD1" <-> "OD2" Residue "Z GLU 878": "OE1" <-> "OE2" Residue "Z GLU 888": "OE1" <-> "OE2" Residue "Z ARG 904": "NH1" <-> "NH2" Residue "Z ASP 909": "OD1" <-> "OD2" Residue "Z GLU 932": "OE1" <-> "OE2" Residue "Z ARG 941": "NH1" <-> "NH2" Residue "Z PHE 1032": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 1043": "OE1" <-> "OE2" Residue "Z ASP 1112": "OD1" <-> "OD2" Residue "Z PHE 1117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 1132": "NH1" <-> "NH2" Residue "Z GLU 1146": "OE1" <-> "OE2" Residue "Z GLU 1219": "OE1" <-> "OE2" Residue "Z GLU 1269": "OE1" <-> "OE2" Residue "Z GLU 1270": "OE1" <-> "OE2" Residue "Z GLU 1284": "OE1" <-> "OE2" Residue "Z ASP 1296": "OD1" <-> "OD2" Residue "Z GLU 1305": "OE1" <-> "OE2" Residue "Z GLU 1334": "OE1" <-> "OE2" Residue "Z PHE 1368": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.27s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 98674 Number of models: 1 Model: "" Number of chains: 26 Chain: "x" Number of atoms: 2328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2328 Classifications: {'peptide': 285} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 277} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "h" Number of atoms: 2398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2398 Classifications: {'peptide': 302} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 284} Chain: "I" Number of atoms: 2349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 296, 2349 Classifications: {'peptide': 296} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 279} Chain breaks: 1 Chain: "H" Number of atoms: 172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 172 Classifications: {'peptide': 20} Link IDs: {'TRANS': 19} Chain: "P" Number of atoms: 172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 172 Classifications: {'peptide': 20} Link IDs: {'TRANS': 19} Chain: "n" Number of atoms: 2334 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 2334 Classifications: {'peptide': 295} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 278} Chain breaks: 1 Chain: "o" Number of atoms: 2291 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2291 Classifications: {'peptide': 289} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 274} Chain breaks: 1 Chain: "g" Number of atoms: 929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 929 Classifications: {'peptide': 112} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 107} Chain breaks: 1 Chain: "m" Number of atoms: 2325 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 2325 Classifications: {'peptide': 290} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 278} Chain: "M" Number of atoms: 3848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 3848 Classifications: {'peptide': 468} Link IDs: {'PTRANS': 20, 'TRANS': 447} Chain breaks: 2 Chain: "N" Number of atoms: 558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 558 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 2, 'TRANS': 63} Chain: "O" Number of atoms: 589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 589 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 3, 'TRANS': 65} Chain breaks: 1 Chain: "1" Number of atoms: 2328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2328 Classifications: {'peptide': 285} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 277} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "Q" Number of atoms: 513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 513 Classifications: {'peptide': 63} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 60} Chain: "R" Number of atoms: 513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 513 Classifications: {'peptide': 63} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 60} Chain: "S" Number of atoms: 513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 513 Classifications: {'peptide': 63} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 60} Chain: "T" Number of atoms: 513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 513 Classifications: {'peptide': 63} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 60} Chain: "i" Number of atoms: 513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 513 Classifications: {'peptide': 63} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 60} Chain: "j" Number of atoms: 513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 513 Classifications: {'peptide': 63} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 60} Chain: "a" Number of atoms: 10260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1297, 10260 Classifications: {'peptide': 1297} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 76, 'TRANS': 1220} Chain breaks: 1 Chain: "A" Number of atoms: 10096 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1271, 10096 Classifications: {'peptide': 1271} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 75, 'TRANS': 1195} Chain breaks: 7 Chain: "B" Number of atoms: 10574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1335, 10574 Classifications: {'peptide': 1335} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 77, 'TRANS': 1257} Chain breaks: 2 Chain: "C" Number of atoms: 10549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1331, 10549 Classifications: {'peptide': 1331} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 77, 'TRANS': 1253} Chain breaks: 3 Chain: "D" Number of atoms: 10269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1297, 10269 Classifications: {'peptide': 1297} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 75, 'TRANS': 1221} Chain breaks: 1 Chain: "Y" Number of atoms: 10676 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1347, 10676 Classifications: {'peptide': 1347} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 78, 'TRANS': 1268} Chain breaks: 1 Chain: "Z" Number of atoms: 10551 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1333, 10551 Classifications: {'peptide': 1333} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 77, 'TRANS': 1255} Chain breaks: 3 Time building chain proxies: 42.02, per 1000 atoms: 0.43 Number of scatterers: 98674 At special positions: 0 Unit cell: (216.125, 271.375, 229.125, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 577 16.00 O 18000 8.00 N 17313 7.00 C 62784 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS a 481 " - pdb=" SG CYS a 542 " distance=2.06 Simple disulfide: pdb=" SG CYS a1292 " - pdb=" SG CYS a1303 " distance=2.04 Simple disulfide: pdb=" SG CYS B1292 " - pdb=" SG CYS B1303 " distance=2.01 Simple disulfide: pdb=" SG CYS C1292 " - pdb=" SG CYS C1303 " distance=2.02 Simple disulfide: pdb=" SG CYS D1292 " - pdb=" SG CYS D1303 " distance=2.09 Simple disulfide: pdb=" SG CYS Y1292 " - pdb=" SG CYS Y1303 " distance=2.02 Simple disulfide: pdb=" SG CYS Z1292 " - pdb=" SG CYS Z1303 " 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: 30.59 Conformation dependent library (CDL) restraints added in 11.6 seconds 24568 Ramachandran restraints generated. 12284 Oldfield, 0 Emsley, 12284 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 23742 Finding SS restraints... Secondary structure from input PDB file: 506 helices and 90 sheets defined 42.5% alpha, 9.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.64 Creating SS restraints... Processing helix chain 'x' and resid 9 through 22 Processing helix chain 'x' and resid 34 through 39 removed outlier: 3.682A pdb=" N LEU x 38 " --> pdb=" O HIS x 34 " (cutoff:3.500A) Processing helix chain 'x' and resid 40 through 42 No H-bonds generated for 'chain 'x' and resid 40 through 42' Processing helix chain 'x' and resid 47 through 69 Processing helix chain 'x' and resid 73 through 93 removed outlier: 3.601A pdb=" N LEU x 77 " --> pdb=" O LEU x 73 " (cutoff:3.500A) Processing helix chain 'x' and resid 99 through 111 removed outlier: 3.639A pdb=" N HIS x 105 " --> pdb=" O LYS x 101 " (cutoff:3.500A) Processing helix chain 'x' and resid 120 through 140 removed outlier: 4.322A pdb=" N GLU x 126 " --> pdb=" O ALA x 122 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ARG x 127 " --> pdb=" O GLU x 123 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N VAL x 140 " --> pdb=" O ALA x 136 " (cutoff:3.500A) Processing helix chain 'x' and resid 160 through 177 Processing helix chain 'x' and resid 194 through 239 Processing helix chain 'x' and resid 244 through 254 Processing helix chain 'x' and resid 260 through 273 Processing helix chain 'x' and resid 277 through 281 removed outlier: 4.131A pdb=" N ASP x 280 " --> pdb=" O ILE x 277 " (cutoff:3.500A) Processing helix chain 'h' and resid 17 through 26 removed outlier: 3.702A pdb=" N LYS h 26 " --> pdb=" O GLY h 22 " (cutoff:3.500A) Processing helix chain 'h' and resid 44 through 46 No H-bonds generated for 'chain 'h' and resid 44 through 46' Processing helix chain 'h' and resid 57 through 68 removed outlier: 3.637A pdb=" N LEU h 61 " --> pdb=" O GLY h 57 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ASN h 67 " --> pdb=" O GLY h 63 " (cutoff:3.500A) Processing helix chain 'h' and resid 140 through 157 removed outlier: 3.512A pdb=" N SER h 157 " --> pdb=" O MET h 153 " (cutoff:3.500A) Processing helix chain 'h' and resid 161 through 173 removed outlier: 4.379A pdb=" N GLN h 171 " --> pdb=" O ALA h 167 " (cutoff:3.500A) Processing helix chain 'h' and resid 190 through 210 Processing helix chain 'h' and resid 217 through 226 Processing helix chain 'h' and resid 228 through 246 removed outlier: 4.357A pdb=" N LEU h 237 " --> pdb=" O LYS h 233 " (cutoff:3.500A) Processing helix chain 'h' and resid 260 through 281 removed outlier: 3.990A pdb=" N GLU h 264 " --> pdb=" O SER h 260 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N LEU h 281 " --> pdb=" O GLN h 277 " (cutoff:3.500A) Processing helix chain 'I' and resid 17 through 25 Processing helix chain 'I' and resid 58 through 67 removed outlier: 3.524A pdb=" N ARG I 66 " --> pdb=" O ARG I 62 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ASN I 67 " --> pdb=" O GLY I 63 " (cutoff:3.500A) Processing helix chain 'I' and resid 140 through 156 Processing helix chain 'I' and resid 157 through 159 No H-bonds generated for 'chain 'I' and resid 157 through 159' Processing helix chain 'I' and resid 163 through 174 removed outlier: 4.004A pdb=" N THR I 174 " --> pdb=" O GLN I 170 " (cutoff:3.500A) Processing helix chain 'I' and resid 194 through 223 removed outlier: 3.535A pdb=" N SER I 212 " --> pdb=" O ALA I 208 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N THR I 215 " --> pdb=" O ALA I 211 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N MET I 216 " --> pdb=" O SER I 212 " (cutoff:3.500A) removed outlier: 5.233A pdb=" N THR I 217 " --> pdb=" O GLU I 213 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N ARG I 220 " --> pdb=" O MET I 216 " (cutoff:3.500A) Processing helix chain 'I' and resid 228 through 246 Processing helix chain 'I' and resid 260 through 277 removed outlier: 3.611A pdb=" N GLU I 264 " --> pdb=" O SER I 260 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLN I 277 " --> pdb=" O VAL I 273 " (cutoff:3.500A) Processing helix chain 'I' and resid 278 through 283 Processing helix chain 'H' and resid 2222 through 2240 removed outlier: 3.828A pdb=" N GLN H2226 " --> pdb=" O ARG H2222 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N VAL H2228 " --> pdb=" O LEU H2224 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N GLN H2233 " --> pdb=" O GLN H2229 " (cutoff:3.500A) Processing helix chain 'P' and resid 2222 through 2237 Processing helix chain 'n' and resid 17 through 25 Processing helix chain 'n' and resid 57 through 66 removed outlier: 3.576A pdb=" N ARG n 66 " --> pdb=" O ARG n 62 " (cutoff:3.500A) Processing helix chain 'n' and resid 140 through 157 removed outlier: 3.714A pdb=" N ASN n 147 " --> pdb=" O ALA n 143 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N LEU n 150 " --> pdb=" O ILE n 146 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N SER n 157 " --> pdb=" O MET n 153 " (cutoff:3.500A) Processing helix chain 'n' and resid 161 through 170 removed outlier: 4.072A pdb=" N GLN n 170 " --> pdb=" O LYS n 166 " (cutoff:3.500A) Processing helix chain 'n' and resid 190 through 210 Processing helix chain 'n' and resid 217 through 223 Processing helix chain 'n' and resid 228 through 236 removed outlier: 3.541A pdb=" N GLU n 236 " --> pdb=" O VAL n 232 " (cutoff:3.500A) Processing helix chain 'n' and resid 260 through 280 removed outlier: 4.105A pdb=" N ALA n 266 " --> pdb=" O ASP n 262 " (cutoff:3.500A) Processing helix chain 'o' and resid 17 through 25 Processing helix chain 'o' and resid 42 through 46 removed outlier: 3.569A pdb=" N GLN o 45 " --> pdb=" O LYS o 42 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LEU o 46 " --> pdb=" O HIS o 43 " (cutoff:3.500A) No H-bonds generated for 'chain 'o' and resid 42 through 46' Processing helix chain 'o' and resid 47 through 51 removed outlier: 3.975A pdb=" N GLN o 50 " --> pdb=" O GLY o 47 " (cutoff:3.500A) Processing helix chain 'o' and resid 58 through 67 removed outlier: 3.565A pdb=" N ARG o 66 " --> pdb=" O ARG o 62 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N ASN o 67 " --> pdb=" O GLY o 63 " (cutoff:3.500A) Processing helix chain 'o' and resid 140 through 156 Processing helix chain 'o' and resid 162 through 174 removed outlier: 3.593A pdb=" N LYS o 166 " --> pdb=" O TYR o 162 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N THR o 174 " --> pdb=" O GLN o 170 " (cutoff:3.500A) Processing helix chain 'o' and resid 194 through 223 removed outlier: 3.613A pdb=" N THR o 215 " --> pdb=" O ALA o 211 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N MET o 216 " --> pdb=" O SER o 212 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N THR o 217 " --> pdb=" O GLU o 213 " (cutoff:3.500A) Processing helix chain 'o' and resid 228 through 243 removed outlier: 3.809A pdb=" N VAL o 232 " --> pdb=" O SER o 228 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LYS o 233 " --> pdb=" O MET o 229 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N CYS o 234 " --> pdb=" O LEU o 230 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLN o 235 " --> pdb=" O LEU o 231 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLU o 236 " --> pdb=" O VAL o 232 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU o 237 " --> pdb=" O LYS o 233 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ARG o 243 " --> pdb=" O MET o 239 " (cutoff:3.500A) Processing helix chain 'o' and resid 260 through 277 Processing helix chain 'o' and resid 278 through 283 removed outlier: 3.781A pdb=" N ARG o 283 " --> pdb=" O ASP o 279 " (cutoff:3.500A) Processing helix chain 'o' and resid 295 through 297 No H-bonds generated for 'chain 'o' and resid 295 through 297' Processing helix chain 'g' and resid 211 through 223 Processing helix chain 'g' and resid 223 through 237 Processing helix chain 'm' and resid 2 through 7 removed outlier: 3.793A pdb=" N VAL m 6 " --> pdb=" O ASP m 2 " (cutoff:3.500A) Processing helix chain 'm' and resid 18 through 28 removed outlier: 3.605A pdb=" N THR m 22 " --> pdb=" O ASN m 18 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ALA m 26 " --> pdb=" O THR m 22 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N LYS m 27 " --> pdb=" O ALA m 23 " (cutoff:3.500A) Processing helix chain 'm' and resid 55 through 57 No H-bonds generated for 'chain 'm' and resid 55 through 57' Processing helix chain 'm' and resid 84 through 88 Processing helix chain 'm' and resid 95 through 103 Processing helix chain 'm' and resid 108 through 119 removed outlier: 4.232A pdb=" N ARG m 112 " --> pdb=" O ALA m 108 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA m 113 " --> pdb=" O SER m 109 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASP m 119 " --> pdb=" O LEU m 115 " (cutoff:3.500A) Processing helix chain 'm' and resid 156 through 160 removed outlier: 3.884A pdb=" N THR m 160 " --> pdb=" O THR m 157 " (cutoff:3.500A) Processing helix chain 'm' and resid 212 through 223 removed outlier: 4.742A pdb=" N VAL m 218 " --> pdb=" O THR m 214 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLY m 221 " --> pdb=" O ASP m 217 " (cutoff:3.500A) Processing helix chain 'm' and resid 223 through 237 Processing helix chain 'M' and resid 2 through 14 removed outlier: 3.930A pdb=" N TYR M 6 " --> pdb=" O GLU M 2 " (cutoff:3.500A) Processing helix chain 'M' and resid 33 through 39 removed outlier: 3.809A pdb=" N THR M 39 " --> pdb=" O GLU M 35 " (cutoff:3.500A) Processing helix chain 'M' and resid 78 through 88 removed outlier: 3.870A pdb=" N PHE M 82 " --> pdb=" O GLY M 78 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N THR M 88 " --> pdb=" O ARG M 84 " (cutoff:3.500A) Processing helix chain 'M' and resid 103 through 110 Processing helix chain 'M' and resid 301 through 310 removed outlier: 3.742A pdb=" N GLU M 305 " --> pdb=" O ALA M 301 " (cutoff:3.500A) Processing helix chain 'M' and resid 336 through 340 removed outlier: 3.990A pdb=" N ARG M 339 " --> pdb=" O TRP M 336 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLU M 340 " --> pdb=" O ARG M 337 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 336 through 340' Processing helix chain 'M' and resid 346 through 382 removed outlier: 3.552A pdb=" N LEU M 350 " --> pdb=" O HIS M 346 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N GLU M 364 " --> pdb=" O ARG M 360 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N TYR M 365 " --> pdb=" O ILE M 361 " (cutoff:3.500A) Processing helix chain 'M' and resid 400 through 417 Processing helix chain 'M' and resid 422 through 429 Processing helix chain 'M' and resid 435 through 448 Processing helix chain 'M' and resid 453 through 459 removed outlier: 3.611A pdb=" N LEU M 457 " --> pdb=" O LYS M 453 " (cutoff:3.500A) Processing helix chain 'M' and resid 552 through 560 removed outlier: 3.656A pdb=" N PHE M 559 " --> pdb=" O LEU M 555 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLN M 560 " --> pdb=" O ARG M 556 " (cutoff:3.500A) Processing helix chain 'N' and resid 31 through 41 Processing helix chain 'N' and resid 49 through 75 removed outlier: 3.891A pdb=" N MET N 53 " --> pdb=" O GLU N 49 " (cutoff:3.500A) Processing helix chain 'O' and resid 27 through 41 Processing helix chain 'O' and resid 55 through 79 Processing helix chain '1' and resid 9 through 22 removed outlier: 3.647A pdb=" N VAL 1 13 " --> pdb=" O GLN 1 9 " (cutoff:3.500A) Processing helix chain '1' and resid 34 through 40 removed outlier: 4.038A pdb=" N LEU 1 38 " --> pdb=" O HIS 1 34 " (cutoff:3.500A) Processing helix chain '1' and resid 47 through 70 removed outlier: 3.776A pdb=" N ASN 1 70 " --> pdb=" O LEU 1 66 " (cutoff:3.500A) Processing helix chain '1' and resid 73 through 93 removed outlier: 3.693A pdb=" N TYR 1 92 " --> pdb=" O ALA 1 88 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N THR 1 93 " --> pdb=" O ARG 1 89 " (cutoff:3.500A) Processing helix chain '1' and resid 98 through 110 removed outlier: 4.232A pdb=" N ALA 1 102 " --> pdb=" O ASP 1 98 " (cutoff:3.500A) Processing helix chain '1' and resid 120 through 141 Processing helix chain '1' and resid 160 through 174 Processing helix chain '1' and resid 194 through 240 Processing helix chain '1' and resid 244 through 254 removed outlier: 3.565A pdb=" N ASN 1 248 " --> pdb=" O SER 1 244 " (cutoff:3.500A) Processing helix chain '1' and resid 260 through 274 removed outlier: 4.057A pdb=" N ASP 1 274 " --> pdb=" O LEU 1 270 " (cutoff:3.500A) Processing helix chain 'Q' and resid 14 through 24 Processing helix chain 'Q' and resid 37 through 50 removed outlier: 4.980A pdb=" N SER Q 45 " --> pdb=" O ALA Q 41 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N LYS Q 46 " --> pdb=" O THR Q 42 " (cutoff:3.500A) Processing helix chain 'Q' and resid 56 through 72 removed outlier: 3.923A pdb=" N PHE Q 60 " --> pdb=" O ASP Q 56 " (cutoff:3.500A) Processing helix chain 'R' and resid 14 through 25 Processing helix chain 'R' and resid 37 through 49 removed outlier: 5.129A pdb=" N SER R 45 " --> pdb=" O ALA R 41 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N LYS R 46 " --> pdb=" O THR R 42 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ARG R 49 " --> pdb=" O SER R 45 " (cutoff:3.500A) Processing helix chain 'R' and resid 56 through 72 removed outlier: 4.149A pdb=" N PHE R 60 " --> pdb=" O ASP R 56 " (cutoff:3.500A) Processing helix chain 'S' and resid 14 through 25 Processing helix chain 'S' and resid 37 through 49 removed outlier: 4.770A pdb=" N SER S 45 " --> pdb=" O ALA S 41 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N LYS S 46 " --> pdb=" O THR S 42 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ARG S 49 " --> pdb=" O SER S 45 " (cutoff:3.500A) Processing helix chain 'S' and resid 56 through 72 removed outlier: 4.177A pdb=" N PHE S 60 " --> pdb=" O ASP S 56 " (cutoff:3.500A) Processing helix chain 'T' and resid 14 through 25 Processing helix chain 'T' and resid 37 through 48 removed outlier: 3.752A pdb=" N ALA T 41 " --> pdb=" O HIS T 37 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N SER T 45 " --> pdb=" O ALA T 41 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N LYS T 46 " --> pdb=" O THR T 42 " (cutoff:3.500A) Processing helix chain 'T' and resid 57 through 71 Processing helix chain 'i' and resid 14 through 24 removed outlier: 3.712A pdb=" N HIS i 18 " --> pdb=" O ARG i 14 " (cutoff:3.500A) Processing helix chain 'i' and resid 37 through 50 removed outlier: 3.710A pdb=" N ALA i 41 " --> pdb=" O HIS i 37 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N SER i 45 " --> pdb=" O ALA i 41 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N LYS i 46 " --> pdb=" O THR i 42 " (cutoff:3.500A) Processing helix chain 'i' and resid 56 through 71 removed outlier: 3.649A pdb=" N PHE i 60 " --> pdb=" O ASP i 56 " (cutoff:3.500A) Processing helix chain 'j' and resid 14 through 24 Processing helix chain 'j' and resid 37 through 49 removed outlier: 4.456A pdb=" N SER j 45 " --> pdb=" O ALA j 41 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N LYS j 46 " --> pdb=" O THR j 42 " (cutoff:3.500A) Processing helix chain 'j' and resid 56 through 72 removed outlier: 4.084A pdb=" N PHE j 60 " --> pdb=" O ASP j 56 " (cutoff:3.500A) Processing helix chain 'a' and resid 69 through 74 Processing helix chain 'a' and resid 82 through 86 removed outlier: 3.508A pdb=" N LYS a 85 " --> pdb=" O ASP a 82 " (cutoff:3.500A) Processing helix chain 'a' and resid 132 through 141 removed outlier: 3.675A pdb=" N GLU a 141 " --> pdb=" O THR a 137 " (cutoff:3.500A) Processing helix chain 'a' and resid 146 through 187 removed outlier: 4.144A pdb=" N LYS a 150 " --> pdb=" O THR a 146 " (cutoff:3.500A) Processing helix chain 'a' and resid 189 through 199 removed outlier: 3.767A pdb=" N VAL a 193 " --> pdb=" O PRO a 189 " (cutoff:3.500A) Processing helix chain 'a' and resid 208 through 226 removed outlier: 3.558A pdb=" N ARG a 212 " --> pdb=" O ASN a 208 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LEU a 224 " --> pdb=" O LYS a 220 " (cutoff:3.500A) Processing helix chain 'a' and resid 235 through 250 removed outlier: 3.953A pdb=" N ALA a 250 " --> pdb=" O LEU a 246 " (cutoff:3.500A) Processing helix chain 'a' and resid 263 through 267 removed outlier: 3.776A pdb=" N GLY a 266 " --> pdb=" O THR a 263 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ALA a 267 " --> pdb=" O SER a 264 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 263 through 267' Processing helix chain 'a' and resid 276 through 287 removed outlier: 3.687A pdb=" N ILE a 282 " --> pdb=" O ASN a 278 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N SER a 285 " --> pdb=" O GLN a 281 " (cutoff:3.500A) Processing helix chain 'a' and resid 308 through 319 removed outlier: 3.508A pdb=" N HIS a 319 " --> pdb=" O ALA a 315 " (cutoff:3.500A) Processing helix chain 'a' and resid 324 through 335 removed outlier: 3.516A pdb=" N THR a 333 " --> pdb=" O LYS a 329 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLY a 335 " --> pdb=" O HIS a 331 " (cutoff:3.500A) Processing helix chain 'a' and resid 419 through 424 Processing helix chain 'a' and resid 445 through 450 removed outlier: 3.685A pdb=" N CYS a 450 " --> pdb=" O LEU a 446 " (cutoff:3.500A) Processing helix chain 'a' and resid 457 through 467 removed outlier: 3.882A pdb=" N ARG a 467 " --> pdb=" O THR a 463 " (cutoff:3.500A) Processing helix chain 'a' and resid 472 through 476 removed outlier: 3.573A pdb=" N MET a 475 " --> pdb=" O GLU a 472 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLN a 476 " --> pdb=" O PRO a 473 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 472 through 476' Processing helix chain 'a' and resid 490 through 499 Proline residue: a 496 - end of helix removed outlier: 4.083A pdb=" N TYR a 499 " --> pdb=" O ILE a 495 " (cutoff:3.500A) Processing helix chain 'a' and resid 508 through 513 Processing helix chain 'a' and resid 527 through 531 removed outlier: 4.166A pdb=" N TYR a 530 " --> pdb=" O ILE a 527 " (cutoff:3.500A) Processing helix chain 'a' and resid 557 through 561 removed outlier: 3.867A pdb=" N ASN a 560 " --> pdb=" O VAL a 557 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU a 561 " --> pdb=" O ILE a 558 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 557 through 561' Processing helix chain 'a' and resid 567 through 582 Processing helix chain 'a' and resid 590 through 602 Processing helix chain 'a' and resid 608 through 616 removed outlier: 3.568A pdb=" N LEU a 612 " --> pdb=" O GLU a 608 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ASP a 614 " --> pdb=" O CYS a 610 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N VAL a 615 " --> pdb=" O TYR a 611 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU a 616 " --> pdb=" O LEU a 612 " (cutoff:3.500A) Processing helix chain 'a' and resid 620 through 626 removed outlier: 3.621A pdb=" N LEU a 626 " --> pdb=" O ASP a 622 " (cutoff:3.500A) Processing helix chain 'a' and resid 627 through 642 removed outlier: 3.974A pdb=" N MET a 638 " --> pdb=" O CYS a 634 " (cutoff:3.500A) Processing helix chain 'a' and resid 651 through 661 removed outlier: 4.693A pdb=" N ILE a 657 " --> pdb=" O LEU a 653 " (cutoff:3.500A) Processing helix chain 'a' and resid 667 through 689 removed outlier: 3.702A pdb=" N LEU a 671 " --> pdb=" O PRO a 667 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ALA a 689 " --> pdb=" O THR a 685 " (cutoff:3.500A) Processing helix chain 'a' and resid 703 through 708 removed outlier: 3.856A pdb=" N VAL a 707 " --> pdb=" O LEU a 703 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ASN a 708 " --> pdb=" O SER a 704 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 703 through 708' Processing helix chain 'a' and resid 753 through 759 removed outlier: 3.925A pdb=" N LEU a 757 " --> pdb=" O ASP a 753 " (cutoff:3.500A) Processing helix chain 'a' and resid 774 through 787 Processing helix chain 'a' and resid 787 through 794 Processing helix chain 'a' and resid 803 through 809 removed outlier: 3.583A pdb=" N LEU a 807 " --> pdb=" O ASN a 803 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N VAL a 809 " --> pdb=" O LYS a 805 " (cutoff:3.500A) Processing helix chain 'a' and resid 814 through 819 Processing helix chain 'a' and resid 845 through 854 Processing helix chain 'a' and resid 854 through 861 removed outlier: 3.708A pdb=" N THR a 858 " --> pdb=" O GLY a 854 " (cutoff:3.500A) Processing helix chain 'a' and resid 871 through 881 Processing helix chain 'a' and resid 945 through 953 Processing helix chain 'a' and resid 954 through 963 Processing helix chain 'a' and resid 964 through 968 removed outlier: 3.540A pdb=" N HIS a 967 " --> pdb=" O PRO a 964 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ARG a 968 " --> pdb=" O HIS a 965 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 964 through 968' Processing helix chain 'a' and resid 981 through 985 removed outlier: 3.800A pdb=" N ASN a 985 " --> pdb=" O GLU a 982 " (cutoff:3.500A) Processing helix chain 'a' and resid 988 through 995 removed outlier: 3.973A pdb=" N SER a 992 " --> pdb=" O ARG a 988 " (cutoff:3.500A) Processing helix chain 'a' and resid 1001 through 1010 Processing helix chain 'a' and resid 1011 through 1013 No H-bonds generated for 'chain 'a' and resid 1011 through 1013' Processing helix chain 'a' and resid 1016 through 1026 removed outlier: 3.543A pdb=" N ALA a1026 " --> pdb=" O LEU a1022 " (cutoff:3.500A) Processing helix chain 'a' and resid 1112 through 1117 removed outlier: 3.625A pdb=" N VAL a1116 " --> pdb=" O ASP a1112 " (cutoff:3.500A) Processing helix chain 'a' and resid 1124 through 1135 removed outlier: 3.561A pdb=" N ASP a1128 " --> pdb=" O HIS a1124 " (cutoff:3.500A) Processing helix chain 'a' and resid 1145 through 1152 Processing helix chain 'a' and resid 1181 through 1186 Processing helix chain 'a' and resid 1198 through 1202 removed outlier: 3.514A pdb=" N ALA a1201 " --> pdb=" O CYS a1198 " (cutoff:3.500A) Processing helix chain 'a' and resid 1206 through 1215 removed outlier: 3.587A pdb=" N ALA a1210 " --> pdb=" O ASP a1206 " (cutoff:3.500A) Processing helix chain 'a' and resid 1238 through 1245 Processing helix chain 'a' and resid 1245 through 1252 removed outlier: 3.523A pdb=" N LEU a1252 " --> pdb=" O HIS a1248 " (cutoff:3.500A) Processing helix chain 'a' and resid 1262 through 1267 Processing helix chain 'a' and resid 1267 through 1274 removed outlier: 3.507A pdb=" N ILE a1271 " --> pdb=" O ASN a1267 " (cutoff:3.500A) Processing helix chain 'a' and resid 1277 through 1288 Processing helix chain 'a' and resid 1313 through 1319 removed outlier: 4.167A pdb=" N LEU a1317 " --> pdb=" O ASN a1313 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N THR a1318 " --> pdb=" O PRO a1314 " (cutoff:3.500A) Processing helix chain 'a' and resid 1329 through 1339 removed outlier: 3.661A pdb=" N MET a1333 " --> pdb=" O THR a1329 " (cutoff:3.500A) Processing helix chain 'a' and resid 1342 through 1346 removed outlier: 3.781A pdb=" N THR a1346 " --> pdb=" O ALA a1343 " (cutoff:3.500A) Processing helix chain 'A' and resid 9 through 14 removed outlier: 4.261A pdb=" N VAL A 13 " --> pdb=" O LEU A 9 " (cutoff:3.500A) Processing helix chain 'A' and resid 31 through 39 Processing helix chain 'A' and resid 69 through 75 removed outlier: 3.564A pdb=" N ALA A 75 " --> pdb=" O ALA A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 141 removed outlier: 3.651A pdb=" N TYR A 138 " --> pdb=" O ALA A 134 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LEU A 139 " --> pdb=" O CYS A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 169 Processing helix chain 'A' and resid 169 through 185 Processing helix chain 'A' and resid 189 through 201 removed outlier: 3.824A pdb=" N THR A 201 " --> pdb=" O VAL A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 226 removed outlier: 3.922A pdb=" N THR A 226 " --> pdb=" O LYS A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 233 removed outlier: 3.560A pdb=" N THR A 233 " --> pdb=" O LEU A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 249 removed outlier: 3.693A pdb=" N VAL A 239 " --> pdb=" O ASP A 235 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA A 249 " --> pdb=" O ARG A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 287 Processing helix chain 'A' and resid 309 through 323 removed outlier: 3.884A pdb=" N VAL A 313 " --> pdb=" O PRO A 309 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N SER A 317 " --> pdb=" O VAL A 313 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N TYR A 318 " --> pdb=" O THR A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 377 removed outlier: 3.933A pdb=" N TYR A 376 " --> pdb=" O LEU A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 450 removed outlier: 3.920A pdb=" N CYS A 450 " --> pdb=" O LEU A 446 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 456 removed outlier: 3.924A pdb=" N GLU A 456 " --> pdb=" O VAL A 453 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 468 Processing helix chain 'A' and resid 494 through 501 removed outlier: 3.722A pdb=" N PHE A 498 " --> pdb=" O ARG A 494 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N TYR A 499 " --> pdb=" O ILE A 495 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N VAL A 501 " --> pdb=" O HIS A 497 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 514 Processing helix chain 'A' and resid 517 through 522 removed outlier: 4.370A pdb=" N TYR A 522 " --> pdb=" O VAL A 518 " (cutoff:3.500A) Processing helix chain 'A' and resid 528 through 532 removed outlier: 3.760A pdb=" N THR A 531 " --> pdb=" O THR A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 557 through 561 Processing helix chain 'A' and resid 567 through 582 Processing helix chain 'A' and resid 590 through 602 Processing helix chain 'A' and resid 609 through 618 Processing helix chain 'A' and resid 620 through 625 Processing helix chain 'A' and resid 630 through 641 removed outlier: 3.546A pdb=" N VAL A 636 " --> pdb=" O ALA A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 650 through 660 removed outlier: 4.231A pdb=" N LEU A 656 " --> pdb=" O ALA A 652 " (cutoff:3.500A) Processing helix chain 'A' and resid 667 through 685 removed outlier: 3.707A pdb=" N LEU A 671 " --> pdb=" O PRO A 667 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU A 681 " --> pdb=" O LEU A 677 " (cutoff:3.500A) Processing helix chain 'A' and resid 686 through 689 Processing helix chain 'A' and resid 703 through 708 removed outlier: 3.648A pdb=" N ASN A 708 " --> pdb=" O SER A 704 " (cutoff:3.500A) Processing helix chain 'A' and resid 753 through 759 removed outlier: 3.558A pdb=" N LEU A 757 " --> pdb=" O ASP A 753 " (cutoff:3.500A) Processing helix chain 'A' and resid 775 through 794 removed outlier: 3.527A pdb=" N LEU A 780 " --> pdb=" O ASP A 776 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLN A 781 " --> pdb=" O GLU A 777 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N MET A 789 " --> pdb=" O TYR A 785 " (cutoff:3.500A) Proline residue: A 790 - end of helix Processing helix chain 'A' and resid 803 through 812 removed outlier: 4.004A pdb=" N VAL A 809 " --> pdb=" O LYS A 805 " (cutoff:3.500A) Processing helix chain 'A' and resid 846 through 854 removed outlier: 3.848A pdb=" N ARG A 850 " --> pdb=" O ILE A 846 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N GLN A 851 " --> pdb=" O ALA A 847 " (cutoff:3.500A) Processing helix chain 'A' and resid 854 through 861 removed outlier: 3.582A pdb=" N THR A 858 " --> pdb=" O GLY A 854 " (cutoff:3.500A) Processing helix chain 'A' and resid 861 through 866 removed outlier: 3.856A pdb=" N THR A 866 " --> pdb=" O GLU A 862 " (cutoff:3.500A) Processing helix chain 'A' and resid 871 through 881 removed outlier: 3.743A pdb=" N ALA A 875 " --> pdb=" O PRO A 871 " (cutoff:3.500A) Processing helix chain 'A' and resid 882 through 886 removed outlier: 3.768A pdb=" N PHE A 885 " --> pdb=" O ALA A 882 " (cutoff:3.500A) Processing helix chain 'A' and resid 927 through 931 removed outlier: 4.039A pdb=" N ILE A 931 " --> pdb=" O LYS A 928 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 950 removed outlier: 3.786A pdb=" N ALA A 950 " --> pdb=" O PRO A 946 " (cutoff:3.500A) Processing helix chain 'A' and resid 953 through 963 Processing helix chain 'A' and resid 964 through 967 Processing helix chain 'A' and resid 988 through 997 removed outlier: 3.697A pdb=" N SER A 992 " --> pdb=" O ARG A 988 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N THR A 997 " --> pdb=" O ARG A 993 " (cutoff:3.500A) Processing helix chain 'A' and resid 1001 through 1011 Processing helix chain 'A' and resid 1016 through 1025 Processing helix chain 'A' and resid 1112 through 1117 Processing helix chain 'A' and resid 1125 through 1136 Processing helix chain 'A' and resid 1182 through 1187 removed outlier: 3.623A pdb=" N LYS A1187 " --> pdb=" O VAL A1183 " (cutoff:3.500A) Processing helix chain 'A' and resid 1206 through 1214 removed outlier: 4.056A pdb=" N LYS A1212 " --> pdb=" O GLU A1208 " (cutoff:3.500A) Processing helix chain 'A' and resid 1239 through 1243 Processing helix chain 'A' and resid 1262 through 1266 Processing helix chain 'A' and resid 1269 through 1287 removed outlier: 3.841A pdb=" N LEU A1278 " --> pdb=" O ALA A1274 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N ASP A1283 " --> pdb=" O PHE A1279 " (cutoff:3.500A) Processing helix chain 'A' and resid 1307 through 1312 removed outlier: 3.733A pdb=" N GLU A1312 " --> pdb=" O GLU A1308 " (cutoff:3.500A) Processing helix chain 'A' and resid 1329 through 1338 Processing helix chain 'A' and resid 1362 through 1367 Processing helix chain 'B' and resid 3 through 10 removed outlier: 3.960A pdb=" N LEU B 7 " --> pdb=" O ASN B 3 " (cutoff:3.500A) Processing helix chain 'B' and resid 22 through 29 Processing helix chain 'B' and resid 42 through 46 removed outlier: 4.443A pdb=" N ARG B 45 " --> pdb=" O ASP B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 69 through 75 Processing helix chain 'B' and resid 133 through 141 removed outlier: 3.752A pdb=" N ARG B 140 " --> pdb=" O LEU B 136 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLU B 141 " --> pdb=" O THR B 137 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 186 removed outlier: 3.720A pdb=" N LYS B 150 " --> pdb=" O THR B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 199 removed outlier: 3.719A pdb=" N THR B 195 " --> pdb=" O PHE B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 226 Processing helix chain 'B' and resid 235 through 250 removed outlier: 3.818A pdb=" N ALA B 250 " --> pdb=" O LEU B 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 265 through 267 No H-bonds generated for 'chain 'B' and resid 265 through 267' Processing helix chain 'B' and resid 276 through 287 Processing helix chain 'B' and resid 311 through 323 removed outlier: 3.910A pdb=" N SER B 317 " --> pdb=" O VAL B 313 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 349 removed outlier: 3.801A pdb=" N ALA B 349 " --> pdb=" O SER B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 377 removed outlier: 3.572A pdb=" N TYR B 376 " --> pdb=" O LEU B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 406 removed outlier: 3.503A pdb=" N ARG B 405 " --> pdb=" O PRO B 402 " (cutoff:3.500A) Processing helix chain 'B' and resid 442 through 444 No H-bonds generated for 'chain 'B' and resid 442 through 444' Processing helix chain 'B' and resid 445 through 450 removed outlier: 3.964A pdb=" N CYS B 450 " --> pdb=" O LEU B 446 " (cutoff:3.500A) Processing helix chain 'B' and resid 457 through 468 removed outlier: 4.113A pdb=" N GLU B 466 " --> pdb=" O GLN B 462 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 479 removed outlier: 3.507A pdb=" N LEU B 478 " --> pdb=" O MET B 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 490 through 494 Processing helix chain 'B' and resid 508 through 513 Processing helix chain 'B' and resid 519 through 523 Processing helix chain 'B' and resid 567 through 582 removed outlier: 3.535A pdb=" N GLU B 577 " --> pdb=" O LEU B 573 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N MET B 582 " --> pdb=" O ILE B 578 " (cutoff:3.500A) Processing helix chain 'B' and resid 591 through 603 removed outlier: 3.582A pdb=" N THR B 602 " --> pdb=" O LYS B 598 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N SER B 603 " --> pdb=" O THR B 599 " (cutoff:3.500A) Processing helix chain 'B' and resid 608 through 618 removed outlier: 3.631A pdb=" N LEU B 612 " --> pdb=" O GLU B 608 " (cutoff:3.500A) Processing helix chain 'B' and resid 620 through 627 Processing helix chain 'B' and resid 627 through 642 removed outlier: 3.798A pdb=" N ARG B 633 " --> pdb=" O THR B 629 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL B 636 " --> pdb=" O ALA B 632 " (cutoff:3.500A) Processing helix chain 'B' and resid 650 through 661 removed outlier: 3.542A pdb=" N VAL B 654 " --> pdb=" O SER B 650 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LEU B 656 " --> pdb=" O ALA B 652 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N GLU B 659 " --> pdb=" O THR B 655 " (cutoff:3.500A) Processing helix chain 'B' and resid 667 through 689 removed outlier: 3.683A pdb=" N TYR B 674 " --> pdb=" O LEU B 670 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA B 689 " --> pdb=" O THR B 685 " (cutoff:3.500A) Processing helix chain 'B' and resid 708 through 712 removed outlier: 3.582A pdb=" N HIS B 711 " --> pdb=" O ASN B 708 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ASP B 712 " --> pdb=" O ALA B 709 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 708 through 712' Processing helix chain 'B' and resid 754 through 759 Processing helix chain 'B' and resid 774 through 788 removed outlier: 3.907A pdb=" N LEU B 788 " --> pdb=" O PHE B 784 " (cutoff:3.500A) Processing helix chain 'B' and resid 788 through 794 Processing helix chain 'B' and resid 803 through 811 Processing helix chain 'B' and resid 814 through 819 removed outlier: 3.812A pdb=" N LEU B 819 " --> pdb=" O PRO B 815 " (cutoff:3.500A) Processing helix chain 'B' and resid 845 through 853 Processing helix chain 'B' and resid 857 through 862 Processing helix chain 'B' and resid 871 through 881 removed outlier: 3.590A pdb=" N ALA B 875 " --> pdb=" O PRO B 871 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LEU B 879 " --> pdb=" O ALA B 875 " (cutoff:3.500A) Processing helix chain 'B' and resid 902 through 906 removed outlier: 3.550A pdb=" N GLN B 905 " --> pdb=" O ALA B 902 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 953 Processing helix chain 'B' and resid 953 through 963 Processing helix chain 'B' and resid 964 through 967 Processing helix chain 'B' and resid 988 through 998 removed outlier: 3.740A pdb=" N SER B 992 " --> pdb=" O ARG B 988 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ALA B 996 " --> pdb=" O SER B 992 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N THR B 997 " --> pdb=" O ARG B 993 " (cutoff:3.500A) Processing helix chain 'B' and resid 1001 through 1011 removed outlier: 3.858A pdb=" N VAL B1005 " --> pdb=" O VAL B1001 " (cutoff:3.500A) Processing helix chain 'B' and resid 1016 through 1026 removed outlier: 3.609A pdb=" N LYS B1025 " --> pdb=" O VAL B1021 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ALA B1026 " --> pdb=" O LEU B1022 " (cutoff:3.500A) Processing helix chain 'B' and resid 1112 through 1117 removed outlier: 3.931A pdb=" N VAL B1116 " --> pdb=" O ASP B1112 " (cutoff:3.500A) Processing helix chain 'B' and resid 1124 through 1135 removed outlier: 3.580A pdb=" N ASP B1128 " --> pdb=" O HIS B1124 " (cutoff:3.500A) Processing helix chain 'B' and resid 1144 through 1153 Processing helix chain 'B' and resid 1181 through 1186 removed outlier: 3.971A pdb=" N PHE B1186 " --> pdb=" O ASP B1182 " (cutoff:3.500A) Processing helix chain 'B' and resid 1206 through 1216 Processing helix chain 'B' and resid 1239 through 1243 Processing helix chain 'B' and resid 1245 through 1250 Processing helix chain 'B' and resid 1260 through 1265 removed outlier: 4.096A pdb=" N GLN B1264 " --> pdb=" O PRO B1261 " (cutoff:3.500A) Processing helix chain 'B' and resid 1277 through 1288 removed outlier: 3.529A pdb=" N LEU B1287 " --> pdb=" O ASP B1283 " (cutoff:3.500A) Processing helix chain 'B' and resid 1314 through 1319 removed outlier: 3.716A pdb=" N THR B1318 " --> pdb=" O PRO B1314 " (cutoff:3.500A) Processing helix chain 'B' and resid 1330 through 1337 Processing helix chain 'B' and resid 1365 through 1370 removed outlier: 3.720A pdb=" N SER B1370 " --> pdb=" O MET B1366 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 10 Processing helix chain 'C' and resid 42 through 47 removed outlier: 4.337A pdb=" N ARG C 45 " --> pdb=" O ASP C 42 " (cutoff:3.500A) Processing helix chain 'C' and resid 69 through 74 removed outlier: 3.578A pdb=" N ALA C 72 " --> pdb=" O SER C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 84 No H-bonds generated for 'chain 'C' and resid 82 through 84' Processing helix chain 'C' and resid 133 through 140 removed outlier: 3.826A pdb=" N ARG C 140 " --> pdb=" O LEU C 136 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 186 removed outlier: 3.866A pdb=" N ILE C 151 " --> pdb=" O ILE C 147 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU C 152 " --> pdb=" O LEU C 148 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N MET C 157 " --> pdb=" O ASN C 153 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LYS C 186 " --> pdb=" O THR C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 189 through 199 removed outlier: 3.696A pdb=" N VAL C 193 " --> pdb=" O PRO C 189 " (cutoff:3.500A) Processing helix chain 'C' and resid 208 through 226 removed outlier: 3.718A pdb=" N LEU C 224 " --> pdb=" O LYS C 220 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N THR C 226 " --> pdb=" O LYS C 222 " (cutoff:3.500A) Processing helix chain 'C' and resid 235 through 250 removed outlier: 3.902A pdb=" N ALA C 250 " --> pdb=" O LEU C 246 " (cutoff:3.500A) Processing helix chain 'C' and resid 263 through 267 removed outlier: 3.949A pdb=" N GLY C 266 " --> pdb=" O THR C 263 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ALA C 267 " --> pdb=" O SER C 264 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 263 through 267' Processing helix chain 'C' and resid 276 through 287 Processing helix chain 'C' and resid 308 through 318 removed outlier: 3.759A pdb=" N ALA C 312 " --> pdb=" O SER C 308 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N VAL C 313 " --> pdb=" O PRO C 309 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N THR C 314 " --> pdb=" O GLU C 310 " (cutoff:3.500A) Processing helix chain 'C' and resid 324 through 335 Processing helix chain 'C' and resid 342 through 347 Processing helix chain 'C' and resid 445 through 450 Processing helix chain 'C' and resid 451 through 456 Processing helix chain 'C' and resid 457 through 468 Processing helix chain 'C' and resid 472 through 477 Processing helix chain 'C' and resid 490 through 501 Proline residue: C 496 - end of helix removed outlier: 4.221A pdb=" N TYR C 499 " --> pdb=" O ILE C 495 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N VAL C 501 " --> pdb=" O HIS C 497 " (cutoff:3.500A) Processing helix chain 'C' and resid 510 through 514 removed outlier: 3.544A pdb=" N LYS C 513 " --> pdb=" O ASN C 510 " (cutoff:3.500A) Processing helix chain 'C' and resid 557 through 561 Processing helix chain 'C' and resid 567 through 582 Processing helix chain 'C' and resid 590 through 602 removed outlier: 3.551A pdb=" N LEU C 596 " --> pdb=" O GLU C 592 " (cutoff:3.500A) Processing helix chain 'C' and resid 608 through 618 removed outlier: 3.843A pdb=" N LEU C 612 " --> pdb=" O GLU C 608 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N HIS C 618 " --> pdb=" O ASP C 614 " (cutoff:3.500A) Processing helix chain 'C' and resid 620 through 643 removed outlier: 6.219A pdb=" N THR C 629 " --> pdb=" O LEU C 625 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N PHE C 630 " --> pdb=" O LEU C 626 " (cutoff:3.500A) Processing helix chain 'C' and resid 650 through 661 removed outlier: 3.704A pdb=" N VAL C 654 " --> pdb=" O SER C 650 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N LEU C 656 " --> pdb=" O ALA C 652 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ALA C 658 " --> pdb=" O VAL C 654 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N GLU C 659 " --> pdb=" O THR C 655 " (cutoff:3.500A) Processing helix chain 'C' and resid 667 through 688 Processing helix chain 'C' and resid 703 through 708 removed outlier: 3.571A pdb=" N VAL C 707 " --> pdb=" O LEU C 703 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ASN C 708 " --> pdb=" O SER C 704 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 703 through 708' Processing helix chain 'C' and resid 709 through 712 Processing helix chain 'C' and resid 753 through 759 removed outlier: 3.512A pdb=" N LEU C 757 " --> pdb=" O ASP C 753 " (cutoff:3.500A) Processing helix chain 'C' and resid 774 through 788 Processing helix chain 'C' and resid 788 through 794 Processing helix chain 'C' and resid 803 through 812 removed outlier: 4.120A pdb=" N VAL C 809 " --> pdb=" O LYS C 805 " (cutoff:3.500A) Processing helix chain 'C' and resid 814 through 819 removed outlier: 3.933A pdb=" N LEU C 819 " --> pdb=" O PRO C 815 " (cutoff:3.500A) Processing helix chain 'C' and resid 846 through 852 Processing helix chain 'C' and resid 854 through 861 Processing helix chain 'C' and resid 871 through 880 Processing helix chain 'C' and resid 881 through 885 removed outlier: 3.593A pdb=" N GLN C 884 " --> pdb=" O LEU C 881 " (cutoff:3.500A) Processing helix chain 'C' and resid 927 through 934 removed outlier: 3.966A pdb=" N ILE C 931 " --> pdb=" O LYS C 928 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N GLU C 932 " --> pdb=" O THR C 929 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N SER C 934 " --> pdb=" O ILE C 931 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 951 removed outlier: 3.746A pdb=" N ALA C 951 " --> pdb=" O THR C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 953 through 963 Processing helix chain 'C' and resid 964 through 967 Processing helix chain 'C' and resid 988 through 996 removed outlier: 3.769A pdb=" N SER C 992 " --> pdb=" O ARG C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1001 through 1011 removed outlier: 3.780A pdb=" N VAL C1005 " --> pdb=" O VAL C1001 " (cutoff:3.500A) Processing helix chain 'C' and resid 1016 through 1025 Processing helix chain 'C' and resid 1112 through 1117 Processing helix chain 'C' and resid 1126 through 1136 Processing helix chain 'C' and resid 1147 through 1154 Processing helix chain 'C' and resid 1181 through 1186 Processing helix chain 'C' and resid 1206 through 1216 Processing helix chain 'C' and resid 1238 through 1243 Processing helix chain 'C' and resid 1245 through 1253 Processing helix chain 'C' and resid 1262 through 1266 removed outlier: 3.552A pdb=" N PHE C1266 " --> pdb=" O ALA C1263 " (cutoff:3.500A) Processing helix chain 'C' and resid 1277 through 1287 removed outlier: 3.681A pdb=" N LEU C1287 " --> pdb=" O ASP C1283 " (cutoff:3.500A) Processing helix chain 'C' and resid 1314 through 1319 Processing helix chain 'C' and resid 1329 through 1339 removed outlier: 3.520A pdb=" N MET C1333 " --> pdb=" O THR C1329 " (cutoff:3.500A) Processing helix chain 'C' and resid 1342 through 1346 removed outlier: 3.931A pdb=" N ALA C1345 " --> pdb=" O GLY C1342 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N THR C1346 " --> pdb=" O ALA C1343 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1342 through 1346' Processing helix chain 'D' and resid 69 through 74 removed outlier: 3.637A pdb=" N ALA D 72 " --> pdb=" O SER D 69 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA D 74 " --> pdb=" O LEU D 71 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 84 No H-bonds generated for 'chain 'D' and resid 82 through 84' Processing helix chain 'D' and resid 132 through 141 removed outlier: 3.922A pdb=" N ARG D 140 " --> pdb=" O LEU D 136 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLU D 141 " --> pdb=" O THR D 137 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 185 Processing helix chain 'D' and resid 189 through 199 removed outlier: 3.752A pdb=" N VAL D 193 " --> pdb=" O PRO D 189 " (cutoff:3.500A) Processing helix chain 'D' and resid 208 through 224 removed outlier: 3.838A pdb=" N LEU D 224 " --> pdb=" O LYS D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 228 through 233 Processing helix chain 'D' and resid 235 through 250 removed outlier: 3.718A pdb=" N ALA D 250 " --> pdb=" O LEU D 246 " (cutoff:3.500A) Processing helix chain 'D' and resid 276 through 287 removed outlier: 3.534A pdb=" N MET D 280 " --> pdb=" O THR D 276 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 318 removed outlier: 3.670A pdb=" N THR D 314 " --> pdb=" O GLU D 310 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ILE D 316 " --> pdb=" O ALA D 312 " (cutoff:3.500A) Processing helix chain 'D' and resid 324 through 335 Processing helix chain 'D' and resid 342 through 347 removed outlier: 3.592A pdb=" N GLN D 346 " --> pdb=" O ASP D 342 " (cutoff:3.500A) Processing helix chain 'D' and resid 372 through 377 Processing helix chain 'D' and resid 419 through 424 Processing helix chain 'D' and resid 445 through 449 removed outlier: 3.755A pdb=" N THR D 448 " --> pdb=" O ALA D 445 " (cutoff:3.500A) Processing helix chain 'D' and resid 451 through 456 removed outlier: 3.865A pdb=" N GLU D 456 " --> pdb=" O VAL D 453 " (cutoff:3.500A) Processing helix chain 'D' and resid 457 through 468 Processing helix chain 'D' and resid 494 through 499 Processing helix chain 'D' and resid 517 through 522 removed outlier: 4.147A pdb=" N TYR D 522 " --> pdb=" O VAL D 518 " (cutoff:3.500A) Processing helix chain 'D' and resid 557 through 561 removed outlier: 3.618A pdb=" N LEU D 561 " --> pdb=" O ILE D 558 " (cutoff:3.500A) Processing helix chain 'D' and resid 567 through 582 Processing helix chain 'D' and resid 590 through 602 removed outlier: 4.024A pdb=" N LEU D 594 " --> pdb=" O TYR D 590 " (cutoff:3.500A) Processing helix chain 'D' and resid 608 through 618 removed outlier: 3.742A pdb=" N LEU D 612 " --> pdb=" O GLU D 608 " (cutoff:3.500A) Processing helix chain 'D' and resid 620 through 627 Processing helix chain 'D' and resid 627 through 642 Processing helix chain 'D' and resid 650 through 661 removed outlier: 3.541A pdb=" N VAL D 654 " --> pdb=" O SER D 650 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLU D 659 " --> pdb=" O THR D 655 " (cutoff:3.500A) Processing helix chain 'D' and resid 667 through 688 removed outlier: 4.290A pdb=" N HIS D 673 " --> pdb=" O GLN D 669 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N TYR D 674 " --> pdb=" O LEU D 670 " (cutoff:3.500A) Processing helix chain 'D' and resid 702 through 708 removed outlier: 3.560A pdb=" N ASN D 708 " --> pdb=" O SER D 704 " (cutoff:3.500A) Processing helix chain 'D' and resid 753 through 759 removed outlier: 3.704A pdb=" N LEU D 757 " --> pdb=" O ASP D 753 " (cutoff:3.500A) Processing helix chain 'D' and resid 774 through 787 Processing helix chain 'D' and resid 789 through 794 Processing helix chain 'D' and resid 803 through 811 removed outlier: 3.872A pdb=" N VAL D 809 " --> pdb=" O LYS D 805 " (cutoff:3.500A) Processing helix chain 'D' and resid 814 through 819 removed outlier: 3.789A pdb=" N LEU D 819 " --> pdb=" O PRO D 815 " (cutoff:3.500A) Processing helix chain 'D' and resid 846 through 848 No H-bonds generated for 'chain 'D' and resid 846 through 848' Processing helix chain 'D' and resid 849 through 854 removed outlier: 3.513A pdb=" N GLY D 854 " --> pdb=" O ARG D 850 " (cutoff:3.500A) Processing helix chain 'D' and resid 857 through 860 Processing helix chain 'D' and resid 861 through 866 Processing helix chain 'D' and resid 871 through 880 removed outlier: 3.969A pdb=" N ALA D 875 " --> pdb=" O PRO D 871 " (cutoff:3.500A) Processing helix chain 'D' and resid 881 through 883 No H-bonds generated for 'chain 'D' and resid 881 through 883' Processing helix chain 'D' and resid 945 through 950 Processing helix chain 'D' and resid 954 through 963 Processing helix chain 'D' and resid 964 through 968 Processing helix chain 'D' and resid 988 through 996 removed outlier: 3.753A pdb=" N SER D 992 " --> pdb=" O ARG D 988 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N TYR D 994 " --> pdb=" O PRO D 990 " (cutoff:3.500A) Processing helix chain 'D' and resid 1001 through 1008 Processing helix chain 'D' and resid 1009 through 1013 removed outlier: 3.756A pdb=" N TYR D1013 " --> pdb=" O ALA D1010 " (cutoff:3.500A) Processing helix chain 'D' and resid 1016 through 1026 removed outlier: 3.954A pdb=" N LEU D1022 " --> pdb=" O VAL D1018 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLN D1023 " --> pdb=" O SER D1019 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N THR D1024 " --> pdb=" O LEU D1020 " (cutoff:3.500A) Processing helix chain 'D' and resid 1112 through 1117 removed outlier: 3.670A pdb=" N VAL D1116 " --> pdb=" O ASP D1112 " (cutoff:3.500A) Processing helix chain 'D' and resid 1124 through 1136 removed outlier: 3.511A pdb=" N ARG D1132 " --> pdb=" O ASP D1128 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLY D1136 " --> pdb=" O ARG D1132 " (cutoff:3.500A) Processing helix chain 'D' and resid 1149 through 1153 removed outlier: 3.728A pdb=" N THR D1152 " --> pdb=" O SER D1149 " (cutoff:3.500A) Processing helix chain 'D' and resid 1239 through 1244 Processing helix chain 'D' and resid 1245 through 1252 removed outlier: 3.855A pdb=" N ARG D1251 " --> pdb=" O ARG D1247 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU D1252 " --> pdb=" O HIS D1248 " (cutoff:3.500A) Processing helix chain 'D' and resid 1262 through 1267 removed outlier: 3.735A pdb=" N ASN D1267 " --> pdb=" O ALA D1263 " (cutoff:3.500A) Processing helix chain 'D' and resid 1268 through 1273 Processing helix chain 'D' and resid 1277 through 1288 removed outlier: 3.786A pdb=" N LEU D1287 " --> pdb=" O ASP D1283 " (cutoff:3.500A) Processing helix chain 'D' and resid 1313 through 1319 removed outlier: 4.138A pdb=" N LEU D1317 " --> pdb=" O ASN D1313 " (cutoff:3.500A) Processing helix chain 'D' and resid 1329 through 1339 Processing helix chain 'Y' and resid 3 through 8 removed outlier: 3.559A pdb=" N GLU Y 8 " --> pdb=" O TRP Y 4 " (cutoff:3.500A) Processing helix chain 'Y' and resid 22 through 28 Processing helix chain 'Y' and resid 70 through 75 Processing helix chain 'Y' and resid 82 through 86 Processing helix chain 'Y' and resid 133 through 137 Processing helix chain 'Y' and resid 146 through 185 removed outlier: 3.796A pdb=" N LYS Y 150 " --> pdb=" O THR Y 146 " (cutoff:3.500A) Processing helix chain 'Y' and resid 189 through 199 removed outlier: 3.547A pdb=" N VAL Y 193 " --> pdb=" O PRO Y 189 " (cutoff:3.500A) Processing helix chain 'Y' and resid 208 through 226 removed outlier: 3.852A pdb=" N LEU Y 224 " --> pdb=" O LYS Y 220 " (cutoff:3.500A) Processing helix chain 'Y' and resid 235 through 250 removed outlier: 3.536A pdb=" N ALA Y 250 " --> pdb=" O LEU Y 246 " (cutoff:3.500A) Processing helix chain 'Y' and resid 276 through 287 Processing helix chain 'Y' and resid 308 through 319 Processing helix chain 'Y' and resid 324 through 335 removed outlier: 3.523A pdb=" N TYR Y 328 " --> pdb=" O ASP Y 324 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N SER Y 334 " --> pdb=" O ALA Y 330 " (cutoff:3.500A) Processing helix chain 'Y' and resid 372 through 377 removed outlier: 3.651A pdb=" N TYR Y 376 " --> pdb=" O LEU Y 372 " (cutoff:3.500A) Processing helix chain 'Y' and resid 402 through 406 Processing helix chain 'Y' and resid 445 through 450 removed outlier: 3.594A pdb=" N CYS Y 450 " --> pdb=" O LEU Y 446 " (cutoff:3.500A) Processing helix chain 'Y' and resid 451 through 456 removed outlier: 3.738A pdb=" N GLU Y 456 " --> pdb=" O VAL Y 453 " (cutoff:3.500A) Processing helix chain 'Y' and resid 457 through 467 removed outlier: 4.353A pdb=" N ARG Y 467 " --> pdb=" O THR Y 463 " (cutoff:3.500A) Processing helix chain 'Y' and resid 472 through 479 removed outlier: 4.114A pdb=" N ARG Y 477 " --> pdb=" O ALA Y 474 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU Y 479 " --> pdb=" O GLN Y 476 " (cutoff:3.500A) Processing helix chain 'Y' and resid 490 through 495 Processing helix chain 'Y' and resid 496 through 500 Processing helix chain 'Y' and resid 508 through 515 removed outlier: 3.832A pdb=" N ASP Y 515 " --> pdb=" O GLU Y 511 " (cutoff:3.500A) Processing helix chain 'Y' and resid 518 through 523 removed outlier: 3.664A pdb=" N TYR Y 522 " --> pdb=" O THR Y 519 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LYS Y 523 " --> pdb=" O ASP Y 520 " (cutoff:3.500A) Processing helix chain 'Y' and resid 557 through 561 Processing helix chain 'Y' and resid 567 through 582 Processing helix chain 'Y' and resid 590 through 603 Processing helix chain 'Y' and resid 608 through 618 removed outlier: 4.033A pdb=" N HIS Y 618 " --> pdb=" O ASP Y 614 " (cutoff:3.500A) Processing helix chain 'Y' and resid 620 through 626 Processing helix chain 'Y' and resid 627 through 642 removed outlier: 3.790A pdb=" N VAL Y 636 " --> pdb=" O ALA Y 632 " (cutoff:3.500A) Processing helix chain 'Y' and resid 650 through 660 removed outlier: 4.018A pdb=" N LEU Y 656 " --> pdb=" O ALA Y 652 " (cutoff:3.500A) Processing helix chain 'Y' and resid 667 through 689 removed outlier: 4.326A pdb=" N TYR Y 674 " --> pdb=" O LEU Y 670 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N LEU Y 677 " --> pdb=" O HIS Y 673 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N ALA Y 689 " --> pdb=" O THR Y 685 " (cutoff:3.500A) Processing helix chain 'Y' and resid 702 through 706 Processing helix chain 'Y' and resid 756 through 760 removed outlier: 3.982A pdb=" N MET Y 760 " --> pdb=" O LEU Y 757 " (cutoff:3.500A) Processing helix chain 'Y' and resid 774 through 787 Processing helix chain 'Y' and resid 789 through 794 Processing helix chain 'Y' and resid 803 through 808 Processing helix chain 'Y' and resid 809 through 811 No H-bonds generated for 'chain 'Y' and resid 809 through 811' Processing helix chain 'Y' and resid 846 through 854 removed outlier: 4.027A pdb=" N GLN Y 851 " --> pdb=" O ALA Y 847 " (cutoff:3.500A) Processing helix chain 'Y' and resid 854 through 866 removed outlier: 3.611A pdb=" N THR Y 858 " --> pdb=" O GLY Y 854 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLU Y 859 " --> pdb=" O GLU Y 855 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N LEU Y 860 " --> pdb=" O MET Y 856 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLU Y 862 " --> pdb=" O THR Y 858 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N ASP Y 863 " --> pdb=" O GLU Y 859 " (cutoff:3.500A) removed outlier: 5.655A pdb=" N VAL Y 864 " --> pdb=" O LEU Y 860 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N THR Y 866 " --> pdb=" O GLU Y 862 " (cutoff:3.500A) Processing helix chain 'Y' and resid 871 through 880 removed outlier: 3.556A pdb=" N LEU Y 879 " --> pdb=" O ALA Y 875 " (cutoff:3.500A) Processing helix chain 'Y' and resid 881 through 885 removed outlier: 3.976A pdb=" N GLN Y 884 " --> pdb=" O LEU Y 881 " (cutoff:3.500A) Processing helix chain 'Y' and resid 945 through 953 removed outlier: 4.506A pdb=" N ALA Y 951 " --> pdb=" O THR Y 947 " (cutoff:3.500A) Processing helix chain 'Y' and resid 953 through 961 Processing helix chain 'Y' and resid 963 through 967 Processing helix chain 'Y' and resid 988 through 996 removed outlier: 4.099A pdb=" N SER Y 992 " --> pdb=" O ARG Y 988 " (cutoff:3.500A) Processing helix chain 'Y' and resid 1003 through 1011 Processing helix chain 'Y' and resid 1016 through 1026 removed outlier: 3.558A pdb=" N LEU Y1020 " --> pdb=" O SER Y1016 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ALA Y1026 " --> pdb=" O LEU Y1022 " (cutoff:3.500A) Processing helix chain 'Y' and resid 1112 through 1117 Processing helix chain 'Y' and resid 1124 through 1135 Processing helix chain 'Y' and resid 1144 through 1153 removed outlier: 3.518A pdb=" N SER Y1149 " --> pdb=" O THR Y1145 " (cutoff:3.500A) Processing helix chain 'Y' and resid 1206 through 1216 removed outlier: 3.683A pdb=" N LYS Y1212 " --> pdb=" O GLU Y1208 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE Y1214 " --> pdb=" O ALA Y1210 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ASP Y1216 " --> pdb=" O LYS Y1212 " (cutoff:3.500A) Processing helix chain 'Y' and resid 1238 through 1245 removed outlier: 3.692A pdb=" N TYR Y1244 " --> pdb=" O SER Y1240 " (cutoff:3.500A) Processing helix chain 'Y' and resid 1245 through 1250 Processing helix chain 'Y' and resid 1260 through 1267 removed outlier: 4.150A pdb=" N GLN Y1264 " --> pdb=" O PRO Y1261 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N ASN Y1267 " --> pdb=" O GLN Y1264 " (cutoff:3.500A) Processing helix chain 'Y' and resid 1268 through 1273 removed outlier: 3.548A pdb=" N ALA Y1273 " --> pdb=" O GLU Y1269 " (cutoff:3.500A) Processing helix chain 'Y' and resid 1277 through 1289 removed outlier: 3.786A pdb=" N ILE Y1282 " --> pdb=" O LEU Y1278 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N ASP Y1283 " --> pdb=" O PHE Y1279 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU Y1287 " --> pdb=" O ASP Y1283 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA Y1289 " --> pdb=" O TYR Y1285 " (cutoff:3.500A) Processing helix chain 'Y' and resid 1314 through 1319 removed outlier: 3.911A pdb=" N THR Y1318 " --> pdb=" O PRO Y1314 " (cutoff:3.500A) Processing helix chain 'Y' and resid 1329 through 1339 removed outlier: 3.534A pdb=" N MET Y1333 " --> pdb=" O THR Y1329 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LYS Y1336 " --> pdb=" O LEU Y1332 " (cutoff:3.500A) Processing helix chain 'Y' and resid 1342 through 1346 Processing helix chain 'Z' and resid 3 through 10 removed outlier: 3.545A pdb=" N LEU Z 7 " --> pdb=" O ASN Z 3 " (cutoff:3.500A) Processing helix chain 'Z' and resid 22 through 29 Processing helix chain 'Z' and resid 42 through 47 removed outlier: 4.054A pdb=" N ARG Z 45 " --> pdb=" O ASP Z 42 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ASN Z 47 " --> pdb=" O GLU Z 44 " (cutoff:3.500A) Processing helix chain 'Z' and resid 69 through 75 Processing helix chain 'Z' and resid 82 through 84 No H-bonds generated for 'chain 'Z' and resid 82 through 84' Processing helix chain 'Z' and resid 132 through 141 removed outlier: 4.121A pdb=" N ARG Z 140 " --> pdb=" O LEU Z 136 " (cutoff:3.500A) Processing helix chain 'Z' and resid 146 through 185 removed outlier: 3.890A pdb=" N LEU Z 152 " --> pdb=" O LEU Z 148 " (cutoff:3.500A) Processing helix chain 'Z' and resid 189 through 199 removed outlier: 3.609A pdb=" N VAL Z 193 " --> pdb=" O PRO Z 189 " (cutoff:3.500A) Processing helix chain 'Z' and resid 208 through 226 removed outlier: 4.044A pdb=" N LEU Z 224 " --> pdb=" O LYS Z 220 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR Z 226 " --> pdb=" O LYS Z 222 " (cutoff:3.500A) Processing helix chain 'Z' and resid 235 through 250 removed outlier: 3.590A pdb=" N ALA Z 250 " --> pdb=" O LEU Z 246 " (cutoff:3.500A) Processing helix chain 'Z' and resid 276 through 287 Processing helix chain 'Z' and resid 308 through 318 removed outlier: 4.051A pdb=" N VAL Z 313 " --> pdb=" O PRO Z 309 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N THR Z 314 " --> pdb=" O GLU Z 310 " (cutoff:3.500A) Processing helix chain 'Z' and resid 324 through 334 Processing helix chain 'Z' and resid 402 through 405 Processing helix chain 'Z' and resid 419 through 424 Processing helix chain 'Z' and resid 445 through 450 removed outlier: 3.716A pdb=" N LEU Z 449 " --> pdb=" O ALA Z 445 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N CYS Z 450 " --> pdb=" O LEU Z 446 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 445 through 450' Processing helix chain 'Z' and resid 457 through 467 removed outlier: 3.739A pdb=" N ARG Z 467 " --> pdb=" O THR Z 463 " (cutoff:3.500A) Processing helix chain 'Z' and resid 489 through 493 removed outlier: 4.160A pdb=" N ALA Z 492 " --> pdb=" O GLY Z 489 " (cutoff:3.500A) Processing helix chain 'Z' and resid 494 through 499 Processing helix chain 'Z' and resid 508 through 513 Processing helix chain 'Z' and resid 517 through 521 removed outlier: 3.765A pdb=" N PHE Z 521 " --> pdb=" O VAL Z 518 " (cutoff:3.500A) Processing helix chain 'Z' and resid 557 through 561 removed outlier: 3.629A pdb=" N ASN Z 560 " --> pdb=" O VAL Z 557 " (cutoff:3.500A) Processing helix chain 'Z' and resid 567 through 582 Processing helix chain 'Z' and resid 590 through 602 Processing helix chain 'Z' and resid 607 through 618 removed outlier: 4.141A pdb=" N TYR Z 611 " --> pdb=" O PRO Z 607 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N HIS Z 618 " --> pdb=" O ASP Z 614 " (cutoff:3.500A) Processing helix chain 'Z' and resid 620 through 625 Processing helix chain 'Z' and resid 627 through 641 Processing helix chain 'Z' and resid 650 through 660 removed outlier: 4.361A pdb=" N LEU Z 656 " --> pdb=" O ALA Z 652 " (cutoff:3.500A) Processing helix chain 'Z' and resid 667 through 688 removed outlier: 3.542A pdb=" N LEU Z 671 " --> pdb=" O PRO Z 667 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N HIS Z 673 " --> pdb=" O GLN Z 669 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N TYR Z 674 " --> pdb=" O LEU Z 670 " (cutoff:3.500A) Processing helix chain 'Z' and resid 703 through 708 removed outlier: 3.891A pdb=" N VAL Z 707 " --> pdb=" O LEU Z 703 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ASN Z 708 " --> pdb=" O SER Z 704 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 703 through 708' Processing helix chain 'Z' and resid 709 through 712 removed outlier: 3.970A pdb=" N ASP Z 712 " --> pdb=" O ALA Z 709 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 709 through 712' Processing helix chain 'Z' and resid 741 through 745 removed outlier: 3.565A pdb=" N GLU Z 745 " --> pdb=" O ALA Z 742 " (cutoff:3.500A) Processing helix chain 'Z' and resid 753 through 759 Processing helix chain 'Z' and resid 774 through 794 removed outlier: 5.291A pdb=" N MET Z 789 " --> pdb=" O TYR Z 785 " (cutoff:3.500A) Proline residue: Z 790 - end of helix Processing helix chain 'Z' and resid 803 through 812 removed outlier: 4.058A pdb=" N ASP Z 810 " --> pdb=" O THR Z 806 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N PHE Z 812 " --> pdb=" O LEU Z 808 " (cutoff:3.500A) Processing helix chain 'Z' and resid 814 through 819 removed outlier: 3.578A pdb=" N LEU Z 818 " --> pdb=" O ARG Z 814 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU Z 819 " --> pdb=" O PRO Z 815 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 814 through 819' Processing helix chain 'Z' and resid 848 through 854 Processing helix chain 'Z' and resid 856 through 860 Processing helix chain 'Z' and resid 875 through 881 removed outlier: 4.269A pdb=" N LEU Z 879 " --> pdb=" O ALA Z 875 " (cutoff:3.500A) Processing helix chain 'Z' and resid 882 through 886 Processing helix chain 'Z' and resid 930 through 932 No H-bonds generated for 'chain 'Z' and resid 930 through 932' Processing helix chain 'Z' and resid 945 through 953 removed outlier: 3.919A pdb=" N CYS Z 949 " --> pdb=" O ASN Z 945 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA Z 951 " --> pdb=" O THR Z 947 " (cutoff:3.500A) Processing helix chain 'Z' and resid 953 through 961 removed outlier: 3.814A pdb=" N TYR Z 959 " --> pdb=" O ASP Z 955 " (cutoff:3.500A) Processing helix chain 'Z' and resid 963 through 968 removed outlier: 3.884A pdb=" N ARG Z 968 " --> pdb=" O HIS Z 965 " (cutoff:3.500A) Processing helix chain 'Z' and resid 988 through 996 removed outlier: 3.793A pdb=" N SER Z 992 " --> pdb=" O ARG Z 988 " (cutoff:3.500A) Processing helix chain 'Z' and resid 1001 through 1007 Processing helix chain 'Z' and resid 1008 through 1013 removed outlier: 4.187A pdb=" N MET Z1011 " --> pdb=" O LEU Z1008 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N TYR Z1013 " --> pdb=" O ALA Z1010 " (cutoff:3.500A) Processing helix chain 'Z' and resid 1016 through 1026 removed outlier: 3.518A pdb=" N THR Z1024 " --> pdb=" O LEU Z1020 " (cutoff:3.500A) Processing helix chain 'Z' and resid 1112 through 1117 removed outlier: 3.634A pdb=" N VAL Z1116 " --> pdb=" O ASP Z1112 " (cutoff:3.500A) Processing helix chain 'Z' and resid 1124 through 1136 removed outlier: 3.580A pdb=" N ASP Z1128 " --> pdb=" O HIS Z1124 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N TRP Z1130 " --> pdb=" O GLU Z1126 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N HIS Z1133 " --> pdb=" O ARG Z1129 " (cutoff:3.500A) Processing helix chain 'Z' and resid 1206 through 1215 removed outlier: 4.290A pdb=" N LYS Z1212 " --> pdb=" O GLU Z1208 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ALA Z1213 " --> pdb=" O ALA Z1209 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ILE Z1214 " --> pdb=" O ALA Z1210 " (cutoff:3.500A) Processing helix chain 'Z' and resid 1238 through 1245 removed outlier: 3.561A pdb=" N TYR Z1244 " --> pdb=" O SER Z1240 " (cutoff:3.500A) Processing helix chain 'Z' and resid 1245 through 1250 removed outlier: 3.753A pdb=" N GLU Z1250 " --> pdb=" O THR Z1246 " (cutoff:3.500A) Processing helix chain 'Z' and resid 1262 through 1266 removed outlier: 3.622A pdb=" N TYR Z1265 " --> pdb=" O CYS Z1262 " (cutoff:3.500A) Processing helix chain 'Z' and resid 1271 through 1275 removed outlier: 4.093A pdb=" N ASN Z1275 " --> pdb=" O ILE Z1272 " (cutoff:3.500A) Processing helix chain 'Z' and resid 1277 through 1288 removed outlier: 3.810A pdb=" N ILE Z1282 " --> pdb=" O LEU Z1278 " (cutoff:3.500A) Processing helix chain 'Z' and resid 1313 through 1319 removed outlier: 3.997A pdb=" N LEU Z1317 " --> pdb=" O ASN Z1313 " (cutoff:3.500A) Processing helix chain 'Z' and resid 1330 through 1339 removed outlier: 3.680A pdb=" N THR Z1335 " --> pdb=" O ALA Z1331 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N LYS Z1336 " --> pdb=" O LEU Z1332 " (cutoff:3.500A) Processing helix chain 'Z' and resid 1342 through 1346 removed outlier: 3.686A pdb=" N ALA Z1345 " --> pdb=" O GLY Z1342 " (cutoff:3.500A) Processing helix chain 'Z' and resid 1361 through 1366 removed outlier: 3.984A pdb=" N SER Z1365 " --> pdb=" O PRO Z1361 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'h' and resid 31 through 34 removed outlier: 8.764A pdb=" N ILE h 41 " --> pdb=" O ASN h 7 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N PHE h 9 " --> pdb=" O ILE h 41 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'h' and resid 92 through 95 removed outlier: 7.224A pdb=" N SER h 299 " --> pdb=" O VAL h 293 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N VAL h 293 " --> pdb=" O SER h 299 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N THR h 301 " --> pdb=" O CYS h 291 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N PHE h 288 " --> pdb=" O LEU h 108 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'h' and resid 175 through 176 removed outlier: 3.540A pdb=" N PHE h 182 " --> pdb=" O ILE h 175 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'I' and resid 31 through 34 removed outlier: 6.851A pdb=" N LEU I 82 " --> pdb=" O ARG I 74 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N VAL I 76 " --> pdb=" O GLN I 80 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N GLN I 80 " --> pdb=" O VAL I 76 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N ILE I 41 " --> pdb=" O ASN I 7 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N PHE I 9 " --> pdb=" O ILE I 41 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'I' and resid 91 through 95 removed outlier: 7.687A pdb=" N SER I 299 " --> pdb=" O VAL I 293 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N VAL I 293 " --> pdb=" O SER I 299 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N THR I 301 " --> pdb=" O CYS I 291 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N VAL I 286 " --> pdb=" O VAL I 110 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N VAL I 110 " --> pdb=" O VAL I 286 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'I' and resid 188 through 189 Processing sheet with id=AA7, first strand: chain 'n' and resid 31 through 34 removed outlier: 5.936A pdb=" N MET n 73 " --> pdb=" O HIS n 84 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N HIS n 84 " --> pdb=" O MET n 73 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N ARG n 75 " --> pdb=" O LEU n 82 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N LEU n 82 " --> pdb=" O ARG n 75 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N PHE n 9 " --> pdb=" O ILE n 41 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'n' and resid 92 through 95 removed outlier: 3.888A pdb=" N CYS n 302 " --> pdb=" O TYR n 92 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N SER n 299 " --> pdb=" O VAL n 293 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N VAL n 293 " --> pdb=" O SER n 299 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N THR n 301 " --> pdb=" O CYS n 291 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'n' and resid 174 through 175 Processing sheet with id=AB1, first strand: chain 'o' and resid 31 through 34 removed outlier: 5.777A pdb=" N MET o 73 " --> pdb=" O HIS o 84 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N HIS o 84 " --> pdb=" O MET o 73 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ARG o 75 " --> pdb=" O LEU o 82 " (cutoff:3.500A) removed outlier: 8.903A pdb=" N ILE o 41 " --> pdb=" O ASN o 7 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N PHE o 9 " --> pdb=" O ILE o 41 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'o' and resid 91 through 95 removed outlier: 6.375A pdb=" N ILE o 303 " --> pdb=" O VAL o 290 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N VAL o 290 " --> pdb=" O ILE o 303 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'o' and resid 188 through 189 removed outlier: 3.656A pdb=" N ILE o 189 " --> pdb=" O HIS o 192 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'g' and resid 172 through 173 WARNING: can't find start of bonding for strands! previous: chain 'g' and resid 172 through 173 current: chain 'g' and resid 203 through 207 WARNING: can't find start of bonding for strands! previous: chain 'g' and resid 203 through 207 current: chain 'g' and resid 280 through 281 No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'm' and resid 34 through 39 removed outlier: 5.102A pdb=" N VAL C1064 " --> pdb=" O TYR m 37 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'm' and resid 46 through 47 WARNING: can't find start of bonding for strands! previous: chain 'm' and resid 46 through 47 current: chain 'm' and resid 79 through 83 WARNING: can't find start of bonding for strands! previous: chain 'm' and resid 79 through 83 current: chain 'm' and resid 143 through 152 WARNING: can't find start of bonding for strands! previous: chain 'm' and resid 143 through 152 current: chain 'm' and resid 201 through 207 WARNING: can't find start of bonding for strands! previous: chain 'm' and resid 201 through 207 current: chain 'm' and resid 280 through 282 No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'm' and resid 165 through 168 Processing sheet with id=AB8, first strand: chain 'M' and resid 93 through 97 removed outlier: 4.416A pdb=" N CYS M 93 " --> pdb=" O THR M 131 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N THR M 131 " --> pdb=" O CYS M 93 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'M' and resid 42 through 44 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 42 through 44 current: chain 'M' and resid 146 through 152 Processing sheet with id=AC1, first strand: chain 'M' and resid 101 through 102 Processing sheet with id=AC2, first strand: chain 'M' and resid 140 through 142 removed outlier: 6.154A pdb=" N LEU M 141 " --> pdb=" O ASP M 344 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'M' and resid 386 through 387 Processing sheet with id=AC4, first strand: chain 'M' and resid 502 through 505 removed outlier: 4.725A pdb=" N GLY M 488 " --> pdb=" O ALA M 475 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N ALA M 475 " --> pdb=" O GLY M 488 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N GLU M 490 " --> pdb=" O TRP M 473 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N TRP M 473 " --> pdb=" O GLU M 490 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N ARG M 492 " --> pdb=" O GLN M 471 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N GLN M 471 " --> pdb=" O ARG M 492 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'N' and resid 14 through 15 Processing sheet with id=AC6, first strand: chain 'a' and resid 78 through 79 WARNING: can't find start of bonding for strands! previous: chain 'a' and resid 78 through 79 current: chain 'a' and resid 1073 through 1085 No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'a' and resid 338 through 339 removed outlier: 4.608A pdb=" N GLY B 14 " --> pdb=" O LEU a 339 " (cutoff:3.500A) removed outlier: 5.754A pdb=" N VAL B 13 " --> pdb=" O CYS Z 58 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N PHE Z 57 " --> pdb=" O LEU a 92 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N GLN a 96 " --> pdb=" O ASN Z 59 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N THR a 113 " --> pdb=" O TYR B 38 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'a' and resid 271 through 275 WARNING: can't find start of bonding for strands! previous: chain 'a' and resid 271 through 275 current: chain 'a' and resid 366 through 371 WARNING: can't find start of bonding for strands! previous: chain 'a' and resid 366 through 371 current: chain 'a' and resid 1033 through 1051 removed outlier: 7.756A pdb=" N THR a1041 " --> pdb=" O ARG a1101 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N ARG a1101 " --> pdb=" O THR a1041 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N GLU a1043 " --> pdb=" O VAL a1099 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N VAL a1099 " --> pdb=" O GLU a1043 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N ASP a1045 " --> pdb=" O ALA a1097 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ALA a1097 " --> pdb=" O ASP a1045 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'a' and resid 295 through 298 Processing sheet with id=AD1, first strand: chain 'a' and resid 407 through 408 Processing sheet with id=AD2, first strand: chain 'a' and resid 427 through 431 Processing sheet with id=AD3, first strand: chain 'a' and resid 537 through 544 Processing sheet with id=AD4, first strand: chain 'a' and resid 697 through 698 Processing sheet with id=AD5, first strand: chain 'a' and resid 719 through 720 removed outlier: 3.660A pdb=" N LYS a 891 " --> pdb=" O TYR a 918 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'a' and resid 723 through 724 removed outlier: 6.923A pdb=" N LEU a 723 " --> pdb=" O ALA a 773 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'a' and resid 921 through 923 Processing sheet with id=AD8, first strand: chain 'a' and resid 1326 through 1327 Processing sheet with id=AD9, first strand: chain 'A' and resid 121 through 130 removed outlier: 6.311A pdb=" N ILE A 78 " --> pdb=" O ILE A1059 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'A' and resid 92 through 94 Processing sheet with id=AE2, first strand: chain 'A' and resid 272 through 275 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 272 through 275 current: chain 'A' and resid 358 through 361 removed outlier: 4.497A pdb=" N ASP A 358 " --> pdb=" O MET A 369 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 366 through 371 current: chain 'A' and resid 1033 through 1050 removed outlier: 7.279A pdb=" N THR A1041 " --> pdb=" O VAL A1102 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N VAL A1102 " --> pdb=" O THR A1041 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N GLU A1043 " --> pdb=" O ASN A1100 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASP A1045 " --> pdb=" O TYR A1098 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N TYR A1098 " --> pdb=" O ASP A1045 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N LEU A1047 " --> pdb=" O VAL A1096 " (cutoff:3.500A) removed outlier: 5.655A pdb=" N VAL A1096 " --> pdb=" O LEU A1047 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N TYR A1049 " --> pdb=" O THR A1094 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N THR A1094 " --> pdb=" O TYR A1049 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'A' and resid 295 through 299 Processing sheet with id=AE4, first strand: chain 'A' and resid 537 through 541 Processing sheet with id=AE5, first strand: chain 'A' and resid 731 through 733 Processing sheet with id=AE6, first strand: chain 'A' and resid 921 through 923 removed outlier: 3.663A pdb=" N CYS A 921 " --> pdb=" O LEU A 800 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU A 800 " --> pdb=" O CYS A 921 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'A' and resid 1326 through 1327 Processing sheet with id=AE8, first strand: chain 'B' and resid 50 through 59 removed outlier: 7.659A pdb=" N PHE B 50 " --> pdb=" O THR C 87 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N GLY C 89 " --> pdb=" O PHE B 50 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ALA B 52 " --> pdb=" O GLY C 89 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N MET C 91 " --> pdb=" O ALA B 52 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N PHE B 54 " --> pdb=" O MET C 91 " (cutoff:3.500A) removed outlier: 7.951A pdb=" N PHE C 93 " --> pdb=" O PHE B 54 " (cutoff:3.500A) removed outlier: 8.633A pdb=" N THR B 56 " --> pdb=" O PHE C 93 " (cutoff:3.500A) removed outlier: 9.457A pdb=" N VAL C 95 " --> pdb=" O THR B 56 " (cutoff:3.500A) removed outlier: 8.691A pdb=" N CYS B 58 " --> pdb=" O VAL C 95 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'B' and resid 78 through 79 Processing sheet with id=AF1, first strand: chain 'B' and resid 91 through 93 Processing sheet with id=AF2, first strand: chain 'B' and resid 125 through 132 Processing sheet with id=AF3, first strand: chain 'B' and resid 262 through 263 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 262 through 263 current: chain 'B' and resid 354 through 360 removed outlier: 12.808A pdb=" N SER B 356 " --> pdb=" O ASN B 371 " (cutoff:3.500A) removed outlier: 9.710A pdb=" N ASN B 371 " --> pdb=" O SER B 356 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N ASP B 358 " --> pdb=" O MET B 369 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N VAL B 367 " --> pdb=" O ILE B 360 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 366 through 371 current: chain 'B' and resid 1034 through 1050 removed outlier: 7.350A pdb=" N THR B1041 " --> pdb=" O ARG B1101 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N ARG B1101 " --> pdb=" O THR B1041 " (cutoff:3.500A) removed outlier: 7.708A pdb=" N GLU B1043 " --> pdb=" O VAL B1099 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N VAL B1099 " --> pdb=" O GLU B1043 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N ASP B1045 " --> pdb=" O ALA B1097 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'B' and resid 415 through 416 Processing sheet with id=AF5, first strand: chain 'B' and resid 428 through 431 Processing sheet with id=AF6, first strand: chain 'B' and resid 537 through 541 Processing sheet with id=AF7, first strand: chain 'B' and resid 719 through 720 Processing sheet with id=AF8, first strand: chain 'B' and resid 921 through 923 Processing sheet with id=AF9, first strand: chain 'C' and resid 50 through 53 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 50 through 53 current: chain 'D' and resid 86 through 96 Processing sheet with id=AG1, first strand: chain 'C' and resid 121 through 122 Processing sheet with id=AG2, first strand: chain 'C' and resid 269 through 274 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 269 through 274 current: chain 'C' and resid 352 through 361 removed outlier: 4.102A pdb=" N ASP C 358 " --> pdb=" O MET C 369 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 366 through 370 current: chain 'C' and resid 1033 through 1051 removed outlier: 7.787A pdb=" N THR C1041 " --> pdb=" O ARG C1101 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N ARG C1101 " --> pdb=" O THR C1041 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N GLU C1043 " --> pdb=" O VAL C1099 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N VAL C1099 " --> pdb=" O GLU C1043 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ASP C1045 " --> pdb=" O ALA C1097 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'C' and resid 415 through 416 Processing sheet with id=AG4, first strand: chain 'C' and resid 427 through 431 Processing sheet with id=AG5, first strand: chain 'C' and resid 537 through 543 Processing sheet with id=AG6, first strand: chain 'C' and resid 697 through 698 Processing sheet with id=AG7, first strand: chain 'C' and resid 719 through 720 Processing sheet with id=AG8, first strand: chain 'C' and resid 798 through 800 removed outlier: 3.570A pdb=" N CYS C 921 " --> pdb=" O LEU C 800 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'C' and resid 1326 through 1327 removed outlier: 4.087A pdb=" N SER C1326 " --> pdb=" O VAL C1356 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'D' and resid 78 through 79 Processing sheet with id=AH2, first strand: chain 'D' and resid 125 through 126 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 125 through 126 current: chain 'D' and resid 1073 through 1079 No H-bonds generated for sheet with id=AH2 Processing sheet with id=AH3, first strand: chain 'D' and resid 269 through 275 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 269 through 275 current: chain 'D' and resid 352 through 361 removed outlier: 4.818A pdb=" N ASP D 358 " --> pdb=" O MET D 369 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 366 through 370 current: chain 'D' and resid 1034 through 1050 removed outlier: 4.429A pdb=" N ARG D1101 " --> pdb=" O GLU D1043 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N ASP D1045 " --> pdb=" O VAL D1099 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N VAL D1099 " --> pdb=" O ASP D1045 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N LEU D1047 " --> pdb=" O ALA D1097 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N ALA D1097 " --> pdb=" O LEU D1047 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N TYR D1049 " --> pdb=" O CYS D1095 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N CYS D1095 " --> pdb=" O TYR D1049 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'D' and resid 428 through 431 Processing sheet with id=AH5, first strand: chain 'D' and resid 537 through 541 Processing sheet with id=AH6, first strand: chain 'D' and resid 731 through 733 removed outlier: 3.520A pdb=" N GLU D 894 " --> pdb=" O VAL D 733 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'D' and resid 921 through 923 removed outlier: 4.231A pdb=" N CYS D 921 " --> pdb=" O LEU D 800 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LEU D 800 " --> pdb=" O CYS D 921 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'Z' and resid 114 through 118 removed outlier: 7.470A pdb=" N PHE Y 50 " --> pdb=" O THR Z 87 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N GLY Z 89 " --> pdb=" O PHE Y 50 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N ALA Y 52 " --> pdb=" O GLY Z 89 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N MET Z 91 " --> pdb=" O ALA Y 52 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'Y' and resid 120 through 122 removed outlier: 6.269A pdb=" N ILE Y 78 " --> pdb=" O ILE Y1059 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'Y' and resid 91 through 92 removed outlier: 3.532A pdb=" N MET Y 91 " --> pdb=" O LYS Y 118 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'Y' and resid 95 through 96 Processing sheet with id=AI3, first strand: chain 'Y' and resid 125 through 132 Processing sheet with id=AI4, first strand: chain 'Y' and resid 271 through 274 WARNING: can't find start of bonding for strands! previous: chain 'Y' and resid 271 through 274 current: chain 'Y' and resid 352 through 361 removed outlier: 4.022A pdb=" N ASP Y 358 " --> pdb=" O MET Y 369 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'Y' and resid 366 through 370 current: chain 'Y' and resid 1033 through 1051 Processing sheet with id=AI5, first strand: chain 'Y' and resid 415 through 416 Processing sheet with id=AI6, first strand: chain 'Y' and resid 427 through 431 Processing sheet with id=AI7, first strand: chain 'Y' and resid 537 through 544 removed outlier: 3.533A pdb=" N GLU Y 547 " --> pdb=" O GLU Y 544 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'Y' and resid 719 through 720 removed outlier: 3.591A pdb=" N ARG Y 896 " --> pdb=" O GLN Y 731 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'Y' and resid 921 through 923 removed outlier: 3.528A pdb=" N CYS Y 921 " --> pdb=" O LEU Y 800 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU Y 800 " --> pdb=" O CYS Y 921 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N GLY Y 799 " --> pdb=" O VAL Y 937 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'Y' and resid 1326 through 1327 Processing sheet with id=AJ2, first strand: chain 'Z' and resid 78 through 79 removed outlier: 3.598A pdb=" N VAL Z1084 " --> pdb=" O SER Z1056 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'Z' and resid 125 through 129 Processing sheet with id=AJ4, first strand: chain 'Z' and resid 262 through 263 WARNING: can't find start of bonding for strands! previous: chain 'Z' and resid 267 through 275 current: chain 'Z' and resid 358 through 360 removed outlier: 4.376A pdb=" N ASP Z 358 " --> pdb=" O MET Z 369 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'Z' and resid 366 through 371 current: chain 'Z' and resid 1034 through 1051 removed outlier: 7.343A pdb=" N THR Z1041 " --> pdb=" O ARG Z1101 " (cutoff:3.500A) removed outlier: 7.305A pdb=" N ARG Z1101 " --> pdb=" O THR Z1041 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N GLU Z1043 " --> pdb=" O VAL Z1099 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N VAL Z1099 " --> pdb=" O GLU Z1043 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N ASP Z1045 " --> pdb=" O ALA Z1097 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ALA Z1097 " --> pdb=" O ASP Z1045 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'Z' and resid 295 through 299 Processing sheet with id=AJ6, first strand: chain 'Z' and resid 428 through 431 Processing sheet with id=AJ7, first strand: chain 'Z' and resid 537 through 540 Processing sheet with id=AJ8, first strand: chain 'Z' and resid 731 through 733 Processing sheet with id=AJ9, first strand: chain 'Z' and resid 921 through 923 3423 hydrogen bonds defined for protein. 9621 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: 41.43 Time building geometry restraints manager: 33.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 32582 1.34 - 1.46: 22739 1.46 - 1.59: 44654 1.59 - 1.71: 0 1.71 - 1.83: 915 Bond restraints: 100890 Sorted by residual: bond pdb=" C ARG a 736 " pdb=" N GLN a 737 " ideal model delta sigma weight residual 1.333 1.230 0.103 2.74e-02 1.33e+03 1.41e+01 bond pdb=" C GLU a 456 " pdb=" N PRO a 457 " ideal model delta sigma weight residual 1.331 1.310 0.021 7.90e-03 1.60e+04 7.17e+00 bond pdb=" C THR C 997 " pdb=" N CYS C 998 " ideal model delta sigma weight residual 1.331 1.262 0.069 2.83e-02 1.25e+03 5.86e+00 bond pdb=" C GLU B 764 " pdb=" N PRO B 765 " ideal model delta sigma weight residual 1.336 1.364 -0.028 1.20e-02 6.94e+03 5.52e+00 bond pdb=" C THR B1327 " pdb=" N THR B1328 " ideal model delta sigma weight residual 1.329 1.289 0.040 1.79e-02 3.12e+03 4.90e+00 ... (remaining 100885 not shown) Histogram of bond angle deviations from ideal: 98.21 - 105.65: 2566 105.65 - 113.10: 55593 113.10 - 120.55: 43585 120.55 - 128.00: 34564 128.00 - 135.45: 909 Bond angle restraints: 137217 Sorted by residual: angle pdb=" N VAL h 247 " pdb=" CA VAL h 247 " pdb=" C VAL h 247 " ideal model delta sigma weight residual 112.29 106.87 5.42 9.40e-01 1.13e+00 3.33e+01 angle pdb=" CA LEU 1 184 " pdb=" CB LEU 1 184 " pdb=" CG LEU 1 184 " ideal model delta sigma weight residual 116.30 133.84 -17.54 3.50e+00 8.16e-02 2.51e+01 angle pdb=" CA LEU m 158 " pdb=" CB LEU m 158 " pdb=" CG LEU m 158 " ideal model delta sigma weight residual 116.30 133.02 -16.72 3.50e+00 8.16e-02 2.28e+01 angle pdb=" C GLU g 177 " pdb=" N THR g 178 " pdb=" CA THR g 178 " ideal model delta sigma weight residual 121.54 130.60 -9.06 1.91e+00 2.74e-01 2.25e+01 angle pdb=" C GLY a 363 " pdb=" N GLU a 364 " pdb=" CA GLU a 364 " ideal model delta sigma weight residual 121.54 130.50 -8.96 1.91e+00 2.74e-01 2.20e+01 ... (remaining 137212 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.15: 55372 19.15 - 38.31: 4798 38.31 - 57.46: 649 57.46 - 76.61: 178 76.61 - 95.77: 52 Dihedral angle restraints: 61049 sinusoidal: 24543 harmonic: 36506 Sorted by residual: dihedral pdb=" CA CYS a 542 " pdb=" C CYS a 542 " pdb=" N GLN a 543 " pdb=" CA GLN a 543 " ideal model delta harmonic sigma weight residual -180.00 -143.94 -36.06 0 5.00e+00 4.00e-02 5.20e+01 dihedral pdb=" CA GLU C 764 " pdb=" C GLU C 764 " pdb=" N PRO C 765 " pdb=" CA PRO C 765 " ideal model delta harmonic sigma weight residual -180.00 -147.56 -32.44 0 5.00e+00 4.00e-02 4.21e+01 dihedral pdb=" CB CYS a1292 " pdb=" SG CYS a1292 " pdb=" SG CYS a1303 " pdb=" CB CYS a1303 " ideal model delta sinusoidal sigma weight residual 93.00 38.63 54.37 1 1.00e+01 1.00e-02 4.01e+01 ... (remaining 61046 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.101: 14620 0.101 - 0.203: 1156 0.203 - 0.304: 57 0.304 - 0.406: 3 0.406 - 0.507: 2 Chirality restraints: 15838 Sorted by residual: chirality pdb=" CB ILE h 303 " pdb=" CA ILE h 303 " pdb=" CG1 ILE h 303 " pdb=" CG2 ILE h 303 " both_signs ideal model delta sigma weight residual False 2.64 2.14 0.51 2.00e-01 2.50e+01 6.44e+00 chirality pdb=" CB ILE a 495 " pdb=" CA ILE a 495 " pdb=" CG1 ILE a 495 " pdb=" CG2 ILE a 495 " both_signs ideal model delta sigma weight residual False 2.64 2.20 0.45 2.00e-01 2.50e+01 5.00e+00 chirality pdb=" CB ILE a 911 " pdb=" CA ILE a 911 " pdb=" CG1 ILE a 911 " pdb=" CG2 ILE a 911 " both_signs ideal model delta sigma weight residual False 2.64 2.27 0.37 2.00e-01 2.50e+01 3.45e+00 ... (remaining 15835 not shown) Planarity restraints: 17656 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER D 989 " 0.050 5.00e-02 4.00e+02 7.53e-02 9.06e+00 pdb=" N PRO D 990 " -0.130 5.00e-02 4.00e+02 pdb=" CA PRO D 990 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO D 990 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU M 511 " -0.014 2.00e-02 2.50e+03 2.91e-02 8.47e+00 pdb=" C LEU M 511 " 0.050 2.00e-02 2.50e+03 pdb=" O LEU M 511 " -0.019 2.00e-02 2.50e+03 pdb=" N ARG M 512 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN A 740 " -0.048 5.00e-02 4.00e+02 7.27e-02 8.46e+00 pdb=" N PRO A 741 " 0.126 5.00e-02 4.00e+02 pdb=" CA PRO A 741 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO A 741 " -0.041 5.00e-02 4.00e+02 ... (remaining 17653 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 19398 2.76 - 3.30: 93018 3.30 - 3.83: 168701 3.83 - 4.37: 188627 4.37 - 4.90: 319749 Nonbonded interactions: 789493 Sorted by model distance: nonbonded pdb=" OH TYR B1185 " pdb=" O ASN B1191 " model vdw 2.228 2.440 nonbonded pdb=" O TYR Y 785 " pdb=" OH TYR Y 943 " model vdw 2.234 2.440 nonbonded pdb=" OH TYR C1185 " pdb=" O ASN C1191 " model vdw 2.237 2.440 nonbonded pdb=" O LEU T 26 " pdb=" OH TYR D 813 " model vdw 2.238 2.440 nonbonded pdb=" OG1 THR C1318 " pdb=" OE1 GLU C1320 " model vdw 2.245 2.440 ... (remaining 789488 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain '1' selection = chain 'x' } ncs_group { reference = (chain 'A' and (resid 55 through 324 or resid 343 through 470 or resid 480 or re \ sid 486 through 821 or resid 846 through 1370)) selection = (chain 'B' and (resid 55 through 204 or resid 210 through 403 or resid 419 throu \ gh 470 or resid 480 or resid 486 through 821 or resid 846 through 1138 or resid \ 1168 through 1288 or resid 1297 through 1370)) selection = (chain 'C' and (resid 55 through 204 or resid 210 through 324 or resid 343 throu \ gh 403 or resid 419 through 470 or resid 480 or resid 486 through 821 or resid 8 \ 46 through 1138 or resid 1168 through 1288 or resid 1297 through 1370)) selection = (chain 'D' and (resid 55 through 204 or resid 210 through 324 or resid 343 throu \ gh 403 or resid 419 through 470 or resid 480 or resid 486 through 1138 or resid \ 1168 through 1288 or resid 1297 through 1370)) selection = (chain 'Y' and (resid 55 through 204 or resid 210 through 324 or resid 343 throu \ gh 403 or resid 419 through 470 or resid 480 or resid 486 through 821 or resid 8 \ 46 through 1138 or resid 1168 through 1288 or resid 1297 through 1370)) selection = (chain 'Z' and (resid 55 through 204 or resid 210 through 324 or resid 343 throu \ gh 403 or resid 419 through 470 or resid 472 through 821 or resid 846 through 11 \ 38 or resid 1168 through 1288 or resid 1297 through 1370)) selection = (chain 'a' and (resid 55 through 204 or resid 210 through 324 or resid 343 throu \ gh 403 or resid 419 through 470 or resid 480 or resid 486 through 821 or resid 8 \ 46 through 1138 or resid 1168 through 1288 or resid 1297 through 1370)) } ncs_group { reference = chain 'H' selection = chain 'P' } ncs_group { reference = (chain 'I' and (resid 6 through 241 or resid 259 through 306)) selection = (chain 'h' and (resid 6 through 117 or resid 123 through 241 or resid 259 throug \ h 306)) selection = (chain 'n' and (resid 6 through 117 or resid 123 through 241 or resid 259 throug \ h 306)) selection = (chain 'o' and (resid 6 through 117 or resid 123 through 241 or resid 259 throug \ h 306)) } ncs_group { reference = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'i' selection = chain 'j' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 577 5.16 5 C 62784 2.51 5 N 17313 2.21 5 O 18000 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.560 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: 0.070 Extract box with map and model: 10.980 Check model and map are aligned: 1.080 Convert atoms to be neutral: 0.670 Process input model: 198.940 Find NCS groups from input model: 6.190 Set up NCS constraints: 0.350 Set refine NCS operators: 0.000 Set scattering table: 0.030 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 221.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 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 : 0.007 0.103 100890 Z= 0.433 Angle : 0.936 17.542 137217 Z= 0.495 Chirality : 0.057 0.507 15838 Planarity : 0.007 0.075 17656 Dihedral : 14.660 95.766 37286 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.64 % Favored : 93.36 % Rotamer Outliers : 0.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.76 % Twisted General : 0.03 % 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: -4.12 (0.06), residues: 12284 helix: -2.88 (0.05), residues: 4533 sheet: -2.53 (0.11), residues: 1581 loop : -2.63 (0.07), residues: 6170 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 24568 Ramachandran restraints generated. 12284 Oldfield, 0 Emsley, 12284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 24568 Ramachandran restraints generated. 12284 Oldfield, 0 Emsley, 12284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 4141 residues out of total 10859 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 4065 time to evaluate : 10.086 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 outliers start: 76 outliers final: 22 residues processed: 4114 average time/residue: 0.8964 time to fit residues: 6211.2610 Evaluate side-chains 2820 residues out of total 10859 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 2798 time to evaluate : 8.848 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 0.6626 time to fit residues: 40.1944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1228 random chunks: chunk 1036 optimal weight: 10.0000 chunk 930 optimal weight: 20.0000 chunk 516 optimal weight: 0.0170 chunk 317 optimal weight: 9.9990 chunk 627 optimal weight: 0.8980 chunk 497 optimal weight: 8.9990 chunk 962 optimal weight: 10.0000 chunk 372 optimal weight: 5.9990 chunk 585 optimal weight: 6.9990 chunk 716 optimal weight: 0.0040 chunk 1115 optimal weight: 0.9990 overall best weight: 1.5834 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: x 54 ASN x 105 HIS x 198 ASN h 14 HIS ** h 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 209 ASN h 235 GLN ** h 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 50 GLN I 79 ASN I 96 ASN ** I 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 257 GLN ** I 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** n 148 GLN n 170 GLN n 171 GLN n 277 GLN ** n 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 14 HIS ** o 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 148 GLN ** o 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 232 ASN m 40 HIS ** m 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** m 249 GLN M 120 GLN M 333 ASN ** M 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 463 ASN M 561 ASN N 70 HIS 1 158 HIS ** 1 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 55 ASN i 20 HIS a 84 ASN a 96 GLN a 231 ASN a 338 HIS ** a 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 534 HIS a 541 HIS ** a 737 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 749 HIS a 794 ASN a 945 ASN a 969 HIS a1000 ASN a1027 HIS a1029 HIS a1076 HIS a1166 HIS a1248 HIS a1319 GLN A 3 ASN A 217 GLN A 319 HIS A 388 ASN A 510 ASN ** A 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 545 ASN A 581 HIS A 676 ASN A 731 GLN A 889 HIS ** A 903 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 967 HIS A1076 HIS A1093 ASN ** A1191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1363 GLN A1369 ASN B 346 GLN B 350 HIS B 485 GLN B 510 ASN B 514 GLN B 534 HIS B 560 ASN B 901 HIS B 903 GLN ** B 919 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 969 HIS ** B1079 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1133 HIS B1229 HIS B1350 HIS B1363 GLN C 484 GLN C 510 ASN C 534 HIS C 543 GLN ** C 560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 676 ASN ** C 708 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 726 ASN ** C 849 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 874 GLN C 903 GLN C 914 GLN C 967 HIS C 985 ASN C1168 GLN C1184 ASN C1191 ASN ** C1255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 94 HIS D 350 HIS D 371 ASN D 510 ASN ** D 526 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 618 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 713 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 731 GLN ** D 914 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 919 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 945 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 969 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1023 GLN D1191 ASN Y 22 HIS ** Y 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 84 ASN Y 231 ASN ** Y 326 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 432 ASN Y 534 HIS Y 543 GLN Y 560 ASN Y 694 ASN Y 695 ASN ** Y 740 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 914 GLN Y1080 ASN Y1093 ASN Y1166 HIS Y1190 ASN Y1229 HIS Y1248 HIS Y1300 GLN ** Z 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 257 ASN Z 545 ASN ** Z 618 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 795 ASN ** Z 849 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z1023 GLN Z1027 HIS Z1060 ASN ** Z1082 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z1166 HIS Z1168 GLN ** Z1230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z1235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 119 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.2403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.068 100890 Z= 0.193 Angle : 0.661 12.545 137217 Z= 0.332 Chirality : 0.043 0.233 15838 Planarity : 0.005 0.097 17656 Dihedral : 5.509 70.356 13654 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 13.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer Outliers : 3.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.89 (0.07), residues: 12284 helix: -1.44 (0.07), residues: 4599 sheet: -2.15 (0.12), residues: 1574 loop : -2.20 (0.07), residues: 6111 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 24568 Ramachandran restraints generated. 12284 Oldfield, 0 Emsley, 12284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 24568 Ramachandran restraints generated. 12284 Oldfield, 0 Emsley, 12284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 3462 residues out of total 10859 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 348 poor density : 3114 time to evaluate : 8.905 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 outliers start: 348 outliers final: 219 residues processed: 3269 average time/residue: 0.8671 time to fit residues: 4876.6087 Evaluate side-chains 2940 residues out of total 10859 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 219 poor density : 2721 time to evaluate : 8.866 Switching outliers to nearest non-outliers outliers start: 219 outliers final: 0 residues processed: 219 average time/residue: 0.7279 time to fit residues: 314.1026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1228 random chunks: chunk 619 optimal weight: 1.9990 chunk 346 optimal weight: 7.9990 chunk 928 optimal weight: 8.9990 chunk 759 optimal weight: 8.9990 chunk 307 optimal weight: 5.9990 chunk 1117 optimal weight: 20.0000 chunk 1206 optimal weight: 5.9990 chunk 994 optimal weight: 10.0000 chunk 1107 optimal weight: 6.9990 chunk 380 optimal weight: 0.7980 chunk 896 optimal weight: 2.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** x 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 201 ASN I 79 ASN I 84 HIS I 148 GLN I 277 GLN ** H2233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** n 171 GLN n 297 ASN o 7 ASN o 14 HIS ** o 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 148 GLN o 173 GLN ** o 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 211 HIS ** M 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 517 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 552 GLN ** M 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 18 HIS S 37 HIS a 96 GLN ** a 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 497 HIS ** a 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 737 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 199 ASN A 545 ASN A 795 ASN ** A 903 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1093 ASN ** A1235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 485 GLN ** B1079 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1350 HIS C 111 GLN C 208 ASN ** C 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 541 HIS ** C 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 726 ASN ** C 748 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 849 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 874 GLN C 965 HIS C 985 ASN C1000 ASN C1029 HIS C1191 ASN ** C1255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 214 ASN D 422 ASN ** D 476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 526 ASN ** D 618 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 713 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 731 GLN ** D 945 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1023 GLN D1120 ASN D1166 HIS ** Y 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 208 ASN ** Y 326 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 455 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 694 ASN ** Y 740 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 795 ASN Y1003 HIS Y1111 GLN ** Z 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 257 ASN Z 462 GLN Z 545 ASN ** Z 618 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 737 GLN ** Z 849 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z1082 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z1235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 49 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.3012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.070 100890 Z= 0.223 Angle : 0.628 14.855 137217 Z= 0.313 Chirality : 0.043 0.243 15838 Planarity : 0.005 0.064 17656 Dihedral : 5.101 71.609 13654 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 12.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer Outliers : 3.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.21 (0.07), residues: 12284 helix: -0.70 (0.07), residues: 4645 sheet: -1.88 (0.12), residues: 1552 loop : -1.95 (0.08), residues: 6087 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 24568 Ramachandran restraints generated. 12284 Oldfield, 0 Emsley, 12284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 24568 Ramachandran restraints generated. 12284 Oldfield, 0 Emsley, 12284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 3258 residues out of total 10859 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 327 poor density : 2931 time to evaluate : 8.916 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 outliers start: 327 outliers final: 177 residues processed: 3106 average time/residue: 0.8870 time to fit residues: 4755.4331 Evaluate side-chains 2830 residues out of total 10859 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 177 poor density : 2653 time to evaluate : 8.859 Switching outliers to nearest non-outliers outliers start: 177 outliers final: 0 residues processed: 177 average time/residue: 0.7136 time to fit residues: 252.7918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1228 random chunks: chunk 1103 optimal weight: 20.0000 chunk 839 optimal weight: 40.0000 chunk 579 optimal weight: 8.9990 chunk 123 optimal weight: 3.9990 chunk 533 optimal weight: 2.9990 chunk 750 optimal weight: 0.8980 chunk 1121 optimal weight: 8.9990 chunk 1186 optimal weight: 0.1980 chunk 585 optimal weight: 9.9990 chunk 1062 optimal weight: 8.9990 chunk 319 optimal weight: 30.0000 overall best weight: 3.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** h 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 79 ASN I 148 GLN I 209 ASN ** n 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** n 43 HIS ** n 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 14 HIS ** o 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 148 GLN ** o 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 333 ASN ** M 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 517 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 63 GLN ** 1 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 37 HIS ** T 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** i 18 HIS ** a 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 231 ASN ** a 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 737 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 781 GLN A 851 GLN A 903 GLN A1029 HIS A1093 ASN ** A1235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1300 GLN ** B 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 208 ASN B 731 GLN ** B 919 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1079 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1166 HIS C 94 HIS ** C 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 795 ASN ** C 849 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1000 ASN ** C1255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 526 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 618 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 945 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 969 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1264 GLN ** Y 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 208 ASN ** Y 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 326 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 455 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 541 HIS Y 660 HIS ** Y 740 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 205 GLN Z 346 GLN Z 462 GLN Z 545 ASN ** Z 618 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 737 GLN ** Z 849 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z1082 ASN ** Z1235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.3425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.063 100890 Z= 0.210 Angle : 0.615 13.487 137217 Z= 0.304 Chirality : 0.042 0.259 15838 Planarity : 0.004 0.068 17656 Dihedral : 4.901 72.843 13654 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 13.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer Outliers : 2.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.84 (0.07), residues: 12284 helix: -0.33 (0.08), residues: 4661 sheet: -1.78 (0.12), residues: 1567 loop : -1.75 (0.08), residues: 6056 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 24568 Ramachandran restraints generated. 12284 Oldfield, 0 Emsley, 12284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 24568 Ramachandran restraints generated. 12284 Oldfield, 0 Emsley, 12284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 3169 residues out of total 10859 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 309 poor density : 2860 time to evaluate : 8.946 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 outliers start: 309 outliers final: 174 residues processed: 3020 average time/residue: 0.9055 time to fit residues: 4750.3505 Evaluate side-chains 2821 residues out of total 10859 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 174 poor density : 2647 time to evaluate : 8.915 Switching outliers to nearest non-outliers outliers start: 174 outliers final: 0 residues processed: 174 average time/residue: 0.6958 time to fit residues: 242.6693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1228 random chunks: chunk 988 optimal weight: 9.9990 chunk 673 optimal weight: 9.9990 chunk 17 optimal weight: 20.0000 chunk 883 optimal weight: 9.9990 chunk 489 optimal weight: 0.0040 chunk 1012 optimal weight: 20.0000 chunk 820 optimal weight: 10.0000 chunk 1 optimal weight: 9.9990 chunk 606 optimal weight: 9.9990 chunk 1065 optimal weight: 20.0000 chunk 299 optimal weight: 10.0000 overall best weight: 8.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** x 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 36 GLN h 80 GLN I 43 HIS I 50 GLN I 67 ASN I 79 ASN I 148 GLN ** n 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 14 HIS ** o 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 249 GLN M 322 HIS M 333 ASN ** M 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 517 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 577 GLN ** 1 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 37 HIS ** T 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 208 ASN a 497 HIS ** a 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 713 HIS a 794 ASN a 984 HIS a1000 ASN ** a1235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 76 HIS ** A 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 618 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 851 GLN A1093 ASN ** A1235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 510 ASN ** B 919 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1027 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1079 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 497 HIS ** C 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 795 ASN ** C 849 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1023 GLN C1120 ASN C1166 HIS ** C1255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 476 GLN ** D 526 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 676 ASN ** D 713 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 901 HIS ** D 914 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 945 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 969 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1100 ASN ** Y 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 326 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 455 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 571 HIS ** Y 708 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 901 HIS Y1029 HIS ** Z 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 462 GLN Z 545 ASN Z 676 ASN Z 737 GLN Z 795 ASN ** Z 849 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z1235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 40 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.3978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.099 100890 Z= 0.368 Angle : 0.711 12.552 137217 Z= 0.353 Chirality : 0.046 0.344 15838 Planarity : 0.005 0.070 17656 Dihedral : 5.078 72.999 13654 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 14.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer Outliers : 3.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.76 (0.07), residues: 12284 helix: -0.26 (0.08), residues: 4683 sheet: -1.67 (0.12), residues: 1584 loop : -1.74 (0.08), residues: 6017 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 24568 Ramachandran restraints generated. 12284 Oldfield, 0 Emsley, 12284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 24568 Ramachandran restraints generated. 12284 Oldfield, 0 Emsley, 12284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 3122 residues out of total 10859 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 398 poor density : 2724 time to evaluate : 12.125 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 outliers start: 398 outliers final: 241 residues processed: 2932 average time/residue: 0.8630 time to fit residues: 4369.0939 Evaluate side-chains 2768 residues out of total 10859 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 241 poor density : 2527 time to evaluate : 8.904 Switching outliers to nearest non-outliers outliers start: 241 outliers final: 0 residues processed: 241 average time/residue: 0.6812 time to fit residues: 325.4698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1228 random chunks: chunk 399 optimal weight: 9.9990 chunk 1068 optimal weight: 4.9990 chunk 234 optimal weight: 5.9990 chunk 696 optimal weight: 8.9990 chunk 293 optimal weight: 8.9990 chunk 1188 optimal weight: 1.9990 chunk 986 optimal weight: 9.9990 chunk 550 optimal weight: 50.0000 chunk 98 optimal weight: 10.0000 chunk 393 optimal weight: 6.9990 chunk 623 optimal weight: 5.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** x 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 67 ASN I 79 ASN I 148 GLN ** n 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 14 HIS ** o 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 249 GLN ** m 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 249 GLN M 333 ASN ** M 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 517 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 37 HIS ** T 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** j 18 HIS a 388 ASN ** a 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 737 GLN ** a1235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 618 HIS A 649 HIS A1093 ASN ** A1191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1229 HIS B 919 ASN B1023 GLN ** B1079 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 199 ASN ** C 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 637 ASN C 726 ASN C 795 ASN ** C1255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 455 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 526 ASN ** D 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 545 ASN ** D 945 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 969 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 326 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 455 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 543 GLN Y 914 GLN Y1111 GLN ** Z 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 257 ASN ** Z 618 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 676 ASN Z 737 GLN ** Z 849 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 919 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z1168 GLN ** Z1235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.4209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.067 100890 Z= 0.269 Angle : 0.667 16.452 137217 Z= 0.327 Chirality : 0.044 0.287 15838 Planarity : 0.005 0.068 17656 Dihedral : 4.954 74.197 13654 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 15.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer Outliers : 2.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.59 (0.07), residues: 12284 helix: -0.11 (0.08), residues: 4674 sheet: -1.61 (0.12), residues: 1582 loop : -1.64 (0.08), residues: 6028 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 24568 Ramachandran restraints generated. 12284 Oldfield, 0 Emsley, 12284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 24568 Ramachandran restraints generated. 12284 Oldfield, 0 Emsley, 12284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2965 residues out of total 10859 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 257 poor density : 2708 time to evaluate : 8.948 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 outliers start: 257 outliers final: 154 residues processed: 2831 average time/residue: 0.8911 time to fit residues: 4358.1731 Evaluate side-chains 2715 residues out of total 10859 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 154 poor density : 2561 time to evaluate : 8.938 Switching outliers to nearest non-outliers outliers start: 154 outliers final: 0 residues processed: 154 average time/residue: 0.6946 time to fit residues: 216.5489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1228 random chunks: chunk 1145 optimal weight: 5.9990 chunk 133 optimal weight: 0.0870 chunk 676 optimal weight: 10.0000 chunk 867 optimal weight: 6.9990 chunk 672 optimal weight: 8.9990 chunk 1000 optimal weight: 7.9990 chunk 663 optimal weight: 5.9990 chunk 1183 optimal weight: 8.9990 chunk 740 optimal weight: 1.9990 chunk 721 optimal weight: 9.9990 chunk 546 optimal weight: 50.0000 overall best weight: 4.2166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** x 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 79 ASN I 148 GLN ** n 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 14 HIS ** o 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 333 ASN ** M 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 517 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 1 193 ASN ** 1 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 37 HIS ** T 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 231 ASN ** a 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 541 HIS ** a1235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a1364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1093 ASN ** A1191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1079 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 795 ASN ** C 849 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 455 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 914 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 945 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 969 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 326 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 455 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 510 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y1190 ASN ** Z 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 462 GLN ** Z 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 618 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 676 ASN Z 737 GLN ** Z 849 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 919 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z1235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.4390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.059 100890 Z= 0.240 Angle : 0.657 15.467 137217 Z= 0.321 Chirality : 0.043 0.260 15838 Planarity : 0.004 0.072 17656 Dihedral : 4.864 75.105 13654 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 14.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer Outliers : 1.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.08), residues: 12284 helix: 0.01 (0.08), residues: 4660 sheet: -1.55 (0.12), residues: 1587 loop : -1.53 (0.08), residues: 6037 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 24568 Ramachandran restraints generated. 12284 Oldfield, 0 Emsley, 12284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 24568 Ramachandran restraints generated. 12284 Oldfield, 0 Emsley, 12284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2862 residues out of total 10859 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 172 poor density : 2690 time to evaluate : 8.981 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 outliers start: 172 outliers final: 97 residues processed: 2767 average time/residue: 0.8979 time to fit residues: 4280.5765 Evaluate side-chains 2660 residues out of total 10859 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 2563 time to evaluate : 8.950 Switching outliers to nearest non-outliers outliers start: 97 outliers final: 0 residues processed: 97 average time/residue: 0.7239 time to fit residues: 144.8990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1228 random chunks: chunk 732 optimal weight: 20.0000 chunk 472 optimal weight: 7.9990 chunk 706 optimal weight: 20.0000 chunk 356 optimal weight: 9.9990 chunk 232 optimal weight: 10.0000 chunk 229 optimal weight: 7.9990 chunk 752 optimal weight: 3.9990 chunk 806 optimal weight: 5.9990 chunk 585 optimal weight: 7.9990 chunk 110 optimal weight: 20.0000 chunk 930 optimal weight: 0.6980 overall best weight: 5.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** x 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 79 ASN I 148 GLN P2229 GLN ** n 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 14 HIS ** o 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 321 GLN M 333 ASN ** M 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 517 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 37 HIS ** T 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 541 HIS a 915 HIS ** a1235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a1364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 510 ASN A1093 ASN ** A1191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 711 HIS B 795 ASN B 919 ASN ** B1079 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1309 GLN C 726 ASN ** C 795 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 849 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1079 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1141 GLN ** C1255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 455 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 914 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 945 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 965 HIS ** D 969 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 455 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 388 ASN ** Z 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 618 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 737 GLN Z 748 HIS ** Z 849 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 919 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z1235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.4583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.072 100890 Z= 0.279 Angle : 0.681 14.458 137217 Z= 0.333 Chirality : 0.044 0.284 15838 Planarity : 0.005 0.073 17656 Dihedral : 4.880 75.833 13654 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 15.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer Outliers : 1.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.08), residues: 12284 helix: 0.06 (0.08), residues: 4663 sheet: -1.52 (0.12), residues: 1623 loop : -1.50 (0.08), residues: 5998 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 24568 Ramachandran restraints generated. 12284 Oldfield, 0 Emsley, 12284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 24568 Ramachandran restraints generated. 12284 Oldfield, 0 Emsley, 12284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2853 residues out of total 10859 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 189 poor density : 2664 time to evaluate : 9.011 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 outliers start: 189 outliers final: 120 residues processed: 2745 average time/residue: 0.9166 time to fit residues: 4350.1388 Evaluate side-chains 2653 residues out of total 10859 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 2533 time to evaluate : 8.901 Switching outliers to nearest non-outliers outliers start: 120 outliers final: 0 residues processed: 120 average time/residue: 0.6906 time to fit residues: 170.7392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1228 random chunks: chunk 1076 optimal weight: 0.9980 chunk 1133 optimal weight: 9.9990 chunk 1034 optimal weight: 0.9990 chunk 1102 optimal weight: 9.9990 chunk 663 optimal weight: 5.9990 chunk 480 optimal weight: 4.9990 chunk 866 optimal weight: 1.9990 chunk 338 optimal weight: 0.0770 chunk 996 optimal weight: 40.0000 chunk 1043 optimal weight: 8.9990 chunk 1099 optimal weight: 0.6980 overall best weight: 0.9542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** x 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 14 HIS ** h 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 67 ASN I 148 GLN ** n 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 14 HIS ** o 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 321 GLN ** M 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 1 193 ASN ** 1 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 37 HIS ** i 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 541 HIS ** a1235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a1364 GLN ** A 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1093 ASN ** A1191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 181 GLN ** B 737 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 795 ASN ** B1079 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 795 ASN ** C1229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 526 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 534 HIS D 914 GLN ** D 945 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 969 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 455 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 945 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 618 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 676 ASN Z 737 GLN ** Z 849 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 919 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z1060 ASN ** Z1235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.4697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.078 100890 Z= 0.176 Angle : 0.667 15.229 137217 Z= 0.321 Chirality : 0.043 0.286 15838 Planarity : 0.004 0.077 17656 Dihedral : 4.744 76.612 13654 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 14.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer Outliers : 0.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.08), residues: 12284 helix: 0.14 (0.08), residues: 4677 sheet: -1.31 (0.13), residues: 1581 loop : -1.40 (0.08), residues: 6026 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 24568 Ramachandran restraints generated. 12284 Oldfield, 0 Emsley, 12284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 24568 Ramachandran restraints generated. 12284 Oldfield, 0 Emsley, 12284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2853 residues out of total 10859 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 2779 time to evaluate : 9.765 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 outliers start: 74 outliers final: 33 residues processed: 2805 average time/residue: 0.8936 time to fit residues: 4320.9088 Evaluate side-chains 2634 residues out of total 10859 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 2601 time to evaluate : 8.991 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 0 residues processed: 33 average time/residue: 0.7187 time to fit residues: 56.8607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1228 random chunks: chunk 724 optimal weight: 7.9990 chunk 1166 optimal weight: 7.9990 chunk 711 optimal weight: 20.0000 chunk 553 optimal weight: 8.9990 chunk 810 optimal weight: 20.0000 chunk 1223 optimal weight: 0.2980 chunk 1126 optimal weight: 0.9980 chunk 974 optimal weight: 7.9990 chunk 101 optimal weight: 9.9990 chunk 752 optimal weight: 5.9990 chunk 597 optimal weight: 6.9990 overall best weight: 4.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: x 34 HIS ** x 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 235 GLN ** h 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 79 ASN I 148 GLN ** n 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 14 HIS o 36 GLN ** o 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 333 ASN ** M 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 517 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 1 54 ASN 1 193 ASN ** 1 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 37 HIS T 20 HIS ** i 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 915 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 889 HIS A1093 ASN ** A1191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 181 GLN B 281 GLN B 795 ASN ** B1079 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 462 GLN ** C 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 543 GLN C 726 ASN ** C 795 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 969 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 981 HIS ** C1255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 290 HIS ** D 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 455 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 526 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 945 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 455 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 510 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 708 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 676 ASN Z 737 GLN ** Z 749 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 849 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z1235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.4830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.089 100890 Z= 0.258 Angle : 0.706 14.221 137217 Z= 0.342 Chirality : 0.044 0.358 15838 Planarity : 0.005 0.077 17656 Dihedral : 4.793 76.701 13654 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 15.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer Outliers : 0.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.08), residues: 12284 helix: 0.18 (0.08), residues: 4682 sheet: -1.35 (0.12), residues: 1635 loop : -1.37 (0.08), residues: 5967 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 24568 Ramachandran restraints generated. 12284 Oldfield, 0 Emsley, 12284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 24568 Ramachandran restraints generated. 12284 Oldfield, 0 Emsley, 12284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2721 residues out of total 10859 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 2658 time to evaluate : 8.869 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 outliers start: 63 outliers final: 39 residues processed: 2680 average time/residue: 0.9646 time to fit residues: 4486.7576 Evaluate side-chains 2603 residues out of total 10859 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 2564 time to evaluate : 8.911 Switching outliers to nearest non-outliers outliers start: 39 outliers final: 0 residues processed: 39 average time/residue: 0.7922 time to fit residues: 70.5014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1228 random chunks: chunk 773 optimal weight: 20.0000 chunk 1037 optimal weight: 8.9990 chunk 298 optimal weight: 40.0000 chunk 898 optimal weight: 30.0000 chunk 143 optimal weight: 10.0000 chunk 270 optimal weight: 9.9990 chunk 975 optimal weight: 0.8980 chunk 408 optimal weight: 7.9990 chunk 1001 optimal weight: 3.9990 chunk 123 optimal weight: 0.6980 chunk 179 optimal weight: 8.9990 overall best weight: 4.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: x 34 HIS h 14 HIS ** h 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 148 GLN ** n 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 14 HIS ** o 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 1 54 ASN ** 1 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 37 HIS ** i 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 326 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 514 GLN a 545 ASN ** a 915 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 510 ASN A 781 GLN A1093 ASN ** A1191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1079 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 795 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 969 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 526 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 914 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 945 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 969 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 326 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 455 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 708 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y1124 HIS ** Z 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 676 ASN Z 737 GLN ** Z 749 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 849 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z1235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.120914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.099980 restraints weight = 172155.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.103003 restraints weight = 101142.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.104696 restraints weight = 61934.518| |-----------------------------------------------------------------------------| r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.4938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.067 100890 Z= 0.254 Angle : 0.717 14.683 137217 Z= 0.346 Chirality : 0.044 0.343 15838 Planarity : 0.005 0.129 17656 Dihedral : 4.826 77.444 13654 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 15.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer Outliers : 0.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (0.08), residues: 12284 helix: 0.18 (0.08), residues: 4692 sheet: -1.35 (0.13), residues: 1595 loop : -1.36 (0.08), residues: 5997 =============================================================================== Job complete usr+sys time: 54098.18 seconds wall clock time: 936 minutes 52.90 seconds (56212.90 seconds total)