Starting phenix.real_space_refine on Mon Mar 11 11:50:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ted_10480/03_2024/6ted_10480_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ted_10480/03_2024/6ted_10480.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ted_10480/03_2024/6ted_10480.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ted_10480/03_2024/6ted_10480.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ted_10480/03_2024/6ted_10480_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ted_10480/03_2024/6ted_10480_updated.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 70 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 9 6.06 5 P 109 5.49 5 Mg 1 5.21 5 S 276 5.16 5 C 35310 2.51 5 N 10289 2.21 5 O 11148 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 10": "OD1" <-> "OD2" Residue "A ARG 16": "NH1" <-> "NH2" Residue "A ASP 29": "OD1" <-> "OD2" Residue "A GLU 38": "OE1" <-> "OE2" Residue "A GLU 48": "OE1" <-> "OE2" Residue "A GLU 80": "OE1" <-> "OE2" Residue "A PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 120": "OD1" <-> "OD2" Residue "A TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 219": "OE1" <-> "OE2" Residue "A ARG 220": "NH1" <-> "NH2" Residue "A ASP 274": "OD1" <-> "OD2" Residue "A ASP 275": "OD1" <-> "OD2" Residue "A ASP 319": "OD1" <-> "OD2" Residue "A GLU 321": "OE1" <-> "OE2" Residue "A ARG 327": "NH1" <-> "NH2" Residue "A GLU 347": "OE1" <-> "OE2" Residue "A ASP 400": "OD1" <-> "OD2" Residue "A ASP 422": "OD1" <-> "OD2" Residue "A ASP 437": "OD1" <-> "OD2" Residue "A ASP 495": "OD1" <-> "OD2" Residue "A ASP 540": "OD1" <-> "OD2" Residue "A ASP 552": "OD1" <-> "OD2" Residue "A PHE 566": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 634": "OE1" <-> "OE2" Residue "A GLU 659": "OE1" <-> "OE2" Residue "A TYR 669": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 695": "OD1" <-> "OD2" Residue "A ASP 712": "OD1" <-> "OD2" Residue "A ARG 743": "NH1" <-> "NH2" Residue "A GLU 762": "OE1" <-> "OE2" Residue "A PHE 766": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 827": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 835": "OE1" <-> "OE2" Residue "A PHE 836": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 849": "OD1" <-> "OD2" Residue "A TYR 924": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 964": "OE1" <-> "OE2" Residue "A GLU 1015": "OE1" <-> "OE2" Residue "A ASP 1026": "OD1" <-> "OD2" Residue "A GLU 1057": "OE1" <-> "OE2" Residue "A PHE 1076": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1149": "NH1" <-> "NH2" Residue "A ARG 1153": "NH1" <-> "NH2" Residue "A ARG 1160": "NH1" <-> "NH2" Residue "A GLU 1191": "OE1" <-> "OE2" Residue "A ARG 1213": "NH1" <-> "NH2" Residue "A ASP 1217": "OD1" <-> "OD2" Residue "A ARG 1218": "NH1" <-> "NH2" Residue "A ASP 1241": "OD1" <-> "OD2" Residue "A ASP 1282": "OD1" <-> "OD2" Residue "A ARG 1286": "NH1" <-> "NH2" Residue "A ASP 1295": "OD1" <-> "OD2" Residue "A GLU 1327": "OE1" <-> "OE2" Residue "A ASP 1339": "OD1" <-> "OD2" Residue "A ASP 1351": "OD1" <-> "OD2" Residue "A ASP 1389": "OD1" <-> "OD2" Residue "A ASP 1423": "OD1" <-> "OD2" Residue "A ASP 1449": "OD1" <-> "OD2" Residue "A GLU 1456": "OE1" <-> "OE2" Residue "A ASP 1472": "OD1" <-> "OD2" Residue "A TYR 1482": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 20": "OD1" <-> "OD2" Residue "B PHE 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 83": "NH1" <-> "NH2" Residue "B TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 102": "OD1" <-> "OD2" Residue "B GLU 135": "OE1" <-> "OE2" Residue "B ASP 168": "OD1" <-> "OD2" Residue "B GLU 173": "OE1" <-> "OE2" Residue "B TYR 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 266": "OE1" <-> "OE2" Residue "B ASP 291": "OD1" <-> "OD2" Residue "B GLU 293": "OE1" <-> "OE2" Residue "B GLU 299": "OE1" <-> "OE2" Residue "B PHE 320": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 355": "OD1" <-> "OD2" Residue "B PHE 364": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 384": "OD1" <-> "OD2" Residue "B ARG 385": "NH1" <-> "NH2" Residue "B ASP 386": "OD1" <-> "OD2" Residue "B TYR 388": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 442": "OD1" <-> "OD2" Residue "B GLU 516": "OE1" <-> "OE2" Residue "B GLU 543": "OE1" <-> "OE2" Residue "B GLU 555": "OE1" <-> "OE2" Residue "B ASP 563": "OD1" <-> "OD2" Residue "B ASP 606": "OD1" <-> "OD2" Residue "B GLU 645": "OE1" <-> "OE2" Residue "B ASP 655": "OD1" <-> "OD2" Residue "B TYR 664": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 680": "OD1" <-> "OD2" Residue "B ASP 681": "OD1" <-> "OD2" Residue "B GLU 684": "OE1" <-> "OE2" Residue "B PHE 713": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 740": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 788": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 814": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 846": "OD1" <-> "OD2" Residue "B ASP 863": "OD1" <-> "OD2" Residue "B PHE 895": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1057": "OD1" <-> "OD2" Residue "B PHE 1086": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 27": "OD1" <-> "OD2" Residue "C ASP 61": "OD1" <-> "OD2" Residue "C PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 76": "OD1" <-> "OD2" Residue "C ASP 77": "OD1" <-> "OD2" Residue "C TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 92": "OE1" <-> "OE2" Residue "C PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 210": "OE1" <-> "OE2" Residue "C GLU 213": "OE1" <-> "OE2" Residue "C GLU 215": "OE1" <-> "OE2" Residue "C ASP 221": "OD1" <-> "OD2" Residue "C TYR 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 15": "OE1" <-> "OE2" Residue "D GLU 30": "OE1" <-> "OE2" Residue "D GLU 59": "OE1" <-> "OE2" Residue "D GLU 109": "OE1" <-> "OE2" Residue "D GLU 125": "OE1" <-> "OE2" Residue "E ASP 2": "OD1" <-> "OD2" Residue "E GLU 4": "OE1" <-> "OE2" Residue "E TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 31": "OD1" <-> "OD2" Residue "E GLU 38": "OE1" <-> "OE2" Residue "E ASP 67": "OD1" <-> "OD2" Residue "E ASP 70": "OD1" <-> "OD2" Residue "E PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 134": "OE1" <-> "OE2" Residue "E GLU 167": "OE1" <-> "OE2" Residue "E PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 88": "OD1" <-> "OD2" Residue "F TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 86": "OD1" <-> "OD2" Residue "G ASP 120": "OD1" <-> "OD2" Residue "G ASP 141": "OD1" <-> "OD2" Residue "G ASP 165": "OD1" <-> "OD2" Residue "H ASP 8": "OD1" <-> "OD2" Residue "H ASP 14": "OD1" <-> "OD2" Residue "H ASP 23": "OD1" <-> "OD2" Residue "H ASP 38": "OD1" <-> "OD2" Residue "H ASP 42": "OD1" <-> "OD2" Residue "H ASP 51": "OD1" <-> "OD2" Residue "H PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 71": "OD1" <-> "OD2" Residue "H ASP 86": "OD1" <-> "OD2" Residue "H PHE 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 40": "NH1" <-> "NH2" Residue "I GLU 61": "OE1" <-> "OE2" Residue "I ASP 71": "OD1" <-> "OD2" Residue "I PHE 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 54": "OD1" <-> "OD2" Residue "K PHE 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 111": "OD1" <-> "OD2" Residue "L GLU 21": "OE1" <-> "OE2" Residue "M GLU 1348": "OE1" <-> "OE2" Residue "M GLU 1364": "OE1" <-> "OE2" Residue "M ASP 1375": "OD1" <-> "OD2" Residue "M ASP 1407": "OD1" <-> "OD2" Residue "M ASP 1409": "OD1" <-> "OD2" Residue "M TYR 1431": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 1439": "OD1" <-> "OD2" Residue "M GLU 1453": "OE1" <-> "OE2" Residue "M PHE 1461": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 1472": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 1485": "OE1" <-> "OE2" Residue "M TYR 1486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 1511": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 1513": "OD1" <-> "OD2" Residue "M ASP 1517": "OD1" <-> "OD2" Residue "Q GLU 7": "OE1" <-> "OE2" Residue "Q ASP 12": "OD1" <-> "OD2" Residue "Q ASP 20": "OD1" <-> "OD2" Residue "Q ASP 22": "OD1" <-> "OD2" Residue "Q GLU 26": "OE1" <-> "OE2" Residue "Q GLU 29": "OE1" <-> "OE2" Residue "Q GLU 37": "OE1" <-> "OE2" Residue "Q TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 58": "OE1" <-> "OE2" Residue "Q PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 65": "OE1" <-> "OE2" Residue "Q ASP 70": "OD1" <-> "OD2" Residue "Q ASP 81": "OD1" <-> "OD2" Residue "Q GLU 100": "OE1" <-> "OE2" Residue "Q ASP 127": "OD1" <-> "OD2" Residue "Q ASP 146": "OD1" <-> "OD2" Residue "Q PHE 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 199": "OE1" <-> "OE2" Residue "Q GLU 226": "OE1" <-> "OE2" Residue "Q GLU 242": "OE1" <-> "OE2" Residue "Q ASP 265": "OD1" <-> "OD2" Residue "Q ASP 284": "OD1" <-> "OD2" Residue "Q GLU 300": "OE1" <-> "OE2" Residue "Q GLU 302": "OE1" <-> "OE2" Residue "Q TYR 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 389": "OE1" <-> "OE2" Residue "Q GLU 392": "OE1" <-> "OE2" Residue "Q ASP 395": "OD1" <-> "OD2" Residue "Q GLU 406": "OE1" <-> "OE2" Residue "Q ASP 426": "OD1" <-> "OD2" Residue "Q GLU 443": "OE1" <-> "OE2" Residue "Q ASP 488": "OD1" <-> "OD2" Residue "Q GLU 489": "OE1" <-> "OE2" Residue "Q PHE 547": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 563": "OD1" <-> "OD2" Residue "Q GLU 580": "OE1" <-> "OE2" Residue "Q PHE 588": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 602": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 648": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 668": "OD1" <-> "OD2" Residue "Q GLU 675": "OE1" <-> "OE2" Residue "Q GLU 735": "OE1" <-> "OE2" Residue "Q ASP 750": "OD1" <-> "OD2" Residue "Q GLU 772": "OE1" <-> "OE2" Residue "Q GLU 778": "OE1" <-> "OE2" Residue "Q PHE 805": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 806": "OD1" <-> "OD2" Residue "Q ASP 819": "OD1" <-> "OD2" Residue "Q ARG 830": "NH1" <-> "NH2" Residue "Q GLU 838": "OE1" <-> "OE2" Residue "Q GLU 846": "OE1" <-> "OE2" Residue "Q GLU 848": "OE1" <-> "OE2" Residue "Q GLU 859": "OE1" <-> "OE2" Residue "Q GLU 867": "OE1" <-> "OE2" Residue "Q GLU 869": "OE1" <-> "OE2" Residue "Q GLU 870": "OE1" <-> "OE2" Residue "R PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 404": "OE1" <-> "OE2" Residue "R GLU 410": "OE1" <-> "OE2" Residue "R ASP 433": "OD1" <-> "OD2" Residue "R GLU 457": "OE1" <-> "OE2" Residue "R PHE 460": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 485": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 494": "OE1" <-> "OE2" Residue "U GLU 395": "OE1" <-> "OE2" Residue "U ASP 396": "OD1" <-> "OD2" Residue "U ARG 409": "NH1" <-> "NH2" Residue "U ASP 445": "OD1" <-> "OD2" Residue "U PHE 457": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 85": "OD1" <-> "OD2" Residue "V ASP 101": "OD1" <-> "OD2" Residue "V ASP 104": "OD1" <-> "OD2" Residue "V GLU 105": "OE1" <-> "OE2" Residue "V GLU 111": "OE1" <-> "OE2" Residue "V GLU 140": "OE1" <-> "OE2" Residue "V PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 184": "OE1" <-> "OE2" Residue "V GLU 203": "OE1" <-> "OE2" Residue "W GLU 12": "OE1" <-> "OE2" Residue "W ARG 50": "NH1" <-> "NH2" Residue "W ASP 51": "OD1" <-> "OD2" Residue "W ARG 147": "NH1" <-> "NH2" Residue "W ASP 201": "OD1" <-> "OD2" Residue "W ASP 243": "OD1" <-> "OD2" Residue "W ASP 244": "OD1" <-> "OD2" Residue "W ASP 260": "OD1" <-> "OD2" Residue "W ASP 272": "OD1" <-> "OD2" Residue "W ASP 275": "OD1" <-> "OD2" Residue "W TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ASP 37": "OD1" <-> "OD2" Residue "Y GLU 47": "OE1" <-> "OE2" Residue "Z ASP 176": "OD1" <-> "OD2" Residue "Z ARG 198": "NH1" <-> "NH2" Residue "Z ASP 207": "OD1" <-> "OD2" Residue "Z ASP 262": "OD1" <-> "OD2" Residue "Z ASP 288": "OD1" <-> "OD2" Residue "Z ASP 289": "OD1" <-> "OD2" Residue "Z GLU 297": "OE1" <-> "OE2" Residue "Z ASP 314": "OD1" <-> "OD2" Residue "Z ASP 351": "OD1" <-> "OD2" Residue "Z ASP 355": "OD1" <-> "OD2" Residue "Z PHE 373": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 384": "OE1" <-> "OE2" Residue "Z GLU 430": "OE1" <-> "OE2" Residue "Z GLU 455": "OE1" <-> "OE2" Residue "Z ASP 456": "OD1" <-> "OD2" Residue "Z PHE 503": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ASP 529": "OD1" <-> "OD2" Residue "Z ASP 543": "OD1" <-> "OD2" Residue "Z ARG 555": "NH1" <-> "NH2" Residue "Z ARG 571": "NH1" <-> "NH2" Residue "Z ARG 577": "NH1" <-> "NH2" Residue "Z ASP 580": "OD1" <-> "OD2" Residue "Z ARG 582": "NH1" <-> "NH2" Residue "Z ASP 588": "OD1" <-> "OD2" Residue "Z PHE 623": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 631": "OE1" <-> "OE2" Residue "Z TYR 720": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 729": "OE1" <-> "OE2" Residue "Z GLU 735": "OE1" <-> "OE2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 57142 Number of models: 1 Model: "" Number of chains: 31 Chain: "A" Number of atoms: 11255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1426, 11255 Classifications: {'peptide': 1426} Link IDs: {'PCIS': 1, 'PTRANS': 71, 'TRANS': 1353} Chain breaks: 7 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'TPO:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 8980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1122, 8980 Classifications: {'peptide': 1122} Link IDs: {'PTRANS': 52, 'TRANS': 1069} Chain breaks: 4 Chain: "C" Number of atoms: 2072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 2072 Classifications: {'peptide': 258} Link IDs: {'PTRANS': 15, 'TRANS': 242} Chain breaks: 1 Chain: "D" Number of atoms: 1004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1004 Classifications: {'peptide': 126} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 3, 'TRANS': 122} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "E" Number of atoms: 1720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1720 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 11, 'TRANS': 197} Chain: "F" Number of atoms: 626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 626 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 5, 'TRANS': 72} Chain: "G" Number of atoms: 1333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1333 Classifications: {'peptide': 171} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 10, 'TRANS': 160} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 10 Chain: "H" Number of atoms: 1197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1197 Classifications: {'peptide': 149} Link IDs: {'PTRANS': 4, 'TRANS': 144} Chain: "I" Number of atoms: 942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 942 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 5, 'TRANS': 110} Chain: "J" Number of atoms: 524 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 524 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 2, 'TRANS': 63} Chain: "K" Number of atoms: 920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 920 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 8, 'TRANS': 106} Chain: "L" Number of atoms: 390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 390 Classifications: {'peptide': 47} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 44} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "M" Number of atoms: 4737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1002, 4737 Classifications: {'peptide': 1002} Incomplete info: {'backbone_only': 780, 'n_c_alpha_c_only': 11, 'truncation_to_alanine': 7} Link IDs: {'PTRANS': 44, 'TRANS': 957} Chain breaks: 12 Unresolved chain link angles: 45 Unresolved non-hydrogen bonds: 3634 Unresolved non-hydrogen angles: 5197 Unresolved non-hydrogen dihedrals: 2360 Unresolved non-hydrogen chiralities: 1014 Planarities with less than four sites: {'GLN:plan1': 42, 'HIS:plan': 21, 'TYR:plan': 32, 'ASN:plan1': 31, 'TRP:plan': 8, 'ASP:plan': 52, 'PHE:plan': 36, 'GLU:plan': 82, 'ARG:plan': 58} Unresolved non-hydrogen planarities: 1828 Chain: "N" Number of atoms: 773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 773 Classifications: {'DNA': 37} Link IDs: {'rna3p': 36} Chain breaks: 1 Chain: "P" Number of atoms: 452 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 452 Classifications: {'RNA': 21} Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 2, 'rna3p_pur': 9, 'rna3p_pyr': 6} Link IDs: {'rna2p': 6, 'rna3p': 14} Chain: "Q" Number of atoms: 7226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 890, 7226 Classifications: {'peptide': 890} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 2, 'PTRANS': 19, 'TRANS': 868} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "R" Number of atoms: 1832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1832 Classifications: {'peptide': 244} Incomplete info: {'truncation_to_alanine': 50} Link IDs: {'CIS': 1, 'PTRANS': 7, 'TRANS': 235} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 180 Unresolved non-hydrogen angles: 220 Unresolved non-hydrogen dihedrals: 145 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 7, 'TYR:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 6, 'GLU:plan': 6, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 101 Chain: "T" Number of atoms: 974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 974 Classifications: {'DNA': 48} Link IDs: {'rna3p': 47} Chain: "U" Number of atoms: 852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 852 Classifications: {'peptide': 125} Incomplete info: {'truncation_to_alanine': 49} Link IDs: {'PTRANS': 6, 'TRANS': 118} Chain breaks: 3 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 175 Unresolved non-hydrogen angles: 220 Unresolved non-hydrogen dihedrals: 146 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 3, 'ASN:plan1': 1, 'HIS:plan': 4, 'PHE:plan': 3, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 90 Chain: "V" Number of atoms: 1703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1703 Classifications: {'peptide': 244} Incomplete info: {'truncation_to_alanine': 83} Link IDs: {'CIS': 2, 'PTRANS': 14, 'TRANS': 227} Chain breaks: 4 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 355 Unresolved non-hydrogen angles: 449 Unresolved non-hydrogen dihedrals: 307 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 9, 'ASN:plan1': 6, 'TRP:plan': 1, 'ASP:plan': 7, 'PHE:plan': 5, 'GLU:plan': 13, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 240 Chain: "W" Number of atoms: 2333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 300, 2333 Classifications: {'peptide': 300} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 291} Chain: "X" Number of atoms: 353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 353 Classifications: {'peptide': 43} Link IDs: {'TRANS': 42} Chain: "Y" Number of atoms: 911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 911 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 4, 'TRANS': 111} Chain: "Z" Number of atoms: 4023 Number of conformers: 1 Conformer: "" Number of residues, atoms: 510, 4023 Classifications: {'peptide': 510} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 19, 'TRANS': 490} Chain breaks: 5 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 1, 'TPO:plan-1': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 23 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "Y" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 472 SG CYS A 71 94.800 77.880 167.032 1.00 48.64 S ATOM 494 SG CYS A 74 94.571 81.674 167.126 1.00 43.97 S ATOM 19805 SG CYS B1119 105.053 90.392 176.486 1.00 32.39 S ATOM 19827 SG CYS B1122 107.643 87.987 176.358 1.00 33.91 S ATOM 19942 SG CYS B1137 103.790 86.825 176.565 1.00 52.14 S ATOM 20929 SG CYS C 88 71.444 91.821 103.019 1.00 25.95 S ATOM 20942 SG CYS C 90 70.713 89.229 105.469 1.00 34.62 S ATOM 20999 SG CYS C 97 73.994 89.271 102.726 1.00 17.28 S ATOM 28249 SG CYS I 17 176.430 39.275 145.158 1.00 41.48 S ATOM 28273 SG CYS I 20 173.350 38.672 146.958 1.00 41.26 S ATOM 28434 SG CYS I 39 174.539 41.692 148.614 1.00 44.80 S ATOM 28811 SG CYS I 86 173.903 57.783 104.965 1.00 35.40 S ATOM 28835 SG CYS I 89 173.165 55.480 102.261 1.00 40.85 S ATOM 29039 SG CYS I 114 170.275 56.425 103.733 1.00 26.20 S ATOM 29074 SG CYS I 119 172.723 54.499 105.483 1.00 34.98 S ATOM 29184 SG CYS J 7 103.959 83.934 94.576 1.00 0.17 S ATOM 29472 SG CYS J 44 106.085 86.192 92.698 1.00 12.81 S ATOM 29478 SG CYS J 45 104.022 84.156 90.933 1.00 12.04 S ATOM 52339 SG CYS Y 19 112.852 22.094 190.278 1.00 74.67 S Residues with excluded nonbonded symmetry interactions: 94 residue: pdb=" N ASN M1145 " occ=0.00 ... (2 atoms not shown) pdb=" O ASN M1145 " occ=0.00 residue: pdb=" N THR M1146 " occ=0.00 ... (2 atoms not shown) pdb=" O THR M1146 " occ=0.00 residue: pdb=" N GLU M1147 " occ=0.00 ... (2 atoms not shown) pdb=" O GLU M1147 " occ=0.00 residue: pdb=" N GLU M1148 " occ=0.00 ... (2 atoms not shown) pdb=" O GLU M1148 " occ=0.00 residue: pdb=" N ILE M1149 " occ=0.00 ... (2 atoms not shown) pdb=" O ILE M1149 " occ=0.00 residue: pdb=" N PHE M1150 " occ=0.00 ... (2 atoms not shown) pdb=" O PHE M1150 " occ=0.00 residue: pdb=" N ASN M1151 " occ=0.00 ... (2 atoms not shown) pdb=" O ASN M1151 " occ=0.00 residue: pdb=" N MET M1152 " occ=0.00 ... (2 atoms not shown) pdb=" O MET M1152 " occ=0.00 residue: pdb=" N LEU M1153 " occ=0.00 ... (2 atoms not shown) pdb=" O LEU M1153 " occ=0.00 residue: pdb=" N THR M1154 " occ=0.00 ... (2 atoms not shown) pdb=" O THR M1154 " occ=0.00 residue: pdb=" N LYS M1155 " occ=0.00 ... (2 atoms not shown) pdb=" O LYS M1155 " occ=0.00 residue: pdb=" N GLU M1156 " occ=0.00 ... (2 atoms not shown) pdb=" O GLU M1156 " occ=0.00 ... (remaining 82 not shown) Time building chain proxies: 23.35, per 1000 atoms: 0.41 Number of scatterers: 57142 At special positions: 0 Unit cell: (207.702, 191.967, 245.466, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 9 29.99 S 276 16.00 P 109 15.00 Mg 1 11.99 O 11148 8.00 N 10289 7.00 C 35310 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 18.17 Conformation dependent library (CDL) restraints added in 7.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2001 " pdb="ZN ZN A2001 " - pdb=" NE2 HIS A 84 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 74 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 71 " pdb=" ZN B1201 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1122 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1119 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1137 " pdb=" ZN C 301 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 88 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 90 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 97 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 17 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 20 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 39 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 114 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 89 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 119 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 86 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 45 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 7 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 44 " pdb=" ZN Y 201 " pdb="ZN ZN Y 201 " - pdb=" SG CYS Y 19 " Number of angles added : 6 14464 Ramachandran restraints generated. 7232 Oldfield, 0 Emsley, 7232 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 12312 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 251 helices and 68 sheets defined 32.4% alpha, 9.6% beta 32 base pairs and 69 stacking pairs defined. Time for finding SS restraints: 19.51 Creating SS restraints... Processing helix chain 'A' and resid 28 through 34 removed outlier: 3.575A pdb=" N ARG A 33 " --> pdb=" O ASP A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 109 Processing helix chain 'A' and resid 124 through 132 removed outlier: 3.918A pdb=" N ILE A 129 " --> pdb=" O LYS A 125 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU A 130 " --> pdb=" O ILE A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 147 removed outlier: 3.899A pdb=" N ASP A 146 " --> pdb=" O THR A 142 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU A 147 " --> pdb=" O HIS A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 227 removed outlier: 3.531A pdb=" N HIS A 222 " --> pdb=" O PRO A 218 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLU A 223 " --> pdb=" O GLU A 219 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ARG A 227 " --> pdb=" O GLU A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 235 No H-bonds generated for 'chain 'A' and resid 232 through 235' Processing helix chain 'A' and resid 245 through 248 Processing helix chain 'A' and resid 275 through 293 removed outlier: 3.997A pdb=" N ASP A 282 " --> pdb=" O HIS A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 318 removed outlier: 3.929A pdb=" N VAL A 318 " --> pdb=" O VAL A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 343 removed outlier: 3.770A pdb=" N LEU A 343 " --> pdb=" O LEU A 339 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 339 through 343' Processing helix chain 'A' and resid 382 through 385 No H-bonds generated for 'chain 'A' and resid 382 through 385' Processing helix chain 'A' and resid 401 through 408 Processing helix chain 'A' and resid 429 through 431 No H-bonds generated for 'chain 'A' and resid 429 through 431' Processing helix chain 'A' and resid 466 through 468 No H-bonds generated for 'chain 'A' and resid 466 through 468' Processing helix chain 'A' and resid 487 through 492 Proline residue: A 491 - end of helix Processing helix chain 'A' and resid 509 through 518 removed outlier: 3.746A pdb=" N GLU A 514 " --> pdb=" O GLU A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 521 through 523 No H-bonds generated for 'chain 'A' and resid 521 through 523' Processing helix chain 'A' and resid 540 through 548 Processing helix chain 'A' and resid 557 through 563 removed outlier: 3.682A pdb=" N ASN A 562 " --> pdb=" O GLY A 558 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 595 removed outlier: 4.253A pdb=" N LEU A 594 " --> pdb=" O GLN A 590 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ILE A 595 " --> pdb=" O ILE A 591 " (cutoff:3.500A) Processing helix chain 'A' and resid 611 through 613 No H-bonds generated for 'chain 'A' and resid 611 through 613' Processing helix chain 'A' and resid 642 through 645 No H-bonds generated for 'chain 'A' and resid 642 through 645' Processing helix chain 'A' and resid 652 through 659 removed outlier: 3.805A pdb=" N TYR A 657 " --> pdb=" O VAL A 653 " (cutoff:3.500A) Processing helix chain 'A' and resid 663 through 683 removed outlier: 3.542A pdb=" N SER A 670 " --> pdb=" O ARG A 666 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLN A 673 " --> pdb=" O TYR A 669 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ASN A 678 " --> pdb=" O THR A 674 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N LEU A 681 " --> pdb=" O ASN A 677 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ILE A 682 " --> pdb=" O ASN A 678 " (cutoff:3.500A) Processing helix chain 'A' and resid 690 through 692 No H-bonds generated for 'chain 'A' and resid 690 through 692' Processing helix chain 'A' and resid 698 through 722 Processing helix chain 'A' and resid 733 through 757 Processing helix chain 'A' and resid 766 through 771 Processing helix chain 'A' and resid 778 through 785 removed outlier: 3.521A pdb=" N GLN A 783 " --> pdb=" O ILE A 779 " (cutoff:3.500A) Processing helix chain 'A' and resid 818 through 820 No H-bonds generated for 'chain 'A' and resid 818 through 820' Processing helix chain 'A' and resid 833 through 868 removed outlier: 3.879A pdb=" N GLU A 845 " --> pdb=" O MET A 841 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N GLY A 846 " --> pdb=" O GLY A 842 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LEU A 847 " --> pdb=" O GLY A 843 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N ALA A 855 " --> pdb=" O ALA A 851 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLY A 858 " --> pdb=" O THR A 854 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N TYR A 859 " --> pdb=" O ALA A 855 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ILE A 860 " --> pdb=" O GLU A 856 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ARG A 862 " --> pdb=" O GLY A 858 " (cutoff:3.500A) Processing helix chain 'A' and resid 891 through 893 No H-bonds generated for 'chain 'A' and resid 891 through 893' Processing helix chain 'A' and resid 917 through 920 No H-bonds generated for 'chain 'A' and resid 917 through 920' Processing helix chain 'A' and resid 927 through 933 removed outlier: 3.542A pdb=" N ARG A 931 " --> pdb=" O GLU A 927 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ARG A 932 " --> pdb=" O ARG A 928 " (cutoff:3.500A) Processing helix chain 'A' and resid 941 through 944 No H-bonds generated for 'chain 'A' and resid 941 through 944' Processing helix chain 'A' and resid 946 through 969 removed outlier: 3.611A pdb=" N GLU A 964 " --> pdb=" O ARG A 960 " (cutoff:3.500A) Processing helix chain 'A' and resid 983 through 993 Processing helix chain 'A' and resid 1006 through 1016 removed outlier: 3.711A pdb=" N VAL A1010 " --> pdb=" O PRO A1006 " (cutoff:3.500A) Processing helix chain 'A' and resid 1028 through 1037 removed outlier: 3.628A pdb=" N ALA A1033 " --> pdb=" O LEU A1029 " (cutoff:3.500A) Processing helix chain 'A' and resid 1039 through 1048 Processing helix chain 'A' and resid 1053 through 1056 No H-bonds generated for 'chain 'A' and resid 1053 through 1056' Processing helix chain 'A' and resid 1062 through 1076 Processing helix chain 'A' and resid 1087 through 1096 Processing helix chain 'A' and resid 1098 through 1101 Processing helix chain 'A' and resid 1121 through 1128 removed outlier: 3.601A pdb=" N GLU A1126 " --> pdb=" O PRO A1122 " (cutoff:3.500A) Processing helix chain 'A' and resid 1151 through 1161 removed outlier: 3.714A pdb=" N ASP A1156 " --> pdb=" O GLU A1152 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ILE A1157 " --> pdb=" O ARG A1153 " (cutoff:3.500A) Processing helix chain 'A' and resid 1166 through 1169 No H-bonds generated for 'chain 'A' and resid 1166 through 1169' Processing helix chain 'A' and resid 1190 through 1194 Processing helix chain 'A' and resid 1228 through 1237 Processing helix chain 'A' and resid 1240 through 1242 No H-bonds generated for 'chain 'A' and resid 1240 through 1242' Processing helix chain 'A' and resid 1282 through 1294 removed outlier: 4.233A pdb=" N ARG A1286 " --> pdb=" O ASP A1282 " (cutoff:3.500A) Processing helix chain 'A' and resid 1344 through 1347 No H-bonds generated for 'chain 'A' and resid 1344 through 1347' Processing helix chain 'A' and resid 1371 through 1387 removed outlier: 3.802A pdb=" N LYS A1376 " --> pdb=" O GLU A1372 " (cutoff:3.500A) Processing helix chain 'A' and resid 1396 through 1405 removed outlier: 3.725A pdb=" N LEU A1401 " --> pdb=" O HIS A1397 " (cutoff:3.500A) Processing helix chain 'A' and resid 1416 through 1419 No H-bonds generated for 'chain 'A' and resid 1416 through 1419' Processing helix chain 'A' and resid 1426 through 1429 No H-bonds generated for 'chain 'A' and resid 1426 through 1429' Processing helix chain 'A' and resid 1437 through 1445 removed outlier: 3.500A pdb=" N GLU A1441 " --> pdb=" O ASP A1437 " (cutoff:3.500A) Processing helix chain 'A' and resid 1456 through 1459 No H-bonds generated for 'chain 'A' and resid 1456 through 1459' Processing helix chain 'A' and resid 1479 through 1481 No H-bonds generated for 'chain 'A' and resid 1479 through 1481' Processing helix chain 'B' and resid 23 through 36 removed outlier: 3.783A pdb=" N TRP B 27 " --> pdb=" O GLN B 23 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ILE B 28 " --> pdb=" O GLU B 24 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N VAL B 29 " --> pdb=" O ALA B 25 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ILE B 30 " --> pdb=" O CYS B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 52 removed outlier: 3.747A pdb=" N SER B 46 " --> pdb=" O GLN B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 54 through 58 Processing helix chain 'B' and resid 110 through 115 Processing helix chain 'B' and resid 168 through 173 removed outlier: 3.517A pdb=" N CYS B 172 " --> pdb=" O ASP B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 275 Processing helix chain 'B' and resid 281 through 288 removed outlier: 3.629A pdb=" N HIS B 287 " --> pdb=" O ASP B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 305 removed outlier: 3.650A pdb=" N GLU B 299 " --> pdb=" O PRO B 295 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N MET B 300 " --> pdb=" O GLU B 296 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N VAL B 301 " --> pdb=" O MET B 297 " (cutoff:3.500A) Proline residue: B 303 - end of helix Processing helix chain 'B' and resid 314 through 324 removed outlier: 4.323A pdb=" N ARG B 324 " --> pdb=" O PHE B 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 339 Processing helix chain 'B' and resid 342 through 345 No H-bonds generated for 'chain 'B' and resid 342 through 345' Processing helix chain 'B' and resid 358 through 376 removed outlier: 3.607A pdb=" N TYR B 363 " --> pdb=" O THR B 359 " (cutoff:3.500A) Processing helix chain 'B' and resid 388 through 390 No H-bonds generated for 'chain 'B' and resid 388 through 390' Processing helix chain 'B' and resid 398 through 423 removed outlier: 3.746A pdb=" N LEU B 403 " --> pdb=" O LEU B 399 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ARG B 405 " --> pdb=" O ALA B 401 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N GLY B 406 " --> pdb=" O PHE B 402 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU B 411 " --> pdb=" O MET B 407 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU B 412 " --> pdb=" O PHE B 408 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N PHE B 422 " --> pdb=" O TYR B 418 " (cutoff:3.500A) Processing helix chain 'B' and resid 440 through 450 removed outlier: 3.622A pdb=" N LYS B 445 " --> pdb=" O SER B 441 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ALA B 449 " --> pdb=" O LYS B 445 " (cutoff:3.500A) Processing helix chain 'B' and resid 456 through 461 removed outlier: 3.919A pdb=" N ALA B 459 " --> pdb=" O GLN B 456 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N HIS B 460 " --> pdb=" O LYS B 457 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 482 removed outlier: 3.582A pdb=" N SER B 480 " --> pdb=" O ALA B 476 " (cutoff:3.500A) Processing helix chain 'B' and resid 539 through 547 removed outlier: 3.582A pdb=" N GLU B 547 " --> pdb=" O GLU B 543 " (cutoff:3.500A) Processing helix chain 'B' and resid 558 through 560 No H-bonds generated for 'chain 'B' and resid 558 through 560' Processing helix chain 'B' and resid 569 through 571 No H-bonds generated for 'chain 'B' and resid 569 through 571' Processing helix chain 'B' and resid 580 through 592 removed outlier: 3.742A pdb=" N ASN B 585 " --> pdb=" O GLU B 581 " (cutoff:3.500A) Processing helix chain 'B' and resid 637 through 644 Processing helix chain 'B' and resid 653 through 659 Processing helix chain 'B' and resid 670 through 672 No H-bonds generated for 'chain 'B' and resid 670 through 672' Processing helix chain 'B' and resid 679 through 682 No H-bonds generated for 'chain 'B' and resid 679 through 682' Processing helix chain 'B' and resid 700 through 703 Processing helix chain 'B' and resid 708 through 710 No H-bonds generated for 'chain 'B' and resid 708 through 710' Processing helix chain 'B' and resid 714 through 716 No H-bonds generated for 'chain 'B' and resid 714 through 716' Processing helix chain 'B' and resid 719 through 728 Processing helix chain 'B' and resid 798 through 802 Processing helix chain 'B' and resid 845 through 847 No H-bonds generated for 'chain 'B' and resid 845 through 847' Processing helix chain 'B' and resid 969 through 971 No H-bonds generated for 'chain 'B' and resid 969 through 971' Processing helix chain 'B' and resid 978 through 993 removed outlier: 3.876A pdb=" N LYS B 988 " --> pdb=" O CYS B 984 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL B 989 " --> pdb=" O LEU B 985 " (cutoff:3.500A) Processing helix chain 'B' and resid 1008 through 1017 removed outlier: 3.777A pdb=" N ASP B1017 " --> pdb=" O ASN B1013 " (cutoff:3.500A) Processing helix chain 'B' and resid 1089 through 1095 removed outlier: 3.579A pdb=" N GLN B1094 " --> pdb=" O GLU B1090 " (cutoff:3.500A) Processing helix chain 'B' and resid 1100 through 1107 Processing helix chain 'B' and resid 1153 through 1165 removed outlier: 4.077A pdb=" N MET B1165 " --> pdb=" O GLU B1161 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 39 removed outlier: 3.576A pdb=" N ARG C 35 " --> pdb=" O ALA C 31 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ILE C 39 " --> pdb=" O ARG C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 69 Processing helix chain 'C' and resid 85 through 87 No H-bonds generated for 'chain 'C' and resid 85 through 87' Processing helix chain 'C' and resid 174 through 176 No H-bonds generated for 'chain 'C' and resid 174 through 176' Processing helix chain 'C' and resid 241 through 268 removed outlier: 3.892A pdb=" N VAL C 245 " --> pdb=" O PRO C 241 " (cutoff:3.500A) Processing helix chain 'D' and resid 24 through 27 No H-bonds generated for 'chain 'D' and resid 24 through 27' Processing helix chain 'D' and resid 34 through 49 removed outlier: 3.705A pdb=" N MET D 39 " --> pdb=" O SER D 35 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU D 40 " --> pdb=" O GLU D 36 " (cutoff:3.500A) Processing helix chain 'D' and resid 59 through 70 removed outlier: 3.712A pdb=" N TYR D 67 " --> pdb=" O LYS D 63 " (cutoff:3.500A) Processing helix chain 'D' and resid 78 through 88 removed outlier: 3.596A pdb=" N SER D 82 " --> pdb=" O GLU D 78 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL D 83 " --> pdb=" O THR D 79 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU D 87 " --> pdb=" O VAL D 83 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 102 removed outlier: 3.962A pdb=" N ALA D 98 " --> pdb=" O PHE D 95 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N CYS D 99 " --> pdb=" O GLU D 96 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N LEU D 100 " --> pdb=" O LEU D 97 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ASN D 102 " --> pdb=" O CYS D 99 " (cutoff:3.500A) Processing helix chain 'D' and resid 108 through 114 Processing helix chain 'D' and resid 116 through 118 No H-bonds generated for 'chain 'D' and resid 116 through 118' Processing helix chain 'D' and resid 124 through 137 removed outlier: 3.646A pdb=" N ILE D 130 " --> pdb=" O GLU D 126 " (cutoff:3.500A) Processing helix chain 'E' and resid 4 through 23 Processing helix chain 'E' and resid 30 through 33 No H-bonds generated for 'chain 'E' and resid 30 through 33' Processing helix chain 'E' and resid 37 through 43 Processing helix chain 'E' and resid 84 through 94 removed outlier: 3.858A pdb=" N VAL E 89 " --> pdb=" O LYS E 85 " (cutoff:3.500A) Processing helix chain 'E' and resid 112 through 120 removed outlier: 3.897A pdb=" N GLN E 116 " --> pdb=" O PRO E 112 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N SER E 117 " --> pdb=" O SER E 113 " (cutoff:3.500A) Processing helix chain 'E' and resid 134 through 136 No H-bonds generated for 'chain 'E' and resid 134 through 136' Processing helix chain 'E' and resid 139 through 141 No H-bonds generated for 'chain 'E' and resid 139 through 141' Processing helix chain 'E' and resid 153 through 162 removed outlier: 3.539A pdb=" N GLU E 158 " --> pdb=" O GLU E 154 " (cutoff:3.500A) Processing helix chain 'E' and resid 167 through 169 No H-bonds generated for 'chain 'E' and resid 167 through 169' Processing helix chain 'E' and resid 178 through 183 removed outlier: 3.636A pdb=" N PHE E 183 " --> pdb=" O VAL E 179 " (cutoff:3.500A) Processing helix chain 'F' and resid 59 through 74 Processing helix chain 'F' and resid 89 through 98 Processing helix chain 'G' and resid 15 through 17 No H-bonds generated for 'chain 'G' and resid 15 through 17' Processing helix chain 'G' and resid 22 through 31 Processing helix chain 'H' and resid 85 through 87 No H-bonds generated for 'chain 'H' and resid 85 through 87' Processing helix chain 'I' and resid 64 through 66 No H-bonds generated for 'chain 'I' and resid 64 through 66' Processing helix chain 'I' and resid 70 through 74 removed outlier: 3.610A pdb=" N SER I 73 " --> pdb=" O ALA I 70 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLN I 74 " --> pdb=" O ASP I 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 70 through 74' Processing helix chain 'J' and resid 15 through 27 removed outlier: 4.330A pdb=" N TRP J 18 " --> pdb=" O GLY J 15 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N GLU J 19 " --> pdb=" O ASN J 16 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ALA J 20 " --> pdb=" O LYS J 17 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU J 25 " --> pdb=" O LEU J 22 " (cutoff:3.500A) Processing helix chain 'J' and resid 31 through 37 removed outlier: 3.710A pdb=" N LEU J 35 " --> pdb=" O GLU J 31 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ASP J 36 " --> pdb=" O GLY J 32 " (cutoff:3.500A) Processing helix chain 'J' and resid 43 through 51 removed outlier: 3.547A pdb=" N ARG J 47 " --> pdb=" O TYR J 43 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N MET J 48 " --> pdb=" O CYS J 44 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N LEU J 49 " --> pdb=" O CYS J 45 " (cutoff:3.500A) Processing helix chain 'J' and resid 56 through 61 removed outlier: 4.115A pdb=" N ASN J 61 " --> pdb=" O GLU J 57 " (cutoff:3.500A) Processing helix chain 'K' and resid 6 through 9 removed outlier: 3.717A pdb=" N SER K 9 " --> pdb=" O ALA K 6 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 6 through 9' Processing helix chain 'K' and resid 40 through 50 removed outlier: 3.576A pdb=" N ASN K 44 " --> pdb=" O HIS K 40 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ILE K 45 " --> pdb=" O THR K 41 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ILE K 46 " --> pdb=" O LEU K 42 " (cutoff:3.500A) Processing helix chain 'K' and resid 83 through 112 removed outlier: 3.754A pdb=" N LEU K 94 " --> pdb=" O ALA K 90 " (cutoff:3.500A) Processing helix chain 'M' and resid 286 through 290 Processing helix chain 'M' and resid 296 through 301 Processing helix chain 'M' and resid 311 through 323 removed outlier: 4.361A pdb=" N GLU M 315 " --> pdb=" O ASP M 311 " (cutoff:3.500A) Processing helix chain 'M' and resid 352 through 369 Processing helix chain 'M' and resid 375 through 378 No H-bonds generated for 'chain 'M' and resid 375 through 378' Processing helix chain 'M' and resid 391 through 428 Processing helix chain 'M' and resid 446 through 452 Processing helix chain 'M' and resid 457 through 470 WARNING: missing atoms! Processing helix chain 'M' and resid 543 through 550 Processing helix chain 'M' and resid 566 through 569 No H-bonds generated for 'chain 'M' and resid 566 through 569' Processing helix chain 'M' and resid 587 through 597 removed outlier: 3.786A pdb=" N MET M 591 " --> pdb=" O GLY M 587 " (cutoff:3.500A) Processing helix chain 'M' and resid 600 through 605 Processing helix chain 'M' and resid 624 through 627 No H-bonds generated for 'chain 'M' and resid 624 through 627' Processing helix chain 'M' and resid 633 through 636 No H-bonds generated for 'chain 'M' and resid 633 through 636' Processing helix chain 'M' and resid 645 through 648 No H-bonds generated for 'chain 'M' and resid 645 through 648' Processing helix chain 'M' and resid 652 through 661 Processing helix chain 'M' and resid 702 through 752 removed outlier: 3.682A pdb=" N GLN M 718 " --> pdb=" O GLU M 714 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N GLN M 719 " --> pdb=" O ARG M 715 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N TYR M 722 " --> pdb=" O GLN M 718 " (cutoff:3.500A) Processing helix chain 'M' and resid 831 through 840 Processing helix chain 'M' and resid 855 through 869 Processing helix chain 'M' and resid 889 through 892 No H-bonds generated for 'chain 'M' and resid 889 through 892' Processing helix chain 'M' and resid 897 through 902 Processing helix chain 'M' and resid 908 through 919 Processing helix chain 'M' and resid 923 through 928 Processing helix chain 'M' and resid 951 through 969 Processing helix chain 'M' and resid 994 through 1007 Processing helix chain 'M' and resid 1016 through 1019 No H-bonds generated for 'chain 'M' and resid 1016 through 1019' Processing helix chain 'M' and resid 1025 through 1030 Processing helix chain 'M' and resid 1063 through 1072 Processing helix chain 'M' and resid 1086 through 1089 No H-bonds generated for 'chain 'M' and resid 1086 through 1089' Processing helix chain 'M' and resid 1104 through 1113 removed outlier: 3.762A pdb=" N ARG M1113 " --> pdb=" O GLU M1109 " (cutoff:3.500A) Processing helix chain 'M' and resid 1122 through 1129 Processing helix chain 'M' and resid 1146 through 1153 Processing helix chain 'M' and resid 1242 through 1245 No H-bonds generated for 'chain 'M' and resid 1242 through 1245' Processing helix chain 'M' and resid 1342 through 1345 removed outlier: 3.508A pdb=" N LYS M1345 " --> pdb=" O GLN M1342 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 1342 through 1345' Processing helix chain 'M' and resid 1404 through 1406 No H-bonds generated for 'chain 'M' and resid 1404 through 1406' Processing helix chain 'M' and resid 1410 through 1413 No H-bonds generated for 'chain 'M' and resid 1410 through 1413' Processing helix chain 'M' and resid 1417 through 1427 removed outlier: 3.892A pdb=" N ASP M1425 " --> pdb=" O SER M1421 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N LEU M1426 " --> pdb=" O PHE M1422 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LEU M1427 " --> pdb=" O ALA M1423 " (cutoff:3.500A) Processing helix chain 'M' and resid 1435 through 1438 No H-bonds generated for 'chain 'M' and resid 1435 through 1438' Processing helix chain 'M' and resid 1440 through 1450 removed outlier: 3.796A pdb=" N GLU M1444 " --> pdb=" O ARG M1440 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N GLU M1445 " --> pdb=" O LYS M1441 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU M1446 " --> pdb=" O LYS M1442 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LEU M1447 " --> pdb=" O LEU M1443 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ILE M1448 " --> pdb=" O GLU M1444 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N LYS M1449 " --> pdb=" O GLU M1445 " (cutoff:3.500A) Processing helix chain 'M' and resid 1504 through 1511 removed outlier: 4.282A pdb=" N PHE M1508 " --> pdb=" O VAL M1504 " (cutoff:3.500A) Processing helix chain 'Q' and resid 30 through 33 No H-bonds generated for 'chain 'Q' and resid 30 through 33' Processing helix chain 'Q' and resid 41 through 53 removed outlier: 3.827A pdb=" N ILE Q 45 " --> pdb=" O LEU Q 41 " (cutoff:3.500A) Processing helix chain 'Q' and resid 57 through 63 removed outlier: 3.734A pdb=" N VAL Q 61 " --> pdb=" O THR Q 57 " (cutoff:3.500A) Processing helix chain 'Q' and resid 66 through 68 No H-bonds generated for 'chain 'Q' and resid 66 through 68' Processing helix chain 'Q' and resid 79 through 97 removed outlier: 3.777A pdb=" N THR Q 88 " --> pdb=" O THR Q 84 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU Q 89 " --> pdb=" O CYS Q 85 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N TYR Q 93 " --> pdb=" O LEU Q 89 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N VAL Q 94 " --> pdb=" O ALA Q 90 " (cutoff:3.500A) Processing helix chain 'Q' and resid 106 through 122 removed outlier: 4.134A pdb=" N GLN Q 112 " --> pdb=" O ASP Q 108 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N LEU Q 116 " --> pdb=" O GLN Q 112 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N TYR Q 117 " --> pdb=" O ALA Q 113 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N THR Q 118 " --> pdb=" O THR Q 114 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N MET Q 119 " --> pdb=" O LEU Q 115 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LYS Q 122 " --> pdb=" O THR Q 118 " (cutoff:3.500A) Processing helix chain 'Q' and resid 130 through 136 removed outlier: 3.561A pdb=" N ARG Q 134 " --> pdb=" O HIS Q 130 " (cutoff:3.500A) Processing helix chain 'Q' and resid 145 through 159 removed outlier: 3.844A pdb=" N PHE Q 154 " --> pdb=" O ALA Q 150 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N VAL Q 155 " --> pdb=" O GLN Q 151 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N LEU Q 156 " --> pdb=" O PHE Q 152 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ASN Q 157 " --> pdb=" O HIS Q 153 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N SER Q 159 " --> pdb=" O VAL Q 155 " (cutoff:3.500A) Processing helix chain 'Q' and resid 167 through 175 removed outlier: 3.507A pdb=" N CYS Q 171 " --> pdb=" O GLY Q 168 " (cutoff:3.500A) Processing helix chain 'Q' and resid 179 through 186 removed outlier: 3.793A pdb=" N TYR Q 185 " --> pdb=" O GLY Q 181 " (cutoff:3.500A) Processing helix chain 'Q' and resid 188 through 191 No H-bonds generated for 'chain 'Q' and resid 188 through 191' Processing helix chain 'Q' and resid 200 through 209 removed outlier: 3.698A pdb=" N PHE Q 208 " --> pdb=" O GLY Q 205 " (cutoff:3.500A) Processing helix chain 'Q' and resid 214 through 227 removed outlier: 3.887A pdb=" N ARG Q 218 " --> pdb=" O LEU Q 214 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N LEU Q 219 " --> pdb=" O GLU Q 215 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ARG Q 223 " --> pdb=" O LEU Q 219 " (cutoff:3.500A) Processing helix chain 'Q' and resid 236 through 242 Processing helix chain 'Q' and resid 251 through 254 No H-bonds generated for 'chain 'Q' and resid 251 through 254' Processing helix chain 'Q' and resid 259 through 264 Processing helix chain 'Q' and resid 269 through 281 removed outlier: 3.978A pdb=" N PHE Q 281 " --> pdb=" O ASN Q 277 " (cutoff:3.500A) Processing helix chain 'Q' and resid 285 through 294 removed outlier: 3.767A pdb=" N GLN Q 289 " --> pdb=" O TYR Q 285 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N HIS Q 290 " --> pdb=" O SER Q 286 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU Q 293 " --> pdb=" O GLN Q 289 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N HIS Q 294 " --> pdb=" O HIS Q 290 " (cutoff:3.500A) Processing helix chain 'Q' and resid 302 through 317 removed outlier: 3.698A pdb=" N ALA Q 306 " --> pdb=" O GLU Q 302 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N GLU Q 307 " --> pdb=" O ALA Q 303 " (cutoff:3.500A) Processing helix chain 'Q' and resid 322 through 335 removed outlier: 4.017A pdb=" N GLN Q 327 " --> pdb=" O ASP Q 323 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N TYR Q 328 " --> pdb=" O GLN Q 324 " (cutoff:3.500A) Processing helix chain 'Q' and resid 342 through 351 Processing helix chain 'Q' and resid 353 through 355 No H-bonds generated for 'chain 'Q' and resid 353 through 355' Processing helix chain 'Q' and resid 357 through 370 removed outlier: 3.813A pdb=" N SER Q 361 " --> pdb=" O LYS Q 357 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLN Q 362 " --> pdb=" O GLU Q 358 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N LYS Q 366 " --> pdb=" O GLN Q 362 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N VAL Q 367 " --> pdb=" O CYS Q 363 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N LEU Q 368 " --> pdb=" O PHE Q 364 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LYS Q 369 " --> pdb=" O GLU Q 365 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ALA Q 370 " --> pdb=" O LYS Q 366 " (cutoff:3.500A) Processing helix chain 'Q' and resid 377 through 382 Processing helix chain 'Q' and resid 391 through 406 removed outlier: 3.825A pdb=" N ASP Q 395 " --> pdb=" O GLN Q 391 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N ILE Q 396 " --> pdb=" O GLU Q 392 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ALA Q 397 " --> pdb=" O LYS Q 393 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LYS Q 403 " --> pdb=" O GLY Q 399 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N GLU Q 406 " --> pdb=" O LYS Q 402 " (cutoff:3.500A) Processing helix chain 'Q' and resid 414 through 419 Processing helix chain 'Q' and resid 427 through 439 removed outlier: 3.652A pdb=" N LEU Q 431 " --> pdb=" O ILE Q 427 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N THR Q 436 " --> pdb=" O SER Q 432 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ARG Q 439 " --> pdb=" O GLY Q 435 " (cutoff:3.500A) Processing helix chain 'Q' and resid 451 through 463 removed outlier: 3.655A pdb=" N ASN Q 456 " --> pdb=" O GLU Q 452 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ARG Q 463 " --> pdb=" O ALA Q 459 " (cutoff:3.500A) Processing helix chain 'Q' and resid 467 through 483 removed outlier: 3.548A pdb=" N ALA Q 483 " --> pdb=" O ASP Q 479 " (cutoff:3.500A) Processing helix chain 'Q' and resid 492 through 509 removed outlier: 3.606A pdb=" N ALA Q 509 " --> pdb=" O ARG Q 505 " (cutoff:3.500A) Processing helix chain 'Q' and resid 513 through 524 Processing helix chain 'Q' and resid 532 through 543 removed outlier: 3.598A pdb=" N LEU Q 537 " --> pdb=" O CYS Q 533 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N GLY Q 538 " --> pdb=" O TYR Q 534 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA Q 539 " --> pdb=" O LEU Q 535 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N MET Q 540 " --> pdb=" O ARG Q 536 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ALA Q 541 " --> pdb=" O LEU Q 537 " (cutoff:3.500A) Processing helix chain 'Q' and resid 549 through 560 removed outlier: 3.832A pdb=" N LYS Q 555 " --> pdb=" O SER Q 551 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LEU Q 558 " --> pdb=" O PHE Q 554 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ILE Q 560 " --> pdb=" O GLU Q 556 " (cutoff:3.500A) Processing helix chain 'Q' and resid 565 through 574 removed outlier: 3.552A pdb=" N ILE Q 571 " --> pdb=" O ALA Q 567 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLY Q 572 " --> pdb=" O TRP Q 568 " (cutoff:3.500A) Processing helix chain 'Q' and resid 584 through 589 removed outlier: 3.541A pdb=" N LYS Q 587 " --> pdb=" O GLY Q 584 " (cutoff:3.500A) Processing helix chain 'Q' and resid 601 through 614 removed outlier: 4.141A pdb=" N THR Q 614 " --> pdb=" O VAL Q 610 " (cutoff:3.500A) Processing helix chain 'Q' and resid 620 through 622 No H-bonds generated for 'chain 'Q' and resid 620 through 622' Processing helix chain 'Q' and resid 625 through 641 Processing helix chain 'Q' and resid 647 through 659 Processing helix chain 'Q' and resid 666 through 676 removed outlier: 3.783A pdb=" N GLN Q 672 " --> pdb=" O ASP Q 668 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N VAL Q 673 " --> pdb=" O VAL Q 669 " (cutoff:3.500A) Processing helix chain 'Q' and resid 683 through 693 removed outlier: 3.716A pdb=" N ALA Q 688 " --> pdb=" O TRP Q 684 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ILE Q 690 " --> pdb=" O ASN Q 686 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N TYR Q 691 " --> pdb=" O LEU Q 687 " (cutoff:3.500A) Processing helix chain 'Q' and resid 701 through 709 Processing helix chain 'Q' and resid 717 through 723 Processing helix chain 'Q' and resid 730 through 744 removed outlier: 3.800A pdb=" N GLN Q 734 " --> pdb=" O CYS Q 730 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N GLU Q 735 " --> pdb=" O GLY Q 731 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N CYS Q 736 " --> pdb=" O LYS Q 732 " (cutoff:3.500A) Processing helix chain 'Q' and resid 751 through 766 removed outlier: 3.865A pdb=" N ALA Q 758 " --> pdb=" O MET Q 754 " (cutoff:3.500A) Processing helix chain 'Q' and resid 776 through 798 removed outlier: 3.617A pdb=" N VAL Q 783 " --> pdb=" O VAL Q 779 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N LYS Q 784 " --> pdb=" O LEU Q 780 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N SER Q 797 " --> pdb=" O PHE Q 793 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N LYS Q 798 " --> pdb=" O SER Q 794 " (cutoff:3.500A) Processing helix chain 'Q' and resid 808 through 891 removed outlier: 4.218A pdb=" N ALA Q 811 " --> pdb=" O ALA Q 808 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N THR Q 812 " --> pdb=" O LEU Q 809 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N VAL Q 828 " --> pdb=" O GLN Q 825 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ALA Q 829 " --> pdb=" O TYR Q 826 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N GLN Q 847 " --> pdb=" O LYS Q 844 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N VAL Q 882 " --> pdb=" O ALA Q 879 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N THR Q 885 " --> pdb=" O VAL Q 882 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LYS Q 886 " --> pdb=" O GLU Q 883 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N MET Q 890 " --> pdb=" O ASN Q 887 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N PHE Q 891 " --> pdb=" O ILE Q 888 " (cutoff:3.500A) Processing helix chain 'R' and resid 358 through 360 No H-bonds generated for 'chain 'R' and resid 358 through 360' Processing helix chain 'R' and resid 366 through 372 removed outlier: 4.155A pdb=" N GLU R 370 " --> pdb=" O ARG R 366 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N ARG R 371 " --> pdb=" O HIS R 367 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N TRP R 372 " --> pdb=" O LYS R 368 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 366 through 372' Processing helix chain 'R' and resid 378 through 381 No H-bonds generated for 'chain 'R' and resid 378 through 381' Processing helix chain 'R' and resid 449 through 460 Processing helix chain 'R' and resid 469 through 483 removed outlier: 4.127A pdb=" N LEU R 477 " --> pdb=" O ASN R 473 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N SER R 478 " --> pdb=" O LYS R 474 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ILE R 479 " --> pdb=" O LYS R 475 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LYS R 480 " --> pdb=" O GLU R 476 " (cutoff:3.500A) Processing helix chain 'R' and resid 491 through 502 removed outlier: 3.607A pdb=" N ARG R 501 " --> pdb=" O LYS R 497 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N PHE R 502 " --> pdb=" O GLU R 498 " (cutoff:3.500A) Processing helix chain 'R' and resid 511 through 523 Processing helix chain 'R' and resid 528 through 554 Processing helix chain 'R' and resid 558 through 584 removed outlier: 3.559A pdb=" N ILE R 563 " --> pdb=" O ALA R 559 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLU R 576 " --> pdb=" O ILE R 572 " (cutoff:3.500A) Processing helix chain 'U' and resid 380 through 382 No H-bonds generated for 'chain 'U' and resid 380 through 382' Processing helix chain 'U' and resid 412 through 414 No H-bonds generated for 'chain 'U' and resid 412 through 414' Processing helix chain 'V' and resid 63 through 67 removed outlier: 3.776A pdb=" N GLU V 67 " --> pdb=" O THR V 64 " (cutoff:3.500A) Processing helix chain 'V' and resid 102 through 108 removed outlier: 3.882A pdb=" N LEU V 107 " --> pdb=" O ALA V 103 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LEU V 108 " --> pdb=" O ASP V 104 " (cutoff:3.500A) Processing helix chain 'V' and resid 123 through 125 No H-bonds generated for 'chain 'V' and resid 123 through 125' Processing helix chain 'V' and resid 173 through 187 removed outlier: 4.067A pdb=" N THR V 177 " --> pdb=" O ASP V 173 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N THR V 182 " --> pdb=" O ALA V 178 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N PHE V 183 " --> pdb=" O ILE V 179 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N GLN V 187 " --> pdb=" O PHE V 183 " (cutoff:3.500A) Processing helix chain 'X' and resid 219 through 222 No H-bonds generated for 'chain 'X' and resid 219 through 222' Processing helix chain 'X' and resid 234 through 238 removed outlier: 3.680A pdb=" N LEU X 238 " --> pdb=" O ARG X 234 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 234 through 238' Processing helix chain 'X' and resid 250 through 259 removed outlier: 3.955A pdb=" N LYS X 257 " --> pdb=" O LEU X 253 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ALA X 258 " --> pdb=" O GLN X 254 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ARG X 259 " --> pdb=" O SER X 255 " (cutoff:3.500A) Processing helix chain 'Y' and resid 25 through 30 removed outlier: 3.649A pdb=" N GLU Y 29 " --> pdb=" O ILE Y 25 " (cutoff:3.500A) Processing helix chain 'Y' and resid 47 through 51 Processing helix chain 'Y' and resid 70 through 74 Processing helix chain 'Y' and resid 99 through 104 removed outlier: 3.875A pdb=" N SER Y 103 " --> pdb=" O ARG Y 99 " (cutoff:3.500A) Processing helix chain 'Z' and resid 189 through 201 removed outlier: 3.636A pdb=" N ARG Z 198 " --> pdb=" O ILE Z 194 " (cutoff:3.500A) Processing helix chain 'Z' and resid 232 through 238 removed outlier: 3.541A pdb=" N LYS Z 236 " --> pdb=" O GLN Z 232 " (cutoff:3.500A) Processing helix chain 'Z' and resid 247 through 249 No H-bonds generated for 'chain 'Z' and resid 247 through 249' Processing helix chain 'Z' and resid 257 through 259 No H-bonds generated for 'chain 'Z' and resid 257 through 259' Processing helix chain 'Z' and resid 378 through 380 No H-bonds generated for 'chain 'Z' and resid 378 through 380' Processing helix chain 'Z' and resid 390 through 395 removed outlier: 3.538A pdb=" N GLU Z 394 " --> pdb=" O LEU Z 390 " (cutoff:3.500A) Processing helix chain 'Z' and resid 465 through 467 No H-bonds generated for 'chain 'Z' and resid 465 through 467' Processing helix chain 'Z' and resid 515 through 517 No H-bonds generated for 'chain 'Z' and resid 515 through 517' Processing helix chain 'Z' and resid 631 through 634 Processing sheet with id= A, first strand: chain 'A' and resid 86 through 88 Processing sheet with id= B, first strand: chain 'A' and resid 192 through 194 removed outlier: 3.829A pdb=" N GLU A 197 " --> pdb=" O SER A 194 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 364 through 366 removed outlier: 3.698A pdb=" N THR A 365 " --> pdb=" O MET A 501 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 367 through 369 removed outlier: 6.164A pdb=" N PHE A 482 " --> pdb=" O THR A 368 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'A' and resid 389 through 393 Processing sheet with id= F, first strand: chain 'A' and resid 601 through 604 Processing sheet with id= G, first strand: chain 'A' and resid 902 through 905 Processing sheet with id= H, first strand: chain 'A' and resid 1308 through 1311 removed outlier: 3.703A pdb=" N GLU A1337 " --> pdb=" O TYR A1308 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 1170 through 1176 removed outlier: 6.835A pdb=" N GLU A1215 " --> pdb=" O ALA A1171 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N THR A1173 " --> pdb=" O ARG A1213 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N ARG A1213 " --> pdb=" O THR A1173 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N ILE A1175 " --> pdb=" O LEU A1211 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N LEU A1211 " --> pdb=" O ILE A1175 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 87 through 89 removed outlier: 3.904A pdb=" N VAL B 132 " --> pdb=" O LEU B 140 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N LEU B 140 " --> pdb=" O VAL B 132 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 192 through 194 Processing sheet with id= L, first strand: chain 'B' and resid 391 through 394 Processing sheet with id= M, first strand: chain 'B' and resid 206 through 208 removed outlier: 6.681A pdb=" N MET B 239 " --> pdb=" O ALA B 216 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N THR B 218 " --> pdb=" O VAL B 237 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N VAL B 237 " --> pdb=" O THR B 218 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N GLU B 220 " --> pdb=" O ILE B 235 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N ILE B 235 " --> pdb=" O GLU B 220 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N ARG B 222 " --> pdb=" O SER B 233 " (cutoff:3.500A) removed outlier: 5.773A pdb=" N SER B 233 " --> pdb=" O ARG B 222 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'B' and resid 530 through 532 Processing sheet with id= O, first strand: chain 'B' and resid 566 through 569 removed outlier: 3.534A pdb=" N GLU B 611 " --> pdb=" O ASP B 606 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'B' and resid 748 through 751 removed outlier: 5.836A pdb=" N ARG B 924 " --> pdb=" O VAL B 904 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N VAL B 904 " --> pdb=" O ARG B 924 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'B' and resid 776 through 782 removed outlier: 4.103A pdb=" N PHE B1042 " --> pdb=" O ILE B 782 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'B' and resid 827 through 829 Processing sheet with id= S, first strand: chain 'B' and resid 1116 through 1119 Processing sheet with id= T, first strand: chain 'B' and resid 121 through 126 removed outlier: 3.872A pdb=" N GLY B 150 " --> pdb=" O LEU B 124 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N VAL B 126 " --> pdb=" O PHE B 148 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N PHE B 148 " --> pdb=" O VAL B 126 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'B' and resid 793 through 797 removed outlier: 6.346A pdb=" N THR B 944 " --> pdb=" O VAL B 794 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N MET B 796 " --> pdb=" O THR B 944 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N GLY B 946 " --> pdb=" O MET B 796 " (cutoff:3.500A) No H-bonds generated for sheet with id= U Processing sheet with id= V, first strand: chain 'C' and resid 229 through 234 removed outlier: 6.669A pdb=" N ILE C 22 " --> pdb=" O ILE C 11 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N ILE C 11 " --> pdb=" O ILE C 22 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N GLU C 24 " --> pdb=" O VAL C 9 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N VAL C 9 " --> pdb=" O GLU C 24 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'C' and resid 99 through 106 removed outlier: 6.109A pdb=" N LYS C 166 " --> pdb=" O ILE C 47 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N ILE C 47 " --> pdb=" O LYS C 166 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N GLY C 168 " --> pdb=" O ILE C 45 " (cutoff:3.500A) removed outlier: 5.489A pdb=" N ILE C 45 " --> pdb=" O GLY C 168 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'C' and resid 113 through 115 Processing sheet with id= Y, first strand: chain 'E' and resid 60 through 63 removed outlier: 3.631A pdb=" N VAL E 60 " --> pdb=" O VAL E 74 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'E' and resid 104 through 106 Processing sheet with id= AA, first strand: chain 'E' and resid 147 through 150 removed outlier: 3.797A pdb=" N GLU E 147 " --> pdb=" O ILE E 194 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'F' and resid 105 through 109 Processing sheet with id= AC, first strand: chain 'G' and resid 2 through 13 removed outlier: 3.666A pdb=" N ALA G 47 " --> pdb=" O ILE G 75 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N PHE G 77 " --> pdb=" O VAL G 45 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N VAL G 45 " --> pdb=" O PHE G 77 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'G' and resid 104 through 108 removed outlier: 6.835A pdb=" N GLU G 100 " --> pdb=" O VAL G 89 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N VAL G 89 " --> pdb=" O GLU G 100 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'G' and resid 50 through 54 removed outlier: 6.930A pdb=" N LYS G 71 " --> pdb=" O ASP G 52 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'H' and resid 30 through 32 removed outlier: 4.738A pdb=" N LYS H 55 " --> pdb=" O LEU H 148 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'H' and resid 25 through 28 Processing sheet with id= AH, first strand: chain 'H' and resid 140 through 142 removed outlier: 3.502A pdb=" N VAL H 141 " --> pdb=" O GLY H 94 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N TYR H 115 " --> pdb=" O TYR H 97 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ILE H 99 " --> pdb=" O SER H 113 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N SER H 113 " --> pdb=" O ILE H 99 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'I' and resid 25 through 29 Processing sheet with id= AJ, first strand: chain 'I' and resid 94 through 97 Processing sheet with id= AK, first strand: chain 'K' and resid 21 through 23 Processing sheet with id= AL, first strand: chain 'L' and resid 25 through 27 Processing sheet with id= AM, first strand: chain 'M' and resid 882 through 884 removed outlier: 5.978A pdb=" N VAL M 848 " --> pdb=" O GLU M 883 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N ASN M 800 " --> pdb=" O VAL M 805 " (cutoff:3.500A) removed outlier: 5.935A pdb=" N VAL M 805 " --> pdb=" O ASN M 800 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'M' and resid 1166 through 1170 removed outlier: 3.607A pdb=" N CYS M1265 " --> pdb=" O ILE M1167 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'M' and resid 1228 through 1231 Processing sheet with id= AP, first strand: chain 'M' and resid 1355 through 1359 removed outlier: 3.735A pdb=" N THR M1370 " --> pdb=" O ILE M1356 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ARG M1358 " --> pdb=" O THR M1368 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N TRP M1371 " --> pdb=" O GLN M1379 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLN M1379 " --> pdb=" O TRP M1371 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N ILE M1377 " --> pdb=" O VAL M1373 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'M' and resid 1471 through 1476 Processing sheet with id= AR, first strand: chain 'Q' and resid 5 through 8 removed outlier: 4.409A pdb=" N ILE Q 6 " --> pdb=" O LEU Q 19 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N LEU Q 19 " --> pdb=" O ILE Q 6 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N ILE Q 17 " --> pdb=" O ILE Q 8 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain 'R' and resid 386 through 390 removed outlier: 3.868A pdb=" N VAL R 387 " --> pdb=" O ALA R 403 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ALA R 403 " --> pdb=" O VAL R 387 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ILE R 389 " --> pdb=" O ARG R 401 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ARG R 401 " --> pdb=" O ILE R 389 " (cutoff:3.500A) No H-bonds generated for sheet with id= AS Processing sheet with id= AT, first strand: chain 'R' and resid 407 through 410 removed outlier: 3.591A pdb=" N GLY R 407 " --> pdb=" O GLN R 427 " (cutoff:3.500A) Processing sheet with id= AU, first strand: chain 'R' and resid 415 through 417 removed outlier: 3.506A pdb=" N TYR R 415 " --> pdb=" O THR R 422 " (cutoff:3.500A) Processing sheet with id= AV, first strand: chain 'R' and resid 428 through 430 removed outlier: 3.751A pdb=" N LEU R 428 " --> pdb=" O ARG R 435 " (cutoff:3.500A) Processing sheet with id= AW, first strand: chain 'U' and resid 448 through 451 removed outlier: 3.783A pdb=" N MET U 448 " --> pdb=" O VAL U 459 " (cutoff:3.500A) Processing sheet with id= AX, first strand: chain 'U' and resid 461 through 463 Processing sheet with id= AY, first strand: chain 'U' and resid 472 through 475 removed outlier: 3.561A pdb=" N ILE U 473 " --> pdb=" O VAL U 484 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N GLN U 475 " --> pdb=" O GLN U 482 " (cutoff:3.500A) Processing sheet with id= AZ, first strand: chain 'W' and resid 19 through 24 removed outlier: 3.507A pdb=" N TRP W 20 " --> pdb=" O GLY W 38 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N GLY W 38 " --> pdb=" O TRP W 20 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N VAL W 22 " --> pdb=" O VAL W 36 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N VAL W 36 " --> pdb=" O VAL W 22 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N TRP W 24 " --> pdb=" O THR W 34 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N THR W 34 " --> pdb=" O TRP W 24 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LYS W 45 " --> pdb=" O THR W 37 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N LYS W 48 " --> pdb=" O LEU W 56 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N LEU W 56 " --> pdb=" O LYS W 48 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N ARG W 50 " --> pdb=" O LEU W 54 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N LEU W 54 " --> pdb=" O ARG W 50 " (cutoff:3.500A) Processing sheet with id= BA, first strand: chain 'W' and resid 89 through 92 removed outlier: 4.313A pdb=" N ALA W 80 " --> pdb=" O ASP W 71 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N ASP W 71 " --> pdb=" O ALA W 80 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N SER W 69 " --> pdb=" O SER W 82 " (cutoff:3.500A) Processing sheet with id= BB, first strand: chain 'W' and resid 120 through 124 removed outlier: 3.731A pdb=" N VAL W 130 " --> pdb=" O LEU W 144 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N TYR W 142 " --> pdb=" O ILE W 132 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N GLY W 134 " --> pdb=" O LYS W 140 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N LYS W 140 " --> pdb=" O GLY W 134 " (cutoff:3.500A) Processing sheet with id= BC, first strand: chain 'W' and resid 153 through 156 removed outlier: 3.770A pdb=" N ALA W 155 " --> pdb=" O ALA W 164 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ALA W 164 " --> pdb=" O ALA W 155 " (cutoff:3.500A) Processing sheet with id= BD, first strand: chain 'W' and resid 213 through 215 Processing sheet with id= BE, first strand: chain 'W' and resid 237 through 240 removed outlier: 3.714A pdb=" N LYS W 257 " --> pdb=" O SER W 249 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N HIS W 268 " --> pdb=" O VAL W 258 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N ASP W 260 " --> pdb=" O CYS W 266 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N CYS W 266 " --> pdb=" O ASP W 260 " (cutoff:3.500A) Processing sheet with id= BF, first strand: chain 'W' and resid 6 through 11 removed outlier: 6.022A pdb=" N ILE W 300 " --> pdb=" O LEU W 8 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N LYS W 10 " --> pdb=" O ILE W 298 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N ILE W 298 " --> pdb=" O LYS W 10 " (cutoff:3.500A) Processing sheet with id= BG, first strand: chain 'W' and resid 172 through 176 removed outlier: 6.700A pdb=" N ASP W 176 " --> pdb=" O LEU W 182 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N LEU W 182 " --> pdb=" O ASP W 176 " (cutoff:3.500A) Processing sheet with id= BH, first strand: chain 'Y' and resid 13 through 15 removed outlier: 3.598A pdb=" N LYS Y 23 " --> pdb=" O ARG Y 14 " (cutoff:3.500A) Processing sheet with id= BI, first strand: chain 'Y' and resid 60 through 62 Processing sheet with id= BJ, first strand: chain 'Z' and resid 179 through 183 Processing sheet with id= BK, first strand: chain 'Z' and resid 302 through 304 Processing sheet with id= BL, first strand: chain 'Z' and resid 352 through 354 Processing sheet with id= BM, first strand: chain 'Z' and resid 477 through 479 removed outlier: 7.512A pdb=" N ILE Z 501 " --> pdb=" O VAL Z 493 " (cutoff:3.500A) Processing sheet with id= BN, first strand: chain 'Z' and resid 567 through 571 removed outlier: 3.592A pdb=" N ARG Z 552 " --> pdb=" O GLN Z 559 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N LEU Z 561 " --> pdb=" O ILE Z 550 " (cutoff:3.500A) removed outlier: 5.182A pdb=" N ILE Z 550 " --> pdb=" O LEU Z 561 " (cutoff:3.500A) Processing sheet with id= BO, first strand: chain 'Z' and resid 599 through 602 removed outlier: 3.728A pdb=" N VAL Z 600 " --> pdb=" O GLY Z 612 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N GLY Z 612 " --> pdb=" O VAL Z 600 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N PHE Z 623 " --> pdb=" O ARG Z 615 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N LEU Z 617 " --> pdb=" O PHE Z 621 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N PHE Z 621 " --> pdb=" O LEU Z 617 " (cutoff:3.500A) Processing sheet with id= BP, first strand: chain 'Z' and resid 750 through 752 removed outlier: 3.829A pdb=" N TYR Z 720 " --> pdb=" O ILE Z 712 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ARG Z 733 " --> pdb=" O LYS Z 725 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N ALA Z 727 " --> pdb=" O THR Z 731 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N THR Z 731 " --> pdb=" O ALA Z 727 " (cutoff:3.500A) 1552 hydrogen bonds defined for protein. 4230 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 85 hydrogen bonds 166 hydrogen bond angles 0 basepair planarities 32 basepair parallelities 69 stacking parallelities Total time for adding SS restraints: 19.88 Time building geometry restraints manager: 19.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.07 - 1.22: 1762 1.22 - 1.37: 20289 1.37 - 1.52: 28516 1.52 - 1.67: 7361 1.67 - 1.82: 434 Bond restraints: 58362 Sorted by residual: bond pdb=" CA GLU B 791 " pdb=" CB GLU B 791 " ideal model delta sigma weight residual 1.527 1.196 0.332 2.48e-02 1.63e+03 1.79e+02 bond pdb=" C SER B 94 " pdb=" N LYS B 95 " ideal model delta sigma weight residual 1.329 1.073 0.256 3.03e-02 1.09e+03 7.15e+01 bond pdb=" CA ASP C 104 " pdb=" CB ASP C 104 " ideal model delta sigma weight residual 1.529 1.403 0.127 1.54e-02 4.22e+03 6.77e+01 bond pdb=" CA TYR A 418 " pdb=" CB TYR A 418 " ideal model delta sigma weight residual 1.534 1.434 0.100 1.45e-02 4.76e+03 4.77e+01 bond pdb=" CB THR B 504 " pdb=" CG2 THR B 504 " ideal model delta sigma weight residual 1.521 1.298 0.223 3.30e-02 9.18e+02 4.55e+01 ... (remaining 58357 not shown) Histogram of bond angle deviations from ideal: 88.86 - 100.54: 155 100.54 - 112.22: 29457 112.22 - 123.89: 47632 123.89 - 135.57: 1722 135.57 - 147.25: 1 Bond angle restraints: 78967 Sorted by residual: angle pdb=" C GLY C 224 " pdb=" N LYS C 225 " pdb=" CA LYS C 225 " ideal model delta sigma weight residual 121.98 147.25 -25.27 3.11e+00 1.03e-01 6.60e+01 angle pdb=" N PRO V 258 " pdb=" CA PRO V 258 " pdb=" CB PRO V 258 " ideal model delta sigma weight residual 103.46 110.89 -7.43 9.30e-01 1.16e+00 6.39e+01 angle pdb=" N PRO R 507 " pdb=" CA PRO R 507 " pdb=" CB PRO R 507 " ideal model delta sigma weight residual 103.25 111.56 -8.31 1.05e+00 9.07e-01 6.26e+01 angle pdb=" N PRO R 506 " pdb=" CA PRO R 506 " pdb=" CB PRO R 506 " ideal model delta sigma weight residual 103.08 110.71 -7.63 9.70e-01 1.06e+00 6.19e+01 angle pdb=" N ILE A 636 " pdb=" CA ILE A 636 " pdb=" C ILE A 636 " ideal model delta sigma weight residual 111.67 105.03 6.64 9.50e-01 1.11e+00 4.88e+01 ... (remaining 78962 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.93: 32839 33.93 - 67.86: 1195 67.86 - 101.78: 72 101.78 - 135.71: 0 135.71 - 169.64: 4 Dihedral angle restraints: 34110 sinusoidal: 14276 harmonic: 19834 Sorted by residual: dihedral pdb=" CA LYS A 910 " pdb=" C LYS A 910 " pdb=" N PRO A 911 " pdb=" CA PRO A 911 " ideal model delta harmonic sigma weight residual 180.00 126.69 53.31 0 5.00e+00 4.00e-02 1.14e+02 dihedral pdb=" CA ASP B 20 " pdb=" C ASP B 20 " pdb=" N LEU B 21 " pdb=" CA LEU B 21 " ideal model delta harmonic sigma weight residual 180.00 144.04 35.96 0 5.00e+00 4.00e-02 5.17e+01 dihedral pdb=" CA GLU A1434 " pdb=" C GLU A1434 " pdb=" N THR A1435 " pdb=" CA THR A1435 " ideal model delta harmonic sigma weight residual 180.00 144.33 35.67 0 5.00e+00 4.00e-02 5.09e+01 ... (remaining 34107 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.127: 7414 0.127 - 0.254: 843 0.254 - 0.382: 88 0.382 - 0.509: 6 0.509 - 0.636: 2 Chirality restraints: 8353 Sorted by residual: chirality pdb=" CB VAL B 759 " pdb=" CA VAL B 759 " pdb=" CG1 VAL B 759 " pdb=" CG2 VAL B 759 " both_signs ideal model delta sigma weight residual False -2.63 -1.99 -0.64 2.00e-01 2.50e+01 1.01e+01 chirality pdb=" CA GLU B 791 " pdb=" N GLU B 791 " pdb=" C GLU B 791 " pdb=" CB GLU B 791 " both_signs ideal model delta sigma weight residual False 2.51 1.96 0.55 2.00e-01 2.50e+01 7.51e+00 chirality pdb=" CB ILE J 2 " pdb=" CA ILE J 2 " pdb=" CG1 ILE J 2 " pdb=" CG2 ILE J 2 " both_signs ideal model delta sigma weight residual False 2.64 2.17 0.47 2.00e-01 2.50e+01 5.62e+00 ... (remaining 8350 not shown) Planarity restraints: 10146 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B1048 " 0.056 2.00e-02 2.50e+03 3.79e-02 2.87e+01 pdb=" CG TYR B1048 " -0.089 2.00e-02 2.50e+03 pdb=" CD1 TYR B1048 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 TYR B1048 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR B1048 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 TYR B1048 " 0.008 2.00e-02 2.50e+03 pdb=" CZ TYR B1048 " 0.008 2.00e-02 2.50e+03 pdb=" OH TYR B1048 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS C 60 " -0.046 2.00e-02 2.50e+03 3.66e-02 2.01e+01 pdb=" CG HIS C 60 " 0.072 2.00e-02 2.50e+03 pdb=" ND1 HIS C 60 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 HIS C 60 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 HIS C 60 " -0.021 2.00e-02 2.50e+03 pdb=" NE2 HIS C 60 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL Q 445 " 0.021 2.00e-02 2.50e+03 4.16e-02 1.73e+01 pdb=" C VAL Q 445 " -0.072 2.00e-02 2.50e+03 pdb=" O VAL Q 445 " 0.027 2.00e-02 2.50e+03 pdb=" N GLN Q 446 " 0.024 2.00e-02 2.50e+03 ... (remaining 10143 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 725 2.55 - 3.14: 47407 3.14 - 3.72: 87886 3.72 - 4.31: 126690 4.31 - 4.90: 205824 Nonbonded interactions: 468532 Sorted by model distance: nonbonded pdb=" OD1 ASP B 953 " pdb=" NH2 ARG C 36 " model vdw 1.961 2.520 nonbonded pdb=" O ASN A1180 " pdb=" OG SER A1183 " model vdw 2.003 2.440 nonbonded pdb=" NE2 GLN A 904 " pdb=" O CYS A 981 " model vdw 2.014 2.520 nonbonded pdb=" OG SER I 101 " pdb=" O ALA I 102 " model vdw 2.030 2.440 nonbonded pdb=" OG1 THR K 77 " pdb=" O TYR K 81 " model vdw 2.036 2.440 ... (remaining 468527 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.250 Construct map_model_manager: 0.060 Extract box with map and model: 11.840 Check model and map are aligned: 0.660 Set scattering table: 0.420 Process input model: 135.010 Find NCS groups from input model: 1.620 Set up NCS constraints: 0.170 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 157.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6954 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 : 0.025 0.332 58362 Z= 1.663 Angle : 1.395 25.272 78967 Z= 0.765 Chirality : 0.083 0.636 8353 Planarity : 0.008 0.099 10146 Dihedral : 16.487 169.640 21798 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 19.36 Ramachandran Plot: Outliers : 0.57 % Allowed : 7.90 % Favored : 91.54 % Rotamer: Outliers : 2.09 % Allowed : 11.07 % Favored : 86.83 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.65 % Cis-general : 0.07 % Twisted Proline : 0.65 % Twisted General : 0.06 % 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: -4.77 (0.07), residues: 7232 helix: -3.51 (0.06), residues: 2474 sheet: -2.77 (0.17), residues: 807 loop : -3.07 (0.08), residues: 3951 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.005 TRP C 176 HIS 0.022 0.004 HIS C 60 PHE 0.058 0.005 PHE A 548 TYR 0.089 0.005 TYR B1048 ARG 0.034 0.002 ARG J 47 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14464 Ramachandran restraints generated. 7232 Oldfield, 0 Emsley, 7232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14464 Ramachandran restraints generated. 7232 Oldfield, 0 Emsley, 7232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 834 residues out of total 6485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 718 time to evaluate : 4.988 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: A 266 MET cc_start: 0.5172 (tmm) cc_final: 0.4868 (tpp) REVERT: A 283 ILE cc_start: 0.8373 (OUTLIER) cc_final: 0.8050 (mp) REVERT: A 301 HIS cc_start: 0.6763 (OUTLIER) cc_final: 0.6218 (t70) REVERT: A 321 GLU cc_start: 0.6585 (tm-30) cc_final: 0.6143 (tm-30) REVERT: A 757 GLN cc_start: 0.8316 (OUTLIER) cc_final: 0.7563 (mm-40) REVERT: A 1412 MET cc_start: 0.8423 (tmm) cc_final: 0.8052 (ttt) REVERT: B 198 GLU cc_start: 0.7906 (OUTLIER) cc_final: 0.7701 (pt0) REVERT: B 348 LEU cc_start: 0.8922 (OUTLIER) cc_final: 0.8210 (mp) REVERT: B 455 ASP cc_start: 0.7016 (m-30) cc_final: 0.6714 (m-30) REVERT: B 597 ILE cc_start: 0.9071 (OUTLIER) cc_final: 0.8758 (mm) REVERT: B 1148 LEU cc_start: 0.8531 (OUTLIER) cc_final: 0.8259 (pt) REVERT: D 15 GLU cc_start: 0.2223 (mm-30) cc_final: 0.1086 (pm20) REVERT: D 62 MET cc_start: 0.6118 (mmp) cc_final: 0.5669 (tpt) REVERT: D 80 ILE cc_start: 0.6034 (mt) cc_final: 0.5729 (mt) REVERT: G 151 ARG cc_start: 0.4917 (ttt90) cc_final: 0.4196 (ttt90) REVERT: K 114 GLU cc_start: 0.6307 (mp0) cc_final: 0.6093 (mp0) REVERT: M 1346 MET cc_start: 0.3067 (mmm) cc_final: 0.0806 (tmm) REVERT: M 1372 LYS cc_start: 0.0154 (mmtm) cc_final: -0.0192 (mmtt) REVERT: Q 125 MET cc_start: 0.0970 (ppp) cc_final: 0.0124 (pmm) REVERT: Q 319 GLN cc_start: 0.4535 (mt0) cc_final: 0.2861 (tp-100) REVERT: Q 640 LEU cc_start: 0.3299 (tp) cc_final: 0.3008 (mt) REVERT: Q 703 MET cc_start: 0.5250 (mtp) cc_final: 0.5048 (mtp) REVERT: R 414 VAL cc_start: 0.2557 (t) cc_final: 0.2115 (m) REVERT: R 566 ARG cc_start: 0.1579 (ptp-110) cc_final: 0.1270 (ttt90) REVERT: R 586 MET cc_start: 0.0757 (ptt) cc_final: 0.0484 (mmt) REVERT: U 378 LEU cc_start: 0.4631 (mp) cc_final: 0.4416 (mt) REVERT: U 412 LEU cc_start: 0.3413 (tt) cc_final: 0.2402 (mm) REVERT: V 47 LYS cc_start: 0.0015 (mmtm) cc_final: -0.0601 (mttp) REVERT: V 140 GLU cc_start: 0.3709 (tt0) cc_final: 0.2721 (mm-30) REVERT: V 198 ARG cc_start: -0.1301 (ppt170) cc_final: -0.1764 (mtm110) REVERT: V 331 ARG cc_start: 0.0035 (ttm170) cc_final: -0.0690 (mtt180) REVERT: Z 197 MET cc_start: 0.3638 (mtp) cc_final: 0.3415 (mtp) outliers start: 116 outliers final: 48 residues processed: 821 average time/residue: 0.5932 time to fit residues: 789.3868 Evaluate side-chains 526 residues out of total 6485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 471 time to evaluate : 5.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 301 HIS Chi-restraints excluded: chain A residue 476 ILE Chi-restraints excluded: chain A residue 605 THR Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain A residue 757 GLN Chi-restraints excluded: chain A residue 942 VAL Chi-restraints excluded: chain A residue 1007 ILE Chi-restraints excluded: chain A residue 1074 SER Chi-restraints excluded: chain A residue 1175 ILE Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1385 VAL Chi-restraints excluded: chain A residue 1424 THR Chi-restraints excluded: chain B residue 20 ASP Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 198 GLU Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 354 SER Chi-restraints excluded: chain B residue 359 THR Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 567 ILE Chi-restraints excluded: chain B residue 597 ILE Chi-restraints excluded: chain B residue 649 ASN Chi-restraints excluded: chain B residue 650 ASN Chi-restraints excluded: chain B residue 659 SER Chi-restraints excluded: chain B residue 738 THR Chi-restraints excluded: chain B residue 750 VAL Chi-restraints excluded: chain B residue 759 VAL Chi-restraints excluded: chain B residue 784 SER Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 958 CYS Chi-restraints excluded: chain B residue 1148 LEU Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 75 SER Chi-restraints excluded: chain E residue 117 SER Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain G residue 37 THR Chi-restraints excluded: chain H residue 67 ASP Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 113 SER Chi-restraints excluded: chain H residue 116 VAL Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain I residue 73 SER Chi-restraints excluded: chain I residue 101 SER Chi-restraints excluded: chain J residue 47 ARG Chi-restraints excluded: chain V residue 45 ASP Chi-restraints excluded: chain W residue 169 ASP Chi-restraints excluded: chain Z residue 720 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 735 random chunks: chunk 620 optimal weight: 0.2980 chunk 557 optimal weight: 7.9990 chunk 309 optimal weight: 0.9990 chunk 190 optimal weight: 0.9990 chunk 375 optimal weight: 0.9980 chunk 297 optimal weight: 8.9990 chunk 576 optimal weight: 0.8980 chunk 222 optimal weight: 0.9990 chunk 350 optimal weight: 4.9990 chunk 428 optimal weight: 50.0000 chunk 667 optimal weight: 10.0000 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 HIS A 288 ASN ** A 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 516 GLN ** A 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 703 GLN A 704 ASN A 746 ASN A 780 ASN A 790 GLN A 809 HIS A 935 GLN A1005 HIS A1093 GLN A1230 GLN A1310 HIS A1462 GLN B 52 GLN B 98 HIS ** B 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 175 ASN B 319 ASN B 471 ASN B 518 HIS B 585 ASN B 593 GLN B 649 ASN B 725 GLN B 741 HIS B 930 GLN B 968 ASN ** B1040 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 111 GLN C 114 HIS C 262 GLN D 19 GLN D 34 ASN ** D 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 168 ASN G 93 ASN G 139 GLN ** I 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 84 HIS I 91 HIS K 2 ASN M1352 GLN Q 38 HIS Q 40 GLN Q 161 ASN Q 244 ASN Q 268 ASN Q 298 ASN ** Q 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 324 GLN Q 349 GLN Q 373 ASN Q 502 ASN ** Q 527 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 573 ASN Q 616 HIS Q 706 ASN ** Q 714 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 781 ASN ** Q 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 880 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 484 ASN R 567 ASN ** R 585 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 588 ASN U 451 HIS V 97 ASN V 193 HIS W 11 GLN ** W 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 223 ASN W 273 HIS ** Z 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 232 GLN Z 251 ASN Z 519 GLN Z 595 HIS Total number of N/Q/H flips: 67 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6829 moved from start: 0.2177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 58362 Z= 0.215 Angle : 0.620 14.990 78967 Z= 0.321 Chirality : 0.044 0.239 8353 Planarity : 0.004 0.060 10146 Dihedral : 12.833 170.165 9201 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.68 % Favored : 94.23 % Rotamer: Outliers : 2.60 % Allowed : 15.06 % Favored : 82.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.65 % Cis-general : 0.07 % Twisted Proline : 0.32 % 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: -3.35 (0.09), residues: 7232 helix: -1.79 (0.09), residues: 2493 sheet: -2.40 (0.17), residues: 831 loop : -2.51 (0.09), residues: 3908 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 176 HIS 0.008 0.001 HIS L 23 PHE 0.019 0.002 PHE B 309 TYR 0.023 0.001 TYR W 142 ARG 0.007 0.001 ARG B 222 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14464 Ramachandran restraints generated. 7232 Oldfield, 0 Emsley, 7232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14464 Ramachandran restraints generated. 7232 Oldfield, 0 Emsley, 7232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 707 residues out of total 6485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 563 time to evaluate : 5.049 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: A 283 ILE cc_start: 0.8193 (OUTLIER) cc_final: 0.7757 (mp) REVERT: A 301 HIS cc_start: 0.6494 (OUTLIER) cc_final: 0.5870 (t70) REVERT: A 501 MET cc_start: 0.8610 (mtp) cc_final: 0.8295 (mtp) REVERT: A 565 MET cc_start: 0.9135 (tpt) cc_final: 0.8809 (tpt) REVERT: A 757 GLN cc_start: 0.8095 (OUTLIER) cc_final: 0.7290 (mm-40) REVERT: B 53 MET cc_start: 0.7649 (mmm) cc_final: 0.7430 (mmm) REVERT: B 348 LEU cc_start: 0.9099 (OUTLIER) cc_final: 0.8887 (mt) REVERT: B 497 LYS cc_start: 0.7848 (pptt) cc_final: 0.7457 (pptt) REVERT: B 576 ILE cc_start: 0.8286 (OUTLIER) cc_final: 0.8018 (tp) REVERT: B 597 ILE cc_start: 0.9049 (OUTLIER) cc_final: 0.8815 (mm) REVERT: B 841 ARG cc_start: 0.7676 (tpp80) cc_final: 0.7215 (mmp-170) REVERT: B 1157 LEU cc_start: 0.8590 (OUTLIER) cc_final: 0.8356 (tp) REVERT: D 15 GLU cc_start: 0.1807 (mm-30) cc_final: 0.0907 (pm20) REVERT: D 62 MET cc_start: 0.5688 (mmp) cc_final: 0.5079 (tpt) REVERT: K 114 GLU cc_start: 0.6362 (mp0) cc_final: 0.6113 (mp0) REVERT: M 1346 MET cc_start: 0.2913 (mmm) cc_final: 0.0605 (tmm) REVERT: M 1347 MET cc_start: -0.3085 (ptt) cc_final: -0.4539 (mpp) REVERT: M 1372 LYS cc_start: 0.0495 (mmtm) cc_final: 0.0057 (mmtt) REVERT: Q 125 MET cc_start: 0.1117 (ppp) cc_final: 0.0115 (pmm) REVERT: Q 206 HIS cc_start: 0.1329 (m170) cc_final: 0.0048 (t-90) REVERT: Q 319 GLN cc_start: 0.4395 (mt0) cc_final: 0.2806 (tp-100) REVERT: R 476 GLU cc_start: 0.1937 (pt0) cc_final: 0.1580 (tp30) REVERT: R 565 GLN cc_start: 0.1770 (pt0) cc_final: 0.1028 (tt0) REVERT: V 26 ARG cc_start: 0.1141 (ttp-170) cc_final: -0.0058 (ttt180) REVERT: V 47 LYS cc_start: 0.0196 (mmtm) cc_final: -0.0375 (mttp) REVERT: V 133 LYS cc_start: 0.4795 (mtpt) cc_final: 0.4048 (mmtt) REVERT: V 140 GLU cc_start: 0.3667 (tt0) cc_final: 0.2768 (mm-30) REVERT: V 198 ARG cc_start: -0.1463 (ppt170) cc_final: -0.2411 (mtm110) REVERT: V 331 ARG cc_start: -0.0451 (ttm170) cc_final: -0.0881 (mtt180) REVERT: Z 307 MET cc_start: 0.2350 (OUTLIER) cc_final: 0.1616 (tmm) REVERT: Z 533 GLN cc_start: 0.1723 (pm20) cc_final: 0.1299 (tt0) outliers start: 144 outliers final: 65 residues processed: 683 average time/residue: 0.5562 time to fit residues: 633.7109 Evaluate side-chains 531 residues out of total 6485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 458 time to evaluate : 4.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 CYS Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 282 ASP Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 301 HIS Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 605 THR Chi-restraints excluded: chain A residue 757 GLN Chi-restraints excluded: chain A residue 1007 ILE Chi-restraints excluded: chain A residue 1129 ASN Chi-restraints excluded: chain A residue 1175 ILE Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1194 ASN Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 354 SER Chi-restraints excluded: chain B residue 388 TYR Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 556 ILE Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain B residue 576 ILE Chi-restraints excluded: chain B residue 597 ILE Chi-restraints excluded: chain B residue 649 ASN Chi-restraints excluded: chain B residue 667 THR Chi-restraints excluded: chain B residue 738 THR Chi-restraints excluded: chain B residue 750 VAL Chi-restraints excluded: chain B residue 759 VAL Chi-restraints excluded: chain B residue 784 SER Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 909 VAL Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 1148 LEU Chi-restraints excluded: chain B residue 1157 LEU Chi-restraints excluded: chain B residue 1174 VAL Chi-restraints excluded: chain C residue 27 ASP Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 75 SER Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 117 SER Chi-restraints excluded: chain E residue 120 ASP Chi-restraints excluded: chain E residue 129 GLN Chi-restraints excluded: chain F residue 123 LEU Chi-restraints excluded: chain G residue 37 THR Chi-restraints excluded: chain H residue 67 ASP Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 116 VAL Chi-restraints excluded: chain H residue 133 HIS Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain K residue 107 VAL Chi-restraints excluded: chain Q residue 697 TYR Chi-restraints excluded: chain Q residue 779 VAL Chi-restraints excluded: chain R residue 389 ILE Chi-restraints excluded: chain R residue 422 THR Chi-restraints excluded: chain V residue 127 VAL Chi-restraints excluded: chain W residue 90 LEU Chi-restraints excluded: chain W residue 169 ASP Chi-restraints excluded: chain W residue 265 THR Chi-restraints excluded: chain Z residue 176 ASP Chi-restraints excluded: chain Z residue 216 VAL Chi-restraints excluded: chain Z residue 307 MET Chi-restraints excluded: chain Z residue 393 LEU Chi-restraints excluded: chain Z residue 495 VAL Chi-restraints excluded: chain Z residue 567 VAL Chi-restraints excluded: chain Z residue 720 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 735 random chunks: chunk 370 optimal weight: 2.9990 chunk 207 optimal weight: 4.9990 chunk 555 optimal weight: 3.9990 chunk 454 optimal weight: 40.0000 chunk 184 optimal weight: 0.9980 chunk 668 optimal weight: 30.0000 chunk 722 optimal weight: 20.0000 chunk 595 optimal weight: 6.9990 chunk 663 optimal weight: 50.0000 chunk 227 optimal weight: 0.5980 chunk 536 optimal weight: 20.0000 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 313 HIS A 441 GLN ** A 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 620 HIS A 671 ASN A 673 GLN A 703 GLN A 742 ASN ** A 982 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1093 GLN B 741 HIS B 906 GLN ** B1040 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 60 HIS C 260 GLN ** D 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 327 GLN Q 527 HIS ** Q 609 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 714 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 880 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 35 ASN ** Z 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7013 moved from start: 0.3024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 58362 Z= 0.361 Angle : 0.618 10.756 78967 Z= 0.320 Chirality : 0.046 0.240 8353 Planarity : 0.004 0.056 10146 Dihedral : 12.563 172.330 9165 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.32 % Favored : 93.63 % Rotamer: Outliers : 3.41 % Allowed : 16.60 % Favored : 79.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.65 % Cis-general : 0.07 % Twisted Proline : 0.32 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.68 (0.09), residues: 7232 helix: -1.01 (0.10), residues: 2504 sheet: -2.12 (0.16), residues: 890 loop : -2.25 (0.09), residues: 3838 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 99 HIS 0.022 0.001 HIS W 268 PHE 0.023 0.002 PHE E 73 TYR 0.029 0.002 TYR B1048 ARG 0.021 0.001 ARG Z 552 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14464 Ramachandran restraints generated. 7232 Oldfield, 0 Emsley, 7232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14464 Ramachandran restraints generated. 7232 Oldfield, 0 Emsley, 7232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 684 residues out of total 6485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 189 poor density : 495 time to evaluate : 5.012 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: A 283 ILE cc_start: 0.8204 (OUTLIER) cc_final: 0.7665 (mp) REVERT: A 301 HIS cc_start: 0.6549 (OUTLIER) cc_final: 0.5521 (t70) REVERT: A 343 LEU cc_start: 0.8640 (OUTLIER) cc_final: 0.8349 (pp) REVERT: A 360 ASP cc_start: 0.7965 (m-30) cc_final: 0.7698 (m-30) REVERT: A 495 ASP cc_start: 0.7318 (t70) cc_final: 0.6959 (t0) REVERT: A 565 MET cc_start: 0.9319 (tpt) cc_final: 0.8981 (tpt) REVERT: A 637 MET cc_start: 0.8601 (OUTLIER) cc_final: 0.8296 (mtp) REVERT: A 952 LEU cc_start: 0.8752 (OUTLIER) cc_final: 0.8469 (mt) REVERT: A 962 ASP cc_start: 0.7667 (m-30) cc_final: 0.7265 (m-30) REVERT: A 1194 ASN cc_start: 0.7257 (OUTLIER) cc_final: 0.6962 (t0) REVERT: B 36 GLU cc_start: 0.7509 (OUTLIER) cc_final: 0.7100 (tp30) REVERT: B 156 LEU cc_start: 0.9024 (OUTLIER) cc_final: 0.8686 (mp) REVERT: B 561 ILE cc_start: 0.9137 (OUTLIER) cc_final: 0.8861 (mt) REVERT: B 576 ILE cc_start: 0.8236 (OUTLIER) cc_final: 0.7981 (tp) REVERT: B 597 ILE cc_start: 0.9251 (OUTLIER) cc_final: 0.8981 (mm) REVERT: C 161 LEU cc_start: 0.9180 (OUTLIER) cc_final: 0.8935 (pp) REVERT: D 47 GLN cc_start: 0.6773 (tm-30) cc_final: 0.6544 (tm-30) REVERT: D 62 MET cc_start: 0.5744 (mmp) cc_final: 0.5024 (tpt) REVERT: E 141 GLU cc_start: 0.7774 (OUTLIER) cc_final: 0.7341 (mp0) REVERT: H 7 GLU cc_start: 0.7358 (OUTLIER) cc_final: 0.6871 (tp30) REVERT: K 100 LEU cc_start: 0.9012 (OUTLIER) cc_final: 0.8778 (tt) REVERT: M 1346 MET cc_start: 0.2929 (mmm) cc_final: 0.0490 (tmm) REVERT: M 1372 LYS cc_start: 0.0970 (mmtm) cc_final: 0.0349 (mmtt) REVERT: Q 125 MET cc_start: 0.1126 (ppp) cc_final: 0.0851 (mtp) REVERT: Q 191 ARG cc_start: 0.0627 (OUTLIER) cc_final: 0.0409 (mtp180) REVERT: Q 206 HIS cc_start: 0.0704 (m170) cc_final: -0.0256 (t-90) REVERT: Q 319 GLN cc_start: 0.4574 (mt0) cc_final: 0.2881 (tp-100) REVERT: Q 368 LEU cc_start: 0.0576 (OUTLIER) cc_final: 0.0337 (tp) REVERT: R 476 GLU cc_start: 0.1888 (pt0) cc_final: 0.1309 (tp30) REVERT: R 565 GLN cc_start: 0.1863 (pt0) cc_final: 0.0928 (tt0) REVERT: V 26 ARG cc_start: 0.1200 (ttp-170) cc_final: 0.0039 (ttt180) REVERT: V 32 ARG cc_start: 0.3180 (mmm-85) cc_final: 0.2890 (mmm-85) REVERT: V 47 LYS cc_start: 0.0466 (mmtm) cc_final: -0.0260 (mttp) REVERT: V 85 ASP cc_start: 0.1496 (OUTLIER) cc_final: 0.1264 (t0) REVERT: V 140 GLU cc_start: 0.3701 (tt0) cc_final: 0.2797 (mm-30) REVERT: V 198 ARG cc_start: -0.1565 (ppt170) cc_final: -0.2307 (mtm110) REVERT: V 205 MET cc_start: 0.3428 (mtt) cc_final: 0.3206 (mtt) REVERT: V 331 ARG cc_start: -0.0341 (ttm170) cc_final: -0.1138 (mtt180) REVERT: Z 307 MET cc_start: 0.2061 (OUTLIER) cc_final: 0.1617 (tmm) REVERT: Z 533 GLN cc_start: 0.1556 (pm20) cc_final: 0.1221 (tt0) outliers start: 189 outliers final: 106 residues processed: 658 average time/residue: 0.5421 time to fit residues: 607.2230 Evaluate side-chains 568 residues out of total 6485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 443 time to evaluate : 4.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 CYS Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 197 GLU Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 282 ASP Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 301 HIS Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 605 THR Chi-restraints excluded: chain A residue 637 MET Chi-restraints excluded: chain A residue 811 ILE Chi-restraints excluded: chain A residue 952 LEU Chi-restraints excluded: chain A residue 996 ILE Chi-restraints excluded: chain A residue 1007 ILE Chi-restraints excluded: chain A residue 1030 SER Chi-restraints excluded: chain A residue 1095 LEU Chi-restraints excluded: chain A residue 1175 ILE Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1194 ASN Chi-restraints excluded: chain A residue 1227 THR Chi-restraints excluded: chain A residue 1314 THR Chi-restraints excluded: chain A residue 1385 VAL Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 36 GLU Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 354 SER Chi-restraints excluded: chain B residue 359 THR Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 556 ILE Chi-restraints excluded: chain B residue 561 ILE Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain B residue 576 ILE Chi-restraints excluded: chain B residue 597 ILE Chi-restraints excluded: chain B residue 647 GLU Chi-restraints excluded: chain B residue 649 ASN Chi-restraints excluded: chain B residue 659 SER Chi-restraints excluded: chain B residue 674 MET Chi-restraints excluded: chain B residue 678 THR Chi-restraints excluded: chain B residue 710 ILE Chi-restraints excluded: chain B residue 715 ASP Chi-restraints excluded: chain B residue 738 THR Chi-restraints excluded: chain B residue 750 VAL Chi-restraints excluded: chain B residue 759 VAL Chi-restraints excluded: chain B residue 794 VAL Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 894 THR Chi-restraints excluded: chain B residue 909 VAL Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 958 CYS Chi-restraints excluded: chain B residue 1130 THR Chi-restraints excluded: chain B residue 1148 LEU Chi-restraints excluded: chain B residue 1149 VAL Chi-restraints excluded: chain B residue 1157 LEU Chi-restraints excluded: chain B residue 1174 VAL Chi-restraints excluded: chain C residue 5 ASN Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 27 ASP Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 75 SER Chi-restraints excluded: chain C residue 132 SER Chi-restraints excluded: chain C residue 147 ASP Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 100 THR Chi-restraints excluded: chain E residue 117 SER Chi-restraints excluded: chain E residue 120 ASP Chi-restraints excluded: chain E residue 129 GLN Chi-restraints excluded: chain E residue 141 GLU Chi-restraints excluded: chain E residue 159 LEU Chi-restraints excluded: chain F residue 123 LEU Chi-restraints excluded: chain G residue 21 ASN Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain H residue 7 GLU Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 67 ASP Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 116 VAL Chi-restraints excluded: chain H residue 133 HIS Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain K residue 107 VAL Chi-restraints excluded: chain M residue 1489 VAL Chi-restraints excluded: chain M residue 1490 THR Chi-restraints excluded: chain Q residue 94 VAL Chi-restraints excluded: chain Q residue 191 ARG Chi-restraints excluded: chain Q residue 301 VAL Chi-restraints excluded: chain Q residue 368 LEU Chi-restraints excluded: chain Q residue 697 TYR Chi-restraints excluded: chain Q residue 707 CYS Chi-restraints excluded: chain Q residue 779 VAL Chi-restraints excluded: chain Q residue 875 LEU Chi-restraints excluded: chain R residue 389 ILE Chi-restraints excluded: chain R residue 422 THR Chi-restraints excluded: chain R residue 563 ILE Chi-restraints excluded: chain U residue 459 VAL Chi-restraints excluded: chain V residue 85 ASP Chi-restraints excluded: chain V residue 94 ILE Chi-restraints excluded: chain V residue 127 VAL Chi-restraints excluded: chain W residue 35 VAL Chi-restraints excluded: chain W residue 90 LEU Chi-restraints excluded: chain W residue 169 ASP Chi-restraints excluded: chain Z residue 176 ASP Chi-restraints excluded: chain Z residue 216 VAL Chi-restraints excluded: chain Z residue 307 MET Chi-restraints excluded: chain Z residue 308 ILE Chi-restraints excluded: chain Z residue 393 LEU Chi-restraints excluded: chain Z residue 451 MET Chi-restraints excluded: chain Z residue 495 VAL Chi-restraints excluded: chain Z residue 551 VAL Chi-restraints excluded: chain Z residue 567 VAL Chi-restraints excluded: chain Z residue 738 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 735 random chunks: chunk 660 optimal weight: 30.0000 chunk 502 optimal weight: 30.0000 chunk 347 optimal weight: 0.7980 chunk 74 optimal weight: 1.9990 chunk 319 optimal weight: 1.9990 chunk 449 optimal weight: 30.0000 chunk 671 optimal weight: 3.9990 chunk 710 optimal weight: 30.0000 chunk 350 optimal weight: 9.9990 chunk 636 optimal weight: 50.0000 chunk 191 optimal weight: 3.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 441 GLN ** A 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 703 GLN ** A 982 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1093 GLN A1244 ASN ** B 650 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M1477 GLN ** Q 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 319 GLN ** Q 609 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 714 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 880 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 427 GLN R 490 GLN ** R 585 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 234 HIS Z 237 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7015 moved from start: 0.3360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 58362 Z= 0.308 Angle : 0.559 11.606 78967 Z= 0.290 Chirality : 0.044 0.368 8353 Planarity : 0.004 0.082 10146 Dihedral : 12.446 171.963 9155 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.66 % Favored : 94.32 % Rotamer: Outliers : 3.36 % Allowed : 18.10 % Favored : 78.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.65 % Cis-general : 0.07 % Twisted Proline : 0.32 % 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: -2.32 (0.09), residues: 7232 helix: -0.60 (0.10), residues: 2504 sheet: -2.06 (0.16), residues: 879 loop : -2.08 (0.09), residues: 3849 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 176 HIS 0.012 0.001 HIS A 809 PHE 0.029 0.002 PHE B 356 TYR 0.023 0.001 TYR D 67 ARG 0.008 0.000 ARG A 67 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14464 Ramachandran restraints generated. 7232 Oldfield, 0 Emsley, 7232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14464 Ramachandran restraints generated. 7232 Oldfield, 0 Emsley, 7232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 645 residues out of total 6485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 186 poor density : 459 time to evaluate : 4.992 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 266 MET cc_start: 0.7017 (tpt) cc_final: 0.6494 (mmm) REVERT: A 283 ILE cc_start: 0.8300 (OUTLIER) cc_final: 0.7790 (mp) REVERT: A 343 LEU cc_start: 0.8755 (OUTLIER) cc_final: 0.8520 (pp) REVERT: A 495 ASP cc_start: 0.7331 (t70) cc_final: 0.6962 (t70) REVERT: A 565 MET cc_start: 0.9234 (tpt) cc_final: 0.8992 (tpt) REVERT: A 637 MET cc_start: 0.8646 (mtp) cc_final: 0.8264 (mtp) REVERT: A 952 LEU cc_start: 0.8676 (OUTLIER) cc_final: 0.8425 (mt) REVERT: A 1095 LEU cc_start: 0.8796 (OUTLIER) cc_final: 0.8583 (mt) REVERT: A 1225 LYS cc_start: 0.7489 (mmtt) cc_final: 0.7286 (mptt) REVERT: B 156 LEU cc_start: 0.9007 (OUTLIER) cc_final: 0.8703 (mp) REVERT: B 597 ILE cc_start: 0.9245 (OUTLIER) cc_final: 0.9008 (mm) REVERT: B 638 ARG cc_start: 0.8170 (mtm110) cc_final: 0.7714 (ptp90) REVERT: B 1130 THR cc_start: 0.8406 (OUTLIER) cc_final: 0.8122 (m) REVERT: B 1157 LEU cc_start: 0.8777 (OUTLIER) cc_final: 0.8481 (tp) REVERT: C 151 VAL cc_start: 0.8978 (OUTLIER) cc_final: 0.8761 (m) REVERT: C 161 LEU cc_start: 0.9123 (OUTLIER) cc_final: 0.8871 (pp) REVERT: D 62 MET cc_start: 0.5799 (mmp) cc_final: 0.5190 (tpt) REVERT: E 141 GLU cc_start: 0.7730 (OUTLIER) cc_final: 0.7311 (mp0) REVERT: H 7 GLU cc_start: 0.7327 (OUTLIER) cc_final: 0.6823 (tp30) REVERT: L 16 ILE cc_start: 0.8721 (tt) cc_final: 0.8502 (tt) REVERT: M 1346 MET cc_start: 0.3001 (mmm) cc_final: 0.0354 (tmm) REVERT: M 1347 MET cc_start: -0.2723 (ptt) cc_final: -0.4211 (mmm) REVERT: M 1372 LYS cc_start: 0.1010 (mmtm) cc_final: 0.0753 (mmtt) REVERT: M 1477 GLN cc_start: 0.1436 (OUTLIER) cc_final: 0.0175 (pt0) REVERT: Q 125 MET cc_start: 0.1161 (ppp) cc_final: 0.0869 (mtp) REVERT: Q 206 HIS cc_start: 0.0742 (m170) cc_final: -0.0197 (t-90) REVERT: Q 580 GLU cc_start: 0.3174 (pp20) cc_final: 0.2268 (mt-10) REVERT: Q 647 LEU cc_start: 0.5636 (OUTLIER) cc_final: 0.5360 (mt) REVERT: Q 698 ILE cc_start: 0.3718 (OUTLIER) cc_final: 0.2514 (mm) REVERT: R 476 GLU cc_start: 0.1877 (pt0) cc_final: 0.1309 (tp30) REVERT: R 565 GLN cc_start: 0.1681 (pt0) cc_final: 0.0937 (tt0) REVERT: V 26 ARG cc_start: 0.1293 (ttp-170) cc_final: 0.0082 (ttt180) REVERT: V 85 ASP cc_start: 0.1515 (OUTLIER) cc_final: 0.1307 (t0) REVERT: V 109 GLU cc_start: 0.4762 (mp0) cc_final: 0.3736 (mm-30) REVERT: V 140 GLU cc_start: 0.3818 (tt0) cc_final: 0.2785 (mm-30) REVERT: V 198 ARG cc_start: -0.1590 (ppt170) cc_final: -0.2227 (mtm110) REVERT: V 205 MET cc_start: 0.3361 (mtt) cc_final: 0.3066 (mtt) REVERT: Z 307 MET cc_start: 0.2523 (OUTLIER) cc_final: 0.1987 (tmm) REVERT: Z 533 GLN cc_start: 0.1674 (pm20) cc_final: 0.1267 (tt0) outliers start: 186 outliers final: 111 residues processed: 620 average time/residue: 0.5474 time to fit residues: 574.7707 Evaluate side-chains 563 residues out of total 6485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 435 time to evaluate : 5.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 CYS Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 81 CYS Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 238 MET Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 282 ASP Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 329 MET Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 605 THR Chi-restraints excluded: chain A residue 886 VAL Chi-restraints excluded: chain A residue 899 GLU Chi-restraints excluded: chain A residue 940 LYS Chi-restraints excluded: chain A residue 952 LEU Chi-restraints excluded: chain A residue 1007 ILE Chi-restraints excluded: chain A residue 1030 SER Chi-restraints excluded: chain A residue 1073 GLU Chi-restraints excluded: chain A residue 1095 LEU Chi-restraints excluded: chain A residue 1128 ILE Chi-restraints excluded: chain A residue 1175 ILE Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1314 THR Chi-restraints excluded: chain A residue 1385 VAL Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 354 SER Chi-restraints excluded: chain B residue 359 THR Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 463 ARG Chi-restraints excluded: chain B residue 556 ILE Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain B residue 597 ILE Chi-restraints excluded: chain B residue 647 GLU Chi-restraints excluded: chain B residue 649 ASN Chi-restraints excluded: chain B residue 662 VAL Chi-restraints excluded: chain B residue 678 THR Chi-restraints excluded: chain B residue 710 ILE Chi-restraints excluded: chain B residue 738 THR Chi-restraints excluded: chain B residue 750 VAL Chi-restraints excluded: chain B residue 759 VAL Chi-restraints excluded: chain B residue 794 VAL Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 842 HIS Chi-restraints excluded: chain B residue 894 THR Chi-restraints excluded: chain B residue 909 VAL Chi-restraints excluded: chain B residue 913 GLN Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 1130 THR Chi-restraints excluded: chain B residue 1148 LEU Chi-restraints excluded: chain B residue 1157 LEU Chi-restraints excluded: chain B residue 1174 VAL Chi-restraints excluded: chain C residue 5 ASN Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 27 ASP Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 147 ASP Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain D residue 136 THR Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 100 THR Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain E residue 117 SER Chi-restraints excluded: chain E residue 120 ASP Chi-restraints excluded: chain E residue 141 GLU Chi-restraints excluded: chain E residue 159 LEU Chi-restraints excluded: chain E residue 168 ASN Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain F residue 105 ILE Chi-restraints excluded: chain F residue 123 LEU Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain H residue 7 GLU Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 67 ASP Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 116 VAL Chi-restraints excluded: chain H residue 133 HIS Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 83 ASP Chi-restraints excluded: chain K residue 107 VAL Chi-restraints excluded: chain M residue 1477 GLN Chi-restraints excluded: chain M residue 1489 VAL Chi-restraints excluded: chain Q residue 94 VAL Chi-restraints excluded: chain Q residue 301 VAL Chi-restraints excluded: chain Q residue 368 LEU Chi-restraints excluded: chain Q residue 647 LEU Chi-restraints excluded: chain Q residue 697 TYR Chi-restraints excluded: chain Q residue 698 ILE Chi-restraints excluded: chain Q residue 779 VAL Chi-restraints excluded: chain Q residue 812 THR Chi-restraints excluded: chain Q residue 875 LEU Chi-restraints excluded: chain R residue 389 ILE Chi-restraints excluded: chain R residue 422 THR Chi-restraints excluded: chain R residue 563 ILE Chi-restraints excluded: chain U residue 452 LEU Chi-restraints excluded: chain V residue 85 ASP Chi-restraints excluded: chain V residue 127 VAL Chi-restraints excluded: chain V residue 202 VAL Chi-restraints excluded: chain W residue 35 VAL Chi-restraints excluded: chain W residue 169 ASP Chi-restraints excluded: chain W residue 243 ASP Chi-restraints excluded: chain Z residue 176 ASP Chi-restraints excluded: chain Z residue 206 THR Chi-restraints excluded: chain Z residue 216 VAL Chi-restraints excluded: chain Z residue 296 VAL Chi-restraints excluded: chain Z residue 307 MET Chi-restraints excluded: chain Z residue 393 LEU Chi-restraints excluded: chain Z residue 451 MET Chi-restraints excluded: chain Z residue 551 VAL Chi-restraints excluded: chain Z residue 567 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 735 random chunks: chunk 591 optimal weight: 0.0040 chunk 403 optimal weight: 20.0000 chunk 10 optimal weight: 9.9990 chunk 528 optimal weight: 10.0000 chunk 293 optimal weight: 0.4980 chunk 606 optimal weight: 30.0000 chunk 491 optimal weight: 40.0000 chunk 0 optimal weight: 8.9990 chunk 362 optimal weight: 0.9990 chunk 637 optimal weight: 50.0000 chunk 179 optimal weight: 2.9990 overall best weight: 2.6998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 459 ASN ** A 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 703 GLN ** A 982 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1194 ASN A1244 ASN A1313 GLN ** B 650 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1003 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1120 ASN C 114 HIS D 76 ASN ** E 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M1477 GLN ** Q 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 609 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 714 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 585 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 274 GLN Y 41 GLN ** Z 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7033 moved from start: 0.3643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 58362 Z= 0.322 Angle : 0.562 11.232 78967 Z= 0.292 Chirality : 0.044 0.259 8353 Planarity : 0.004 0.063 10146 Dihedral : 12.419 172.181 9151 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.95 % Favored : 94.03 % Rotamer: Outliers : 3.97 % Allowed : 18.30 % Favored : 77.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.65 % Cis-general : 0.07 % Twisted Proline : 0.32 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.08 (0.09), residues: 7232 helix: -0.36 (0.11), residues: 2505 sheet: -2.00 (0.16), residues: 885 loop : -1.95 (0.09), residues: 3842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 479 HIS 0.011 0.001 HIS A 809 PHE 0.052 0.002 PHE Q 152 TYR 0.022 0.001 TYR D 67 ARG 0.007 0.000 ARG A 67 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14464 Ramachandran restraints generated. 7232 Oldfield, 0 Emsley, 7232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14464 Ramachandran restraints generated. 7232 Oldfield, 0 Emsley, 7232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 677 residues out of total 6485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 220 poor density : 457 time to evaluate : 5.027 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 266 MET cc_start: 0.6884 (tpt) cc_final: 0.6548 (mmm) REVERT: A 283 ILE cc_start: 0.8314 (OUTLIER) cc_final: 0.7767 (mp) REVERT: A 343 LEU cc_start: 0.8804 (OUTLIER) cc_final: 0.8586 (pp) REVERT: A 565 MET cc_start: 0.9254 (tpt) cc_final: 0.8985 (tpt) REVERT: A 637 MET cc_start: 0.8677 (mtp) cc_final: 0.8280 (mtp) REVERT: A 952 LEU cc_start: 0.8647 (OUTLIER) cc_final: 0.8402 (mt) REVERT: A 1095 LEU cc_start: 0.8810 (OUTLIER) cc_final: 0.8600 (mt) REVERT: A 1440 MET cc_start: 0.8506 (mmt) cc_final: 0.7798 (mmt) REVERT: B 156 LEU cc_start: 0.9004 (OUTLIER) cc_final: 0.8709 (mp) REVERT: B 561 ILE cc_start: 0.9175 (OUTLIER) cc_final: 0.8957 (mt) REVERT: B 597 ILE cc_start: 0.9271 (OUTLIER) cc_final: 0.9011 (mm) REVERT: B 638 ARG cc_start: 0.8186 (mtm110) cc_final: 0.7755 (ptp90) REVERT: B 1130 THR cc_start: 0.8408 (OUTLIER) cc_final: 0.8169 (m) REVERT: B 1157 LEU cc_start: 0.8809 (OUTLIER) cc_final: 0.8497 (tp) REVERT: C 161 LEU cc_start: 0.9119 (OUTLIER) cc_final: 0.8872 (pp) REVERT: D 45 LYS cc_start: 0.6371 (tptp) cc_final: 0.6031 (tptp) REVERT: D 62 MET cc_start: 0.5745 (mmp) cc_final: 0.5501 (tpt) REVERT: E 141 GLU cc_start: 0.7742 (OUTLIER) cc_final: 0.7313 (mp0) REVERT: H 7 GLU cc_start: 0.7317 (OUTLIER) cc_final: 0.6798 (tp30) REVERT: M 1346 MET cc_start: 0.3104 (mmm) cc_final: 0.0458 (tmm) REVERT: M 1347 MET cc_start: -0.2775 (ptt) cc_final: -0.3760 (mmm) REVERT: M 1372 LYS cc_start: 0.1228 (mmtm) cc_final: 0.0527 (mmtt) REVERT: M 1477 GLN cc_start: 0.1171 (OUTLIER) cc_final: -0.0086 (pt0) REVERT: Q 125 MET cc_start: 0.1103 (ppp) cc_final: 0.0823 (mtp) REVERT: Q 206 HIS cc_start: 0.0882 (m170) cc_final: -0.0405 (t-90) REVERT: Q 540 MET cc_start: 0.4078 (ptp) cc_final: 0.3578 (ptm) REVERT: Q 580 GLU cc_start: 0.3320 (pp20) cc_final: 0.2364 (mt-10) REVERT: Q 647 LEU cc_start: 0.5738 (OUTLIER) cc_final: 0.5423 (mt) REVERT: R 464 MET cc_start: 0.3795 (tmm) cc_final: 0.3413 (ttt) REVERT: R 565 GLN cc_start: 0.1397 (pt0) cc_final: 0.0702 (tt0) REVERT: V 85 ASP cc_start: 0.1939 (OUTLIER) cc_final: 0.1646 (t0) REVERT: V 109 GLU cc_start: 0.4618 (mp0) cc_final: 0.3551 (mm-30) REVERT: V 140 GLU cc_start: 0.3896 (tt0) cc_final: 0.2773 (mm-30) REVERT: V 198 ARG cc_start: -0.1004 (ppt170) cc_final: -0.1841 (mtm110) REVERT: V 205 MET cc_start: 0.3418 (mtt) cc_final: 0.3162 (mtt) REVERT: W 302 ASP cc_start: 0.3187 (p0) cc_final: 0.1710 (p0) REVERT: Z 533 GLN cc_start: 0.1549 (pm20) cc_final: 0.1106 (tt0) outliers start: 220 outliers final: 142 residues processed: 643 average time/residue: 0.5945 time to fit residues: 641.4950 Evaluate side-chains 592 residues out of total 6485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 157 poor density : 435 time to evaluate : 5.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 CYS Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 81 CYS Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 197 GLU Chi-restraints excluded: chain A residue 238 MET Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 282 ASP Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 321 GLU Chi-restraints excluded: chain A residue 329 MET Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 555 LEU Chi-restraints excluded: chain A residue 605 THR Chi-restraints excluded: chain A residue 886 VAL Chi-restraints excluded: chain A residue 899 GLU Chi-restraints excluded: chain A residue 940 LYS Chi-restraints excluded: chain A residue 952 LEU Chi-restraints excluded: chain A residue 996 ILE Chi-restraints excluded: chain A residue 1007 ILE Chi-restraints excluded: chain A residue 1030 SER Chi-restraints excluded: chain A residue 1073 GLU Chi-restraints excluded: chain A residue 1095 LEU Chi-restraints excluded: chain A residue 1175 ILE Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1385 VAL Chi-restraints excluded: chain A residue 1458 ILE Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 65 ILE Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 323 SER Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 354 SER Chi-restraints excluded: chain B residue 359 THR Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 429 PHE Chi-restraints excluded: chain B residue 463 ARG Chi-restraints excluded: chain B residue 556 ILE Chi-restraints excluded: chain B residue 561 ILE Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain B residue 597 ILE Chi-restraints excluded: chain B residue 647 GLU Chi-restraints excluded: chain B residue 649 ASN Chi-restraints excluded: chain B residue 659 SER Chi-restraints excluded: chain B residue 662 VAL Chi-restraints excluded: chain B residue 674 MET Chi-restraints excluded: chain B residue 678 THR Chi-restraints excluded: chain B residue 710 ILE Chi-restraints excluded: chain B residue 715 ASP Chi-restraints excluded: chain B residue 738 THR Chi-restraints excluded: chain B residue 750 VAL Chi-restraints excluded: chain B residue 759 VAL Chi-restraints excluded: chain B residue 794 VAL Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 836 THR Chi-restraints excluded: chain B residue 842 HIS Chi-restraints excluded: chain B residue 894 THR Chi-restraints excluded: chain B residue 909 VAL Chi-restraints excluded: chain B residue 913 GLN Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 958 CYS Chi-restraints excluded: chain B residue 1130 THR Chi-restraints excluded: chain B residue 1148 LEU Chi-restraints excluded: chain B residue 1149 VAL Chi-restraints excluded: chain B residue 1157 LEU Chi-restraints excluded: chain B residue 1174 VAL Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 108 ASN Chi-restraints excluded: chain C residue 132 SER Chi-restraints excluded: chain C residue 147 ASP Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain D residue 136 THR Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 100 THR Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain E residue 117 SER Chi-restraints excluded: chain E residue 120 ASP Chi-restraints excluded: chain E residue 141 GLU Chi-restraints excluded: chain E residue 159 LEU Chi-restraints excluded: chain E residue 168 ASN Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain F residue 105 ILE Chi-restraints excluded: chain F residue 123 LEU Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 21 ASN Chi-restraints excluded: chain G residue 38 CYS Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain H residue 7 GLU Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 67 ASP Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 116 VAL Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain H residue 147 LYS Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 83 ASP Chi-restraints excluded: chain J residue 65 LEU Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain M residue 1477 GLN Chi-restraints excluded: chain M residue 1489 VAL Chi-restraints excluded: chain M residue 1490 THR Chi-restraints excluded: chain Q residue 94 VAL Chi-restraints excluded: chain Q residue 301 VAL Chi-restraints excluded: chain Q residue 368 LEU Chi-restraints excluded: chain Q residue 647 LEU Chi-restraints excluded: chain Q residue 692 VAL Chi-restraints excluded: chain Q residue 779 VAL Chi-restraints excluded: chain Q residue 812 THR Chi-restraints excluded: chain Q residue 875 LEU Chi-restraints excluded: chain R residue 389 ILE Chi-restraints excluded: chain R residue 422 THR Chi-restraints excluded: chain R residue 563 ILE Chi-restraints excluded: chain U residue 452 LEU Chi-restraints excluded: chain U residue 459 VAL Chi-restraints excluded: chain V residue 30 VAL Chi-restraints excluded: chain V residue 85 ASP Chi-restraints excluded: chain V residue 94 ILE Chi-restraints excluded: chain V residue 127 VAL Chi-restraints excluded: chain V residue 202 VAL Chi-restraints excluded: chain V residue 203 GLU Chi-restraints excluded: chain W residue 26 THR Chi-restraints excluded: chain W residue 35 VAL Chi-restraints excluded: chain W residue 36 VAL Chi-restraints excluded: chain W residue 42 ASP Chi-restraints excluded: chain W residue 107 VAL Chi-restraints excluded: chain W residue 169 ASP Chi-restraints excluded: chain W residue 243 ASP Chi-restraints excluded: chain Y residue 71 VAL Chi-restraints excluded: chain Y residue 84 VAL Chi-restraints excluded: chain Z residue 176 ASP Chi-restraints excluded: chain Z residue 206 THR Chi-restraints excluded: chain Z residue 216 VAL Chi-restraints excluded: chain Z residue 221 VAL Chi-restraints excluded: chain Z residue 296 VAL Chi-restraints excluded: chain Z residue 393 LEU Chi-restraints excluded: chain Z residue 451 MET Chi-restraints excluded: chain Z residue 551 VAL Chi-restraints excluded: chain Z residue 567 VAL Chi-restraints excluded: chain Z residue 738 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 735 random chunks: chunk 239 optimal weight: 1.9990 chunk 639 optimal weight: 20.0000 chunk 140 optimal weight: 0.0770 chunk 417 optimal weight: 6.9990 chunk 175 optimal weight: 0.9990 chunk 711 optimal weight: 30.0000 chunk 590 optimal weight: 8.9990 chunk 329 optimal weight: 30.0000 chunk 59 optimal weight: 0.9990 chunk 235 optimal weight: 0.7980 chunk 373 optimal weight: 0.8980 overall best weight: 0.7542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 703 GLN A1313 GLN ** B 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 906 GLN B 941 GLN ** B1003 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 93 ASN K 89 ASN ** Q 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 714 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 585 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 13 GLN ** W 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 41 GLN ** Z 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 519 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6965 moved from start: 0.3918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 58362 Z= 0.153 Angle : 0.485 10.918 78967 Z= 0.252 Chirality : 0.041 0.232 8353 Planarity : 0.003 0.050 10146 Dihedral : 12.253 171.942 9151 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.01 % Allowed : 4.89 % Favored : 95.09 % Rotamer: Outliers : 2.84 % Allowed : 19.70 % Favored : 77.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.65 % Cis-general : 0.07 % 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: -1.72 (0.10), residues: 7232 helix: -0.03 (0.11), residues: 2524 sheet: -1.72 (0.17), residues: 849 loop : -1.79 (0.09), residues: 3859 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 203 HIS 0.009 0.001 HIS W 268 PHE 0.056 0.001 PHE Q 152 TYR 0.024 0.001 TYR D 67 ARG 0.007 0.000 ARG A 407 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14464 Ramachandran restraints generated. 7232 Oldfield, 0 Emsley, 7232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14464 Ramachandran restraints generated. 7232 Oldfield, 0 Emsley, 7232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 616 residues out of total 6485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 157 poor density : 459 time to evaluate : 5.033 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 283 ILE cc_start: 0.8169 (OUTLIER) cc_final: 0.7680 (mp) REVERT: A 327 ARG cc_start: 0.7361 (mpt90) cc_final: 0.7101 (mmt-90) REVERT: A 343 LEU cc_start: 0.8729 (OUTLIER) cc_final: 0.8515 (pp) REVERT: A 952 LEU cc_start: 0.8409 (OUTLIER) cc_final: 0.8177 (mt) REVERT: A 1190 GLN cc_start: 0.6930 (OUTLIER) cc_final: 0.6535 (mt0) REVERT: B 235 ILE cc_start: 0.8369 (mm) cc_final: 0.8144 (mm) REVERT: B 335 ARG cc_start: 0.7411 (mtm110) cc_final: 0.7144 (mtm-85) REVERT: B 550 MET cc_start: 0.7127 (ttt) cc_final: 0.6909 (ttt) REVERT: B 561 ILE cc_start: 0.9216 (OUTLIER) cc_final: 0.8994 (mt) REVERT: B 597 ILE cc_start: 0.9188 (OUTLIER) cc_final: 0.8950 (mm) REVERT: B 638 ARG cc_start: 0.8158 (mtm110) cc_final: 0.7809 (ptp90) REVERT: B 1081 ASP cc_start: 0.8168 (t0) cc_final: 0.7579 (t0) REVERT: B 1157 LEU cc_start: 0.8672 (OUTLIER) cc_final: 0.8387 (tp) REVERT: C 161 LEU cc_start: 0.9127 (OUTLIER) cc_final: 0.8878 (pp) REVERT: D 45 LYS cc_start: 0.6279 (tptp) cc_final: 0.6012 (tptp) REVERT: D 62 MET cc_start: 0.5709 (mmp) cc_final: 0.5366 (tpt) REVERT: E 110 MET cc_start: 0.7388 (ptp) cc_final: 0.7005 (ptp) REVERT: H 7 GLU cc_start: 0.7098 (OUTLIER) cc_final: 0.6680 (tp30) REVERT: M 1346 MET cc_start: 0.3135 (mmm) cc_final: 0.0416 (tmm) REVERT: M 1347 MET cc_start: -0.2912 (ptt) cc_final: -0.4095 (mmm) REVERT: M 1372 LYS cc_start: 0.0940 (mmtm) cc_final: 0.0678 (mmtt) REVERT: M 1375 ASP cc_start: -0.0121 (OUTLIER) cc_final: -0.0374 (p0) REVERT: Q 125 MET cc_start: 0.1013 (ppp) cc_final: 0.0733 (mtp) REVERT: Q 206 HIS cc_start: 0.0687 (m170) cc_final: -0.0452 (t-90) REVERT: Q 375 TYR cc_start: 0.3803 (m-80) cc_final: 0.3280 (p90) REVERT: Q 392 GLU cc_start: 0.0177 (pm20) cc_final: -0.0359 (tp30) REVERT: Q 540 MET cc_start: 0.4247 (ptp) cc_final: 0.3731 (ptm) REVERT: Q 580 GLU cc_start: 0.3102 (pp20) cc_final: 0.2295 (mt-10) REVERT: Q 779 VAL cc_start: 0.4470 (OUTLIER) cc_final: 0.3811 (p) REVERT: Q 890 MET cc_start: 0.4823 (tpp) cc_final: 0.4482 (ptm) REVERT: R 464 MET cc_start: 0.3461 (tmm) cc_final: 0.3119 (ttm) REVERT: R 565 GLN cc_start: 0.1251 (pt0) cc_final: 0.0460 (tt0) REVERT: V 85 ASP cc_start: 0.1995 (OUTLIER) cc_final: 0.1688 (t0) REVERT: V 109 GLU cc_start: 0.4561 (mp0) cc_final: 0.3490 (mm-30) REVERT: V 140 GLU cc_start: 0.3794 (tt0) cc_final: 0.2680 (mm-30) REVERT: V 198 ARG cc_start: -0.0853 (ppt170) cc_final: -0.1717 (mtm110) REVERT: V 203 GLU cc_start: 0.4105 (OUTLIER) cc_final: 0.2205 (pm20) REVERT: V 205 MET cc_start: 0.3499 (mtt) cc_final: 0.3288 (mtt) REVERT: W 302 ASP cc_start: 0.2673 (p0) cc_final: 0.1436 (p0) REVERT: Z 290 ILE cc_start: -0.1054 (OUTLIER) cc_final: -0.1539 (mp) REVERT: Z 533 GLN cc_start: 0.1898 (pm20) cc_final: 0.1434 (tt0) outliers start: 157 outliers final: 94 residues processed: 592 average time/residue: 0.5505 time to fit residues: 553.1105 Evaluate side-chains 539 residues out of total 6485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 431 time to evaluate : 5.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 CYS Chi-restraints excluded: chain A residue 81 CYS Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 321 GLU Chi-restraints excluded: chain A residue 329 MET Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 555 LEU Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 605 THR Chi-restraints excluded: chain A residue 689 ILE Chi-restraints excluded: chain A residue 899 GLU Chi-restraints excluded: chain A residue 940 LYS Chi-restraints excluded: chain A residue 952 LEU Chi-restraints excluded: chain A residue 996 ILE Chi-restraints excluded: chain A residue 1007 ILE Chi-restraints excluded: chain A residue 1030 SER Chi-restraints excluded: chain A residue 1128 ILE Chi-restraints excluded: chain A residue 1175 ILE Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1190 GLN Chi-restraints excluded: chain A residue 1314 THR Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 291 ASP Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 354 SER Chi-restraints excluded: chain B residue 429 PHE Chi-restraints excluded: chain B residue 561 ILE Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain B residue 597 ILE Chi-restraints excluded: chain B residue 616 THR Chi-restraints excluded: chain B residue 647 GLU Chi-restraints excluded: chain B residue 649 ASN Chi-restraints excluded: chain B residue 738 THR Chi-restraints excluded: chain B residue 750 VAL Chi-restraints excluded: chain B residue 759 VAL Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 842 HIS Chi-restraints excluded: chain B residue 909 VAL Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 1148 LEU Chi-restraints excluded: chain B residue 1157 LEU Chi-restraints excluded: chain B residue 1174 VAL Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 108 ASN Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain E residue 120 ASP Chi-restraints excluded: chain E residue 168 ASN Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain F residue 123 LEU Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain H residue 7 GLU Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 34 SER Chi-restraints excluded: chain H residue 52 LEU Chi-restraints excluded: chain H residue 67 ASP Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 116 VAL Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 83 ASP Chi-restraints excluded: chain K residue 94 LEU Chi-restraints excluded: chain M residue 1375 ASP Chi-restraints excluded: chain M residue 1489 VAL Chi-restraints excluded: chain M residue 1490 THR Chi-restraints excluded: chain Q residue 94 VAL Chi-restraints excluded: chain Q residue 301 VAL Chi-restraints excluded: chain Q residue 692 VAL Chi-restraints excluded: chain Q residue 779 VAL Chi-restraints excluded: chain Q residue 875 LEU Chi-restraints excluded: chain R residue 389 ILE Chi-restraints excluded: chain U residue 452 LEU Chi-restraints excluded: chain U residue 459 VAL Chi-restraints excluded: chain V residue 85 ASP Chi-restraints excluded: chain V residue 94 ILE Chi-restraints excluded: chain V residue 127 VAL Chi-restraints excluded: chain V residue 203 GLU Chi-restraints excluded: chain W residue 26 THR Chi-restraints excluded: chain W residue 35 VAL Chi-restraints excluded: chain W residue 36 VAL Chi-restraints excluded: chain W residue 169 ASP Chi-restraints excluded: chain W residue 219 VAL Chi-restraints excluded: chain W residue 243 ASP Chi-restraints excluded: chain Y residue 84 VAL Chi-restraints excluded: chain Z residue 176 ASP Chi-restraints excluded: chain Z residue 216 VAL Chi-restraints excluded: chain Z residue 290 ILE Chi-restraints excluded: chain Z residue 393 LEU Chi-restraints excluded: chain Z residue 495 VAL Chi-restraints excluded: chain Z residue 547 VAL Chi-restraints excluded: chain Z residue 551 VAL Chi-restraints excluded: chain Z residue 567 VAL Chi-restraints excluded: chain Z residue 738 SER Chi-restraints excluded: chain Z residue 777 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 735 random chunks: chunk 685 optimal weight: 7.9990 chunk 80 optimal weight: 0.8980 chunk 405 optimal weight: 10.0000 chunk 519 optimal weight: 3.9990 chunk 402 optimal weight: 8.9990 chunk 598 optimal weight: 8.9990 chunk 397 optimal weight: 20.0000 chunk 708 optimal weight: 0.0570 chunk 443 optimal weight: 40.0000 chunk 431 optimal weight: 50.0000 chunk 327 optimal weight: 20.0000 overall best weight: 4.3904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 122 ASN A 152 ASN A 372 ASN A 441 GLN ** A 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 982 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1093 GLN B 111 ASN ** B 716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 941 GLN B1003 ASN ** B1040 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 89 ASN ** Q 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 609 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 714 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 187 GLN W 13 GLN ** W 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 519 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7083 moved from start: 0.4098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.092 58362 Z= 0.475 Angle : 0.631 11.737 78967 Z= 0.326 Chirality : 0.048 0.248 8353 Planarity : 0.005 0.088 10146 Dihedral : 12.470 172.936 9148 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.01 % Allowed : 6.68 % Favored : 93.31 % Rotamer: Outliers : 3.38 % Allowed : 19.38 % Favored : 77.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.65 % Cis-general : 0.07 % Twisted Proline : 0.32 % 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: -1.83 (0.10), residues: 7232 helix: -0.16 (0.11), residues: 2507 sheet: -1.80 (0.17), residues: 885 loop : -1.80 (0.10), residues: 3840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 479 HIS 0.011 0.001 HIS L 23 PHE 0.041 0.002 PHE Q 152 TYR 0.027 0.002 TYR H 97 ARG 0.009 0.001 ARG A 190 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14464 Ramachandran restraints generated. 7232 Oldfield, 0 Emsley, 7232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14464 Ramachandran restraints generated. 7232 Oldfield, 0 Emsley, 7232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 623 residues out of total 6485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 187 poor density : 436 time to evaluate : 5.046 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 283 ILE cc_start: 0.8301 (OUTLIER) cc_final: 0.7836 (mp) REVERT: A 343 LEU cc_start: 0.8834 (OUTLIER) cc_final: 0.8470 (pp) REVERT: A 1190 GLN cc_start: 0.6868 (OUTLIER) cc_final: 0.6442 (mt0) REVERT: B 36 GLU cc_start: 0.7468 (OUTLIER) cc_final: 0.7077 (tt0) REVERT: B 305 LEU cc_start: 0.9005 (OUTLIER) cc_final: 0.8642 (mp) REVERT: B 561 ILE cc_start: 0.9178 (OUTLIER) cc_final: 0.8941 (mt) REVERT: B 597 ILE cc_start: 0.9308 (OUTLIER) cc_final: 0.9052 (mm) REVERT: B 1148 LEU cc_start: 0.8903 (OUTLIER) cc_final: 0.8651 (tp) REVERT: C 161 LEU cc_start: 0.9189 (OUTLIER) cc_final: 0.8942 (pp) REVERT: C 211 LEU cc_start: 0.8837 (OUTLIER) cc_final: 0.8378 (mp) REVERT: D 45 LYS cc_start: 0.6286 (tptp) cc_final: 0.5968 (tptp) REVERT: E 141 GLU cc_start: 0.7764 (OUTLIER) cc_final: 0.7319 (mp0) REVERT: H 7 GLU cc_start: 0.7201 (OUTLIER) cc_final: 0.6739 (tp30) REVERT: M 1346 MET cc_start: 0.3101 (mmm) cc_final: 0.0739 (tmm) REVERT: M 1347 MET cc_start: -0.2868 (ptt) cc_final: -0.4129 (mmm) REVERT: M 1372 LYS cc_start: 0.1366 (mmtm) cc_final: 0.0986 (mmtt) REVERT: M 1419 MET cc_start: 0.1957 (ttp) cc_final: 0.1659 (ptp) REVERT: Q 206 HIS cc_start: 0.1281 (m170) cc_final: -0.0099 (t-90) REVERT: Q 540 MET cc_start: 0.3895 (ptp) cc_final: 0.3349 (ptm) REVERT: Q 580 GLU cc_start: 0.3305 (pp20) cc_final: 0.2394 (mt-10) REVERT: Q 647 LEU cc_start: 0.5808 (OUTLIER) cc_final: 0.5471 (mt) REVERT: Q 779 VAL cc_start: 0.4011 (OUTLIER) cc_final: 0.3376 (p) REVERT: Q 890 MET cc_start: 0.4695 (tpp) cc_final: 0.4452 (ptm) REVERT: R 565 GLN cc_start: 0.1338 (pt0) cc_final: 0.0544 (tt0) REVERT: V 85 ASP cc_start: 0.2125 (OUTLIER) cc_final: 0.1653 (t0) REVERT: V 109 GLU cc_start: 0.4754 (mp0) cc_final: 0.3538 (mm-30) REVERT: V 140 GLU cc_start: 0.3940 (tt0) cc_final: 0.2753 (mm-30) REVERT: V 188 LYS cc_start: 0.3209 (mtpt) cc_final: 0.2890 (mmtt) REVERT: V 198 ARG cc_start: -0.0492 (ppt170) cc_final: -0.1522 (mtm110) REVERT: V 203 GLU cc_start: 0.4460 (OUTLIER) cc_final: 0.2035 (pm20) REVERT: W 302 ASP cc_start: 0.2587 (p0) cc_final: 0.1460 (p0) REVERT: Y 42 MET cc_start: 0.2833 (ptm) cc_final: 0.2291 (ptm) REVERT: Z 197 MET cc_start: 0.4448 (mtp) cc_final: 0.4229 (mtp) REVERT: Z 307 MET cc_start: 0.3163 (tmm) cc_final: 0.2772 (ttt) REVERT: Z 533 GLN cc_start: 0.1887 (pm20) cc_final: 0.1286 (tt0) REVERT: Z 581 ASN cc_start: 0.0223 (OUTLIER) cc_final: -0.0158 (m-40) outliers start: 187 outliers final: 131 residues processed: 599 average time/residue: 0.5488 time to fit residues: 555.3376 Evaluate side-chains 561 residues out of total 6485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 413 time to evaluate : 4.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 CYS Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 88 ILE Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 197 GLU Chi-restraints excluded: chain A residue 238 MET Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 329 MET Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 605 THR Chi-restraints excluded: chain A residue 689 ILE Chi-restraints excluded: chain A residue 886 VAL Chi-restraints excluded: chain A residue 899 GLU Chi-restraints excluded: chain A residue 940 LYS Chi-restraints excluded: chain A residue 952 LEU Chi-restraints excluded: chain A residue 996 ILE Chi-restraints excluded: chain A residue 1007 ILE Chi-restraints excluded: chain A residue 1030 SER Chi-restraints excluded: chain A residue 1175 ILE Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1190 GLN Chi-restraints excluded: chain A residue 1314 THR Chi-restraints excluded: chain A residue 1358 THR Chi-restraints excluded: chain A residue 1385 VAL Chi-restraints excluded: chain A residue 1458 ILE Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 36 GLU Chi-restraints excluded: chain B residue 65 ILE Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 323 SER Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 354 SER Chi-restraints excluded: chain B residue 359 THR Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 429 PHE Chi-restraints excluded: chain B residue 463 ARG Chi-restraints excluded: chain B residue 561 ILE Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain B residue 597 ILE Chi-restraints excluded: chain B residue 616 THR Chi-restraints excluded: chain B residue 647 GLU Chi-restraints excluded: chain B residue 649 ASN Chi-restraints excluded: chain B residue 659 SER Chi-restraints excluded: chain B residue 738 THR Chi-restraints excluded: chain B residue 750 VAL Chi-restraints excluded: chain B residue 759 VAL Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 836 THR Chi-restraints excluded: chain B residue 842 HIS Chi-restraints excluded: chain B residue 844 ILE Chi-restraints excluded: chain B residue 894 THR Chi-restraints excluded: chain B residue 909 VAL Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 958 CYS Chi-restraints excluded: chain B residue 1148 LEU Chi-restraints excluded: chain B residue 1149 VAL Chi-restraints excluded: chain B residue 1174 VAL Chi-restraints excluded: chain C residue 5 ASN Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 27 ASP Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 108 ASN Chi-restraints excluded: chain C residue 132 SER Chi-restraints excluded: chain C residue 147 ASP Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 120 ASP Chi-restraints excluded: chain E residue 141 GLU Chi-restraints excluded: chain E residue 159 LEU Chi-restraints excluded: chain E residue 168 ASN Chi-restraints excluded: chain F residue 105 ILE Chi-restraints excluded: chain F residue 123 LEU Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 21 ASN Chi-restraints excluded: chain G residue 38 CYS Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain H residue 7 GLU Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 52 LEU Chi-restraints excluded: chain H residue 67 ASP Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 116 VAL Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain H residue 147 LYS Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 83 ASP Chi-restraints excluded: chain I residue 101 SER Chi-restraints excluded: chain K residue 94 LEU Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain M residue 1362 LYS Chi-restraints excluded: chain M residue 1489 VAL Chi-restraints excluded: chain M residue 1490 THR Chi-restraints excluded: chain Q residue 94 VAL Chi-restraints excluded: chain Q residue 301 VAL Chi-restraints excluded: chain Q residue 511 CYS Chi-restraints excluded: chain Q residue 647 LEU Chi-restraints excluded: chain Q residue 669 VAL Chi-restraints excluded: chain Q residue 692 VAL Chi-restraints excluded: chain Q residue 779 VAL Chi-restraints excluded: chain Q residue 875 LEU Chi-restraints excluded: chain R residue 389 ILE Chi-restraints excluded: chain R residue 563 ILE Chi-restraints excluded: chain U residue 382 LEU Chi-restraints excluded: chain U residue 452 LEU Chi-restraints excluded: chain U residue 459 VAL Chi-restraints excluded: chain V residue 64 THR Chi-restraints excluded: chain V residue 85 ASP Chi-restraints excluded: chain V residue 94 ILE Chi-restraints excluded: chain V residue 127 VAL Chi-restraints excluded: chain V residue 202 VAL Chi-restraints excluded: chain V residue 203 GLU Chi-restraints excluded: chain W residue 26 THR Chi-restraints excluded: chain W residue 35 VAL Chi-restraints excluded: chain W residue 36 VAL Chi-restraints excluded: chain W residue 42 ASP Chi-restraints excluded: chain W residue 165 SER Chi-restraints excluded: chain W residue 169 ASP Chi-restraints excluded: chain W residue 243 ASP Chi-restraints excluded: chain W residue 250 SER Chi-restraints excluded: chain Y residue 84 VAL Chi-restraints excluded: chain Z residue 206 THR Chi-restraints excluded: chain Z residue 216 VAL Chi-restraints excluded: chain Z residue 221 VAL Chi-restraints excluded: chain Z residue 251 ASN Chi-restraints excluded: chain Z residue 393 LEU Chi-restraints excluded: chain Z residue 451 MET Chi-restraints excluded: chain Z residue 551 VAL Chi-restraints excluded: chain Z residue 567 VAL Chi-restraints excluded: chain Z residue 581 ASN Chi-restraints excluded: chain Z residue 738 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 735 random chunks: chunk 438 optimal weight: 0.0270 chunk 282 optimal weight: 8.9990 chunk 423 optimal weight: 50.0000 chunk 213 optimal weight: 0.9990 chunk 139 optimal weight: 5.9990 chunk 137 optimal weight: 0.9980 chunk 450 optimal weight: 20.0000 chunk 482 optimal weight: 20.0000 chunk 350 optimal weight: 0.0980 chunk 66 optimal weight: 0.8980 chunk 556 optimal weight: 4.9990 overall best weight: 0.6040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 372 ASN A 441 GLN A 982 ASN A1093 GLN A1194 ASN B 941 GLN ** D 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 89 ASN Q 289 GLN ** Q 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 319 GLN ** Q 714 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 95 GLN ** Z 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 519 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6978 moved from start: 0.4329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 58362 Z= 0.151 Angle : 0.492 10.226 78967 Z= 0.256 Chirality : 0.041 0.285 8353 Planarity : 0.003 0.054 10146 Dihedral : 12.261 171.716 9148 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.01 % Allowed : 4.63 % Favored : 95.35 % Rotamer: Outliers : 2.40 % Allowed : 20.64 % Favored : 76.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.65 % Cis-general : 0.07 % Twisted Proline : 0.32 % 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: -1.47 (0.10), residues: 7232 helix: 0.19 (0.11), residues: 2517 sheet: -1.49 (0.17), residues: 841 loop : -1.68 (0.10), residues: 3874 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 176 HIS 0.010 0.001 HIS W 268 PHE 0.037 0.001 PHE Q 152 TYR 0.022 0.001 TYR D 67 ARG 0.006 0.000 ARG A 16 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14464 Ramachandran restraints generated. 7232 Oldfield, 0 Emsley, 7232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14464 Ramachandran restraints generated. 7232 Oldfield, 0 Emsley, 7232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 583 residues out of total 6485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 450 time to evaluate : 5.544 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 266 MET cc_start: 0.6387 (mmm) cc_final: 0.5913 (mmm) REVERT: A 283 ILE cc_start: 0.8099 (OUTLIER) cc_final: 0.7698 (mp) REVERT: A 343 LEU cc_start: 0.8763 (OUTLIER) cc_final: 0.8473 (pp) REVERT: A 1190 GLN cc_start: 0.6868 (OUTLIER) cc_final: 0.6177 (mp10) REVERT: A 1262 MET cc_start: 0.5479 (tpt) cc_final: 0.4648 (tpt) REVERT: A 1412 MET cc_start: 0.8132 (tmm) cc_final: 0.7753 (ttt) REVERT: B 156 LEU cc_start: 0.8976 (OUTLIER) cc_final: 0.8692 (mp) REVERT: B 235 ILE cc_start: 0.8311 (mm) cc_final: 0.8059 (mm) REVERT: B 305 LEU cc_start: 0.8839 (OUTLIER) cc_final: 0.8555 (mp) REVERT: B 561 ILE cc_start: 0.9194 (OUTLIER) cc_final: 0.8985 (mt) REVERT: B 597 ILE cc_start: 0.9197 (OUTLIER) cc_final: 0.8959 (mm) REVERT: B 638 ARG cc_start: 0.8130 (mtm110) cc_final: 0.7841 (ptp90) REVERT: B 1081 ASP cc_start: 0.8258 (t0) cc_final: 0.7654 (t0) REVERT: C 161 LEU cc_start: 0.9125 (OUTLIER) cc_final: 0.8879 (pp) REVERT: D 45 LYS cc_start: 0.6250 (tptp) cc_final: 0.5956 (tttm) REVERT: H 7 GLU cc_start: 0.7012 (OUTLIER) cc_final: 0.6619 (tp30) REVERT: L 16 ILE cc_start: 0.8958 (tt) cc_final: 0.8751 (tt) REVERT: M 1346 MET cc_start: 0.2898 (mmm) cc_final: 0.0547 (tmm) REVERT: M 1347 MET cc_start: -0.2944 (ptt) cc_final: -0.4100 (mmm) REVERT: M 1372 LYS cc_start: 0.1168 (mmtm) cc_final: 0.0782 (mmtt) REVERT: M 1375 ASP cc_start: -0.0141 (OUTLIER) cc_final: -0.0416 (p0) REVERT: Q 206 HIS cc_start: 0.0768 (m170) cc_final: -0.0403 (t-90) REVERT: Q 375 TYR cc_start: 0.3814 (m-80) cc_final: 0.3175 (p90) REVERT: Q 392 GLU cc_start: 0.0144 (pm20) cc_final: -0.0346 (tp30) REVERT: Q 580 GLU cc_start: 0.3258 (pp20) cc_final: 0.2449 (mt-10) REVERT: Q 779 VAL cc_start: 0.4236 (OUTLIER) cc_final: 0.3649 (p) REVERT: R 565 GLN cc_start: 0.1165 (pt0) cc_final: 0.0489 (tt0) REVERT: R 596 ARG cc_start: 0.3340 (mmm160) cc_final: 0.2004 (mmp-170) REVERT: V 109 GLU cc_start: 0.4775 (mp0) cc_final: 0.3576 (mm-30) REVERT: V 122 GLN cc_start: 0.6137 (tm-30) cc_final: 0.5094 (mp10) REVERT: V 140 GLU cc_start: 0.3837 (tt0) cc_final: 0.2665 (mm-30) REVERT: V 198 ARG cc_start: -0.0338 (ppt170) cc_final: -0.1348 (mtm110) REVERT: W 302 ASP cc_start: 0.2400 (p0) cc_final: 0.1342 (p0) REVERT: Z 533 GLN cc_start: 0.2103 (pm20) cc_final: 0.1460 (tt0) outliers start: 133 outliers final: 103 residues processed: 567 average time/residue: 0.5588 time to fit residues: 534.8582 Evaluate side-chains 545 residues out of total 6485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 431 time to evaluate : 5.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 CYS Chi-restraints excluded: chain A residue 81 CYS Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 238 MET Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 321 GLU Chi-restraints excluded: chain A residue 329 MET Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 555 LEU Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 605 THR Chi-restraints excluded: chain A residue 689 ILE Chi-restraints excluded: chain A residue 940 LYS Chi-restraints excluded: chain A residue 996 ILE Chi-restraints excluded: chain A residue 1030 SER Chi-restraints excluded: chain A residue 1175 ILE Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1190 GLN Chi-restraints excluded: chain A residue 1194 ASN Chi-restraints excluded: chain A residue 1314 THR Chi-restraints excluded: chain A residue 1358 THR Chi-restraints excluded: chain A residue 1458 ILE Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 65 ILE Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 291 ASP Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 429 PHE Chi-restraints excluded: chain B residue 463 ARG Chi-restraints excluded: chain B residue 561 ILE Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain B residue 597 ILE Chi-restraints excluded: chain B residue 616 THR Chi-restraints excluded: chain B residue 647 GLU Chi-restraints excluded: chain B residue 649 ASN Chi-restraints excluded: chain B residue 659 SER Chi-restraints excluded: chain B residue 738 THR Chi-restraints excluded: chain B residue 750 VAL Chi-restraints excluded: chain B residue 759 VAL Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 842 HIS Chi-restraints excluded: chain B residue 903 ILE Chi-restraints excluded: chain B residue 913 GLN Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 1149 VAL Chi-restraints excluded: chain B residue 1157 LEU Chi-restraints excluded: chain B residue 1174 VAL Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 132 SER Chi-restraints excluded: chain C residue 147 ASP Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 120 ASP Chi-restraints excluded: chain E residue 159 LEU Chi-restraints excluded: chain E residue 168 ASN Chi-restraints excluded: chain F residue 123 LEU Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 21 ASN Chi-restraints excluded: chain G residue 38 CYS Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain H residue 7 GLU Chi-restraints excluded: chain H residue 34 SER Chi-restraints excluded: chain H residue 67 ASP Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 116 VAL Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 83 ASP Chi-restraints excluded: chain K residue 94 LEU Chi-restraints excluded: chain M residue 1362 LYS Chi-restraints excluded: chain M residue 1375 ASP Chi-restraints excluded: chain M residue 1489 VAL Chi-restraints excluded: chain M residue 1490 THR Chi-restraints excluded: chain Q residue 301 VAL Chi-restraints excluded: chain Q residue 351 TYR Chi-restraints excluded: chain Q residue 669 VAL Chi-restraints excluded: chain Q residue 692 VAL Chi-restraints excluded: chain Q residue 779 VAL Chi-restraints excluded: chain Q residue 875 LEU Chi-restraints excluded: chain R residue 389 ILE Chi-restraints excluded: chain R residue 563 ILE Chi-restraints excluded: chain U residue 382 LEU Chi-restraints excluded: chain U residue 452 LEU Chi-restraints excluded: chain U residue 459 VAL Chi-restraints excluded: chain V residue 94 ILE Chi-restraints excluded: chain V residue 127 VAL Chi-restraints excluded: chain W residue 26 THR Chi-restraints excluded: chain W residue 35 VAL Chi-restraints excluded: chain W residue 36 VAL Chi-restraints excluded: chain W residue 42 ASP Chi-restraints excluded: chain W residue 169 ASP Chi-restraints excluded: chain W residue 219 VAL Chi-restraints excluded: chain W residue 243 ASP Chi-restraints excluded: chain W residue 250 SER Chi-restraints excluded: chain Y residue 84 VAL Chi-restraints excluded: chain Z residue 176 ASP Chi-restraints excluded: chain Z residue 393 LEU Chi-restraints excluded: chain Z residue 495 VAL Chi-restraints excluded: chain Z residue 567 VAL Chi-restraints excluded: chain Z residue 738 SER Chi-restraints excluded: chain Z residue 777 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 735 random chunks: chunk 644 optimal weight: 6.9990 chunk 678 optimal weight: 30.0000 chunk 619 optimal weight: 9.9990 chunk 660 optimal weight: 0.9980 chunk 397 optimal weight: 30.0000 chunk 287 optimal weight: 30.0000 chunk 518 optimal weight: 20.0000 chunk 202 optimal weight: 3.9990 chunk 596 optimal weight: 7.9990 chunk 624 optimal weight: 0.0270 chunk 657 optimal weight: 6.9990 overall best weight: 3.8044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 441 GLN ** A 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1093 GLN A1194 ASN ** B 716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 941 GLN ** B1040 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 128 GLN ** E 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 89 ASN ** Q 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 609 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 714 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 745 HIS ** R 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 27 ASN ** Z 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 519 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7082 moved from start: 0.4405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.086 58362 Z= 0.438 Angle : 0.623 9.576 78967 Z= 0.320 Chirality : 0.047 0.234 8353 Planarity : 0.005 0.077 10146 Dihedral : 12.397 173.249 9143 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.01 % Allowed : 6.35 % Favored : 93.64 % Rotamer: Outliers : 2.80 % Allowed : 20.46 % Favored : 76.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.65 % Cis-general : 0.07 % Twisted Proline : 0.32 % 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: -1.60 (0.10), residues: 7232 helix: 0.05 (0.11), residues: 2503 sheet: -1.61 (0.17), residues: 879 loop : -1.69 (0.10), residues: 3850 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 479 HIS 0.014 0.001 HIS L 23 PHE 0.036 0.002 PHE Q 152 TYR 0.024 0.002 TYR H 97 ARG 0.007 0.001 ARG J 47 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14464 Ramachandran restraints generated. 7232 Oldfield, 0 Emsley, 7232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14464 Ramachandran restraints generated. 7232 Oldfield, 0 Emsley, 7232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 589 residues out of total 6485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 155 poor density : 434 time to evaluate : 5.055 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: A 266 MET cc_start: 0.6283 (mmm) cc_final: 0.5889 (mmm) REVERT: A 283 ILE cc_start: 0.8331 (OUTLIER) cc_final: 0.7893 (mp) REVERT: A 343 LEU cc_start: 0.8868 (OUTLIER) cc_final: 0.8496 (pp) REVERT: A 1190 GLN cc_start: 0.6894 (OUTLIER) cc_final: 0.6149 (mp10) REVERT: A 1440 MET cc_start: 0.8614 (mmt) cc_final: 0.8195 (mmt) REVERT: B 156 LEU cc_start: 0.9018 (OUTLIER) cc_final: 0.8753 (mp) REVERT: B 305 LEU cc_start: 0.8999 (OUTLIER) cc_final: 0.8618 (mp) REVERT: B 347 MET cc_start: 0.8584 (ppp) cc_final: 0.8220 (ptm) REVERT: B 561 ILE cc_start: 0.9218 (OUTLIER) cc_final: 0.8994 (mt) REVERT: B 597 ILE cc_start: 0.9315 (OUTLIER) cc_final: 0.9033 (mm) REVERT: B 733 MET cc_start: 0.8507 (ttm) cc_final: 0.8267 (mtt) REVERT: C 161 LEU cc_start: 0.9179 (OUTLIER) cc_final: 0.8934 (pp) REVERT: C 211 LEU cc_start: 0.8844 (OUTLIER) cc_final: 0.8386 (mp) REVERT: E 141 GLU cc_start: 0.7744 (OUTLIER) cc_final: 0.7303 (mp0) REVERT: H 7 GLU cc_start: 0.7209 (OUTLIER) cc_final: 0.6727 (tp30) REVERT: K 14 GLU cc_start: 0.7274 (mm-30) cc_final: 0.7030 (mm-30) REVERT: M 1346 MET cc_start: 0.2961 (mmm) cc_final: 0.0713 (tmm) REVERT: Q 206 HIS cc_start: 0.1611 (m170) cc_final: 0.0165 (t-90) REVERT: Q 289 GLN cc_start: -0.2414 (OUTLIER) cc_final: -0.3663 (tt0) REVERT: Q 580 GLU cc_start: 0.3202 (pp20) cc_final: 0.2349 (mt-10) REVERT: Q 779 VAL cc_start: 0.4212 (OUTLIER) cc_final: 0.3606 (p) REVERT: R 565 GLN cc_start: 0.1344 (pt0) cc_final: 0.0629 (tt0) REVERT: V 109 GLU cc_start: 0.4727 (mp0) cc_final: 0.3498 (mm-30) REVERT: V 140 GLU cc_start: 0.3882 (tt0) cc_final: 0.2739 (mm-30) REVERT: V 188 LYS cc_start: 0.3438 (mtpt) cc_final: 0.2974 (mmtt) REVERT: V 198 ARG cc_start: -0.0550 (ppt170) cc_final: -0.1100 (mtm110) REVERT: V 203 GLU cc_start: 0.4586 (OUTLIER) cc_final: 0.2117 (pm20) REVERT: Z 533 GLN cc_start: 0.1924 (pm20) cc_final: 0.1327 (tt0) outliers start: 155 outliers final: 120 residues processed: 565 average time/residue: 0.5535 time to fit residues: 528.5553 Evaluate side-chains 549 residues out of total 6485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 415 time to evaluate : 4.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 CYS Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 81 CYS Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 238 MET Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 321 GLU Chi-restraints excluded: chain A residue 329 MET Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 555 LEU Chi-restraints excluded: chain A residue 605 THR Chi-restraints excluded: chain A residue 689 ILE Chi-restraints excluded: chain A residue 940 LYS Chi-restraints excluded: chain A residue 996 ILE Chi-restraints excluded: chain A residue 1007 ILE Chi-restraints excluded: chain A residue 1030 SER Chi-restraints excluded: chain A residue 1175 ILE Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1190 GLN Chi-restraints excluded: chain A residue 1314 THR Chi-restraints excluded: chain A residue 1358 THR Chi-restraints excluded: chain A residue 1458 ILE Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 65 ILE Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 429 PHE Chi-restraints excluded: chain B residue 463 ARG Chi-restraints excluded: chain B residue 561 ILE Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain B residue 597 ILE Chi-restraints excluded: chain B residue 616 THR Chi-restraints excluded: chain B residue 647 GLU Chi-restraints excluded: chain B residue 649 ASN Chi-restraints excluded: chain B residue 659 SER Chi-restraints excluded: chain B residue 738 THR Chi-restraints excluded: chain B residue 750 VAL Chi-restraints excluded: chain B residue 759 VAL Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 836 THR Chi-restraints excluded: chain B residue 842 HIS Chi-restraints excluded: chain B residue 844 ILE Chi-restraints excluded: chain B residue 894 THR Chi-restraints excluded: chain B residue 909 VAL Chi-restraints excluded: chain B residue 913 GLN Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 1149 VAL Chi-restraints excluded: chain B residue 1157 LEU Chi-restraints excluded: chain B residue 1174 VAL Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 132 SER Chi-restraints excluded: chain C residue 147 ASP Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 120 ASP Chi-restraints excluded: chain E residue 141 GLU Chi-restraints excluded: chain E residue 159 LEU Chi-restraints excluded: chain E residue 168 ASN Chi-restraints excluded: chain F residue 105 ILE Chi-restraints excluded: chain F residue 123 LEU Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 21 ASN Chi-restraints excluded: chain G residue 38 CYS Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain H residue 7 GLU Chi-restraints excluded: chain H residue 34 SER Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 52 LEU Chi-restraints excluded: chain H residue 67 ASP Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 116 VAL Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain H residue 147 LYS Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 83 ASP Chi-restraints excluded: chain K residue 94 LEU Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain M residue 1362 LYS Chi-restraints excluded: chain M residue 1489 VAL Chi-restraints excluded: chain M residue 1490 THR Chi-restraints excluded: chain Q residue 289 GLN Chi-restraints excluded: chain Q residue 301 VAL Chi-restraints excluded: chain Q residue 511 CYS Chi-restraints excluded: chain Q residue 669 VAL Chi-restraints excluded: chain Q residue 692 VAL Chi-restraints excluded: chain Q residue 779 VAL Chi-restraints excluded: chain Q residue 875 LEU Chi-restraints excluded: chain R residue 389 ILE Chi-restraints excluded: chain R residue 563 ILE Chi-restraints excluded: chain U residue 382 LEU Chi-restraints excluded: chain U residue 452 LEU Chi-restraints excluded: chain U residue 459 VAL Chi-restraints excluded: chain V residue 64 THR Chi-restraints excluded: chain V residue 94 ILE Chi-restraints excluded: chain V residue 127 VAL Chi-restraints excluded: chain V residue 137 ILE Chi-restraints excluded: chain V residue 203 GLU Chi-restraints excluded: chain W residue 26 THR Chi-restraints excluded: chain W residue 35 VAL Chi-restraints excluded: chain W residue 36 VAL Chi-restraints excluded: chain W residue 42 ASP Chi-restraints excluded: chain W residue 165 SER Chi-restraints excluded: chain W residue 169 ASP Chi-restraints excluded: chain W residue 219 VAL Chi-restraints excluded: chain W residue 243 ASP Chi-restraints excluded: chain W residue 250 SER Chi-restraints excluded: chain Y residue 84 VAL Chi-restraints excluded: chain Y residue 115 ILE Chi-restraints excluded: chain Z residue 176 ASP Chi-restraints excluded: chain Z residue 221 VAL Chi-restraints excluded: chain Z residue 251 ASN Chi-restraints excluded: chain Z residue 393 LEU Chi-restraints excluded: chain Z residue 551 VAL Chi-restraints excluded: chain Z residue 567 VAL Chi-restraints excluded: chain Z residue 738 SER Chi-restraints excluded: chain Z residue 777 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 735 random chunks: chunk 433 optimal weight: 30.0000 chunk 698 optimal weight: 20.0000 chunk 426 optimal weight: 10.0000 chunk 331 optimal weight: 30.0000 chunk 485 optimal weight: 9.9990 chunk 732 optimal weight: 0.6980 chunk 673 optimal weight: 0.0770 chunk 583 optimal weight: 8.9990 chunk 60 optimal weight: 1.9990 chunk 450 optimal weight: 8.9990 chunk 357 optimal weight: 0.0470 overall best weight: 2.3640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 441 GLN ** A 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1093 GLN A1422 GLN B 716 HIS C 60 HIS ** E 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 89 ASN ** Q 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 305 GLN ** Q 609 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 714 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 745 HIS ** R 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 567 ASN ** R 585 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 519 GLN Z 607 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7048 moved from start: 0.4552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 58362 Z= 0.288 Angle : 0.550 9.435 78967 Z= 0.284 Chirality : 0.044 0.230 8353 Planarity : 0.004 0.055 10146 Dihedral : 12.355 172.532 9143 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.01 % Allowed : 5.45 % Favored : 94.54 % Rotamer: Outliers : 2.67 % Allowed : 20.53 % Favored : 76.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.65 % Cis-general : 0.07 % Twisted Proline : 0.32 % 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: -1.48 (0.10), residues: 7232 helix: 0.16 (0.11), residues: 2498 sheet: -1.58 (0.17), residues: 867 loop : -1.63 (0.10), residues: 3867 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 479 HIS 0.012 0.001 HIS W 268 PHE 0.036 0.001 PHE Q 152 TYR 0.018 0.001 TYR H 115 ARG 0.008 0.000 ARG E 93 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14464 Ramachandran restraints generated. 7232 Oldfield, 0 Emsley, 7232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14464 Ramachandran restraints generated. 7232 Oldfield, 0 Emsley, 7232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 582 residues out of total 6485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 434 time to evaluate : 5.053 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: A 266 MET cc_start: 0.6277 (mmm) cc_final: 0.5928 (mmm) REVERT: A 283 ILE cc_start: 0.8224 (OUTLIER) cc_final: 0.7815 (mp) REVERT: A 343 LEU cc_start: 0.8831 (OUTLIER) cc_final: 0.8504 (pp) REVERT: A 1262 MET cc_start: 0.5577 (tpt) cc_final: 0.4697 (tpt) REVERT: B 156 LEU cc_start: 0.8996 (OUTLIER) cc_final: 0.8716 (mp) REVERT: B 305 LEU cc_start: 0.8907 (OUTLIER) cc_final: 0.8578 (mp) REVERT: B 561 ILE cc_start: 0.9224 (OUTLIER) cc_final: 0.9016 (mt) REVERT: B 597 ILE cc_start: 0.9290 (OUTLIER) cc_final: 0.9022 (mm) REVERT: B 733 MET cc_start: 0.8378 (ttm) cc_final: 0.8067 (mtt) REVERT: B 1081 ASP cc_start: 0.8295 (t0) cc_final: 0.7648 (t0) REVERT: C 161 LEU cc_start: 0.9129 (OUTLIER) cc_final: 0.8889 (pp) REVERT: D 45 LYS cc_start: 0.6181 (tptp) cc_final: 0.5970 (tttm) REVERT: E 141 GLU cc_start: 0.7707 (OUTLIER) cc_final: 0.7256 (mp0) REVERT: H 7 GLU cc_start: 0.7149 (OUTLIER) cc_final: 0.6722 (tp30) REVERT: M 1346 MET cc_start: 0.2980 (mmm) cc_final: 0.0703 (tmm) REVERT: Q 206 HIS cc_start: 0.1763 (m170) cc_final: 0.0303 (t-90) REVERT: Q 580 GLU cc_start: 0.3085 (pp20) cc_final: 0.2236 (mt-10) REVERT: Q 647 LEU cc_start: 0.5815 (OUTLIER) cc_final: 0.5478 (mt) REVERT: Q 779 VAL cc_start: 0.4380 (OUTLIER) cc_final: 0.3785 (p) REVERT: R 565 GLN cc_start: 0.1266 (pt0) cc_final: 0.0602 (tt0) REVERT: V 85 ASP cc_start: 0.1978 (OUTLIER) cc_final: 0.1526 (t0) REVERT: V 109 GLU cc_start: 0.4773 (mp0) cc_final: 0.3516 (mm-30) REVERT: V 126 LYS cc_start: 0.5626 (mtpt) cc_final: 0.5176 (mmtt) REVERT: V 140 GLU cc_start: 0.3942 (tt0) cc_final: 0.2773 (mm-30) REVERT: V 188 LYS cc_start: 0.3312 (mtpt) cc_final: 0.2924 (mmtt) REVERT: V 198 ARG cc_start: -0.0280 (ppt170) cc_final: -0.0942 (mtm110) REVERT: V 203 GLU cc_start: 0.4586 (OUTLIER) cc_final: 0.1995 (pm20) REVERT: W 302 ASP cc_start: 0.3108 (p0) cc_final: 0.1673 (p0) REVERT: Z 533 GLN cc_start: 0.2393 (pm20) cc_final: 0.1579 (tt0) outliers start: 148 outliers final: 124 residues processed: 558 average time/residue: 0.5708 time to fit residues: 537.8989 Evaluate side-chains 557 residues out of total 6485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 420 time to evaluate : 5.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 CYS Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 81 CYS Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 238 MET Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 321 GLU Chi-restraints excluded: chain A residue 329 MET Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 555 LEU Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 605 THR Chi-restraints excluded: chain A residue 689 ILE Chi-restraints excluded: chain A residue 940 LYS Chi-restraints excluded: chain A residue 942 VAL Chi-restraints excluded: chain A residue 996 ILE Chi-restraints excluded: chain A residue 1007 ILE Chi-restraints excluded: chain A residue 1030 SER Chi-restraints excluded: chain A residue 1128 ILE Chi-restraints excluded: chain A residue 1175 ILE Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1247 PHE Chi-restraints excluded: chain A residue 1314 THR Chi-restraints excluded: chain A residue 1358 THR Chi-restraints excluded: chain A residue 1458 ILE Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 65 ILE Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 429 PHE Chi-restraints excluded: chain B residue 463 ARG Chi-restraints excluded: chain B residue 561 ILE Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain B residue 597 ILE Chi-restraints excluded: chain B residue 616 THR Chi-restraints excluded: chain B residue 647 GLU Chi-restraints excluded: chain B residue 649 ASN Chi-restraints excluded: chain B residue 659 SER Chi-restraints excluded: chain B residue 678 THR Chi-restraints excluded: chain B residue 710 ILE Chi-restraints excluded: chain B residue 738 THR Chi-restraints excluded: chain B residue 750 VAL Chi-restraints excluded: chain B residue 759 VAL Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 836 THR Chi-restraints excluded: chain B residue 842 HIS Chi-restraints excluded: chain B residue 894 THR Chi-restraints excluded: chain B residue 913 GLN Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 1149 VAL Chi-restraints excluded: chain B residue 1157 LEU Chi-restraints excluded: chain B residue 1174 VAL Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 132 SER Chi-restraints excluded: chain C residue 147 ASP Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 120 ASP Chi-restraints excluded: chain E residue 141 GLU Chi-restraints excluded: chain E residue 159 LEU Chi-restraints excluded: chain E residue 168 ASN Chi-restraints excluded: chain F residue 105 ILE Chi-restraints excluded: chain F residue 123 LEU Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 21 ASN Chi-restraints excluded: chain G residue 38 CYS Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain H residue 7 GLU Chi-restraints excluded: chain H residue 34 SER Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 52 LEU Chi-restraints excluded: chain H residue 67 ASP Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 116 VAL Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain H residue 147 LYS Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 83 ASP Chi-restraints excluded: chain K residue 94 LEU Chi-restraints excluded: chain M residue 1362 LYS Chi-restraints excluded: chain M residue 1489 VAL Chi-restraints excluded: chain M residue 1490 THR Chi-restraints excluded: chain Q residue 301 VAL Chi-restraints excluded: chain Q residue 511 CYS Chi-restraints excluded: chain Q residue 647 LEU Chi-restraints excluded: chain Q residue 669 VAL Chi-restraints excluded: chain Q residue 692 VAL Chi-restraints excluded: chain Q residue 779 VAL Chi-restraints excluded: chain Q residue 875 LEU Chi-restraints excluded: chain R residue 389 ILE Chi-restraints excluded: chain R residue 563 ILE Chi-restraints excluded: chain U residue 382 LEU Chi-restraints excluded: chain U residue 452 LEU Chi-restraints excluded: chain U residue 459 VAL Chi-restraints excluded: chain V residue 64 THR Chi-restraints excluded: chain V residue 85 ASP Chi-restraints excluded: chain V residue 94 ILE Chi-restraints excluded: chain V residue 127 VAL Chi-restraints excluded: chain V residue 203 GLU Chi-restraints excluded: chain W residue 26 THR Chi-restraints excluded: chain W residue 35 VAL Chi-restraints excluded: chain W residue 36 VAL Chi-restraints excluded: chain W residue 42 ASP Chi-restraints excluded: chain W residue 107 VAL Chi-restraints excluded: chain W residue 165 SER Chi-restraints excluded: chain W residue 169 ASP Chi-restraints excluded: chain W residue 219 VAL Chi-restraints excluded: chain W residue 243 ASP Chi-restraints excluded: chain W residue 250 SER Chi-restraints excluded: chain Y residue 84 VAL Chi-restraints excluded: chain Y residue 115 ILE Chi-restraints excluded: chain Z residue 176 ASP Chi-restraints excluded: chain Z residue 216 VAL Chi-restraints excluded: chain Z residue 221 VAL Chi-restraints excluded: chain Z residue 251 ASN Chi-restraints excluded: chain Z residue 393 LEU Chi-restraints excluded: chain Z residue 551 VAL Chi-restraints excluded: chain Z residue 567 VAL Chi-restraints excluded: chain Z residue 738 SER Chi-restraints excluded: chain Z residue 777 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 735 random chunks: chunk 463 optimal weight: 0.0980 chunk 621 optimal weight: 0.3980 chunk 178 optimal weight: 0.4980 chunk 537 optimal weight: 20.0000 chunk 86 optimal weight: 0.5980 chunk 162 optimal weight: 1.9990 chunk 584 optimal weight: 20.0000 chunk 244 optimal weight: 0.9990 chunk 599 optimal weight: 20.0000 chunk 73 optimal weight: 2.9990 chunk 107 optimal weight: 0.7980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 941 GLN ** B1142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 28 GLN J 52 HIS K 89 ASN L 23 HIS ** Q 714 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 745 HIS ** R 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 607 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4571 r_free = 0.4571 target = 0.199900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.163184 restraints weight = 91585.655| |-----------------------------------------------------------------------------| r_work (start): 0.4137 rms_B_bonded: 2.07 r_work: 0.3804 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3669 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3669 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3655 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3655 r_free = 0.3655 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 433 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3655 r_free = 0.3655 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 435 | |-----------------------------------------------------------------------------| r_final: 0.3655 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7385 moved from start: 0.4723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 58362 Z= 0.142 Angle : 0.488 9.388 78967 Z= 0.252 Chirality : 0.041 0.224 8353 Planarity : 0.003 0.060 10146 Dihedral : 12.197 173.615 9143 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.01 % Allowed : 5.02 % Favored : 94.97 % Rotamer: Outliers : 2.17 % Allowed : 21.06 % Favored : 76.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.65 % Cis-general : 0.07 % 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: -1.20 (0.10), residues: 7232 helix: 0.45 (0.11), residues: 2496 sheet: -1.36 (0.18), residues: 839 loop : -1.52 (0.10), residues: 3897 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 203 HIS 0.013 0.001 HIS W 268 PHE 0.035 0.001 PHE Q 152 TYR 0.020 0.001 TYR D 67 ARG 0.007 0.000 ARG E 93 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11748.14 seconds wall clock time: 208 minutes 11.13 seconds (12491.13 seconds total)