Starting phenix.real_space_refine on Tue Mar 12 14:09:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fik_31600/03_2024/7fik_31600.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fik_31600/03_2024/7fik_31600.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fik_31600/03_2024/7fik_31600.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fik_31600/03_2024/7fik_31600.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fik_31600/03_2024/7fik_31600.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fik_31600/03_2024/7fik_31600.pdb" } resolution = 3.7 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= 0.040 sd= 0.082 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 297 5.16 5 C 71120 2.51 5 N 22197 2.21 5 O 22549 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 1250": "NH1" <-> "NH2" Residue "A GLU 1255": "OE1" <-> "OE2" Residue "A GLU 1289": "OE1" <-> "OE2" Residue "B TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 60": "OD1" <-> "OD2" Residue "B GLU 74": "OE1" <-> "OE2" Residue "B PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 121": "OE1" <-> "OE2" Residue "B GLU 125": "OE1" <-> "OE2" Residue "B GLU 153": "OE1" <-> "OE2" Residue "B GLU 166": "OE1" <-> "OE2" Residue "B GLU 190": "OE1" <-> "OE2" Residue "B GLU 192": "OE1" <-> "OE2" Residue "B PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 196": "OD1" <-> "OD2" Residue "B GLU 209": "OE1" <-> "OE2" Residue "B GLU 217": "OE1" <-> "OE2" Residue "B ASP 233": "OD1" <-> "OD2" Residue "B GLU 251": "OE1" <-> "OE2" Residue "B PHE 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 261": "OE1" <-> "OE2" Residue "B GLU 262": "OE1" <-> "OE2" Residue "B GLU 279": "OE1" <-> "OE2" Residue "B GLU 289": "OE1" <-> "OE2" Residue "B GLU 290": "OE1" <-> "OE2" Residue "B GLU 294": "OE1" <-> "OE2" Residue "B TYR 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 321": "OE1" <-> "OE2" Residue "B PHE 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 325": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 333": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 344": "OD1" <-> "OD2" Residue "B PHE 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 380": "OD1" <-> "OD2" Residue "B GLU 398": "OE1" <-> "OE2" Residue "B PHE 399": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 404": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 420": "OD1" <-> "OD2" Residue "B GLU 431": "OE1" <-> "OE2" Residue "B TYR 432": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 456": "OE1" <-> "OE2" Residue "B GLU 462": "OE1" <-> "OE2" Residue "B TYR 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 510": "OE1" <-> "OE2" Residue "B PHE 535": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 539": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 541": "OE1" <-> "OE2" Residue "B TYR 546": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 553": "OE1" <-> "OE2" Residue "B PHE 571": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 584": "OE1" <-> "OE2" Residue "B PHE 590": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 593": "OE1" <-> "OE2" Residue "B GLU 603": "OE1" <-> "OE2" Residue "B GLU 611": "OE1" <-> "OE2" Residue "B ASP 626": "OD1" <-> "OD2" Residue "B GLU 648": "OE1" <-> "OE2" Residue "C PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 41": "OE1" <-> "OE2" Residue "C GLU 42": "OE1" <-> "OE2" Residue "C GLU 61": "OE1" <-> "OE2" Residue "C ASP 71": "OD1" <-> "OD2" Residue "C PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 85": "OD1" <-> "OD2" Residue "C GLU 87": "OE1" <-> "OE2" Residue "C GLU 105": "OE1" <-> "OE2" Residue "C GLU 117": "OE1" <-> "OE2" Residue "C GLU 140": "OE1" <-> "OE2" Residue "C GLU 146": "OE1" <-> "OE2" Residue "C GLU 156": "OE1" <-> "OE2" Residue "C GLU 182": "OE1" <-> "OE2" Residue "C GLU 213": "OE1" <-> "OE2" Residue "C GLU 258": "OE1" <-> "OE2" Residue "C GLU 263": "OE1" <-> "OE2" Residue "C PHE 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 279": "OE1" <-> "OE2" Residue "C GLU 336": "OE1" <-> "OE2" Residue "C GLU 365": "OE1" <-> "OE2" Residue "C TYR 368": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 10": "OD1" <-> "OD2" Residue "D PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 43": "OE1" <-> "OE2" Residue "D GLU 69": "OE1" <-> "OE2" Residue "D PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 87": "OE1" <-> "OE2" Residue "D GLU 88": "OE1" <-> "OE2" Residue "D ASP 111": "OD1" <-> "OD2" Residue "D ASP 118": "OD1" <-> "OD2" Residue "D TYR 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 143": "OE1" <-> "OE2" Residue "D GLU 158": "OE1" <-> "OE2" Residue "D TYR 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 204": "OE1" <-> "OE2" Residue "D TYR 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 213": "OE1" <-> "OE2" Residue "D PHE 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 267": "OE1" <-> "OE2" Residue "D ASP 298": "OD1" <-> "OD2" Residue "E TYR 957": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 984": "OE1" <-> "OE2" Residue "E PHE 1000": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 1013": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 1038": "OE1" <-> "OE2" Residue "E GLU 1047": "OE1" <-> "OE2" Residue "E GLU 1056": "OE1" <-> "OE2" Residue "E TYR 1076": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 1077": "OE1" <-> "OE2" Residue "E TYR 1080": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 1082": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 1085": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 1086": "NH1" <-> "NH2" Residue "E ARG 1111": "NH1" <-> "NH2" Residue "E ARG 1128": "NH1" <-> "NH2" Residue "E GLU 1171": "OE1" <-> "OE2" Residue "E ASP 1177": "OD1" <-> "OD2" Residue "E GLU 1181": "OE1" <-> "OE2" Residue "E TYR 1182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 1208": "OE1" <-> "OE2" Residue "E ASP 1221": "OD1" <-> "OD2" Residue "E PHE 1230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 1258": "OE1" <-> "OE2" Residue "E GLU 1261": "OE1" <-> "OE2" Residue "E ASP 1340": "OD1" <-> "OD2" Residue "E GLU 1343": "OE1" <-> "OE2" Residue "E GLU 1347": "OE1" <-> "OE2" Residue "E GLU 1351": "OE1" <-> "OE2" Residue "E TYR 1352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 1363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 1381": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 1393": "OE1" <-> "OE2" Residue "E ASP 1412": "OD1" <-> "OD2" Residue "E GLU 1413": "OE1" <-> "OE2" Residue "E TYR 1414": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 1425": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 1065": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 1070": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 1145": "OE1" <-> "OE2" Residue "G PHE 1162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 1211": "OE1" <-> "OE2" Residue "G GLU 1218": "OE1" <-> "OE2" Residue "G TYR 1222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 1227": "OE1" <-> "OE2" Residue "G PHE 1232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 1242": "OE1" <-> "OE2" Residue "G GLU 1245": "OE1" <-> "OE2" Residue "G PHE 1261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 1271": "OD1" <-> "OD2" Residue "G ASP 1281": "OD1" <-> "OD2" Residue "G ARG 1283": "NH1" <-> "NH2" Residue "G ARG 1298": "NH1" <-> "NH2" Residue "G GLU 1299": "OE1" <-> "OE2" Residue "G TYR 1316": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 1319": "OE1" <-> "OE2" Residue "G ASP 1338": "OD1" <-> "OD2" Residue "G TYR 1375": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 1379": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 1381": "OE1" <-> "OE2" Residue "G GLU 1384": "OE1" <-> "OE2" Residue "G GLU 1386": "OE1" <-> "OE2" Residue "G TYR 1388": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 1391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 1432": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 1446": "OD1" <-> "OD2" Residue "G TYR 1480": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 1485": "OE1" <-> "OE2" Residue "G PHE 1495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 1507": "OE1" <-> "OE2" Residue "G GLU 1546": "OE1" <-> "OE2" Residue "G ARG 1553": "NH1" <-> "NH2" Residue "G GLU 1561": "OE1" <-> "OE2" Residue "H ASP 18": "OD1" <-> "OD2" Residue "H TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 88": "OE1" <-> "OE2" Residue "H GLU 89": "OE1" <-> "OE2" Residue "H GLU 94": "OE1" <-> "OE2" Residue "H TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 141": "OE1" <-> "OE2" Residue "H GLU 197": "OE1" <-> "OE2" Residue "H ASP 198": "OD1" <-> "OD2" Residue "H ASP 216": "OD1" <-> "OD2" Residue "H TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 260": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 262": "OD1" <-> "OD2" Residue "S PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 120": "NH1" <-> "NH2" Residue "S PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 127": "OE1" <-> "OE2" Residue "S TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 131": "OE1" <-> "OE2" Residue "S GLU 136": "OE1" <-> "OE2" Residue "W GLU 1058": "OE1" <-> "OE2" Residue "W ASP 1076": "OD1" <-> "OD2" Residue "W ARG 1086": "NH1" <-> "NH2" Residue "W PHE 1088": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 1113": "OE1" <-> "OE2" Residue "W TYR 1114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 1136": "OE1" <-> "OE2" Residue "W PHE 1137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 1140": "OE1" <-> "OE2" Residue "W GLU 1142": "OE1" <-> "OE2" Residue "W GLU 1143": "OE1" <-> "OE2" Residue "W GLU 1197": "OE1" <-> "OE2" Residue "W GLU 1225": "OE1" <-> "OE2" Residue "W PHE 1259": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 1262": "OE1" <-> "OE2" Residue "W PHE 1263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W TYR 1267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 1269": "OE1" <-> "OE2" Residue "W PHE 1281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W TYR 1284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 1288": "OE1" <-> "OE2" Residue "W GLU 1298": "OE1" <-> "OE2" Residue "W PHE 1304": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 1322": "OE1" <-> "OE2" Residue "W TYR 1325": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W TYR 1331": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 1334": "OE1" <-> "OE2" Residue "W GLU 1342": "OE1" <-> "OE2" Residue "W PHE 1346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 1385": "OE1" <-> "OE2" Residue "s ARG 120": "NH1" <-> "NH2" Residue "s PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s GLU 131": "OE1" <-> "OE2" Residue "s GLU 136": "OE1" <-> "OE2" Residue "a ARG 1220": "NH1" <-> "NH2" Residue "a GLU 1256": "OE1" <-> "OE2" Residue "a ARG 1285": "NH1" <-> "NH2" Residue "b ASP 31": "OD1" <-> "OD2" Residue "b TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 61": "OE1" <-> "OE2" Residue "b GLU 74": "OE1" <-> "OE2" Residue "b PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 87": "OE1" <-> "OE2" Residue "b GLU 88": "OE1" <-> "OE2" Residue "b GLU 121": "OE1" <-> "OE2" Residue "b GLU 125": "OE1" <-> "OE2" Residue "b GLU 153": "OE1" <-> "OE2" Residue "b GLU 166": "OE1" <-> "OE2" Residue "b ASP 233": "OD1" <-> "OD2" Residue "b GLU 251": "OE1" <-> "OE2" Residue "b PHE 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 261": "OE1" <-> "OE2" Residue "b GLU 262": "OE1" <-> "OE2" Residue "b TYR 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 333": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ASP 380": "OD1" <-> "OD2" Residue "b GLU 398": "OE1" <-> "OE2" Residue "b PHE 399": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b TYR 404": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ASP 420": "OD1" <-> "OD2" Residue "b GLU 431": "OE1" <-> "OE2" Residue "b GLU 456": "OE1" <-> "OE2" Residue "b GLU 462": "OE1" <-> "OE2" Residue "b ARG 465": "NH1" <-> "NH2" Residue "b TYR 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 510": "OE1" <-> "OE2" Residue "b PHE 535": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b TYR 539": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 541": "OE1" <-> "OE2" Residue "b GLU 553": "OE1" <-> "OE2" Residue "b PHE 571": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 590": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 593": "OE1" <-> "OE2" Residue "b GLU 603": "OE1" <-> "OE2" Residue "b GLU 611": "OE1" <-> "OE2" Residue "c PHE 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c GLU 41": "OE1" <-> "OE2" Residue "c GLU 42": "OE1" <-> "OE2" Residue "c ASP 71": "OD1" <-> "OD2" Residue "c ASP 77": "OD1" <-> "OD2" Residue "c ASP 85": "OD1" <-> "OD2" Residue "c GLU 87": "OE1" <-> "OE2" Residue "c GLU 105": "OE1" <-> "OE2" Residue "c GLU 117": "OE1" <-> "OE2" Residue "c GLU 146": "OE1" <-> "OE2" Residue "c ARG 149": "NH1" <-> "NH2" Residue "c GLU 182": "OE1" <-> "OE2" Residue "c GLU 213": "OE1" <-> "OE2" Residue "c GLU 258": "OE1" <-> "OE2" Residue "c GLU 260": "OE1" <-> "OE2" Residue "c GLU 263": "OE1" <-> "OE2" Residue "c GLU 279": "OE1" <-> "OE2" Residue "c GLU 336": "OE1" <-> "OE2" Residue "c GLU 365": "OE1" <-> "OE2" Residue "c TYR 368": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 371": "NH1" <-> "NH2" Residue "d ASP 10": "OD1" <-> "OD2" Residue "d PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d GLU 43": "OE1" <-> "OE2" Residue "d GLU 69": "OE1" <-> "OE2" Residue "d PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d GLU 87": "OE1" <-> "OE2" Residue "d ASP 118": "OD1" <-> "OD2" Residue "d TYR 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d GLU 143": "OE1" <-> "OE2" Residue "d GLU 158": "OE1" <-> "OE2" Residue "d TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d TYR 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d GLU 204": "OE1" <-> "OE2" Residue "d GLU 213": "OE1" <-> "OE2" Residue "d PHE 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d PHE 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d GLU 267": "OE1" <-> "OE2" Residue "d ASP 298": "OD1" <-> "OD2" Residue "e TYR 705": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e GLU 759": "OE1" <-> "OE2" Residue "e TYR 772": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e GLU 791": "OE1" <-> "OE2" Residue "e GLU 821": "OE1" <-> "OE2" Residue "e PHE 823": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e GLU 825": "OE1" <-> "OE2" Residue "e PHE 836": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e TYR 860": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e PHE 872": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e PHE 874": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e GLU 876": "OE1" <-> "OE2" Residue "e GLU 889": "OE1" <-> "OE2" Residue "e TYR 890": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e GLU 918": "OE1" <-> "OE2" Residue "e GLU 932": "OE1" <-> "OE2" Residue "e GLU 934": "OE1" <-> "OE2" Residue "e PHE 938": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e TYR 957": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e GLU 966": "OE1" <-> "OE2" Residue "e GLU 984": "OE1" <-> "OE2" Residue "e PHE 1000": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e TYR 1013": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e GLU 1038": "OE1" <-> "OE2" Residue "e GLU 1047": "OE1" <-> "OE2" Residue "e GLU 1062": "OE1" <-> "OE2" Residue "e TYR 1076": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e GLU 1077": "OE1" <-> "OE2" Residue "e TYR 1080": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e PHE 1082": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e TYR 1085": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e PHE 1097": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e GLU 1098": "OE1" <-> "OE2" Residue "e GLU 1106": "OE1" <-> "OE2" Residue "e GLU 1179": "OE1" <-> "OE2" Residue "e GLU 1181": "OE1" <-> "OE2" Residue "e TYR 1182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e GLU 1208": "OE1" <-> "OE2" Residue "e GLU 1209": "OE1" <-> "OE2" Residue "e ASP 1221": "OD1" <-> "OD2" Residue "e PHE 1230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e GLU 1239": "OE1" <-> "OE2" Residue "e GLU 1253": "OE1" <-> "OE2" Residue "e GLU 1258": "OE1" <-> "OE2" Residue "e GLU 1261": "OE1" <-> "OE2" Residue "e GLU 1282": "OE1" <-> "OE2" Residue "e TYR 1324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e GLU 1331": "OE1" <-> "OE2" Residue "e TYR 1339": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e GLU 1343": "OE1" <-> "OE2" Residue "e GLU 1347": "OE1" <-> "OE2" Residue "e GLU 1351": "OE1" <-> "OE2" Residue "e TYR 1352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e PHE 1364": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e GLU 1395": "OE1" <-> "OE2" Residue "e GLU 1413": "OE1" <-> "OE2" Residue "e TYR 1414": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e TYR 1425": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f GLU 16": "OE1" <-> "OE2" Residue "f TYR 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f GLU 23": "OE1" <-> "OE2" Residue "f GLU 53": "OE1" <-> "OE2" Residue "f GLU 54": "OE1" <-> "OE2" Residue "f GLU 59": "OE1" <-> "OE2" Residue "f GLU 62": "OE1" <-> "OE2" Residue "f PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f GLU 73": "OE1" <-> "OE2" Residue "f GLU 83": "OE1" <-> "OE2" Residue "f PHE 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ASP 113": "OD1" <-> "OD2" Residue "f GLU 116": "OE1" <-> "OE2" Residue "f GLU 121": "OE1" <-> "OE2" Residue "f PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f GLU 136": "OE1" <-> "OE2" Residue "f GLU 176": "OE1" <-> "OE2" Residue "f GLU 185": "OE1" <-> "OE2" Residue "f GLU 205": "OE1" <-> "OE2" Residue "f GLU 236": "OE1" <-> "OE2" Residue "f GLU 264": "OE1" <-> "OE2" Residue "f TYR 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f PHE 321": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f GLU 325": "OE1" <-> "OE2" Residue "g PHE 1070": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g TYR 1140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g GLU 1145": "OE1" <-> "OE2" Residue "g GLU 1184": "OE1" <-> "OE2" Residue "g GLU 1187": "OE1" <-> "OE2" Residue "g TYR 1222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g GLU 1227": "OE1" <-> "OE2" Residue "g PHE 1232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g GLU 1242": "OE1" <-> "OE2" Residue "g GLU 1245": "OE1" <-> "OE2" Residue "g PHE 1261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g ASP 1271": "OD1" <-> "OD2" Residue "g ARG 1283": "NH1" <-> "NH2" Residue "g GLU 1299": "OE1" <-> "OE2" Residue "g GLU 1319": "OE1" <-> "OE2" Residue "g ASP 1338": "OD1" <-> "OD2" Residue "g TYR 1375": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g PHE 1379": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g GLU 1386": "OE1" <-> "OE2" Residue "g TYR 1391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g TYR 1432": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g ASP 1446": "OD1" <-> "OD2" Residue "g TYR 1450": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g TYR 1465": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g TYR 1480": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g GLU 1485": "OE1" <-> "OE2" Residue "g PHE 1495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g GLU 1507": "OE1" <-> "OE2" Residue "g GLU 1525": "OE1" <-> "OE2" Residue "g PHE 1532": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g GLU 1546": "OE1" <-> "OE2" Residue "g GLU 1561": "OE1" <-> "OE2" Residue "g TYR 1594": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g PHE 1598": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g GLU 1601": "OE1" <-> "OE2" Residue "g GLU 1606": "OE1" <-> "OE2" Residue "g TYR 1624": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g ASP 1637": "OD1" <-> "OD2" Residue "g GLU 1643": "OE1" <-> "OE2" Residue "g GLU 1659": "OE1" <-> "OE2" Residue "h ASP 9": "OD1" <-> "OD2" Residue "h GLU 13": "OE1" <-> "OE2" Residue "h ASP 18": "OD1" <-> "OD2" Residue "h TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h GLU 88": "OE1" <-> "OE2" Residue "h GLU 89": "OE1" <-> "OE2" Residue "h GLU 94": "OE1" <-> "OE2" Residue "h TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h GLU 141": "OE1" <-> "OE2" Residue "h ARG 181": "NH1" <-> "NH2" Residue "h GLU 197": "OE1" <-> "OE2" Residue "h ASP 198": "OD1" <-> "OD2" Residue "h ASP 216": "OD1" <-> "OD2" Residue "h PHE 260": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h ASP 262": "OD1" <-> "OD2" Residue "h ASP 293": "OD1" <-> "OD2" Time to flip residues: 0.19s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 116163 Number of models: 1 Model: "" Number of chains: 32 Chain: "A" Number of atoms: 9238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1795, 9238 Classifications: {'peptide': 1795} Incomplete info: {'truncation_to_alanine': 1497} Link IDs: {'PCIS': 1, 'PTRANS': 74, 'TRANS': 1719} Chain breaks: 17 Unresolved chain link angles: 72 Unresolved non-hydrogen bonds: 5355 Unresolved non-hydrogen angles: 6841 Unresolved non-hydrogen dihedrals: 4414 Unresolved non-hydrogen chiralities: 526 Planarities with less than four sites: {'GLN:plan1': 108, 'ASP:plan': 81, 'TYR:plan': 49, 'ASN:plan1': 47, 'TRP:plan': 17, 'HIS:plan': 42, 'PHE:plan': 61, 'GLU:plan': 110, 'ARG:plan': 103} Unresolved non-hydrogen planarities: 2842 Chain: "B" Number of atoms: 4799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 598, 4799 Classifications: {'peptide': 598} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 15, 'TRANS': 582} Chain breaks: 6 Unresolved non-hydrogen bonds: 76 Unresolved non-hydrogen angles: 98 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 3, 'ASN:plan1': 1, 'ASP:plan': 2, 'PHE:plan': 2, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 46 Chain: "C" Number of atoms: 2557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2557 Classifications: {'peptide': 324} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 309} Chain breaks: 4 Chain: "D" Number of atoms: 2473 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2473 Classifications: {'peptide': 316} Link IDs: {'PTRANS': 10, 'TRANS': 305} Chain breaks: 2 Chain: "E" Number of atoms: 7891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1310, 7891 Classifications: {'peptide': 1310} Incomplete info: {'truncation_to_alanine': 771} Link IDs: {'PCIS': 1, 'PTRANS': 47, 'TRANS': 1261} Chain breaks: 5 Unresolved chain link angles: 37 Unresolved non-hydrogen bonds: 2718 Unresolved non-hydrogen angles: 3518 Unresolved non-hydrogen dihedrals: 2234 Unresolved non-hydrogen chiralities: 272 Planarities with less than four sites: {'GLN:plan1': 51, 'HIS:plan': 25, 'TYR:plan': 29, 'ASN:plan1': 43, 'TRP:plan': 12, 'ASP:plan': 49, 'PHE:plan': 29, 'GLU:plan': 52, 'ARG:plan': 41} Unresolved non-hydrogen planarities: 1503 Chain: "F" Number of atoms: 1607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 1607 Classifications: {'peptide': 326} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 274} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 310} Unresolved chain link angles: 15 Unresolved non-hydrogen bonds: 1037 Unresolved non-hydrogen angles: 1341 Unresolved non-hydrogen dihedrals: 897 Unresolved non-hydrogen chiralities: 85 Planarities with less than four sites: {'GLN:plan1': 9, 'ARG:plan': 17, 'TYR:plan': 10, 'ASN:plan1': 9, 'TRP:plan': 9, 'HIS:plan': 12, 'PHE:plan': 16, 'GLU:plan': 18, 'ASP:plan': 20} Unresolved non-hydrogen planarities: 587 Chain: "G" Number of atoms: 4209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 567, 4209 Classifications: {'peptide': 567} Incomplete info: {'truncation_to_alanine': 123} Link IDs: {'PTRANS': 25, 'TRANS': 541} Chain breaks: 10 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 446 Unresolved non-hydrogen angles: 565 Unresolved non-hydrogen dihedrals: 373 Unresolved non-hydrogen chiralities: 40 Planarities with less than four sites: {'GLN:plan1': 7, 'ASP:plan': 5, 'TYR:plan': 4, 'ASN:plan1': 6, 'TRP:plan': 2, 'HIS:plan': 6, 'PHE:plan': 2, 'GLU:plan': 11, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 233 Chain: "H" Number of atoms: 2235 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2235 Classifications: {'peptide': 288} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 10, 'TRANS': 277} Chain breaks: 1 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 1, 'HIS:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 18 Chain: "I" Number of atoms: 3626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 729, 3626 Classifications: {'peptide': 729} Incomplete info: {'truncation_to_alanine': 655} Link IDs: {'PTRANS': 20, 'TRANS': 708} Chain breaks: 4 Unresolved chain link angles: 20 Unresolved non-hydrogen bonds: 2490 Unresolved non-hydrogen angles: 3187 Unresolved non-hydrogen dihedrals: 2100 Unresolved non-hydrogen chiralities: 204 Planarities with less than four sites: {'GLN:plan1': 38, 'ARG:plan': 38, 'TYR:plan': 22, 'ASN:plan1': 24, 'TRP:plan': 17, 'HIS:plan': 20, 'PHE:plan': 31, 'GLU:plan': 72, 'ASP:plan': 48} Unresolved non-hydrogen planarities: 1439 Chain: "J" Number of atoms: 5029 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1015, 5029 Classifications: {'peptide': 1015} Incomplete info: {'backbone_only': 32, 'truncation_to_alanine': 937} Link IDs: {'PTRANS': 9, 'TRANS': 1005} Chain breaks: 4 Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 2658 Unresolved non-hydrogen angles: 3665 Unresolved non-hydrogen dihedrals: 1809 Unresolved non-hydrogen chiralities: 162 Planarities with less than four sites: {'GLN:plan1': 27, 'HIS:plan': 8, 'ASN:plan1': 22, 'TYR:plan': 19, 'UNK:plan-1': 561, 'TRP:plan': 6, 'ASP:plan': 25, 'PHE:plan': 17, 'GLU:plan': 49, 'ARG:plan': 15} Unresolved non-hydrogen planarities: 1410 Chain: "K" Number of atoms: 3460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 697, 3460 Classifications: {'peptide': 697} Incomplete info: {'truncation_to_alanine': 630} Link IDs: {'PTRANS': 29, 'TRANS': 667} Chain breaks: 7 Unresolved chain link angles: 29 Unresolved non-hydrogen bonds: 2324 Unresolved non-hydrogen angles: 2971 Unresolved non-hydrogen dihedrals: 1960 Unresolved non-hydrogen chiralities: 197 Planarities with less than four sites: {'GLN:plan1': 39, 'HIS:plan': 16, 'TYR:plan': 26, 'ASN:plan1': 27, 'TRP:plan': 12, 'ASP:plan': 36, 'PHE:plan': 30, 'GLU:plan': 55, 'ARG:plan': 34} Unresolved non-hydrogen planarities: 1285 Chain: "L" Number of atoms: 3372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 679, 3372 Classifications: {'peptide': 679} Incomplete info: {'truncation_to_alanine': 613} Link IDs: {'PTRANS': 28, 'TRANS': 650} Chain breaks: 9 Unresolved chain link angles: 28 Unresolved non-hydrogen bonds: 2266 Unresolved non-hydrogen angles: 2895 Unresolved non-hydrogen dihedrals: 1914 Unresolved non-hydrogen chiralities: 193 Planarities with less than four sites: {'GLN:plan1': 39, 'ASP:plan': 34, 'TYR:plan': 25, 'ASN:plan1': 23, 'TRP:plan': 12, 'HIS:plan': 16, 'PHE:plan': 29, 'GLU:plan': 53, 'ARG:plan': 34} Unresolved non-hydrogen planarities: 1246 Chain: "M" Number of atoms: 3246 Number of conformers: 1 Conformer: "" Number of residues, atoms: 654, 3246 Classifications: {'peptide': 654} Incomplete info: {'truncation_to_alanine': 590} Link IDs: {'PTRANS': 28, 'TRANS': 625} Chain breaks: 7 Unresolved chain link angles: 28 Unresolved non-hydrogen bonds: 2163 Unresolved non-hydrogen angles: 2768 Unresolved non-hydrogen dihedrals: 1821 Unresolved non-hydrogen chiralities: 190 Planarities with less than four sites: {'GLN:plan1': 37, 'ASP:plan': 36, 'TYR:plan': 21, 'ASN:plan1': 24, 'TRP:plan': 12, 'HIS:plan': 16, 'PHE:plan': 28, 'GLU:plan': 49, 'ARG:plan': 30} Unresolved non-hydrogen planarities: 1177 Chain: "N" Number of atoms: 3480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 701, 3480 Classifications: {'peptide': 701} Incomplete info: {'truncation_to_alanine': 632} Link IDs: {'PTRANS': 29, 'TRANS': 671} Chain breaks: 8 Unresolved chain link angles: 29 Unresolved non-hydrogen bonds: 2324 Unresolved non-hydrogen angles: 2970 Unresolved non-hydrogen dihedrals: 1961 Unresolved non-hydrogen chiralities: 197 Planarities with less than four sites: {'GLN:plan1': 39, 'HIS:plan': 16, 'TYR:plan': 26, 'ASN:plan1': 27, 'TRP:plan': 12, 'ASP:plan': 36, 'PHE:plan': 30, 'GLU:plan': 55, 'ARG:plan': 33} Unresolved non-hydrogen planarities: 1280 Chain: "O" Number of atoms: 3391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 683, 3391 Classifications: {'peptide': 683} Incomplete info: {'truncation_to_alanine': 614} Link IDs: {'PTRANS': 29, 'TRANS': 653} Chain breaks: 10 Unresolved chain link angles: 29 Unresolved non-hydrogen bonds: 2261 Unresolved non-hydrogen angles: 2893 Unresolved non-hydrogen dihedrals: 1909 Unresolved non-hydrogen chiralities: 192 Planarities with less than four sites: {'GLN:plan1': 37, 'HIS:plan': 16, 'TYR:plan': 25, 'ASN:plan1': 27, 'TRP:plan': 12, 'ASP:plan': 34, 'PHE:plan': 30, 'GLU:plan': 53, 'ARG:plan': 33} Unresolved non-hydrogen planarities: 1251 Chain: "P" Number of atoms: 2945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 593, 2945 Classifications: {'peptide': 593} Incomplete info: {'truncation_to_alanine': 529} Link IDs: {'PTRANS': 18, 'TRANS': 574} Chain breaks: 5 Unresolved chain link angles: 18 Unresolved non-hydrogen bonds: 1964 Unresolved non-hydrogen angles: 2497 Unresolved non-hydrogen dihedrals: 1630 Unresolved non-hydrogen chiralities: 162 Planarities with less than four sites: {'GLN:plan1': 34, 'ASP:plan': 33, 'TYR:plan': 26, 'ASN:plan1': 29, 'TRP:plan': 3, 'HIS:plan': 11, 'PHE:plan': 30, 'GLU:plan': 40, 'ARG:plan': 42} Unresolved non-hydrogen planarities: 1136 Chain: "S" Number of atoms: 432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 432 Classifications: {'peptide': 52} Link IDs: {'TRANS': 51} Chain: "W" Number of atoms: 2636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2636 Classifications: {'peptide': 324} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 310} Chain breaks: 2 Chain: "X" Number of atoms: 794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 794 Classifications: {'peptide': 161} Incomplete info: {'backbone_only': 11, 'truncation_to_alanine': 150} Link IDs: {'TRANS': 160} Unresolved non-hydrogen bonds: 333 Unresolved non-hydrogen angles: 505 Unresolved non-hydrogen dihedrals: 161 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'UNK:plan-1': 161} Unresolved non-hydrogen planarities: 161 Chain: "Y" Number of atoms: 1676 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 1676 Classifications: {'peptide': 339} Incomplete info: {'truncation_to_alanine': 302} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 317} Chain breaks: 7 Unresolved chain link angles: 21 Unresolved non-hydrogen bonds: 1026 Unresolved non-hydrogen angles: 1336 Unresolved non-hydrogen dihedrals: 847 Unresolved non-hydrogen chiralities: 124 Planarities with less than four sites: {'GLN:plan1': 8, 'HIS:plan': 10, 'TYR:plan': 14, 'ASN:plan1': 9, 'TRP:plan': 4, 'ASP:plan': 13, 'PHE:plan': 10, 'GLU:plan': 23, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 484 Chain: "i" Number of atoms: 3347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 673, 3347 Classifications: {'peptide': 673} Incomplete info: {'truncation_to_alanine': 603} Link IDs: {'PTRANS': 16, 'TRANS': 656} Chain breaks: 7 Unresolved chain link angles: 16 Unresolved non-hydrogen bonds: 2275 Unresolved non-hydrogen angles: 2910 Unresolved non-hydrogen dihedrals: 1910 Unresolved non-hydrogen chiralities: 194 Planarities with less than four sites: {'GLN:plan1': 34, 'ARG:plan': 36, 'TYR:plan': 20, 'ASN:plan1': 21, 'TRP:plan': 14, 'HIS:plan': 20, 'PHE:plan': 28, 'GLU:plan': 64, 'ASP:plan': 44} Unresolved non-hydrogen planarities: 1301 Chain: "s" Number of atoms: 432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 432 Classifications: {'peptide': 52} Link IDs: {'TRANS': 51} Chain: "a" Number of atoms: 8811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1725, 8811 Classifications: {'peptide': 1725} Incomplete info: {'truncation_to_alanine': 1456} Link IDs: {'PCIS': 1, 'PTRANS': 73, 'TRANS': 1650} Chain breaks: 16 Unresolved chain link angles: 71 Unresolved non-hydrogen bonds: 5195 Unresolved non-hydrogen angles: 6640 Unresolved non-hydrogen dihedrals: 4282 Unresolved non-hydrogen chiralities: 515 Planarities with less than four sites: {'GLN:plan1': 106, 'ASP:plan': 78, 'TYR:plan': 48, 'ASN:plan1': 48, 'TRP:plan': 17, 'HIS:plan': 39, 'PHE:plan': 60, 'GLU:plan': 105, 'ARG:plan': 95} Unresolved non-hydrogen planarities: 2739 Chain: "b" Number of atoms: 4549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 595, 4549 Classifications: {'peptide': 595} Incomplete info: {'truncation_to_alanine': 85} Link IDs: {'PTRANS': 15, 'TRANS': 579} Chain breaks: 7 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 294 Unresolved non-hydrogen angles: 374 Unresolved non-hydrogen dihedrals: 231 Unresolved non-hydrogen chiralities: 31 Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 7, 'TYR:plan': 1, 'ASN:plan1': 4, 'TRP:plan': 1, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 11, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 165 Chain: "c" Number of atoms: 2445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2445 Classifications: {'peptide': 309} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 295} Chain breaks: 4 Chain: "d" Number of atoms: 2435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 2435 Classifications: {'peptide': 312} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 10, 'TRANS': 301} Chain breaks: 2 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "e" Number of atoms: 8134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1247, 8134 Classifications: {'peptide': 1247} Incomplete info: {'truncation_to_alanine': 555} Link IDs: {'PCIS': 1, 'PTRANS': 43, 'TRANS': 1202} Chain breaks: 9 Unresolved chain link angles: 29 Unresolved non-hydrogen bonds: 1964 Unresolved non-hydrogen angles: 2547 Unresolved non-hydrogen dihedrals: 1617 Unresolved non-hydrogen chiralities: 196 Planarities with less than four sites: {'GLN:plan1': 28, 'HIS:plan': 18, 'TYR:plan': 22, 'ASN:plan1': 30, 'TRP:plan': 9, 'ASP:plan': 40, 'PHE:plan': 21, 'GLU:plan': 40, 'ARG:plan': 31} Unresolved non-hydrogen planarities: 1088 Chain: "f" Number of atoms: 2524 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2524 Classifications: {'peptide': 322} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 306} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "g" Number of atoms: 4770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 603, 4770 Classifications: {'peptide': 603} Incomplete info: {'truncation_to_alanine': 46} Link IDs: {'PTRANS': 25, 'TRANS': 577} Chain breaks: 3 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 145 Unresolved non-hydrogen angles: 180 Unresolved non-hydrogen dihedrals: 118 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'ASP:plan': 3, 'PHE:plan': 2, 'GLU:plan': 6, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 68 Chain: "h" Number of atoms: 2259 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2259 Classifications: {'peptide': 288} Link IDs: {'PTRANS': 8, 'TRANS': 279} Chain breaks: 1 Chain: "j" Number of atoms: 5094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1028, 5094 Classifications: {'peptide': 1028} Incomplete info: {'truncation_to_alanine': 901} Link IDs: {'PTRANS': 32, 'TRANS': 995} Chain breaks: 2 Unresolved chain link angles: 32 Unresolved non-hydrogen bonds: 3187 Unresolved non-hydrogen angles: 4090 Unresolved non-hydrogen dihedrals: 2660 Unresolved non-hydrogen chiralities: 289 Planarities with less than four sites: {'GLN:plan1': 53, 'ARG:plan': 33, 'TYR:plan': 34, 'ASN:plan1': 45, 'TRP:plan': 18, 'ASP:plan': 64, 'PHE:plan': 37, 'GLU:plan': 79, 'HIS:plan': 21} Unresolved non-hydrogen planarities: 1747 Chain: "p" Number of atoms: 2267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 456, 2267 Classifications: {'peptide': 456} Incomplete info: {'truncation_to_alanine': 408} Link IDs: {'PTRANS': 10, 'TRANS': 445} Chain breaks: 14 Unresolved chain link angles: 10 Unresolved non-hydrogen bonds: 1555 Unresolved non-hydrogen angles: 1980 Unresolved non-hydrogen dihedrals: 1304 Unresolved non-hydrogen chiralities: 126 Planarities with less than four sites: {'GLN:plan1': 23, 'ASP:plan': 23, 'TYR:plan': 25, 'ASN:plan1': 22, 'TRP:plan': 3, 'HIS:plan': 9, 'PHE:plan': 25, 'GLU:plan': 30, 'ARG:plan': 33} Unresolved non-hydrogen planarities: 909 Time building chain proxies: 46.44, per 1000 atoms: 0.40 Number of scatterers: 116163 At special positions: 0 Unit cell: (466.032, 448.001, 314.849, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 297 16.00 O 22549 8.00 N 22197 7.00 C 71120 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=0, symmetry=0 Time building additional restraints: 36.50 Conformation dependent library (CDL) restraints added in 21.2 seconds 37268 Ramachandran restraints generated. 18634 Oldfield, 0 Emsley, 18634 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 37838 Finding SS restraints... Secondary structure from input PDB file: 821 helices and 104 sheets defined 62.2% alpha, 10.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 11.67 Creating SS restraints... Processing helix chain 'A' and resid 16 through 29 Processing helix chain 'A' and resid 32 through 52 removed outlier: 4.125A pdb=" N HIS A 37 " --> pdb=" O PRO A 33 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N SER A 38 " --> pdb=" O GLU A 34 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ILE A 41 " --> pdb=" O HIS A 37 " (cutoff:3.500A) Proline residue: A 48 - end of helix Processing helix chain 'A' and resid 60 through 69 Processing helix chain 'A' and resid 87 through 99 Processing helix chain 'A' and resid 107 through 122 removed outlier: 3.530A pdb=" N ILE A 114 " --> pdb=" O GLU A 110 " (cutoff:3.500A) Proline residue: A 120 - end of helix Processing helix chain 'A' and resid 126 through 153 Processing helix chain 'A' and resid 165 through 179 removed outlier: 4.346A pdb=" N MET A 169 " --> pdb=" O GLU A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 202 removed outlier: 3.647A pdb=" N ILE A 186 " --> pdb=" O LEU A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 239 Processing helix chain 'A' and resid 242 through 254 Processing helix chain 'A' and resid 265 through 280 Processing helix chain 'A' and resid 281 through 285 Processing helix chain 'A' and resid 290 through 298 Processing helix chain 'A' and resid 303 through 316 removed outlier: 3.681A pdb=" N ILE A 307 " --> pdb=" O ASP A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 340 removed outlier: 3.794A pdb=" N GLN A 326 " --> pdb=" O SER A 322 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N VAL A 329 " --> pdb=" O MET A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 363 removed outlier: 3.706A pdb=" N MET A 356 " --> pdb=" O ALA A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 373 removed outlier: 3.842A pdb=" N THR A 370 " --> pdb=" O PHE A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 381 removed outlier: 3.530A pdb=" N CYS A 380 " --> pdb=" O GLU A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 400 removed outlier: 3.734A pdb=" N ILE A 386 " --> pdb=" O ASP A 382 " (cutoff:3.500A) Proline residue: A 397 - end of helix Processing helix chain 'A' and resid 400 through 423 removed outlier: 3.686A pdb=" N VAL A 404 " --> pdb=" O MET A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 434 through 449 removed outlier: 4.624A pdb=" N LYS A 449 " --> pdb=" O GLU A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 461 removed outlier: 3.558A pdb=" N GLU A 459 " --> pdb=" O LEU A 456 " (cutoff:3.500A) Processing helix chain 'A' and resid 485 through 498 Processing helix chain 'A' and resid 503 through 505 No H-bonds generated for 'chain 'A' and resid 503 through 505' Processing helix chain 'A' and resid 506 through 518 Processing helix chain 'A' and resid 520 through 535 removed outlier: 3.678A pdb=" N GLY A 535 " --> pdb=" O LEU A 531 " (cutoff:3.500A) Processing helix chain 'A' and resid 551 through 569 Processing helix chain 'A' and resid 587 through 608 Processing helix chain 'A' and resid 608 through 618 removed outlier: 3.697A pdb=" N GLU A 617 " --> pdb=" O LEU A 613 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N HIS A 618 " --> pdb=" O ALA A 614 " (cutoff:3.500A) Processing helix chain 'A' and resid 622 through 632 removed outlier: 4.208A pdb=" N GLN A 632 " --> pdb=" O LEU A 628 " (cutoff:3.500A) Processing helix chain 'A' and resid 636 through 650 Processing helix chain 'A' and resid 653 through 668 removed outlier: 3.558A pdb=" N GLN A 668 " --> pdb=" O LEU A 664 " (cutoff:3.500A) Processing helix chain 'A' and resid 683 through 691 Processing helix chain 'A' and resid 691 through 696 Processing helix chain 'A' and resid 698 through 715 removed outlier: 3.744A pdb=" N ARG A 702 " --> pdb=" O TYR A 698 " (cutoff:3.500A) Processing helix chain 'A' and resid 729 through 746 removed outlier: 3.945A pdb=" N LEU A 733 " --> pdb=" O PHE A 729 " (cutoff:3.500A) Processing helix chain 'A' and resid 753 through 772 removed outlier: 3.601A pdb=" N GLU A 757 " --> pdb=" O ALA A 753 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N VAL A 758 " --> pdb=" O GLU A 754 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ALA A 759 " --> pdb=" O LYS A 755 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N VAL A 765 " --> pdb=" O ALA A 761 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ASP A 772 " --> pdb=" O LYS A 768 " (cutoff:3.500A) Processing helix chain 'A' and resid 797 through 805 removed outlier: 3.601A pdb=" N SER A 801 " --> pdb=" O PRO A 797 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N HIS A 805 " --> pdb=" O SER A 801 " (cutoff:3.500A) Processing helix chain 'A' and resid 810 through 829 Processing helix chain 'A' and resid 835 through 867 removed outlier: 3.503A pdb=" N LEU A 854 " --> pdb=" O LEU A 850 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N GLN A 855 " --> pdb=" O ASN A 851 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LYS A 856 " --> pdb=" O LEU A 852 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLU A 866 " --> pdb=" O ASP A 862 " (cutoff:3.500A) Processing helix chain 'A' and resid 875 through 880 Processing helix chain 'A' and resid 891 through 899 removed outlier: 4.058A pdb=" N TYR A 899 " --> pdb=" O ASN A 895 " (cutoff:3.500A) Processing helix chain 'A' and resid 906 through 922 removed outlier: 3.623A pdb=" N CYS A 922 " --> pdb=" O CYS A 918 " (cutoff:3.500A) Processing helix chain 'A' and resid 926 through 936 Processing helix chain 'A' and resid 937 through 953 Processing helix chain 'A' and resid 969 through 993 Processing helix chain 'A' and resid 998 through 1004 Processing helix chain 'A' and resid 1011 through 1015 Processing helix chain 'A' and resid 1021 through 1025 removed outlier: 3.825A pdb=" N GLY A1024 " --> pdb=" O GLY A1021 " (cutoff:3.500A) Processing helix chain 'A' and resid 1028 through 1040 removed outlier: 3.635A pdb=" N LYS A1039 " --> pdb=" O ASP A1035 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N GLY A1040 " --> pdb=" O ILE A1036 " (cutoff:3.500A) Processing helix chain 'A' and resid 1047 through 1051 removed outlier: 3.882A pdb=" N TRP A1051 " --> pdb=" O VAL A1048 " (cutoff:3.500A) Processing helix chain 'A' and resid 1057 through 1067 Processing helix chain 'A' and resid 1070 through 1074 removed outlier: 3.762A pdb=" N SER A1074 " --> pdb=" O ALA A1071 " (cutoff:3.500A) Processing helix chain 'A' and resid 1075 through 1084 Processing helix chain 'A' and resid 1086 through 1092 removed outlier: 3.636A pdb=" N SER A1090 " --> pdb=" O ASP A1086 " (cutoff:3.500A) Processing helix chain 'A' and resid 1093 through 1095 No H-bonds generated for 'chain 'A' and resid 1093 through 1095' Processing helix chain 'A' and resid 1102 through 1126 Processing helix chain 'A' and resid 1129 through 1142 Processing helix chain 'A' and resid 1178 through 1187 removed outlier: 3.637A pdb=" N ILE A1187 " --> pdb=" O ILE A1183 " (cutoff:3.500A) Processing helix chain 'A' and resid 1203 through 1214 Processing helix chain 'A' and resid 1228 through 1242 Processing helix chain 'A' and resid 1246 through 1248 No H-bonds generated for 'chain 'A' and resid 1246 through 1248' Processing helix chain 'A' and resid 1249 through 1295 removed outlier: 3.517A pdb=" N LEU A1253 " --> pdb=" O GLN A1249 " (cutoff:3.500A) Processing helix chain 'A' and resid 1301 through 1321 Processing helix chain 'A' and resid 1328 through 1352 removed outlier: 3.915A pdb=" N ILE A1332 " --> pdb=" O GLU A1328 " (cutoff:3.500A) Processing helix chain 'A' and resid 1391 through 1408 Processing helix chain 'A' and resid 1413 through 1432 removed outlier: 4.081A pdb=" N ALA A1431 " --> pdb=" O TYR A1427 " (cutoff:3.500A) Processing helix chain 'A' and resid 1439 through 1445 removed outlier: 3.804A pdb=" N LYS A1445 " --> pdb=" O SER A1442 " (cutoff:3.500A) Processing helix chain 'A' and resid 1446 through 1452 Processing helix chain 'A' and resid 1456 through 1472 Processing helix chain 'A' and resid 1472 through 1486 removed outlier: 3.809A pdb=" N LEU A1476 " --> pdb=" O TYR A1472 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N MET A1477 " --> pdb=" O GLY A1473 " (cutoff:3.500A) Processing helix chain 'A' and resid 1488 through 1506 Processing helix chain 'A' and resid 1509 through 1518 Processing helix chain 'A' and resid 1519 through 1528 removed outlier: 3.501A pdb=" N VAL A1523 " --> pdb=" O GLY A1519 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU A1528 " --> pdb=" O LEU A1524 " (cutoff:3.500A) Processing helix chain 'A' and resid 1531 through 1539 removed outlier: 3.515A pdb=" N ARG A1536 " --> pdb=" O ASP A1532 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ASN A1537 " --> pdb=" O VAL A1533 " (cutoff:3.500A) Processing helix chain 'A' and resid 1546 through 1564 removed outlier: 3.515A pdb=" N LYS A1564 " --> pdb=" O THR A1560 " (cutoff:3.500A) Processing helix chain 'A' and resid 1565 through 1575 Processing helix chain 'A' and resid 1576 through 1583 Processing helix chain 'A' and resid 1585 through 1589 removed outlier: 3.551A pdb=" N MET A1589 " --> pdb=" O VAL A1586 " (cutoff:3.500A) Processing helix chain 'A' and resid 1610 through 1627 Proline residue: A1621 - end of helix Processing helix chain 'A' and resid 1628 through 1631 Processing helix chain 'A' and resid 1638 through 1650 removed outlier: 3.639A pdb=" N GLY A1642 " --> pdb=" O LEU A1638 " (cutoff:3.500A) Processing helix chain 'A' and resid 1651 through 1660 Processing helix chain 'A' and resid 1665 through 1683 Processing helix chain 'A' and resid 1684 through 1691 removed outlier: 4.076A pdb=" N LEU A1688 " --> pdb=" O LEU A1684 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ASN A1689 " --> pdb=" O PRO A1685 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N GLU A1690 " --> pdb=" O GLY A1686 " (cutoff:3.500A) Processing helix chain 'A' and resid 1698 through 1716 Processing helix chain 'A' and resid 1717 through 1722 Processing helix chain 'A' and resid 1724 through 1732 removed outlier: 4.149A pdb=" N ARG A1728 " --> pdb=" O SER A1724 " (cutoff:3.500A) Processing helix chain 'A' and resid 1738 through 1771 removed outlier: 3.648A pdb=" N ASN A1770 " --> pdb=" O LEU A1766 " (cutoff:3.500A) Processing helix chain 'A' and resid 1772 through 1774 No H-bonds generated for 'chain 'A' and resid 1772 through 1774' Processing helix chain 'A' and resid 1811 through 1844 removed outlier: 3.949A pdb=" N ILE A1815 " --> pdb=" O LEU A1811 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N PHE A1826 " --> pdb=" O ALA A1822 " (cutoff:3.500A) Processing helix chain 'A' and resid 1846 through 1855 Processing helix chain 'A' and resid 1866 through 1913 removed outlier: 4.574A pdb=" N LEU A1912 " --> pdb=" O GLU A1908 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N HIS A1913 " --> pdb=" O TYR A1909 " (cutoff:3.500A) Processing helix chain 'A' and resid 1957 through 1972 removed outlier: 4.292A pdb=" N GLY A1966 " --> pdb=" O LEU A1962 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N ALA A1967 " --> pdb=" O LEU A1963 " (cutoff:3.500A) Processing helix chain 'A' and resid 1995 through 2011 Processing helix chain 'B' and resid 61 through 64 removed outlier: 3.865A pdb=" N TYR B 64 " --> pdb=" O GLU B 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 61 through 64' Processing helix chain 'B' and resid 65 through 85 Processing helix chain 'B' and resid 91 through 123 Processing helix chain 'B' and resid 126 through 152 Processing helix chain 'B' and resid 156 through 172 removed outlier: 3.617A pdb=" N LEU B 161 " --> pdb=" O ALA B 157 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ILE B 162 " --> pdb=" O GLY B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 185 Processing helix chain 'B' and resid 187 through 191 Processing helix chain 'B' and resid 193 through 204 Processing helix chain 'B' and resid 206 through 220 removed outlier: 3.791A pdb=" N LYS B 216 " --> pdb=" O GLN B 212 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N THR B 220 " --> pdb=" O LYS B 216 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 238 Processing helix chain 'B' and resid 248 through 269 Processing helix chain 'B' and resid 275 through 287 Processing helix chain 'B' and resid 288 through 295 Processing helix chain 'B' and resid 301 through 314 Processing helix chain 'B' and resid 321 through 334 Processing helix chain 'B' and resid 341 through 352 Processing helix chain 'B' and resid 354 through 366 Processing helix chain 'B' and resid 369 through 382 Processing helix chain 'B' and resid 396 through 411 Processing helix chain 'B' and resid 414 through 425 removed outlier: 3.663A pdb=" N TYR B 424 " --> pdb=" O ASP B 420 " (cutoff:3.500A) Processing helix chain 'B' and resid 428 through 440 Processing helix chain 'B' and resid 444 through 458 removed outlier: 3.553A pdb=" N ALA B 448 " --> pdb=" O THR B 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 460 through 478 Processing helix chain 'B' and resid 480 through 491 Processing helix chain 'B' and resid 493 through 512 Processing helix chain 'B' and resid 516 through 522 Processing helix chain 'B' and resid 523 through 529 removed outlier: 3.785A pdb=" N MET B 527 " --> pdb=" O GLY B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 530 through 548 Processing helix chain 'B' and resid 550 through 564 Processing helix chain 'B' and resid 568 through 585 removed outlier: 4.001A pdb=" N LEU B 573 " --> pdb=" O CYS B 569 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N THR B 574 " --> pdb=" O SER B 570 " (cutoff:3.500A) Proline residue: B 581 - end of helix removed outlier: 3.663A pdb=" N GLN B 585 " --> pdb=" O PRO B 581 " (cutoff:3.500A) Processing helix chain 'B' and resid 591 through 612 Processing helix chain 'B' and resid 623 through 648 Processing helix chain 'C' and resid 323 through 327 Processing helix chain 'D' and resid 67 through 71 Processing helix chain 'D' and resid 123 through 127 Processing helix chain 'E' and resid 168 through 173 removed outlier: 4.127A pdb=" N TYR E 173 " --> pdb=" O PRO E 169 " (cutoff:3.500A) Processing helix chain 'E' and resid 179 through 183 removed outlier: 3.727A pdb=" N ILE E 183 " --> pdb=" O ASP E 180 " (cutoff:3.500A) Processing helix chain 'E' and resid 280 through 283 Processing helix chain 'E' and resid 325 through 327 No H-bonds generated for 'chain 'E' and resid 325 through 327' Processing helix chain 'E' and resid 333 through 337 Processing helix chain 'E' and resid 455 through 465 Processing helix chain 'E' and resid 471 through 483 Processing helix chain 'E' and resid 493 through 513 Processing helix chain 'E' and resid 519 through 546 Processing helix chain 'E' and resid 575 through 583 Processing helix chain 'E' and resid 584 through 588 Processing helix chain 'E' and resid 592 through 597 removed outlier: 4.117A pdb=" N ILE E 596 " --> pdb=" O ASP E 592 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N SER E 597 " --> pdb=" O GLU E 593 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 592 through 597' Processing helix chain 'E' and resid 599 through 618 Processing helix chain 'E' and resid 621 through 634 Processing helix chain 'E' and resid 637 through 652 Processing helix chain 'E' and resid 656 through 667 Processing helix chain 'E' and resid 670 through 682 Processing helix chain 'E' and resid 698 through 702 Processing helix chain 'E' and resid 707 through 744 removed outlier: 3.935A pdb=" N ASP E 744 " --> pdb=" O LEU E 740 " (cutoff:3.500A) Processing helix chain 'E' and resid 749 through 759 Processing helix chain 'E' and resid 759 through 780 Processing helix chain 'E' and resid 786 through 799 removed outlier: 3.664A pdb=" N VAL E 799 " --> pdb=" O GLN E 795 " (cutoff:3.500A) Processing helix chain 'E' and resid 818 through 827 Processing helix chain 'E' and resid 831 through 839 removed outlier: 3.774A pdb=" N SER E 839 " --> pdb=" O VAL E 835 " (cutoff:3.500A) Processing helix chain 'E' and resid 849 through 866 Processing helix chain 'E' and resid 873 through 881 Processing helix chain 'E' and resid 883 through 895 Processing helix chain 'E' and resid 901 through 916 Processing helix chain 'E' and resid 918 through 929 Processing helix chain 'E' and resid 953 through 969 removed outlier: 3.625A pdb=" N GLY E 969 " --> pdb=" O LEU E 965 " (cutoff:3.500A) Processing helix chain 'E' and resid 972 through 985 Processing helix chain 'E' and resid 988 through 1007 Processing helix chain 'E' and resid 1008 through 1019 Processing helix chain 'E' and resid 1023 through 1040 removed outlier: 4.172A pdb=" N ASP E1027 " --> pdb=" O SER E1023 " (cutoff:3.500A) Processing helix chain 'E' and resid 1041 through 1048 Processing helix chain 'E' and resid 1053 through 1068 Processing helix chain 'E' and resid 1074 through 1085 Processing helix chain 'E' and resid 1088 through 1106 Processing helix chain 'E' and resid 1111 through 1130 removed outlier: 3.540A pdb=" N ILE E1130 " --> pdb=" O CYS E1126 " (cutoff:3.500A) Processing helix chain 'E' and resid 1174 through 1195 removed outlier: 3.548A pdb=" N ASN E1195 " --> pdb=" O LEU E1191 " (cutoff:3.500A) Processing helix chain 'E' and resid 1196 through 1203 removed outlier: 4.335A pdb=" N ALA E1200 " --> pdb=" O PRO E1196 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N ILE E1201 " --> pdb=" O SER E1197 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLY E1203 " --> pdb=" O ALA E1199 " (cutoff:3.500A) Processing helix chain 'E' and resid 1206 through 1218 removed outlier: 3.654A pdb=" N GLY E1218 " --> pdb=" O LEU E1214 " (cutoff:3.500A) Processing helix chain 'E' and resid 1219 through 1230 Processing helix chain 'E' and resid 1234 through 1250 removed outlier: 3.595A pdb=" N GLN E1250 " --> pdb=" O ILE E1246 " (cutoff:3.500A) Processing helix chain 'E' and resid 1252 through 1267 Processing helix chain 'E' and resid 1278 through 1294 Processing helix chain 'E' and resid 1302 through 1312 Processing helix chain 'E' and resid 1317 through 1328 removed outlier: 3.707A pdb=" N MET E1327 " --> pdb=" O ARG E1323 " (cutoff:3.500A) Processing helix chain 'E' and resid 1328 through 1339 removed outlier: 3.926A pdb=" N LEU E1332 " --> pdb=" O ASP E1328 " (cutoff:3.500A) Processing helix chain 'E' and resid 1341 through 1358 Processing helix chain 'E' and resid 1361 through 1365 Processing helix chain 'E' and resid 1380 through 1392 Processing helix chain 'E' and resid 1397 through 1430 Processing helix chain 'G' and resid 1048 through 1055 removed outlier: 3.669A pdb=" N ARG G1055 " --> pdb=" O VAL G1051 " (cutoff:3.500A) Processing helix chain 'G' and resid 1061 through 1066 Processing helix chain 'G' and resid 1075 through 1079 removed outlier: 3.649A pdb=" N TRP G1078 " --> pdb=" O GLY G1075 " (cutoff:3.500A) Processing helix chain 'G' and resid 1136 through 1151 removed outlier: 3.777A pdb=" N TYR G1140 " --> pdb=" O GLU G1136 " (cutoff:3.500A) Proline residue: G1143 - end of helix Processing helix chain 'G' and resid 1169 through 1182 removed outlier: 3.509A pdb=" N ASP G1173 " --> pdb=" O ALA G1169 " (cutoff:3.500A) Processing helix chain 'G' and resid 1192 through 1205 Processing helix chain 'G' and resid 1220 through 1251 removed outlier: 5.014A pdb=" N GLU G1242 " --> pdb=" O HIS G1238 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N ARG G1243 " --> pdb=" O THR G1239 " (cutoff:3.500A) Processing helix chain 'G' and resid 1258 through 1267 Processing helix chain 'G' and resid 1268 through 1276 Processing helix chain 'G' and resid 1284 through 1289 Processing helix chain 'G' and resid 1293 through 1310 Processing helix chain 'G' and resid 1320 through 1330 Processing helix chain 'G' and resid 1349 through 1360 Processing helix chain 'G' and resid 1367 through 1380 Processing helix chain 'G' and resid 1418 through 1429 Processing helix chain 'G' and resid 1439 through 1443 removed outlier: 3.570A pdb=" N VAL G1443 " --> pdb=" O PRO G1440 " (cutoff:3.500A) Processing helix chain 'G' and resid 1450 through 1463 Processing helix chain 'G' and resid 1469 through 1488 Processing helix chain 'G' and resid 1490 through 1498 Processing helix chain 'G' and resid 1502 through 1518 removed outlier: 3.527A pdb=" N ARG G1506 " --> pdb=" O HIS G1502 " (cutoff:3.500A) Processing helix chain 'G' and resid 1524 through 1536 Processing helix chain 'G' and resid 1540 through 1556 removed outlier: 4.237A pdb=" N VAL G1544 " --> pdb=" O PRO G1540 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ARG G1554 " --> pdb=" O ILE G1550 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ASP G1555 " --> pdb=" O ARG G1551 " (cutoff:3.500A) Processing helix chain 'G' and resid 1560 through 1569 Processing helix chain 'G' and resid 1573 through 1585 Processing helix chain 'G' and resid 1592 through 1602 removed outlier: 4.277A pdb=" N SER G1597 " --> pdb=" O ARG G1593 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N PHE G1598 " --> pdb=" O TYR G1594 " (cutoff:3.500A) Processing helix chain 'G' and resid 1613 through 1634 removed outlier: 3.574A pdb=" N ALA G1617 " --> pdb=" O ASP G1613 " (cutoff:3.500A) Processing helix chain 'G' and resid 1641 through 1658 removed outlier: 3.746A pdb=" N CYS G1655 " --> pdb=" O VAL G1651 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N LYS G1656 " --> pdb=" O MET G1652 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N TRP G1657 " --> pdb=" O SER G1653 " (cutoff:3.500A) Processing helix chain 'G' and resid 1659 through 1661 No H-bonds generated for 'chain 'G' and resid 1659 through 1661' Processing helix chain 'G' and resid 1668 through 1691 removed outlier: 3.535A pdb=" N GLN G1691 " --> pdb=" O LEU G1687 " (cutoff:3.500A) Processing helix chain 'H' and resid 67 through 71 Processing helix chain 'I' and resid 145 through 157 removed outlier: 3.833A pdb=" N ASP I 149 " --> pdb=" O SER I 145 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N PHE I 150 " --> pdb=" O MET I 146 " (cutoff:3.500A) Processing helix chain 'I' and resid 161 through 183 removed outlier: 3.503A pdb=" N LEU I 165 " --> pdb=" O ALA I 161 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N ILE I 183 " --> pdb=" O LEU I 179 " (cutoff:3.500A) Processing helix chain 'I' and resid 189 through 223 removed outlier: 4.036A pdb=" N LYS I 193 " --> pdb=" O PRO I 189 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU I 203 " --> pdb=" O SER I 199 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N LEU I 204 " --> pdb=" O ILE I 200 " (cutoff:3.500A) Processing helix chain 'I' and resid 224 through 227 Processing helix chain 'I' and resid 240 through 252 Processing helix chain 'I' and resid 252 through 268 Processing helix chain 'I' and resid 289 through 298 Processing helix chain 'I' and resid 316 through 322 removed outlier: 3.570A pdb=" N ILE I 320 " --> pdb=" O PRO I 316 " (cutoff:3.500A) Processing helix chain 'I' and resid 327 through 348 Processing helix chain 'I' and resid 349 through 361 Processing helix chain 'I' and resid 362 through 369 Processing helix chain 'I' and resid 395 through 408 Processing helix chain 'I' and resid 412 through 424 Processing helix chain 'I' and resid 429 through 434 removed outlier: 3.925A pdb=" N GLU I 434 " --> pdb=" O PRO I 431 " (cutoff:3.500A) Processing helix chain 'I' and resid 435 through 459 Processing helix chain 'I' and resid 463 through 467 Processing helix chain 'I' and resid 479 through 489 Processing helix chain 'I' and resid 496 through 501 Processing helix chain 'I' and resid 501 through 513 Processing helix chain 'I' and resid 515 through 529 removed outlier: 3.577A pdb=" N SER I 527 " --> pdb=" O SER I 523 " (cutoff:3.500A) Processing helix chain 'I' and resid 536 through 552 Processing helix chain 'I' and resid 556 through 574 Processing helix chain 'I' and resid 576 through 587 removed outlier: 3.928A pdb=" N PHE I 582 " --> pdb=" O GLU I 578 " (cutoff:3.500A) Processing helix chain 'I' and resid 590 through 603 removed outlier: 3.588A pdb=" N GLN I 595 " --> pdb=" O LEU I 591 " (cutoff:3.500A) Processing helix chain 'I' and resid 611 through 614 removed outlier: 4.285A pdb=" N GLU I 614 " --> pdb=" O ARG I 611 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 611 through 614' Processing helix chain 'I' and resid 615 through 622 removed outlier: 3.974A pdb=" N ALA I 619 " --> pdb=" O LEU I 615 " (cutoff:3.500A) Processing helix chain 'I' and resid 628 through 642 removed outlier: 3.811A pdb=" N GLU I 641 " --> pdb=" O LYS I 637 " (cutoff:3.500A) Processing helix chain 'I' and resid 653 through 671 Processing helix chain 'I' and resid 676 through 692 Processing helix chain 'I' and resid 695 through 705 Processing helix chain 'I' and resid 709 through 715 Processing helix chain 'I' and resid 719 through 727 removed outlier: 4.013A pdb=" N SER I 725 " --> pdb=" O GLN I 721 " (cutoff:3.500A) Processing helix chain 'I' and resid 730 through 760 removed outlier: 3.710A pdb=" N PHE I 751 " --> pdb=" O SER I 747 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ASN I 759 " --> pdb=" O PHE I 755 " (cutoff:3.500A) Processing helix chain 'I' and resid 772 through 813 removed outlier: 3.574A pdb=" N MET I 788 " --> pdb=" O LYS I 784 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLY I 791 " --> pdb=" O GLU I 787 " (cutoff:3.500A) Processing helix chain 'I' and resid 830 through 859 Proline residue: I 846 - end of helix Processing helix chain 'I' and resid 861 through 867 Processing helix chain 'I' and resid 867 through 874 Processing helix chain 'I' and resid 878 through 882 Processing helix chain 'I' and resid 884 through 905 Processing helix chain 'J' and resid 83 through 93 Processing helix chain 'J' and resid 127 through 131 Processing helix chain 'J' and resid 146 through 148 No H-bonds generated for 'chain 'J' and resid 146 through 148' Processing helix chain 'J' and resid 156 through 158 No H-bonds generated for 'chain 'J' and resid 156 through 158' Processing helix chain 'J' and resid 301 through 316 removed outlier: 3.545A pdb=" N UNK J 307 " --> pdb=" O UNK J 303 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N UNK J 308 " --> pdb=" O UNK J 304 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N UNK J 309 " --> pdb=" O UNK J 305 " (cutoff:3.500A) Processing helix chain 'J' and resid 320 through 326 removed outlier: 4.015A pdb=" N UNK J 326 " --> pdb=" O UNK J 322 " (cutoff:3.500A) Processing helix chain 'J' and resid 389 through 393 Processing helix chain 'J' and resid 435 through 439 removed outlier: 4.053A pdb=" N UNK J 438 " --> pdb=" O UNK J 435 " (cutoff:3.500A) Processing helix chain 'J' and resid 506 through 520 removed outlier: 3.704A pdb=" N UNK J 520 " --> pdb=" O UNK J 516 " (cutoff:3.500A) Processing helix chain 'J' and resid 523 through 534 Processing helix chain 'J' and resid 542 through 560 removed outlier: 3.704A pdb=" N UNK J 550 " --> pdb=" O UNK J 546 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N UNK J 553 " --> pdb=" O UNK J 549 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N UNK J 559 " --> pdb=" O UNK J 555 " (cutoff:3.500A) Processing helix chain 'J' and resid 583 through 604 removed outlier: 3.587A pdb=" N UNK J 604 " --> pdb=" O UNK J 600 " (cutoff:3.500A) Processing helix chain 'J' and resid 623 through 643 Processing helix chain 'J' and resid 645 through 660 Processing helix chain 'J' and resid 672 through 678 removed outlier: 3.921A pdb=" N ARG J 677 " --> pdb=" O UNK J 673 " (cutoff:3.500A) Processing helix chain 'J' and resid 680 through 686 removed outlier: 3.952A pdb=" N ILE J 684 " --> pdb=" O SER J 680 " (cutoff:3.500A) Processing helix chain 'J' and resid 687 through 698 removed outlier: 3.626A pdb=" N ASP J 696 " --> pdb=" O LYS J 692 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N GLU J 698 " --> pdb=" O GLU J 694 " (cutoff:3.500A) Processing helix chain 'J' and resid 705 through 731 removed outlier: 3.651A pdb=" N VAL J 712 " --> pdb=" O ALA J 708 " (cutoff:3.500A) Processing helix chain 'J' and resid 761 through 772 Processing helix chain 'J' and resid 773 through 777 Processing helix chain 'J' and resid 780 through 808 removed outlier: 3.997A pdb=" N TYR J 800 " --> pdb=" O LEU J 796 " (cutoff:3.500A) Processing helix chain 'J' and resid 813 through 835 removed outlier: 3.956A pdb=" N LEU J 830 " --> pdb=" O LYS J 826 " (cutoff:3.500A) Proline residue: J 833 - end of helix Processing helix chain 'J' and resid 842 through 850 Processing helix chain 'J' and resid 853 through 864 removed outlier: 3.602A pdb=" N ILE J 859 " --> pdb=" O ILE J 855 " (cutoff:3.500A) Processing helix chain 'J' and resid 866 through 876 Processing helix chain 'J' and resid 879 through 891 Processing helix chain 'J' and resid 908 through 915 removed outlier: 3.573A pdb=" N ALA J 915 " --> pdb=" O ALA J 911 " (cutoff:3.500A) Processing helix chain 'J' and resid 921 through 927 Processing helix chain 'J' and resid 929 through 944 Processing helix chain 'J' and resid 947 through 964 Processing helix chain 'J' and resid 968 through 991 removed outlier: 3.733A pdb=" N HIS J 988 " --> pdb=" O HIS J 984 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N GLN J 989 " --> pdb=" O PHE J 985 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLU J 990 " --> pdb=" O LEU J 986 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N THR J 991 " --> pdb=" O LEU J 987 " (cutoff:3.500A) Processing helix chain 'J' and resid 993 through 1001 removed outlier: 3.857A pdb=" N GLU J 998 " --> pdb=" O LYS J 994 " (cutoff:3.500A) Processing helix chain 'J' and resid 1011 through 1021 Processing helix chain 'J' and resid 1028 through 1038 Processing helix chain 'J' and resid 1044 through 1049 Processing helix chain 'J' and resid 1049 through 1064 removed outlier: 3.558A pdb=" N ILE J1062 " --> pdb=" O LEU J1058 " (cutoff:3.500A) Processing helix chain 'J' and resid 1078 through 1089 removed outlier: 3.909A pdb=" N LEU J1089 " --> pdb=" O PHE J1085 " (cutoff:3.500A) Processing helix chain 'J' and resid 1091 through 1096 removed outlier: 3.973A pdb=" N LYS J1095 " --> pdb=" O ASN J1091 " (cutoff:3.500A) Processing helix chain 'J' and resid 1108 through 1118 Processing helix chain 'J' and resid 1120 through 1138 removed outlier: 5.995A pdb=" N PHE J1126 " --> pdb=" O SER J1122 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N SER J1127 " --> pdb=" O TYR J1123 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N CYS J1134 " --> pdb=" O ALA J1130 " (cutoff:3.500A) Processing helix chain 'K' and resid 9 through 21 Processing helix chain 'K' and resid 25 through 39 Processing helix chain 'K' and resid 41 through 56 Processing helix chain 'K' and resid 59 through 74 Processing helix chain 'K' and resid 75 through 90 Processing helix chain 'K' and resid 95 through 107 removed outlier: 3.863A pdb=" N ARG K 99 " --> pdb=" O ASP K 95 " (cutoff:3.500A) Processing helix chain 'K' and resid 113 through 125 removed outlier: 4.101A pdb=" N TRP K 117 " --> pdb=" O ARG K 113 " (cutoff:3.500A) Processing helix chain 'K' and resid 128 through 140 Processing helix chain 'K' and resid 147 through 161 Processing helix chain 'K' and resid 164 through 178 Processing helix chain 'K' and resid 183 through 196 Proline residue: K 191 - end of helix Processing helix chain 'K' and resid 198 through 214 Processing helix chain 'K' and resid 223 through 243 removed outlier: 3.711A pdb=" N LYS K 230 " --> pdb=" O ARG K 226 " (cutoff:3.500A) Processing helix chain 'K' and resid 249 through 270 removed outlier: 3.976A pdb=" N ALA K 255 " --> pdb=" O LYS K 251 " (cutoff:3.500A) Processing helix chain 'K' and resid 277 through 305 Processing helix chain 'K' and resid 312 through 324 Processing helix chain 'K' and resid 339 through 362 removed outlier: 4.231A pdb=" N LEU K 343 " --> pdb=" O GLY K 339 " (cutoff:3.500A) Processing helix chain 'K' and resid 367 through 375 Processing helix chain 'K' and resid 379 through 390 removed outlier: 3.705A pdb=" N PHE K 388 " --> pdb=" O ILE K 384 " (cutoff:3.500A) Processing helix chain 'K' and resid 415 through 427 removed outlier: 3.629A pdb=" N SER K 420 " --> pdb=" O LEU K 416 " (cutoff:3.500A) Processing helix chain 'K' and resid 433 through 447 Processing helix chain 'K' and resid 452 through 461 Processing helix chain 'K' and resid 480 through 501 Processing helix chain 'K' and resid 524 through 539 Processing helix chain 'K' and resid 551 through 562 Processing helix chain 'K' and resid 570 through 588 removed outlier: 4.332A pdb=" N LEU K 574 " --> pdb=" O GLN K 570 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU K 588 " --> pdb=" O THR K 584 " (cutoff:3.500A) Processing helix chain 'K' and resid 590 through 614 removed outlier: 4.212A pdb=" N GLU K 596 " --> pdb=" O TYR K 592 " (cutoff:3.500A) Proline residue: K 610 - end of helix removed outlier: 3.887A pdb=" N LEU K 614 " --> pdb=" O PRO K 610 " (cutoff:3.500A) Processing helix chain 'K' and resid 640 through 659 removed outlier: 4.463A pdb=" N ASP K 644 " --> pdb=" O SER K 640 " (cutoff:3.500A) Processing helix chain 'K' and resid 662 through 671 Processing helix chain 'K' and resid 675 through 690 removed outlier: 3.884A pdb=" N TYR K 679 " --> pdb=" O ASN K 675 " (cutoff:3.500A) Processing helix chain 'K' and resid 697 through 713 removed outlier: 3.762A pdb=" N GLU K 701 " --> pdb=" O CYS K 697 " (cutoff:3.500A) Processing helix chain 'K' and resid 722 through 734 removed outlier: 3.813A pdb=" N ALA K 726 " --> pdb=" O ASP K 722 " (cutoff:3.500A) Proline residue: K 728 - end of helix Processing helix chain 'L' and resid 5 through 21 Processing helix chain 'L' and resid 25 through 36 Processing helix chain 'L' and resid 43 through 53 Processing helix chain 'L' and resid 61 through 74 Processing helix chain 'L' and resid 75 through 90 Processing helix chain 'L' and resid 95 through 107 removed outlier: 3.876A pdb=" N ARG L 99 " --> pdb=" O ASP L 95 " (cutoff:3.500A) Processing helix chain 'L' and resid 113 through 125 removed outlier: 3.994A pdb=" N TRP L 117 " --> pdb=" O ARG L 113 " (cutoff:3.500A) Processing helix chain 'L' and resid 128 through 142 Processing helix chain 'L' and resid 148 through 161 Processing helix chain 'L' and resid 163 through 174 Processing helix chain 'L' and resid 181 through 194 removed outlier: 4.081A pdb=" N LYS L 190 " --> pdb=" O LEU L 186 " (cutoff:3.500A) Proline residue: L 191 - end of helix Processing helix chain 'L' and resid 197 through 213 removed outlier: 4.109A pdb=" N GLU L 201 " --> pdb=" O ARG L 197 " (cutoff:3.500A) Processing helix chain 'L' and resid 223 through 243 Processing helix chain 'L' and resid 249 through 270 removed outlier: 4.116A pdb=" N ALA L 255 " --> pdb=" O LYS L 251 " (cutoff:3.500A) Processing helix chain 'L' and resid 277 through 305 Processing helix chain 'L' and resid 312 through 324 Processing helix chain 'L' and resid 341 through 361 Processing helix chain 'L' and resid 367 through 375 Processing helix chain 'L' and resid 379 through 390 removed outlier: 3.738A pdb=" N PHE L 388 " --> pdb=" O ILE L 384 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU L 389 " --> pdb=" O LEU L 385 " (cutoff:3.500A) Processing helix chain 'L' and resid 415 through 427 Processing helix chain 'L' and resid 433 through 447 Processing helix chain 'L' and resid 452 through 461 Processing helix chain 'L' and resid 480 through 501 Processing helix chain 'L' and resid 524 through 539 Processing helix chain 'L' and resid 551 through 562 Processing helix chain 'L' and resid 570 through 588 removed outlier: 3.900A pdb=" N LEU L 574 " --> pdb=" O GLN L 570 " (cutoff:3.500A) Processing helix chain 'L' and resid 590 through 612 removed outlier: 4.680A pdb=" N GLU L 596 " --> pdb=" O TYR L 592 " (cutoff:3.500A) Proline residue: L 610 - end of helix Processing helix chain 'L' and resid 638 through 659 removed outlier: 3.631A pdb=" N VAL L 642 " --> pdb=" O LYS L 638 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N LYS L 643 " --> pdb=" O VAL L 639 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N ASP L 644 " --> pdb=" O SER L 640 " (cutoff:3.500A) Processing helix chain 'L' and resid 662 through 671 Processing helix chain 'L' and resid 675 through 690 removed outlier: 3.699A pdb=" N TYR L 679 " --> pdb=" O ASN L 675 " (cutoff:3.500A) Processing helix chain 'L' and resid 697 through 713 removed outlier: 3.803A pdb=" N GLU L 701 " --> pdb=" O CYS L 697 " (cutoff:3.500A) Processing helix chain 'L' and resid 722 through 734 removed outlier: 3.688A pdb=" N ALA L 726 " --> pdb=" O ASP L 722 " (cutoff:3.500A) Proline residue: L 728 - end of helix Processing helix chain 'M' and resid 60 through 73 Processing helix chain 'M' and resid 75 through 90 Processing helix chain 'M' and resid 95 through 107 removed outlier: 4.582A pdb=" N ARG M 99 " --> pdb=" O ASP M 95 " (cutoff:3.500A) Processing helix chain 'M' and resid 114 through 125 Processing helix chain 'M' and resid 128 through 142 Processing helix chain 'M' and resid 146 through 161 Processing helix chain 'M' and resid 164 through 177 Processing helix chain 'M' and resid 181 through 196 Proline residue: M 191 - end of helix Processing helix chain 'M' and resid 198 through 217 Processing helix chain 'M' and resid 223 through 243 removed outlier: 5.036A pdb=" N LYS M 230 " --> pdb=" O ARG M 226 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N GLU M 231 " --> pdb=" O MET M 227 " (cutoff:3.500A) Processing helix chain 'M' and resid 249 through 270 removed outlier: 3.748A pdb=" N LYS M 253 " --> pdb=" O VAL M 249 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N ALA M 255 " --> pdb=" O LYS M 251 " (cutoff:3.500A) Processing helix chain 'M' and resid 277 through 305 Processing helix chain 'M' and resid 312 through 324 Processing helix chain 'M' and resid 340 through 361 Processing helix chain 'M' and resid 367 through 375 Processing helix chain 'M' and resid 379 through 390 removed outlier: 3.951A pdb=" N PHE M 388 " --> pdb=" O ILE M 384 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N LEU M 389 " --> pdb=" O LEU M 385 " (cutoff:3.500A) Processing helix chain 'M' and resid 415 through 427 Processing helix chain 'M' and resid 433 through 447 Processing helix chain 'M' and resid 452 through 461 removed outlier: 3.673A pdb=" N TRP M 456 " --> pdb=" O PRO M 452 " (cutoff:3.500A) Processing helix chain 'M' and resid 480 through 502 Processing helix chain 'M' and resid 524 through 539 Processing helix chain 'M' and resid 551 through 562 Processing helix chain 'M' and resid 570 through 587 removed outlier: 3.798A pdb=" N LEU M 574 " --> pdb=" O GLN M 570 " (cutoff:3.500A) Processing helix chain 'M' and resid 590 through 614 removed outlier: 3.950A pdb=" N GLU M 596 " --> pdb=" O TYR M 592 " (cutoff:3.500A) Proline residue: M 610 - end of helix Processing helix chain 'M' and resid 641 through 659 Processing helix chain 'M' and resid 662 through 671 removed outlier: 3.609A pdb=" N ILE M 667 " --> pdb=" O THR M 663 " (cutoff:3.500A) Processing helix chain 'M' and resid 675 through 691 Processing helix chain 'M' and resid 697 through 713 removed outlier: 3.695A pdb=" N GLU M 701 " --> pdb=" O CYS M 697 " (cutoff:3.500A) Processing helix chain 'M' and resid 725 through 734 removed outlier: 4.111A pdb=" N SER M 729 " --> pdb=" O SER M 725 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE M 730 " --> pdb=" O ALA M 726 " (cutoff:3.500A) Processing helix chain 'N' and resid 5 through 21 removed outlier: 3.662A pdb=" N GLN N 9 " --> pdb=" O LYS N 5 " (cutoff:3.500A) Processing helix chain 'N' and resid 25 through 39 Processing helix chain 'N' and resid 41 through 55 Processing helix chain 'N' and resid 60 through 74 Processing helix chain 'N' and resid 75 through 90 Processing helix chain 'N' and resid 96 through 107 Processing helix chain 'N' and resid 114 through 125 Processing helix chain 'N' and resid 128 through 142 Processing helix chain 'N' and resid 148 through 161 Processing helix chain 'N' and resid 164 through 178 Processing helix chain 'N' and resid 182 through 196 Proline residue: N 191 - end of helix Processing helix chain 'N' and resid 198 through 213 Processing helix chain 'N' and resid 223 through 243 removed outlier: 3.998A pdb=" N LYS N 230 " --> pdb=" O ARG N 226 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N GLU N 231 " --> pdb=" O MET N 227 " (cutoff:3.500A) Processing helix chain 'N' and resid 249 through 270 removed outlier: 4.716A pdb=" N ALA N 255 " --> pdb=" O LYS N 251 " (cutoff:3.500A) Processing helix chain 'N' and resid 277 through 305 Processing helix chain 'N' and resid 312 through 324 Processing helix chain 'N' and resid 339 through 361 removed outlier: 3.899A pdb=" N LEU N 343 " --> pdb=" O GLY N 339 " (cutoff:3.500A) Processing helix chain 'N' and resid 367 through 375 Processing helix chain 'N' and resid 379 through 390 removed outlier: 4.087A pdb=" N LEU N 389 " --> pdb=" O LEU N 385 " (cutoff:3.500A) Processing helix chain 'N' and resid 415 through 427 Processing helix chain 'N' and resid 433 through 447 Processing helix chain 'N' and resid 452 through 461 Processing helix chain 'N' and resid 480 through 502 removed outlier: 3.652A pdb=" N LEU N 484 " --> pdb=" O CYS N 480 " (cutoff:3.500A) Processing helix chain 'N' and resid 524 through 539 Processing helix chain 'N' and resid 551 through 562 Processing helix chain 'N' and resid 570 through 588 removed outlier: 4.110A pdb=" N LEU N 574 " --> pdb=" O GLN N 570 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N LEU N 588 " --> pdb=" O THR N 584 " (cutoff:3.500A) Processing helix chain 'N' and resid 590 through 613 removed outlier: 4.256A pdb=" N GLU N 596 " --> pdb=" O TYR N 592 " (cutoff:3.500A) Proline residue: N 610 - end of helix Processing helix chain 'N' and resid 640 through 659 removed outlier: 4.025A pdb=" N ASP N 644 " --> pdb=" O SER N 640 " (cutoff:3.500A) Processing helix chain 'N' and resid 662 through 671 removed outlier: 3.535A pdb=" N ILE N 667 " --> pdb=" O THR N 663 " (cutoff:3.500A) Processing helix chain 'N' and resid 675 through 690 removed outlier: 4.042A pdb=" N TYR N 679 " --> pdb=" O ASN N 675 " (cutoff:3.500A) Processing helix chain 'N' and resid 697 through 713 removed outlier: 3.753A pdb=" N GLU N 701 " --> pdb=" O CYS N 697 " (cutoff:3.500A) Processing helix chain 'N' and resid 722 through 734 removed outlier: 3.542A pdb=" N ALA N 726 " --> pdb=" O ASP N 722 " (cutoff:3.500A) Proline residue: N 728 - end of helix Processing helix chain 'O' and resid 14 through 21 Processing helix chain 'O' and resid 26 through 39 Processing helix chain 'O' and resid 41 through 56 Processing helix chain 'O' and resid 59 through 74 Processing helix chain 'O' and resid 75 through 90 Processing helix chain 'O' and resid 94 through 107 removed outlier: 4.244A pdb=" N LEU O 98 " --> pdb=" O LYS O 94 " (cutoff:3.500A) Processing helix chain 'O' and resid 113 through 125 removed outlier: 4.162A pdb=" N TRP O 117 " --> pdb=" O ARG O 113 " (cutoff:3.500A) Processing helix chain 'O' and resid 128 through 141 Processing helix chain 'O' and resid 147 through 161 Processing helix chain 'O' and resid 164 through 178 Processing helix chain 'O' and resid 183 through 196 Proline residue: O 191 - end of helix removed outlier: 3.505A pdb=" N ALA O 195 " --> pdb=" O PRO O 191 " (cutoff:3.500A) Processing helix chain 'O' and resid 198 through 216 Processing helix chain 'O' and resid 223 through 243 removed outlier: 4.059A pdb=" N LYS O 230 " --> pdb=" O ARG O 226 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N GLU O 231 " --> pdb=" O MET O 227 " (cutoff:3.500A) Processing helix chain 'O' and resid 249 through 270 removed outlier: 3.932A pdb=" N ALA O 255 " --> pdb=" O LYS O 251 " (cutoff:3.500A) Processing helix chain 'O' and resid 276 through 305 removed outlier: 4.499A pdb=" N VAL O 280 " --> pdb=" O SER O 276 " (cutoff:3.500A) Processing helix chain 'O' and resid 312 through 325 Processing helix chain 'O' and resid 339 through 362 removed outlier: 4.338A pdb=" N LEU O 343 " --> pdb=" O GLY O 339 " (cutoff:3.500A) Processing helix chain 'O' and resid 366 through 375 removed outlier: 3.941A pdb=" N SER O 370 " --> pdb=" O GLN O 366 " (cutoff:3.500A) Processing helix chain 'O' and resid 379 through 390 removed outlier: 3.601A pdb=" N PHE O 388 " --> pdb=" O ILE O 384 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N LEU O 389 " --> pdb=" O LEU O 385 " (cutoff:3.500A) Processing helix chain 'O' and resid 400 through 404 removed outlier: 3.686A pdb=" N SER O 403 " --> pdb=" O PHE O 400 " (cutoff:3.500A) Processing helix chain 'O' and resid 417 through 427 Processing helix chain 'O' and resid 433 through 447 Processing helix chain 'O' and resid 452 through 461 removed outlier: 3.816A pdb=" N TRP O 456 " --> pdb=" O PRO O 452 " (cutoff:3.500A) Processing helix chain 'O' and resid 480 through 502 removed outlier: 3.556A pdb=" N LEU O 484 " --> pdb=" O CYS O 480 " (cutoff:3.500A) Processing helix chain 'O' and resid 524 through 539 Processing helix chain 'O' and resid 551 through 562 Processing helix chain 'O' and resid 570 through 588 removed outlier: 3.900A pdb=" N LEU O 574 " --> pdb=" O GLN O 570 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LEU O 588 " --> pdb=" O THR O 584 " (cutoff:3.500A) Processing helix chain 'O' and resid 590 through 612 removed outlier: 4.730A pdb=" N GLU O 596 " --> pdb=" O TYR O 592 " (cutoff:3.500A) Proline residue: O 610 - end of helix Processing helix chain 'O' and resid 646 through 659 Processing helix chain 'O' and resid 664 through 671 Processing helix chain 'O' and resid 675 through 690 Processing helix chain 'O' and resid 696 through 713 removed outlier: 3.759A pdb=" N ALA O 700 " --> pdb=" O ASP O 696 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU O 701 " --> pdb=" O CYS O 697 " (cutoff:3.500A) Processing helix chain 'O' and resid 722 through 734 removed outlier: 4.193A pdb=" N ALA O 726 " --> pdb=" O ASP O 722 " (cutoff:3.500A) Proline residue: O 728 - end of helix Processing helix chain 'P' and resid 181 through 199 Processing helix chain 'P' and resid 204 through 216 Processing helix chain 'P' and resid 218 through 233 Processing helix chain 'P' and resid 241 through 248 Processing helix chain 'P' and resid 248 through 275 removed outlier: 3.759A pdb=" N GLN P 252 " --> pdb=" O SER P 248 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N ILE P 273 " --> pdb=" O ASN P 269 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N SER P 274 " --> pdb=" O TYR P 270 " (cutoff:3.500A) Processing helix chain 'P' and resid 290 through 301 Processing helix chain 'P' and resid 320 through 330 Processing helix chain 'P' and resid 331 through 342 Processing helix chain 'P' and resid 342 through 347 removed outlier: 4.019A pdb=" N LEU P 346 " --> pdb=" O ALA P 342 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N GLY P 347 " --> pdb=" O GLN P 343 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 342 through 347' Processing helix chain 'P' and resid 347 through 359 removed outlier: 4.330A pdb=" N ASN P 351 " --> pdb=" O GLY P 347 " (cutoff:3.500A) Processing helix chain 'P' and resid 365 through 379 Processing helix chain 'P' and resid 386 through 397 Processing helix chain 'P' and resid 410 through 422 Processing helix chain 'P' and resid 437 through 447 Processing helix chain 'P' and resid 462 through 470 Processing helix chain 'P' and resid 472 through 483 Processing helix chain 'P' and resid 486 through 500 Processing helix chain 'P' and resid 528 through 541 removed outlier: 4.391A pdb=" N PHE P 540 " --> pdb=" O TYR P 536 " (cutoff:3.500A) Processing helix chain 'P' and resid 544 through 553 Processing helix chain 'P' and resid 565 through 579 Processing helix chain 'P' and resid 580 through 585 Processing helix chain 'P' and resid 605 through 620 Processing helix chain 'P' and resid 622 through 633 Processing helix chain 'P' and resid 635 through 651 Proline residue: P 649 - end of helix Processing helix chain 'P' and resid 660 through 679 Processing helix chain 'P' and resid 684 through 706 Processing helix chain 'P' and resid 707 through 719 removed outlier: 3.592A pdb=" N LYS P 719 " --> pdb=" O ILE P 715 " (cutoff:3.500A) Processing helix chain 'P' and resid 726 through 736 removed outlier: 4.277A pdb=" N GLU P 730 " --> pdb=" O ASP P 726 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ARG P 736 " --> pdb=" O VAL P 732 " (cutoff:3.500A) Processing helix chain 'P' and resid 739 through 767 removed outlier: 4.738A pdb=" N SER P 747 " --> pdb=" O ARG P 743 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N GLU P 748 " --> pdb=" O HIS P 744 " (cutoff:3.500A) Processing helix chain 'P' and resid 784 through 800 Processing helix chain 'P' and resid 805 through 820 Processing helix chain 'S' and resid 102 through 152 Processing helix chain 'W' and resid 1057 through 1067 Processing helix chain 'W' and resid 1071 through 1085 Processing helix chain 'W' and resid 1087 through 1101 Processing helix chain 'W' and resid 1110 through 1126 Processing helix chain 'W' and resid 1131 through 1162 Processing helix chain 'W' and resid 1165 through 1178 removed outlier: 3.565A pdb=" N GLY W1169 " --> pdb=" O HIS W1165 " (cutoff:3.500A) Processing helix chain 'W' and resid 1181 through 1191 Processing helix chain 'W' and resid 1195 through 1207 Processing helix chain 'W' and resid 1210 through 1230 Processing helix chain 'W' and resid 1233 through 1252 Processing helix chain 'W' and resid 1260 through 1276 Processing helix chain 'W' and resid 1280 through 1289 Processing helix chain 'W' and resid 1292 through 1306 Processing helix chain 'W' and resid 1308 through 1314 removed outlier: 4.239A pdb=" N SER W1312 " --> pdb=" O ASP W1308 " (cutoff:3.500A) Processing helix chain 'W' and resid 1316 through 1334 removed outlier: 3.595A pdb=" N LEU W1320 " --> pdb=" O LYS W1316 " (cutoff:3.500A) Processing helix chain 'W' and resid 1335 through 1338 Processing helix chain 'W' and resid 1339 through 1341 No H-bonds generated for 'chain 'W' and resid 1339 through 1341' Processing helix chain 'W' and resid 1342 through 1364 Processing helix chain 'W' and resid 1367 through 1388 Processing helix chain 'X' and resid 686 through 692 Processing helix chain 'X' and resid 726 through 730 Processing helix chain 'X' and resid 743 through 747 Processing helix chain 'X' and resid 778 through 785 Processing helix chain 'X' and resid 786 through 798 removed outlier: 3.589A pdb=" N UNK X 790 " --> pdb=" O UNK X 786 " (cutoff:3.500A) Processing helix chain 'X' and resid 825 through 831 removed outlier: 3.905A pdb=" N UNK X 829 " --> pdb=" O UNK X 825 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N UNK X 830 " --> pdb=" O UNK X 826 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N UNK X 831 " --> pdb=" O UNK X 827 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 825 through 831' Processing helix chain 'X' and resid 831 through 836 removed outlier: 4.078A pdb=" N UNK X 835 " --> pdb=" O UNK X 831 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N UNK X 836 " --> pdb=" O UNK X 832 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 831 through 836' Processing helix chain 'Y' and resid 148 through 155 removed outlier: 3.501A pdb=" N PHE Y 152 " --> pdb=" O ALA Y 148 " (cutoff:3.500A) Processing helix chain 'Y' and resid 216 through 222 Processing helix chain 'i' and resid 145 through 157 removed outlier: 3.588A pdb=" N ASP i 149 " --> pdb=" O SER i 145 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N PHE i 150 " --> pdb=" O MET i 146 " (cutoff:3.500A) Processing helix chain 'i' and resid 158 through 160 No H-bonds generated for 'chain 'i' and resid 158 through 160' Processing helix chain 'i' and resid 161 through 181 removed outlier: 3.938A pdb=" N LEU i 165 " --> pdb=" O ALA i 161 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ILE i 166 " --> pdb=" O VAL i 162 " (cutoff:3.500A) Processing helix chain 'i' and resid 201 through 223 Processing helix chain 'i' and resid 224 through 227 removed outlier: 3.552A pdb=" N GLU i 227 " --> pdb=" O SER i 224 " (cutoff:3.500A) No H-bonds generated for 'chain 'i' and resid 224 through 227' Processing helix chain 'i' and resid 240 through 252 Processing helix chain 'i' and resid 252 through 268 Processing helix chain 'i' and resid 289 through 295 Processing helix chain 'i' and resid 317 through 322 Processing helix chain 'i' and resid 327 through 348 Processing helix chain 'i' and resid 349 through 361 Processing helix chain 'i' and resid 362 through 370 Processing helix chain 'i' and resid 414 through 424 Processing helix chain 'i' and resid 429 through 434 removed outlier: 3.752A pdb=" N VAL i 432 " --> pdb=" O LEU i 429 " (cutoff:3.500A) Processing helix chain 'i' and resid 435 through 458 Processing helix chain 'i' and resid 479 through 489 Processing helix chain 'i' and resid 496 through 501 Processing helix chain 'i' and resid 501 through 513 Processing helix chain 'i' and resid 514 through 528 removed outlier: 3.779A pdb=" N LEU i 518 " --> pdb=" O ASP i 514 " (cutoff:3.500A) Processing helix chain 'i' and resid 534 through 552 removed outlier: 4.064A pdb=" N LEU i 538 " --> pdb=" O LEU i 534 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ARG i 539 " --> pdb=" O GLY i 535 " (cutoff:3.500A) Processing helix chain 'i' and resid 556 through 574 Processing helix chain 'i' and resid 576 through 587 removed outlier: 3.848A pdb=" N PHE i 582 " --> pdb=" O GLU i 578 " (cutoff:3.500A) Processing helix chain 'i' and resid 590 through 605 removed outlier: 4.108A pdb=" N GLN i 595 " --> pdb=" O LEU i 591 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ASP i 605 " --> pdb=" O GLU i 601 " (cutoff:3.500A) Processing helix chain 'i' and resid 614 through 625 removed outlier: 3.654A pdb=" N VAL i 623 " --> pdb=" O ALA i 619 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N SER i 625 " --> pdb=" O LEU i 621 " (cutoff:3.500A) Processing helix chain 'i' and resid 629 through 641 removed outlier: 3.720A pdb=" N GLU i 641 " --> pdb=" O LYS i 637 " (cutoff:3.500A) Processing helix chain 'i' and resid 653 through 671 Processing helix chain 'i' and resid 676 through 693 removed outlier: 3.756A pdb=" N SER i 693 " --> pdb=" O LYS i 689 " (cutoff:3.500A) Processing helix chain 'i' and resid 695 through 706 removed outlier: 3.800A pdb=" N ILE i 706 " --> pdb=" O VAL i 702 " (cutoff:3.500A) Processing helix chain 'i' and resid 709 through 715 Processing helix chain 'i' and resid 719 through 727 removed outlier: 3.603A pdb=" N SER i 725 " --> pdb=" O GLN i 721 " (cutoff:3.500A) Processing helix chain 'i' and resid 732 through 759 removed outlier: 3.641A pdb=" N PHE i 751 " --> pdb=" O SER i 747 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ASN i 759 " --> pdb=" O PHE i 755 " (cutoff:3.500A) Processing helix chain 'i' and resid 773 through 827 removed outlier: 4.470A pdb=" N LYS i 807 " --> pdb=" O ASP i 803 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ILE i 808 " --> pdb=" O VAL i 804 " (cutoff:3.500A) Processing helix chain 'i' and resid 831 through 859 Proline residue: i 846 - end of helix Processing helix chain 'i' and resid 861 through 874 removed outlier: 4.403A pdb=" N ALA i 869 " --> pdb=" O CYS i 865 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ASP i 870 " --> pdb=" O LEU i 866 " (cutoff:3.500A) Processing helix chain 'i' and resid 878 through 883 removed outlier: 3.550A pdb=" N PHE i 883 " --> pdb=" O TYR i 880 " (cutoff:3.500A) Processing helix chain 'i' and resid 884 through 903 Processing helix chain 's' and resid 102 through 152 Processing helix chain 'a' and resid 14 through 28 removed outlier: 3.894A pdb=" N ARG a 18 " --> pdb=" O TRP a 14 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N TRP a 21 " --> pdb=" O TYR a 17 " (cutoff:3.500A) Processing helix chain 'a' and resid 32 through 46 removed outlier: 3.524A pdb=" N SER a 38 " --> pdb=" O GLU a 34 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N ILE a 41 " --> pdb=" O HIS a 37 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N LYS a 44 " --> pdb=" O ASP a 40 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LYS a 45 " --> pdb=" O ILE a 41 " (cutoff:3.500A) Processing helix chain 'a' and resid 46 through 52 removed outlier: 3.641A pdb=" N PHE a 50 " --> pdb=" O TYR a 46 " (cutoff:3.500A) Processing helix chain 'a' and resid 62 through 67 Processing helix chain 'a' and resid 90 through 96 removed outlier: 3.538A pdb=" N ILE a 96 " --> pdb=" O LYS a 92 " (cutoff:3.500A) Processing helix chain 'a' and resid 97 through 100 removed outlier: 3.703A pdb=" N LEU a 100 " --> pdb=" O LEU a 97 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 97 through 100' Processing helix chain 'a' and resid 104 through 118 removed outlier: 3.502A pdb=" N GLU a 110 " --> pdb=" O ILE a 106 " (cutoff:3.500A) Processing helix chain 'a' and resid 126 through 153 removed outlier: 3.629A pdb=" N LYS a 139 " --> pdb=" O TYR a 135 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU a 146 " --> pdb=" O MET a 142 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA a 152 " --> pdb=" O HIS a 148 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ARG a 153 " --> pdb=" O LEU a 149 " (cutoff:3.500A) Processing helix chain 'a' and resid 166 through 179 Processing helix chain 'a' and resid 183 through 201 removed outlier: 3.603A pdb=" N ASN a 196 " --> pdb=" O GLN a 192 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLU a 198 " --> pdb=" O ASP a 194 " (cutoff:3.500A) Processing helix chain 'a' and resid 212 through 239 removed outlier: 3.536A pdb=" N GLN a 238 " --> pdb=" O SER a 234 " (cutoff:3.500A) Processing helix chain 'a' and resid 242 through 254 Processing helix chain 'a' and resid 265 through 280 removed outlier: 3.574A pdb=" N THR a 270 " --> pdb=" O LYS a 266 " (cutoff:3.500A) Processing helix chain 'a' and resid 281 through 284 Processing helix chain 'a' and resid 290 through 298 Processing helix chain 'a' and resid 303 through 315 removed outlier: 3.603A pdb=" N ILE a 307 " --> pdb=" O ASP a 303 " (cutoff:3.500A) Processing helix chain 'a' and resid 322 through 340 removed outlier: 3.969A pdb=" N GLN a 326 " --> pdb=" O SER a 322 " (cutoff:3.500A) Processing helix chain 'a' and resid 350 through 352 No H-bonds generated for 'chain 'a' and resid 350 through 352' Processing helix chain 'a' and resid 353 through 363 Processing helix chain 'a' and resid 364 through 372 removed outlier: 3.867A pdb=" N THR a 370 " --> pdb=" O PHE a 366 " (cutoff:3.500A) Processing helix chain 'a' and resid 383 through 400 removed outlier: 3.509A pdb=" N ARG a 388 " --> pdb=" O PHE a 384 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ILE a 389 " --> pdb=" O PHE a 385 " (cutoff:3.500A) Proline residue: a 397 - end of helix removed outlier: 3.593A pdb=" N MET a 400 " --> pdb=" O PHE a 396 " (cutoff:3.500A) Processing helix chain 'a' and resid 400 through 425 removed outlier: 3.775A pdb=" N ALA a 411 " --> pdb=" O LEU a 407 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ILE a 418 " --> pdb=" O ASP a 414 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N MET a 424 " --> pdb=" O MET a 420 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N GLY a 425 " --> pdb=" O SER a 421 " (cutoff:3.500A) Processing helix chain 'a' and resid 434 through 447 removed outlier: 3.963A pdb=" N TYR a 447 " --> pdb=" O ILE a 443 " (cutoff:3.500A) Processing helix chain 'a' and resid 455 through 460 Processing helix chain 'a' and resid 485 through 498 Processing helix chain 'a' and resid 503 through 505 No H-bonds generated for 'chain 'a' and resid 503 through 505' Processing helix chain 'a' and resid 506 through 518 Processing helix chain 'a' and resid 520 through 534 Processing helix chain 'a' and resid 551 through 568 Processing helix chain 'a' and resid 587 through 608 removed outlier: 3.503A pdb=" N THR a 601 " --> pdb=" O CYS a 597 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N TRP a 607 " --> pdb=" O THR a 603 " (cutoff:3.500A) Processing helix chain 'a' and resid 608 through 617 removed outlier: 3.674A pdb=" N ARG a 612 " --> pdb=" O SER a 608 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N CYS a 616 " --> pdb=" O ARG a 612 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLU a 617 " --> pdb=" O LEU a 613 " (cutoff:3.500A) Processing helix chain 'a' and resid 622 through 632 removed outlier: 3.766A pdb=" N VAL a 626 " --> pdb=" O MET a 622 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLN a 632 " --> pdb=" O LEU a 628 " (cutoff:3.500A) Processing helix chain 'a' and resid 636 through 652 Processing helix chain 'a' and resid 653 through 668 removed outlier: 3.540A pdb=" N GLN a 662 " --> pdb=" O ALA a 658 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLU a 665 " --> pdb=" O TRP a 661 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N TYR a 666 " --> pdb=" O GLN a 662 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLN a 668 " --> pdb=" O LEU a 664 " (cutoff:3.500A) Processing helix chain 'a' and resid 683 through 691 Processing helix chain 'a' and resid 691 through 696 Processing helix chain 'a' and resid 698 through 715 removed outlier: 3.809A pdb=" N ARG a 702 " --> pdb=" O TYR a 698 " (cutoff:3.500A) Processing helix chain 'a' and resid 729 through 746 removed outlier: 3.754A pdb=" N ARG a 745 " --> pdb=" O PHE a 741 " (cutoff:3.500A) Processing helix chain 'a' and resid 751 through 772 removed outlier: 4.128A pdb=" N LYS a 755 " --> pdb=" O ARG a 751 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N TRP a 756 " --> pdb=" O ALA a 752 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N VAL a 765 " --> pdb=" O ALA a 761 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ASP a 772 " --> pdb=" O LYS a 768 " (cutoff:3.500A) Processing helix chain 'a' and resid 776 through 780 Processing helix chain 'a' and resid 797 through 807 removed outlier: 3.978A pdb=" N HIS a 805 " --> pdb=" O SER a 801 " (cutoff:3.500A) Processing helix chain 'a' and resid 810 through 828 Processing helix chain 'a' and resid 835 through 868 removed outlier: 3.634A pdb=" N LEU a 854 " --> pdb=" O LEU a 850 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N GLN a 855 " --> pdb=" O ASN a 851 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ARG a 859 " --> pdb=" O GLN a 855 " (cutoff:3.500A) Processing helix chain 'a' and resid 875 through 881 removed outlier: 3.797A pdb=" N GLN a 881 " --> pdb=" O GLU a 877 " (cutoff:3.500A) Processing helix chain 'a' and resid 891 through 898 Processing helix chain 'a' and resid 899 through 904 removed outlier: 3.542A pdb=" N HIS a 902 " --> pdb=" O TYR a 899 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ASN a 904 " --> pdb=" O CYS a 901 " (cutoff:3.500A) Processing helix chain 'a' and resid 906 through 921 removed outlier: 3.657A pdb=" N ALA a 910 " --> pdb=" O ASN a 906 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N SER a 919 " --> pdb=" O LYS a 915 " (cutoff:3.500A) Processing helix chain 'a' and resid 922 through 924 No H-bonds generated for 'chain 'a' and resid 922 through 924' Processing helix chain 'a' and resid 925 through 935 removed outlier: 4.200A pdb=" N LYS a 929 " --> pdb=" O LYS a 925 " (cutoff:3.500A) Processing helix chain 'a' and resid 937 through 953 Processing helix chain 'a' and resid 970 through 995 removed outlier: 3.710A pdb=" N MET a 994 " --> pdb=" O THR a 990 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N LYS a 995 " --> pdb=" O SER a 991 " (cutoff:3.500A) Processing helix chain 'a' and resid 998 through 1004 removed outlier: 3.575A pdb=" N PHE a1002 " --> pdb=" O ASN a 998 " (cutoff:3.500A) Processing helix chain 'a' and resid 1011 through 1015 removed outlier: 3.606A pdb=" N THR a1015 " --> pdb=" O VAL a1012 " (cutoff:3.500A) Processing helix chain 'a' and resid 1021 through 1025 Processing helix chain 'a' and resid 1028 through 1039 removed outlier: 3.517A pdb=" N ILE a1033 " --> pdb=" O CYS a1029 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LYS a1039 " --> pdb=" O ASP a1035 " (cutoff:3.500A) Processing helix chain 'a' and resid 1047 through 1051 removed outlier: 4.134A pdb=" N TRP a1051 " --> pdb=" O VAL a1048 " (cutoff:3.500A) Processing helix chain 'a' and resid 1056 through 1070 removed outlier: 3.858A pdb=" N CYS a1060 " --> pdb=" O LEU a1056 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N CYS a1068 " --> pdb=" O ILE a1064 " (cutoff:3.500A) Processing helix chain 'a' and resid 1073 through 1084 removed outlier: 3.775A pdb=" N MET a1078 " --> pdb=" O SER a1074 " (cutoff:3.500A) Processing helix chain 'a' and resid 1086 through 1093 removed outlier: 3.529A pdb=" N GLN a1093 " --> pdb=" O PHE a1089 " (cutoff:3.500A) Processing helix chain 'a' and resid 1099 through 1101 No H-bonds generated for 'chain 'a' and resid 1099 through 1101' Processing helix chain 'a' and resid 1102 through 1127 removed outlier: 4.091A pdb=" N THR a1116 " --> pdb=" O TRP a1112 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ILE a1119 " --> pdb=" O LYS a1115 " (cutoff:3.500A) Processing helix chain 'a' and resid 1129 through 1142 Processing helix chain 'a' and resid 1178 through 1186 removed outlier: 3.682A pdb=" N LEU a1184 " --> pdb=" O ILE a1180 " (cutoff:3.500A) Processing helix chain 'a' and resid 1206 through 1215 removed outlier: 3.918A pdb=" N VAL a1210 " --> pdb=" O GLN a1206 " (cutoff:3.500A) Processing helix chain 'a' and resid 1226 through 1241 removed outlier: 3.666A pdb=" N VAL a1238 " --> pdb=" O LEU a1234 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASN a1239 " --> pdb=" O VAL a1235 " (cutoff:3.500A) Processing helix chain 'a' and resid 1249 through 1295 Processing helix chain 'a' and resid 1301 through 1321 Processing helix chain 'a' and resid 1328 through 1352 removed outlier: 4.334A pdb=" N ILE a1332 " --> pdb=" O GLU a1328 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ALA a1342 " --> pdb=" O PHE a1338 " (cutoff:3.500A) Processing helix chain 'a' and resid 1391 through 1409 Processing helix chain 'a' and resid 1413 through 1429 Processing helix chain 'a' and resid 1455 through 1472 removed outlier: 3.600A pdb=" N SER a1459 " --> pdb=" O GLU a1455 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLN a1462 " --> pdb=" O PHE a1458 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ARG a1463 " --> pdb=" O SER a1459 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N TYR a1472 " --> pdb=" O ILE a1468 " (cutoff:3.500A) Processing helix chain 'a' and resid 1474 through 1486 Processing helix chain 'a' and resid 1490 through 1504 removed outlier: 3.660A pdb=" N ARG a1501 " --> pdb=" O ALA a1497 " (cutoff:3.500A) Processing helix chain 'a' and resid 1509 through 1518 Processing helix chain 'a' and resid 1519 through 1539 Processing helix chain 'a' and resid 1547 through 1563 removed outlier: 3.521A pdb=" N ALA a1563 " --> pdb=" O LEU a1559 " (cutoff:3.500A) Processing helix chain 'a' and resid 1566 through 1575 removed outlier: 3.517A pdb=" N ILE a1570 " --> pdb=" O SER a1566 " (cutoff:3.500A) Processing helix chain 'a' and resid 1578 through 1583 Processing helix chain 'a' and resid 1584 through 1588 removed outlier: 3.600A pdb=" N TYR a1587 " --> pdb=" O CYS a1584 " (cutoff:3.500A) Processing helix chain 'a' and resid 1610 through 1633 Proline residue: a1621 - end of helix removed outlier: 4.105A pdb=" N LEU a1630 " --> pdb=" O CYS a1626 " (cutoff:3.500A) Processing helix chain 'a' and resid 1639 through 1651 removed outlier: 4.104A pdb=" N VAL a1644 " --> pdb=" O ALA a1640 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N HIS a1651 " --> pdb=" O PHE a1647 " (cutoff:3.500A) Processing helix chain 'a' and resid 1651 through 1660 removed outlier: 3.562A pdb=" N ARG a1660 " --> pdb=" O GLN a1656 " (cutoff:3.500A) Processing helix chain 'a' and resid 1666 through 1683 removed outlier: 3.991A pdb=" N LYS a1681 " --> pdb=" O GLY a1677 " (cutoff:3.500A) Processing helix chain 'a' and resid 1684 through 1689 removed outlier: 4.017A pdb=" N LEU a1688 " --> pdb=" O LEU a1684 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ASN a1689 " --> pdb=" O PRO a1685 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 1684 through 1689' Processing helix chain 'a' and resid 1698 through 1716 Processing helix chain 'a' and resid 1717 through 1722 Processing helix chain 'a' and resid 1724 through 1732 removed outlier: 4.144A pdb=" N ARG a1728 " --> pdb=" O SER a1724 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU a1730 " --> pdb=" O ARG a1726 " (cutoff:3.500A) Processing helix chain 'a' and resid 1738 through 1771 removed outlier: 3.746A pdb=" N CYS a1756 " --> pdb=" O MET a1752 " (cutoff:3.500A) Processing helix chain 'a' and resid 1811 through 1844 removed outlier: 4.273A pdb=" N ILE a1815 " --> pdb=" O LEU a1811 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N PHE a1826 " --> pdb=" O ALA a1822 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N THR a1827 " --> pdb=" O ASN a1823 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLN a1834 " --> pdb=" O ASP a1830 " (cutoff:3.500A) Processing helix chain 'a' and resid 1866 through 1913 removed outlier: 3.931A pdb=" N TYR a1871 " --> pdb=" O THR a1867 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ARG a1876 " --> pdb=" O GLY a1872 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE a1896 " --> pdb=" O CYS a1892 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLU a1897 " --> pdb=" O SER a1893 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N LEU a1912 " --> pdb=" O GLU a1908 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N HIS a1913 " --> pdb=" O TYR a1909 " (cutoff:3.500A) Processing helix chain 'b' and resid 61 through 64 Processing helix chain 'b' and resid 65 through 86 Processing helix chain 'b' and resid 90 through 123 Processing helix chain 'b' and resid 126 through 152 Processing helix chain 'b' and resid 156 through 172 removed outlier: 3.923A pdb=" N LEU b 161 " --> pdb=" O ALA b 157 " (cutoff:3.500A) Processing helix chain 'b' and resid 173 through 184 Processing helix chain 'b' and resid 187 through 191 Processing helix chain 'b' and resid 193 through 204 Processing helix chain 'b' and resid 206 through 218 removed outlier: 3.703A pdb=" N ALA b 210 " --> pdb=" O ARG b 206 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LYS b 216 " --> pdb=" O GLN b 212 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N GLU b 217 " --> pdb=" O LEU b 213 " (cutoff:3.500A) Processing helix chain 'b' and resid 221 through 237 Processing helix chain 'b' and resid 249 through 271 Processing helix chain 'b' and resid 277 through 287 Processing helix chain 'b' and resid 288 through 295 removed outlier: 3.720A pdb=" N LYS b 295 " --> pdb=" O VAL b 291 " (cutoff:3.500A) Processing helix chain 'b' and resid 301 through 314 Processing helix chain 'b' and resid 321 through 334 Processing helix chain 'b' and resid 341 through 352 Processing helix chain 'b' and resid 354 through 366 Processing helix chain 'b' and resid 369 through 382 Processing helix chain 'b' and resid 397 through 409 Processing helix chain 'b' and resid 414 through 425 removed outlier: 3.849A pdb=" N TYR b 424 " --> pdb=" O ASP b 420 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N CYS b 425 " --> pdb=" O TYR b 421 " (cutoff:3.500A) Processing helix chain 'b' and resid 428 through 439 removed outlier: 3.983A pdb=" N TYR b 432 " --> pdb=" O LEU b 428 " (cutoff:3.500A) Processing helix chain 'b' and resid 444 through 458 removed outlier: 3.743A pdb=" N ARG b 458 " --> pdb=" O ILE b 454 " (cutoff:3.500A) Processing helix chain 'b' and resid 460 through 478 Processing helix chain 'b' and resid 480 through 492 Processing helix chain 'b' and resid 493 through 512 Processing helix chain 'b' and resid 516 through 522 Processing helix chain 'b' and resid 525 through 529 Processing helix chain 'b' and resid 530 through 548 Processing helix chain 'b' and resid 550 through 564 Processing helix chain 'b' and resid 568 through 585 removed outlier: 3.815A pdb=" N LEU b 573 " --> pdb=" O CYS b 569 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N THR b 574 " --> pdb=" O SER b 570 " (cutoff:3.500A) Proline residue: b 581 - end of helix Processing helix chain 'b' and resid 591 through 611 Processing helix chain 'b' and resid 622 through 647 Processing helix chain 'd' and resid 67 through 71 Processing helix chain 'e' and resid 168 through 173 removed outlier: 4.075A pdb=" N TYR e 173 " --> pdb=" O PRO e 169 " (cutoff:3.500A) Processing helix chain 'e' and resid 179 through 183 removed outlier: 3.792A pdb=" N ILE e 183 " --> pdb=" O ASP e 180 " (cutoff:3.500A) Processing helix chain 'e' and resid 189 through 193 removed outlier: 3.502A pdb=" N THR e 193 " --> pdb=" O ILE e 190 " (cutoff:3.500A) Processing helix chain 'e' and resid 280 through 283 Processing helix chain 'e' and resid 325 through 328 removed outlier: 3.572A pdb=" N VAL e 328 " --> pdb=" O LEU e 325 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 325 through 328' Processing helix chain 'e' and resid 333 through 337 removed outlier: 3.575A pdb=" N GLN e 336 " --> pdb=" O ASP e 333 " (cutoff:3.500A) Processing helix chain 'e' and resid 455 through 465 Processing helix chain 'e' and resid 471 through 483 Processing helix chain 'e' and resid 493 through 513 Processing helix chain 'e' and resid 519 through 546 Processing helix chain 'e' and resid 575 through 583 Processing helix chain 'e' and resid 584 through 591 removed outlier: 4.166A pdb=" N LEU e 589 " --> pdb=" O GLU e 586 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N THR e 590 " --> pdb=" O HIS e 587 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N VAL e 591 " --> pdb=" O LEU e 588 " (cutoff:3.500A) Processing helix chain 'e' and resid 592 through 597 removed outlier: 4.018A pdb=" N ILE e 596 " --> pdb=" O ASP e 592 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N SER e 597 " --> pdb=" O GLU e 593 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 592 through 597' Processing helix chain 'e' and resid 599 through 618 Processing helix chain 'e' and resid 670 through 682 Processing helix chain 'e' and resid 707 through 742 Processing helix chain 'e' and resid 760 through 780 Processing helix chain 'e' and resid 786 through 800 Processing helix chain 'e' and resid 818 through 827 Processing helix chain 'e' and resid 831 through 837 Processing helix chain 'e' and resid 850 through 866 Processing helix chain 'e' and resid 873 through 881 Processing helix chain 'e' and resid 883 through 895 Processing helix chain 'e' and resid 901 through 917 Processing helix chain 'e' and resid 918 through 932 removed outlier: 3.926A pdb=" N GLU e 932 " --> pdb=" O GLN e 928 " (cutoff:3.500A) Processing helix chain 'e' and resid 936 through 941 Processing helix chain 'e' and resid 953 through 969 Processing helix chain 'e' and resid 970 through 985 Processing helix chain 'e' and resid 988 through 1007 Processing helix chain 'e' and resid 1008 through 1017 Processing helix chain 'e' and resid 1021 through 1039 Processing helix chain 'e' and resid 1041 through 1048 removed outlier: 3.645A pdb=" N LEU e1045 " --> pdb=" O GLN e1041 " (cutoff:3.500A) Processing helix chain 'e' and resid 1053 through 1066 Processing helix chain 'e' and resid 1074 through 1086 Processing helix chain 'e' and resid 1088 through 1107 Processing helix chain 'e' and resid 1109 through 1129 Processing helix chain 'e' and resid 1175 through 1195 Processing helix chain 'e' and resid 1195 through 1204 Processing helix chain 'e' and resid 1206 through 1218 Processing helix chain 'e' and resid 1219 through 1230 removed outlier: 3.633A pdb=" N ALA e1223 " --> pdb=" O LEU e1219 " (cutoff:3.500A) Processing helix chain 'e' and resid 1234 through 1250 removed outlier: 3.538A pdb=" N GLN e1250 " --> pdb=" O ILE e1246 " (cutoff:3.500A) Processing helix chain 'e' and resid 1252 through 1266 Processing helix chain 'e' and resid 1277 through 1294 Processing helix chain 'e' and resid 1297 through 1310 removed outlier: 3.529A pdb=" N TYR e1301 " --> pdb=" O LYS e1297 " (cutoff:3.500A) Processing helix chain 'e' and resid 1317 through 1339 removed outlier: 4.123A pdb=" N ALA e1329 " --> pdb=" O LYS e1325 " (cutoff:3.500A) removed outlier: 9.103A pdb=" N ALA e1330 " --> pdb=" O ALA e1326 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N GLU e1331 " --> pdb=" O MET e1327 " (cutoff:3.500A) Processing helix chain 'e' and resid 1341 through 1357 Processing helix chain 'e' and resid 1360 through 1365 Processing helix chain 'e' and resid 1380 through 1392 removed outlier: 3.576A pdb=" N ILE e1384 " --> pdb=" O PRO e1380 " (cutoff:3.500A) Processing helix chain 'e' and resid 1397 through 1430 Processing helix chain 'g' and resid 1050 through 1055 Processing helix chain 'g' and resid 1061 through 1066 Processing helix chain 'g' and resid 1075 through 1079 removed outlier: 3.684A pdb=" N TRP g1078 " --> pdb=" O GLY g1075 " (cutoff:3.500A) Processing helix chain 'g' and resid 1136 through 1150 removed outlier: 3.782A pdb=" N TYR g1140 " --> pdb=" O GLU g1136 " (cutoff:3.500A) Proline residue: g1143 - end of helix Processing helix chain 'g' and resid 1169 through 1185 removed outlier: 4.221A pdb=" N GLU g1184 " --> pdb=" O ASN g1180 " (cutoff:3.500A) Processing helix chain 'g' and resid 1189 through 1207 removed outlier: 4.638A pdb=" N LYS g1193 " --> pdb=" O GLU g1189 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU g1205 " --> pdb=" O LEU g1201 " (cutoff:3.500A) Processing helix chain 'g' and resid 1221 through 1252 removed outlier: 4.510A pdb=" N GLU g1242 " --> pdb=" O HIS g1238 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N ARG g1243 " --> pdb=" O THR g1239 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLY g1252 " --> pdb=" O VAL g1248 " (cutoff:3.500A) Processing helix chain 'g' and resid 1258 through 1266 Processing helix chain 'g' and resid 1268 through 1276 removed outlier: 3.795A pdb=" N ARG g1274 " --> pdb=" O SER g1270 " (cutoff:3.500A) Processing helix chain 'g' and resid 1277 through 1279 No H-bonds generated for 'chain 'g' and resid 1277 through 1279' Processing helix chain 'g' and resid 1282 through 1290 Processing helix chain 'g' and resid 1293 through 1311 Processing helix chain 'g' and resid 1318 through 1330 Processing helix chain 'g' and resid 1349 through 1360 Processing helix chain 'g' and resid 1367 through 1380 removed outlier: 3.565A pdb=" N ALA g1371 " --> pdb=" O THR g1367 " (cutoff:3.500A) Processing helix chain 'g' and resid 1408 through 1413 Processing helix chain 'g' and resid 1418 through 1429 removed outlier: 4.100A pdb=" N HIS g1422 " --> pdb=" O ASP g1418 " (cutoff:3.500A) Processing helix chain 'g' and resid 1433 through 1438 removed outlier: 3.522A pdb=" N LEU g1437 " --> pdb=" O ASP g1433 " (cutoff:3.500A) Processing helix chain 'g' and resid 1439 through 1443 removed outlier: 3.589A pdb=" N VAL g1443 " --> pdb=" O PRO g1440 " (cutoff:3.500A) Processing helix chain 'g' and resid 1450 through 1463 Processing helix chain 'g' and resid 1469 through 1488 Processing helix chain 'g' and resid 1490 through 1498 Processing helix chain 'g' and resid 1502 through 1518 Processing helix chain 'g' and resid 1523 through 1537 Processing helix chain 'g' and resid 1540 through 1555 Processing helix chain 'g' and resid 1557 through 1568 removed outlier: 3.704A pdb=" N LYS g1567 " --> pdb=" O LEU g1563 " (cutoff:3.500A) Processing helix chain 'g' and resid 1571 through 1581 Processing helix chain 'g' and resid 1581 through 1590 removed outlier: 3.518A pdb=" N ASP g1585 " --> pdb=" O HIS g1581 " (cutoff:3.500A) Processing helix chain 'g' and resid 1591 through 1602 removed outlier: 4.062A pdb=" N LEU g1595 " --> pdb=" O ASN g1591 " (cutoff:3.500A) Processing helix chain 'g' and resid 1604 through 1611 Processing helix chain 'g' and resid 1613 through 1637 Processing helix chain 'g' and resid 1640 through 1659 removed outlier: 3.621A pdb=" N GLU g1659 " --> pdb=" O CYS g1655 " (cutoff:3.500A) Processing helix chain 'g' and resid 1665 through 1691 removed outlier: 3.807A pdb=" N ARG g1669 " --> pdb=" O THR g1665 " (cutoff:3.500A) Processing helix chain 'h' and resid 67 through 71 Processing helix chain 'j' and resid 83 through 93 Processing helix chain 'j' and resid 127 through 131 Processing helix chain 'j' and resid 146 through 148 No H-bonds generated for 'chain 'j' and resid 146 through 148' Processing helix chain 'j' and resid 156 through 158 No H-bonds generated for 'chain 'j' and resid 156 through 158' Processing helix chain 'j' and resid 301 through 316 removed outlier: 3.592A pdb=" N ARG j 307 " --> pdb=" O SER j 303 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N GLU j 308 " --> pdb=" O ARG j 304 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N TYR j 309 " --> pdb=" O VAL j 305 " (cutoff:3.500A) Processing helix chain 'j' and resid 320 through 326 removed outlier: 4.065A pdb=" N ALA j 326 " --> pdb=" O ASP j 322 " (cutoff:3.500A) Processing helix chain 'j' and resid 389 through 393 Processing helix chain 'j' and resid 435 through 439 removed outlier: 4.044A pdb=" N GLY j 438 " --> pdb=" O GLU j 435 " (cutoff:3.500A) Processing helix chain 'j' and resid 506 through 520 removed outlier: 3.713A pdb=" N ASP j 520 " --> pdb=" O TYR j 516 " (cutoff:3.500A) Processing helix chain 'j' and resid 523 through 534 Processing helix chain 'j' and resid 542 through 558 removed outlier: 3.509A pdb=" N GLN j 549 " --> pdb=" O LEU j 545 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ILE j 550 " --> pdb=" O ALA j 546 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASP j 553 " --> pdb=" O GLN j 549 " (cutoff:3.500A) Processing helix chain 'j' and resid 583 through 604 removed outlier: 3.541A pdb=" N VAL j 604 " --> pdb=" O PHE j 600 " (cutoff:3.500A) Processing helix chain 'j' and resid 622 through 643 removed outlier: 3.822A pdb=" N LEU j 626 " --> pdb=" O THR j 622 " (cutoff:3.500A) Processing helix chain 'j' and resid 645 through 660 Processing helix chain 'j' and resid 672 through 678 removed outlier: 3.953A pdb=" N ARG j 677 " --> pdb=" O ASP j 673 " (cutoff:3.500A) Processing helix chain 'j' and resid 680 through 697 removed outlier: 3.514A pdb=" N ILE j 684 " --> pdb=" O SER j 680 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N PHE j 686 " --> pdb=" O MET j 682 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLU j 687 " --> pdb=" O GLU j 683 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N CYS j 688 " --> pdb=" O ILE j 684 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ASP j 696 " --> pdb=" O LYS j 692 " (cutoff:3.500A) Processing helix chain 'j' and resid 705 through 731 removed outlier: 4.100A pdb=" N VAL j 711 " --> pdb=" O TRP j 707 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL j 712 " --> pdb=" O ALA j 708 " (cutoff:3.500A) Processing helix chain 'j' and resid 761 through 772 Processing helix chain 'j' and resid 773 through 778 Processing helix chain 'j' and resid 780 through 808 removed outlier: 3.848A pdb=" N TYR j 800 " --> pdb=" O LEU j 796 " (cutoff:3.500A) Processing helix chain 'j' and resid 813 through 837 removed outlier: 3.652A pdb=" N ASN j 817 " --> pdb=" O GLU j 813 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N LEU j 830 " --> pdb=" O LYS j 826 " (cutoff:3.500A) Proline residue: j 833 - end of helix removed outlier: 4.158A pdb=" N LEU j 837 " --> pdb=" O PRO j 833 " (cutoff:3.500A) Processing helix chain 'j' and resid 839 through 841 No H-bonds generated for 'chain 'j' and resid 839 through 841' Processing helix chain 'j' and resid 842 through 850 Processing helix chain 'j' and resid 854 through 864 removed outlier: 3.504A pdb=" N ILE j 859 " --> pdb=" O ILE j 855 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ASP j 864 " --> pdb=" O CYS j 860 " (cutoff:3.500A) Processing helix chain 'j' and resid 866 through 876 Processing helix chain 'j' and resid 879 through 891 Processing helix chain 'j' and resid 905 through 915 removed outlier: 3.852A pdb=" N LEU j 913 " --> pdb=" O LEU j 909 " (cutoff:3.500A) Processing helix chain 'j' and resid 919 through 928 removed outlier: 3.531A pdb=" N LEU j 925 " --> pdb=" O TRP j 921 " (cutoff:3.500A) Processing helix chain 'j' and resid 929 through 944 Processing helix chain 'j' and resid 947 through 965 Processing helix chain 'j' and resid 968 through 991 removed outlier: 3.526A pdb=" N GLN j 982 " --> pdb=" O GLU j 978 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N HIS j 988 " --> pdb=" O HIS j 984 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N GLN j 989 " --> pdb=" O PHE j 985 " (cutoff:3.500A) Processing helix chain 'j' and resid 993 through 1001 Processing helix chain 'j' and resid 1011 through 1020 Processing helix chain 'j' and resid 1028 through 1038 Processing helix chain 'j' and resid 1044 through 1049 Processing helix chain 'j' and resid 1049 through 1064 removed outlier: 3.501A pdb=" N LEU j1053 " --> pdb=" O ASP j1049 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE j1062 " --> pdb=" O LEU j1058 " (cutoff:3.500A) Processing helix chain 'j' and resid 1078 through 1089 removed outlier: 4.065A pdb=" N LEU j1089 " --> pdb=" O PHE j1085 " (cutoff:3.500A) Processing helix chain 'j' and resid 1108 through 1118 Processing helix chain 'j' and resid 1120 through 1137 removed outlier: 5.714A pdb=" N PHE j1126 " --> pdb=" O SER j1122 " (cutoff:3.500A) removed outlier: 5.368A pdb=" N SER j1127 " --> pdb=" O TYR j1123 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N CYS j1134 " --> pdb=" O ALA j1130 " (cutoff:3.500A) Processing helix chain 'p' and resid 181 through 199 Processing helix chain 'p' and resid 204 through 215 Processing helix chain 'p' and resid 220 through 233 Processing helix chain 'p' and resid 243 through 248 Processing helix chain 'p' and resid 249 through 275 removed outlier: 4.587A pdb=" N ILE p 273 " --> pdb=" O ASN p 269 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N SER p 274 " --> pdb=" O TYR p 270 " (cutoff:3.500A) Processing helix chain 'p' and resid 292 through 301 Processing helix chain 'p' and resid 320 through 330 Processing helix chain 'p' and resid 331 through 342 Processing helix chain 'p' and resid 342 through 347 removed outlier: 4.019A pdb=" N LEU p 346 " --> pdb=" O ALA p 342 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N GLY p 347 " --> pdb=" O GLN p 343 " (cutoff:3.500A) No H-bonds generated for 'chain 'p' and resid 342 through 347' Processing helix chain 'p' and resid 347 through 359 removed outlier: 4.330A pdb=" N ASN p 351 " --> pdb=" O GLY p 347 " (cutoff:3.500A) Processing helix chain 'p' and resid 365 through 379 Processing helix chain 'p' and resid 386 through 397 Processing helix chain 'p' and resid 411 through 421 Processing helix chain 'p' and resid 442 through 447 Processing helix chain 'p' and resid 462 through 468 Processing helix chain 'p' and resid 473 through 483 Processing helix chain 'p' and resid 486 through 500 Processing helix chain 'p' and resid 529 through 541 removed outlier: 4.390A pdb=" N PHE p 540 " --> pdb=" O TYR p 536 " (cutoff:3.500A) Processing helix chain 'p' and resid 544 through 553 Processing helix chain 'p' and resid 566 through 579 removed outlier: 3.554A pdb=" N ILE p 576 " --> pdb=" O SER p 572 " (cutoff:3.500A) Processing helix chain 'p' and resid 580 through 585 Processing helix chain 'p' and resid 607 through 620 Processing helix chain 'p' and resid 622 through 633 Processing helix chain 'p' and resid 638 through 651 Proline residue: p 649 - end of helix Processing helix chain 'p' and resid 661 through 679 Processing helix chain 'p' and resid 684 through 704 Processing helix chain 'p' and resid 709 through 717 Processing helix chain 'p' and resid 784 through 800 Processing helix chain 'p' and resid 805 through 820 Processing sheet with id=AA1, first strand: chain 'A' and resid 75 through 76 Processing sheet with id=AA2, first strand: chain 'A' and resid 784 through 787 removed outlier: 3.634A pdb=" N LEU A 787 " --> pdb=" O GLU A 790 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 23 through 27 removed outlier: 3.671A pdb=" N TYR B 55 " --> pdb=" O LEU B 34 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 6 through 9 removed outlier: 4.028A pdb=" N ALA C 366 " --> pdb=" O THR C 362 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N SER C 350 " --> pdb=" O GLY C 361 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 13 through 19 removed outlier: 5.754A pdb=" N ILE C 14 " --> pdb=" O TRP C 38 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N TRP C 38 " --> pdb=" O ILE C 14 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N LYS C 44 " --> pdb=" O SER C 37 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N VAL C 45 " --> pdb=" O ASP C 71 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N ASP C 71 " --> pdb=" O VAL C 45 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N VAL C 47 " --> pdb=" O LEU C 69 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 78 through 83 removed outlier: 3.774A pdb=" N ASP C 80 " --> pdb=" O GLY C 92 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL C 98 " --> pdb=" O ARG C 115 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N ARG C 115 " --> pdb=" O VAL C 98 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N ILE C 100 " --> pdb=" O ASN C 113 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 133 through 137 Processing sheet with id=AA8, first strand: chain 'C' and resid 174 through 177 removed outlier: 3.722A pdb=" N GLY C 174 " --> pdb=" O VAL C 186 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLN C 206 " --> pdb=" O LEU C 194 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 217 through 222 removed outlier: 3.525A pdb=" N VAL C 230 " --> pdb=" O TRP C 242 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 261 through 266 removed outlier: 3.691A pdb=" N GLU C 263 " --> pdb=" O CYS C 277 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 15 through 20 removed outlier: 3.689A pdb=" N ASP D 17 " --> pdb=" O CYS D 30 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N SER D 31 " --> pdb=" O SER D 35 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N SER D 35 " --> pdb=" O SER D 31 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N VAL D 36 " --> pdb=" O SER D 52 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N SER D 52 " --> pdb=" O VAL D 36 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N VAL D 38 " --> pdb=" O THR D 50 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 62 through 65 removed outlier: 4.029A pdb=" N ARG D 62 " --> pdb=" O CYS D 77 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N CYS D 77 " --> pdb=" O ARG D 62 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ALA D 84 " --> pdb=" O SER D 76 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N ALA D 83 " --> pdb=" O THR D 108 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N THR D 108 " --> pdb=" O ALA D 83 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N VAL D 85 " --> pdb=" O ARG D 106 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 118 through 121 removed outlier: 4.025A pdb=" N ASP D 118 " --> pdb=" O CYS D 133 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N HIS D 157 " --> pdb=" O ILE D 141 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N GLU D 143 " --> pdb=" O LEU D 155 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N LEU D 155 " --> pdb=" O GLU D 143 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 165 through 170 removed outlier: 4.317A pdb=" N CYS D 167 " --> pdb=" O GLY D 185 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N VAL D 197 " --> pdb=" O THR D 214 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N THR D 214 " --> pdb=" O VAL D 197 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N ILE D 199 " --> pdb=" O ALA D 212 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LYS D 208 " --> pdb=" O ASN D 203 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 224 through 228 removed outlier: 3.639A pdb=" N ASP D 224 " --> pdb=" O ALA D 241 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N ILE D 237 " --> pdb=" O ALA D 228 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ALA D 272 " --> pdb=" O ILE D 247 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N THR D 249 " --> pdb=" O THR D 270 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N THR D 270 " --> pdb=" O THR D 249 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N LYS D 251 " --> pdb=" O ASN D 268 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N ASN D 268 " --> pdb=" O LYS D 251 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 281 through 286 removed outlier: 6.645A pdb=" N SER D 296 " --> pdb=" O TRP D 282 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N VAL D 284 " --> pdb=" O ALA D 294 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ALA D 294 " --> pdb=" O VAL D 284 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N TRP D 286 " --> pdb=" O VAL D 292 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N VAL D 292 " --> pdb=" O TRP D 286 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 396 through 402 removed outlier: 6.991A pdb=" N LEU E 412 " --> pdb=" O ILE E 398 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N PHE E 400 " --> pdb=" O TRP E 410 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N TRP E 410 " --> pdb=" O PHE E 400 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N PHE E 402 " --> pdb=" O ASP E 408 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N ASP E 408 " --> pdb=" O PHE E 402 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N VAL E 422 " --> pdb=" O VAL E 438 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N TYR E 46 " --> pdb=" O PHE E 439 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N LEU E 568 " --> pdb=" O GLY E 51 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N VAL E 560 " --> pdb=" O LEU E 571 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 62 through 66 removed outlier: 5.894A pdb=" N ARG E 62 " --> pdb=" O ARG E 129 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N ARG E 131 " --> pdb=" O ARG E 62 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N LEU E 64 " --> pdb=" O ARG E 131 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 137 through 146 removed outlier: 5.323A pdb=" N GLY E 141 " --> pdb=" O LEU E 156 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N THR E 160 " --> pdb=" O THR E 157 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 218 through 221 Processing sheet with id=AC3, first strand: chain 'E' and resid 285 through 293 removed outlier: 3.519A pdb=" N ASP E 296 " --> pdb=" O LEU E 293 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N LYS E 307 " --> pdb=" O CYS E 303 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N MET E 320 " --> pdb=" O MET E 310 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N SER E 312 " --> pdb=" O CYS E 318 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N CYS E 318 " --> pdb=" O SER E 312 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 343 through 349 removed outlier: 5.242A pdb=" N LEU E 355 " --> pdb=" O LEU E 374 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N GLN E 373 " --> pdb=" O HIS E 386 " (cutoff:3.500A) removed outlier: 5.583A pdb=" N HIS E 386 " --> pdb=" O GLN E 373 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N MET E 375 " --> pdb=" O LEU E 384 " (cutoff:3.500A) removed outlier: 5.323A pdb=" N LEU E 384 " --> pdb=" O MET E 375 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 11 through 14 Processing sheet with id=AC6, first strand: chain 'F' and resid 21 through 24 removed outlier: 6.515A pdb=" N SER F 48 " --> pdb=" O THR F 65 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N THR F 65 " --> pdb=" O SER F 48 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N ARG F 50 " --> pdb=" O PHE F 63 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N PHE F 63 " --> pdb=" O ARG F 50 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 75 through 80 removed outlier: 3.811A pdb=" N ALA F 77 " --> pdb=" O ALA F 98 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 127 through 132 removed outlier: 3.582A pdb=" N GLY F 144 " --> pdb=" O THR F 148 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N THR F 148 " --> pdb=" O GLY F 144 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N CYS F 149 " --> pdb=" O MET F 161 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N MET F 161 " --> pdb=" O CYS F 149 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ILE F 151 " --> pdb=" O ILE F 159 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 168 through 173 removed outlier: 4.072A pdb=" N THR F 189 " --> pdb=" O GLU F 185 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N ILE F 190 " --> pdb=" O SER F 203 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N SER F 203 " --> pdb=" O ILE F 190 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N PHE F 192 " --> pdb=" O ILE F 201 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLN F 199 " --> pdb=" O ASP F 194 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 211 through 216 removed outlier: 3.708A pdb=" N SER F 213 " --> pdb=" O VAL F 227 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 254 through 259 removed outlier: 6.518A pdb=" N THR F 270 " --> pdb=" O ARG F 255 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N PHE F 257 " --> pdb=" O ALA F 268 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N ALA F 268 " --> pdb=" O PHE F 257 " (cutoff:3.500A) removed outlier: 5.382A pdb=" N TRP F 259 " --> pdb=" O VAL F 266 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N VAL F 266 " --> pdb=" O TRP F 259 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N PHE F 267 " --> pdb=" O HIS F 283 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N GLN F 279 " --> pdb=" O GLY F 271 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'G' and resid 1080 through 1081 removed outlier: 4.073A pdb=" N LEU G1080 " --> pdb=" O GLU G1126 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N GLU G1126 " --> pdb=" O LEU G1080 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'G' and resid 1152 through 1154 Processing sheet with id=AD5, first strand: chain 'G' and resid 1333 through 1335 Processing sheet with id=AD6, first strand: chain 'H' and resid 18 through 21 removed outlier: 3.797A pdb=" N ASP H 18 " --> pdb=" O CYS H 31 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ALA H 51 " --> pdb=" O ILE H 39 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'H' and resid 60 through 65 removed outlier: 4.053A pdb=" N GLN H 62 " --> pdb=" O CYS H 77 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N VAL H 83 " --> pdb=" O GLU H 98 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N GLU H 98 " --> pdb=" O VAL H 83 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N ILE H 85 " --> pdb=" O THR H 96 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'H' and resid 106 through 111 removed outlier: 6.713A pdb=" N GLY H 123 " --> pdb=" O ASN H 107 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N VAL H 109 " --> pdb=" O ALA H 121 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ALA H 121 " --> pdb=" O VAL H 109 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N TRP H 111 " --> pdb=" O LEU H 119 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N LEU H 119 " --> pdb=" O TRP H 111 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N LEU H 118 " --> pdb=" O TYR H 134 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N TYR H 134 " --> pdb=" O LEU H 118 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'H' and resid 153 through 158 removed outlier: 3.553A pdb=" N ALA H 155 " --> pdb=" O GLY H 185 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N VAL H 191 " --> pdb=" O LYS H 206 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N LYS H 206 " --> pdb=" O VAL H 191 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ILE H 193 " --> pdb=" O ASP H 204 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'H' and resid 214 through 219 removed outlier: 3.734A pdb=" N ASP H 216 " --> pdb=" O CYS H 233 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N SER H 234 " --> pdb=" O ARG H 238 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N ARG H 238 " --> pdb=" O SER H 234 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N VAL H 239 " --> pdb=" O LEU H 257 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'H' and resid 267 through 269 removed outlier: 4.203A pdb=" N SER H 300 " --> pdb=" O LEU H 287 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N LYS H 289 " --> pdb=" O CYS H 298 " (cutoff:3.500A) removed outlier: 5.532A pdb=" N CYS H 298 " --> pdb=" O LYS H 289 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'J' and resid 73 through 77 removed outlier: 4.455A pdb=" N UNK J 451 " --> pdb=" O UNK J 463 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'J' and resid 100 through 103 removed outlier: 3.977A pdb=" N UNK J 100 " --> pdb=" O UNK J 112 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'J' and resid 150 through 154 Processing sheet with id=AE6, first strand: chain 'J' and resid 202 through 206 removed outlier: 3.796A pdb=" N UNK J 210 " --> pdb=" O UNK J 206 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'J' and resid 265 through 270 removed outlier: 6.453A pdb=" N UNK J 284 " --> pdb=" O UNK J 299 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N UNK J 299 " --> pdb=" O UNK J 284 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N UNK J 286 " --> pdb=" O UNK J 297 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'J' and resid 329 through 338 removed outlier: 6.665A pdb=" N UNK J 345 " --> pdb=" O UNK J 333 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N UNK J 335 " --> pdb=" O UNK J 343 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N UNK J 343 " --> pdb=" O UNK J 335 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N UNK J 337 " --> pdb=" O UNK J 341 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N UNK J 341 " --> pdb=" O UNK J 337 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N UNK J 366 " --> pdb=" O UNK J 375 " (cutoff:3.500A) removed outlier: 7.886A pdb=" N UNK J 375 " --> pdb=" O UNK J 366 " (cutoff:3.500A) removed outlier: 8.971A pdb=" N UNK J 368 " --> pdb=" O UNK J 373 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N UNK J 373 " --> pdb=" O UNK J 368 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'J' and resid 396 through 398 Processing sheet with id=AF1, first strand: chain 'J' and resid 1069 through 1070 Processing sheet with id=AF2, first strand: chain 'P' and resid 514 through 515 Processing sheet with id=AF3, first strand: chain 'P' and resid 586 through 588 Processing sheet with id=AF4, first strand: chain 'X' and resid 680 through 682 removed outlier: 4.403A pdb=" N UNK X 700 " --> pdb=" O UNK X 720 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N UNK X 720 " --> pdb=" O UNK X 700 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N UNK X 702 " --> pdb=" O UNK X 718 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N UNK X 718 " --> pdb=" O UNK X 702 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N UNK X 811 " --> pdb=" O UNK X 805 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N UNK X 805 " --> pdb=" O UNK X 811 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N UNK X 813 " --> pdb=" O UNK X 803 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'X' and resid 731 through 734 Processing sheet with id=AF6, first strand: chain 'Y' and resid 48 through 51 removed outlier: 8.395A pdb=" N VAL Y 140 " --> pdb=" O GLU Y 85 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N LYS Y 87 " --> pdb=" O VAL Y 140 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N CYS Y 142 " --> pdb=" O LYS Y 87 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N LEU Y 89 " --> pdb=" O CYS Y 142 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'Y' and resid 100 through 103 removed outlier: 4.092A pdb=" N VAL Y 118 " --> pdb=" O ILE Y 147 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'Y' and resid 126 through 127 Processing sheet with id=AF9, first strand: chain 'Y' and resid 160 through 165 removed outlier: 3.782A pdb=" N ILE Y 183 " --> pdb=" O THR Y 179 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'Y' and resid 225 through 230 Processing sheet with id=AG2, first strand: chain 'Y' and resid 297 through 303 removed outlier: 3.907A pdb=" N ILE Y 309 " --> pdb=" O LEU Y 303 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N LEU Y 318 " --> pdb=" O THR Y 314 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N LEU Y 319 " --> pdb=" O CYS Y 354 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N CYS Y 354 " --> pdb=" O LEU Y 319 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N HIS Y 321 " --> pdb=" O PHE Y 352 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'Y' and resid 380 through 383 removed outlier: 6.553A pdb=" N VAL Y 399 " --> pdb=" O ILE Y 438 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'Y' and resid 452 through 460 Processing sheet with id=AG5, first strand: chain 'a' and resid 784 through 787 Processing sheet with id=AG6, first strand: chain 'b' and resid 23 through 27 Processing sheet with id=AG7, first strand: chain 'c' and resid 6 through 9 removed outlier: 4.176A pdb=" N ALA c 366 " --> pdb=" O THR c 362 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N ASN c 357 " --> pdb=" O VAL c 353 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N VAL c 353 " --> pdb=" O ASN c 357 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N VAL c 359 " --> pdb=" O LEU c 351 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N LEU c 351 " --> pdb=" O VAL c 359 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N GLY c 361 " --> pdb=" O ASN c 349 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'c' and resid 14 through 19 removed outlier: 4.315A pdb=" N LYS c 44 " --> pdb=" O SER c 37 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N VAL c 45 " --> pdb=" O ASP c 71 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N ASP c 71 " --> pdb=" O VAL c 45 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N VAL c 47 " --> pdb=" O LEU c 69 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'c' and resid 80 through 85 removed outlier: 3.625A pdb=" N ASP c 80 " --> pdb=" O GLY c 92 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ARG c 88 " --> pdb=" O LEU c 84 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N VAL c 98 " --> pdb=" O ARG c 115 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N ARG c 115 " --> pdb=" O VAL c 98 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N ILE c 100 " --> pdb=" O ASN c 113 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'c' and resid 134 through 137 removed outlier: 3.606A pdb=" N ILE c 141 " --> pdb=" O PHE c 153 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ILE c 164 " --> pdb=" O ILE c 150 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ARG c 162 " --> pdb=" O CYS c 152 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'c' and resid 172 through 177 removed outlier: 3.861A pdb=" N GLY c 174 " --> pdb=" O VAL c 186 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N GLN c 191 " --> pdb=" O ASN c 187 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLN c 206 " --> pdb=" O LEU c 194 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'c' and resid 217 through 222 removed outlier: 3.676A pdb=" N GLY c 234 " --> pdb=" O MET c 238 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N MET c 238 " --> pdb=" O GLY c 234 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'c' and resid 261 through 266 removed outlier: 3.649A pdb=" N GLU c 263 " --> pdb=" O CYS c 277 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'd' and resid 15 through 20 removed outlier: 7.104A pdb=" N CYS d 30 " --> pdb=" O HIS d 16 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N VAL d 18 " --> pdb=" O ALA d 28 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ALA d 28 " --> pdb=" O VAL d 18 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N PHE d 20 " --> pdb=" O ARG d 26 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N ARG d 26 " --> pdb=" O PHE d 20 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N SER d 35 " --> pdb=" O SER d 31 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ALA d 51 " --> pdb=" O VAL d 38 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N ASP d 40 " --> pdb=" O CYS d 49 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N CYS d 49 " --> pdb=" O ASP d 40 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'd' and resid 60 through 63 removed outlier: 6.804A pdb=" N CYS d 77 " --> pdb=" O TRP d 61 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N VAL d 63 " --> pdb=" O ALA d 75 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N ALA d 75 " --> pdb=" O VAL d 63 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N ALA d 83 " --> pdb=" O THR d 108 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N THR d 108 " --> pdb=" O ALA d 83 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL d 85 " --> pdb=" O ARG d 106 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'd' and resid 116 through 120 removed outlier: 3.747A pdb=" N ASP d 118 " --> pdb=" O CYS d 133 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N VAL d 138 " --> pdb=" O SER d 134 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N GLU d 143 " --> pdb=" O LEU d 155 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N LEU d 155 " --> pdb=" O GLU d 143 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'd' and resid 165 through 170 removed outlier: 4.496A pdb=" N CYS d 167 " --> pdb=" O GLY d 185 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N VAL d 197 " --> pdb=" O THR d 214 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N THR d 214 " --> pdb=" O VAL d 197 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ILE d 199 " --> pdb=" O ALA d 212 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'd' and resid 224 through 227 removed outlier: 3.654A pdb=" N ASP d 224 " --> pdb=" O ALA d 241 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ALA d 272 " --> pdb=" O ILE d 247 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N THR d 249 " --> pdb=" O THR d 270 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N THR d 270 " --> pdb=" O THR d 249 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N LYS d 251 " --> pdb=" O ASN d 268 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N ASN d 268 " --> pdb=" O LYS d 251 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'd' and resid 281 through 286 removed outlier: 4.681A pdb=" N ARG d 283 " --> pdb=" O SER d 296 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N LEU d 304 " --> pdb=" O ILE d 316 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'e' and resid 396 through 402 removed outlier: 6.955A pdb=" N LEU e 412 " --> pdb=" O ILE e 398 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N PHE e 400 " --> pdb=" O TRP e 410 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N TRP e 410 " --> pdb=" O PHE e 400 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N PHE e 402 " --> pdb=" O ASP e 408 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ASP e 408 " --> pdb=" O PHE e 402 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N VAL e 422 " --> pdb=" O VAL e 438 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N TYR e 46 " --> pdb=" O PHE e 439 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N VAL e 560 " --> pdb=" O LEU e 571 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA e 550 " --> pdb=" O LEU e 563 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'e' and resid 62 through 66 removed outlier: 5.851A pdb=" N ARG e 62 " --> pdb=" O ARG e 129 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N ARG e 131 " --> pdb=" O ARG e 62 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N LEU e 64 " --> pdb=" O ARG e 131 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'e' and resid 137 through 146 removed outlier: 5.490A pdb=" N GLY e 141 " --> pdb=" O LEU e 156 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N THR e 160 " --> pdb=" O THR e 157 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'e' and resid 218 through 221 Processing sheet with id=AI6, first strand: chain 'e' and resid 285 through 292 removed outlier: 4.402A pdb=" N LYS e 307 " --> pdb=" O CYS e 303 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N MET e 320 " --> pdb=" O MET e 310 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N SER e 312 " --> pdb=" O CYS e 318 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N CYS e 318 " --> pdb=" O SER e 312 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'e' and resid 343 through 349 removed outlier: 4.968A pdb=" N LEU e 355 " --> pdb=" O LEU e 374 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLN e 368 " --> pdb=" O LEU e 361 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N SER e 388 " --> pdb=" O VAL e 371 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N GLN e 373 " --> pdb=" O HIS e 386 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N HIS e 386 " --> pdb=" O GLN e 373 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N MET e 375 " --> pdb=" O LEU e 384 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N LEU e 384 " --> pdb=" O MET e 375 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'f' and resid 11 through 14 Processing sheet with id=AI9, first strand: chain 'f' and resid 21 through 24 removed outlier: 6.370A pdb=" N SER f 48 " --> pdb=" O THR f 65 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N THR f 65 " --> pdb=" O SER f 48 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N ARG f 50 " --> pdb=" O PHE f 63 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N PHE f 63 " --> pdb=" O ARG f 50 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'f' and resid 75 through 80 removed outlier: 3.700A pdb=" N ALA f 77 " --> pdb=" O ALA f 98 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'f' and resid 75 through 80 removed outlier: 3.700A pdb=" N ALA f 77 " --> pdb=" O ALA f 98 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'f' and resid 127 through 131 removed outlier: 3.505A pdb=" N ASP f 129 " --> pdb=" O VAL f 143 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLY f 144 " --> pdb=" O THR f 148 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N THR f 148 " --> pdb=" O GLY f 144 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ALA f 160 " --> pdb=" O ILE f 151 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ASP f 153 " --> pdb=" O GLN f 158 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N GLN f 158 " --> pdb=" O ASP f 153 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'f' and resid 168 through 173 removed outlier: 3.508A pdb=" N SER f 170 " --> pdb=" O ALA f 184 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N THR f 189 " --> pdb=" O GLU f 185 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU f 202 " --> pdb=" O PHE f 192 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ASP f 194 " --> pdb=" O ALA f 200 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N ALA f 200 " --> pdb=" O ASP f 194 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'f' and resid 211 through 216 removed outlier: 3.852A pdb=" N SER f 213 " --> pdb=" O VAL f 227 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'f' and resid 254 through 259 removed outlier: 6.466A pdb=" N THR f 270 " --> pdb=" O ARG f 255 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N PHE f 257 " --> pdb=" O ALA f 268 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N ALA f 268 " --> pdb=" O PHE f 257 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N TRP f 259 " --> pdb=" O VAL f 266 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N VAL f 266 " --> pdb=" O TRP f 259 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N GLN f 279 " --> pdb=" O GLY f 271 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain 'g' and resid 1151 through 1154 Processing sheet with id=AJ8, first strand: chain 'g' and resid 1333 through 1335 Processing sheet with id=AJ9, first strand: chain 'h' and resid 16 through 21 removed outlier: 3.718A pdb=" N ASP h 18 " --> pdb=" O CYS h 31 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N SER h 32 " --> pdb=" O SER h 36 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N SER h 36 " --> pdb=" O SER h 32 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N VAL h 37 " --> pdb=" O ASP h 52 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N ASP h 52 " --> pdb=" O VAL h 37 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ILE h 39 " --> pdb=" O ILE h 50 " (cutoff:3.500A) Processing sheet with id=AK1, first strand: chain 'h' and resid 60 through 65 removed outlier: 4.367A pdb=" N GLN h 62 " --> pdb=" O CYS h 77 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N VAL h 83 " --> pdb=" O GLU h 98 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N GLU h 98 " --> pdb=" O VAL h 83 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N ILE h 85 " --> pdb=" O THR h 96 " (cutoff:3.500A) Processing sheet with id=AK2, first strand: chain 'h' and resid 106 through 111 removed outlier: 6.778A pdb=" N GLY h 123 " --> pdb=" O ASN h 107 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N VAL h 109 " --> pdb=" O ALA h 121 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ALA h 121 " --> pdb=" O VAL h 109 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N TRP h 111 " --> pdb=" O LEU h 119 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N LEU h 119 " --> pdb=" O TRP h 111 " (cutoff:3.500A) Processing sheet with id=AK3, first strand: chain 'h' and resid 153 through 158 removed outlier: 6.536A pdb=" N VAL h 191 " --> pdb=" O LYS h 206 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N LYS h 206 " --> pdb=" O VAL h 191 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ILE h 193 " --> pdb=" O ASP h 204 " (cutoff:3.500A) Processing sheet with id=AK4, first strand: chain 'h' and resid 214 through 219 removed outlier: 3.671A pdb=" N ASP h 216 " --> pdb=" O CYS h 233 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N SER h 234 " --> pdb=" O ARG h 238 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N ARG h 238 " --> pdb=" O SER h 234 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N VAL h 239 " --> pdb=" O LEU h 257 " (cutoff:3.500A) Processing sheet with id=AK5, first strand: chain 'h' and resid 267 through 268 removed outlier: 3.979A pdb=" N SER h 300 " --> pdb=" O LEU h 287 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N LYS h 289 " --> pdb=" O CYS h 298 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N CYS h 298 " --> pdb=" O LYS h 289 " (cutoff:3.500A) Processing sheet with id=AK6, first strand: chain 'j' and resid 73 through 77 Processing sheet with id=AK7, first strand: chain 'j' and resid 100 through 103 removed outlier: 3.964A pdb=" N ALA j 100 " --> pdb=" O ALA j 112 " (cutoff:3.500A) Processing sheet with id=AK8, first strand: chain 'j' and resid 150 through 154 Processing sheet with id=AK9, first strand: chain 'j' and resid 202 through 206 removed outlier: 3.792A pdb=" N SER j 210 " --> pdb=" O VAL j 206 " (cutoff:3.500A) Processing sheet with id=AL1, first strand: chain 'j' and resid 265 through 270 removed outlier: 6.459A pdb=" N ILE j 284 " --> pdb=" O ASN j 299 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N ASN j 299 " --> pdb=" O ILE j 284 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N LYS j 286 " --> pdb=" O VAL j 297 " (cutoff:3.500A) Processing sheet with id=AL2, first strand: chain 'j' and resid 329 through 338 removed outlier: 6.665A pdb=" N LEU j 345 " --> pdb=" O LEU j 333 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N LEU j 335 " --> pdb=" O VAL j 343 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N VAL j 343 " --> pdb=" O LEU j 335 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N GLN j 337 " --> pdb=" O GLY j 341 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N GLY j 341 " --> pdb=" O GLN j 337 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N LYS j 366 " --> pdb=" O GLU j 375 " (cutoff:3.500A) removed outlier: 7.904A pdb=" N GLU j 375 " --> pdb=" O LYS j 366 " (cutoff:3.500A) removed outlier: 8.980A pdb=" N GLU j 368 " --> pdb=" O SER j 373 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N SER j 373 " --> pdb=" O GLU j 368 " (cutoff:3.500A) Processing sheet with id=AL3, first strand: chain 'j' and resid 396 through 398 Processing sheet with id=AL4, first strand: chain 'j' and resid 1068 through 1070 removed outlier: 4.033A pdb=" N SER j1068 " --> pdb=" O ASP j1075 " (cutoff:3.500A) Processing sheet with id=AL5, first strand: chain 'p' and resid 586 through 588 9224 hydrogen bonds defined for protein. 26991 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 82.32 Time building geometry restraints manager: 40.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.52: 73950 1.52 - 1.87: 43158 1.87 - 2.22: 0 2.22 - 2.58: 0 2.58 - 2.93: 1 Bond restraints: 117109 Sorted by residual: bond pdb=" C VAL p 680 " pdb=" N GLU p 683 " ideal model delta sigma weight residual 1.329 2.931 -1.602 1.76e-02 3.23e+03 8.29e+03 bond pdb=" C TRP g1614 " pdb=" O TRP g1614 " ideal model delta sigma weight residual 1.236 1.161 0.074 1.16e-02 7.43e+03 4.11e+01 bond pdb=" C TYR g1594 " pdb=" O TYR g1594 " ideal model delta sigma weight residual 1.237 1.308 -0.071 1.16e-02 7.43e+03 3.79e+01 bond pdb=" N LEU E1234 " pdb=" CA LEU E1234 " ideal model delta sigma weight residual 1.458 1.526 -0.068 1.12e-02 7.97e+03 3.72e+01 bond pdb=" C PRO g1540 " pdb=" O PRO g1540 " ideal model delta sigma weight residual 1.233 1.290 -0.058 9.90e-03 1.02e+04 3.39e+01 ... (remaining 117104 not shown) Histogram of bond angle deviations from ideal: 70.40 - 88.47: 1 88.47 - 106.54: 1974 106.54 - 124.60: 157817 124.60 - 142.67: 1421 142.67 - 160.74: 1 Bond angle restraints: 161214 Sorted by residual: angle pdb=" O VAL p 680 " pdb=" C VAL p 680 " pdb=" N GLU p 683 " ideal model delta sigma weight residual 122.69 70.40 52.29 9.30e-01 1.16e+00 3.16e+03 angle pdb=" CA VAL p 680 " pdb=" C VAL p 680 " pdb=" N GLU p 683 " ideal model delta sigma weight residual 115.54 160.74 -45.20 1.14e+00 7.69e-01 1.57e+03 angle pdb=" C VAL p 680 " pdb=" N GLU p 683 " pdb=" CA GLU p 683 " ideal model delta sigma weight residual 123.20 95.66 27.54 2.05e+00 2.38e-01 1.80e+02 angle pdb=" N GLY A 683 " pdb=" CA GLY A 683 " pdb=" C GLY A 683 " ideal model delta sigma weight residual 110.21 119.40 -9.19 9.10e-01 1.21e+00 1.02e+02 angle pdb=" N ARG g1321 " pdb=" CA ARG g1321 " pdb=" C ARG g1321 " ideal model delta sigma weight residual 111.14 100.73 10.41 1.08e+00 8.57e-01 9.28e+01 ... (remaining 161209 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.84: 67019 17.84 - 35.68: 1693 35.68 - 53.52: 416 53.52 - 71.36: 74 71.36 - 89.20: 10 Dihedral angle restraints: 69212 sinusoidal: 11633 harmonic: 57579 Sorted by residual: dihedral pdb=" CA THR A1053 " pdb=" C THR A1053 " pdb=" N PRO A1054 " pdb=" CA PRO A1054 " ideal model delta harmonic sigma weight residual -180.00 -121.11 -58.89 0 5.00e+00 4.00e-02 1.39e+02 dihedral pdb=" CA THR a1053 " pdb=" C THR a1053 " pdb=" N PRO a1054 " pdb=" CA PRO a1054 " ideal model delta harmonic sigma weight residual -180.00 -122.58 -57.42 0 5.00e+00 4.00e-02 1.32e+02 dihedral pdb=" CA SER A1771 " pdb=" C SER A1771 " pdb=" N PRO A1772 " pdb=" CA PRO A1772 " ideal model delta harmonic sigma weight residual -180.00 -126.41 -53.59 0 5.00e+00 4.00e-02 1.15e+02 ... (remaining 69209 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.088: 19058 0.088 - 0.175: 1419 0.175 - 0.263: 82 0.263 - 0.351: 9 0.351 - 0.438: 6 Chirality restraints: 20574 Sorted by residual: chirality pdb=" CB VAL e 968 " pdb=" CA VAL e 968 " pdb=" CG1 VAL e 968 " pdb=" CG2 VAL e 968 " both_signs ideal model delta sigma weight residual False -2.63 -2.19 -0.44 2.00e-01 2.50e+01 4.80e+00 chirality pdb=" CG LEU G1287 " pdb=" CB LEU G1287 " pdb=" CD1 LEU G1287 " pdb=" CD2 LEU G1287 " both_signs ideal model delta sigma weight residual False -2.59 -2.18 -0.41 2.00e-01 2.50e+01 4.28e+00 chirality pdb=" CG LEU B 637 " pdb=" CB LEU B 637 " pdb=" CD1 LEU B 637 " pdb=" CD2 LEU B 637 " both_signs ideal model delta sigma weight residual False -2.59 -2.19 -0.40 2.00e-01 2.50e+01 4.01e+00 ... (remaining 20571 not shown) Planarity restraints: 22056 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL p 680 " -0.090 2.00e-02 2.50e+03 9.53e-02 9.09e+01 pdb=" C VAL p 680 " 0.160 2.00e-02 2.50e+03 pdb=" O VAL p 680 " -0.028 2.00e-02 2.50e+03 pdb=" N GLU p 683 " -0.041 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU g1286 " -0.026 2.00e-02 2.50e+03 5.20e-02 2.70e+01 pdb=" C LEU g1286 " 0.090 2.00e-02 2.50e+03 pdb=" O LEU g1286 " -0.033 2.00e-02 2.50e+03 pdb=" N LEU g1287 " -0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG G1417 " -0.024 2.00e-02 2.50e+03 4.87e-02 2.37e+01 pdb=" C ARG G1417 " 0.084 2.00e-02 2.50e+03 pdb=" O ARG G1417 " -0.032 2.00e-02 2.50e+03 pdb=" N ASP G1418 " -0.028 2.00e-02 2.50e+03 ... (remaining 22053 not shown) Histogram of nonbonded interaction distances: 1.87 - 2.47: 38 2.47 - 3.08: 82851 3.08 - 3.69: 170712 3.69 - 4.29: 223510 4.29 - 4.90: 357774 Nonbonded interactions: 834885 Sorted by model distance: nonbonded pdb=" O GLN a1627 " pdb=" CB THR a1631 " model vdw 1.868 2.776 nonbonded pdb=" O GLN I 428 " pdb=" N VAL I 432 " model vdw 2.220 2.520 nonbonded pdb=" O VAL I 187 " pdb=" N GLN I 191 " model vdw 2.229 2.520 nonbonded pdb=" O TRP E 866 " pdb=" N SER E 868 " model vdw 2.273 2.520 nonbonded pdb=" O SER I 459 " pdb=" N ILE I 461 " model vdw 2.324 2.520 ... (remaining 834880 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 16 through 154 or resid 164 through 179 or resid 182 throu \ gh 463 or resid 484 through 571 or resid 583 through 673 or resid 683 through 95 \ 4 or (resid 969 through 1213 and (name N or name CA or name C or name O or name \ CB )) or resid 1214 through 1301 or (resid 1302 through 1334 and (name N or name \ CA or name C or name O or name CB )) or resid 1335 through 1437 or resid 1455 t \ hrough 1486 or resid 1489 through 1633 or resid 1638 through 1661 or resid 1665 \ through 1690 or resid 1697 through 1846 or resid 1865 through 1916)) selection = (chain 'a' and (resid 16 through 55 or resid 57 through 69 or resid 74 through 1 \ 03 or resid 107 through 1217 or (resid 1218 and (name N or name CA or name C or \ name O or name CB or name CG )) or resid 1227 through 1352 or resid 1382 through \ 1593 or resid 1608 through 1916)) } ncs_group { reference = (chain 'B' and (resid 18 through 58 or resid 61 through 184 or (resid 185 throug \ h 196 and (name N or name CA or name C or name O or name CB )) or resid 197 or ( \ resid 198 through 199 and (name N or name CA or name C or name O or name CB )) o \ r resid 200 or (resid 201 through 204 and (name N or name CA or name C or name O \ or name CB )) or resid 205 or (resid 206 through 222 and (name N or name CA or \ name C or name O or name CB )) or resid 223 through 242 or resid 248 through 271 \ or (resid 276 through 286 and (name N or name CA or name C or name O or name CB \ )) or resid 287 or (resid 288 through 297 and (name N or name CA or name C or n \ ame O or name CB )) or resid 300 through 385 or resid 396 through 611 or (resid \ 622 through 647 and (name N or name CA or name C or name O or name CB )))) selection = (chain 'b' and (resid 18 through 42 or resid 47 through 86 or resid 90 through 3 \ 34 or resid 340 through 356 or (resid 357 through 365 and (name N or name CA or \ name C or name O or name CB )) or resid 366 through 384 or (resid 385 and (name \ N or name CA or name C or name O or name CB )) or resid 396 through 611 or resid \ 622 through 647)) } ncs_group { reference = (chain 'C' and (resid 3 through 50 or resid 66 through 246 or resid 250 through \ 289 or resid 334 through 342 or resid 346 through 375)) selection = (chain 'c' and (resid 3 through 22 or resid 27 through 50 or resid 66 through 37 \ 5)) } ncs_group { reference = (chain 'D' and (resid 2 through 90 or resid 102 through 109 or (resid 110 throug \ h 114 and (name N or name CA or name C or name O or name CB )) or resid 115 thro \ ugh 255 or resid 260 through 327)) selection = (chain 'd' and resid 2 through 327) } ncs_group { reference = (chain 'E' and (resid 41 through 484 or resid 490 through 620 or resid 668 throu \ gh 689 or resid 703 through 742 or resid 759 through 837 or resid 849 through 11 \ 30 or (resid 1131 through 1174 and (name N or name CA or name C or name O or nam \ e CB )) or resid 1175 through 1368 or resid 1373 through 1430)) selection = (chain 'e' and (resid 41 through 259 or (resid 279 through 705 and (name N or na \ me CA or name C or name O or name CB )) or resid 706 or (resid 707 through 776 a \ nd (name N or name CA or name C or name O or name CB )) or resid 777 or (resid 7 \ 78 through 814 and (name N or name CA or name C or name O or name CB )) or (resi \ d 815 through 902 and (name N or name CA or name C or name O or name CB )) or re \ sid 903 or (resid 904 through 916 and (name N or name CA or name C or name O or \ name CB )) or resid 917 or (resid 918 and (name N or name CA or name C or name O \ or name CB )) or resid 919 through 931 or resid 953 through 969 or resid 971 th \ rough 1138 or resid 1170 through 1267 or resid 1277 through 1430)) } ncs_group { reference = (chain 'F' and resid 5 through 326) selection = (chain 'f' and ((resid 5 through 29 and (name N or name CA or name C or name O o \ r name CB )) or (resid 30 through 38 and (name N or name CA or name C or name O \ or name CB )) or resid 39 through 40 or (resid 41 through 59 and (name N or name \ CA or name C or name O or name CB )) or resid 60 or (resid 61 through 71 and (n \ ame N or name CA or name C or name O or name CB )) or resid 72 or (resid 73 thro \ ugh 99 and (name N or name CA or name C or name O or name CB )) or resid 100 or \ (resid 101 through 121 and (name N or name CA or name C or name O or name CB )) \ or resid 122 or (resid 123 through 124 and (name N or name CA or name C or name \ O or name CB )) or resid 125 or (resid 126 through 136 and (name N or name CA or \ name C or name O or name CB )) or resid 137 or (resid 138 through 143 and (name \ N or name CA or name C or name O or name CB )) or resid 144 or (resid 145 throu \ gh 155 and (name N or name CA or name C or name O or name CB )) or resid 156 or \ (resid 157 through 167 and (name N or name CA or name C or name O or name CB )) \ or resid 168 or (resid 169 through 176 and (name N or name CA or name C or name \ O or name CB )) or (resid 177 through 187 and (name N or name CA or name C or na \ me O or name CB )) or resid 188 or (resid 189 through 224 and (name N or name CA \ or name C or name O or name CB )) or (resid 225 through 228 and (name N or name \ CA or name C or name O or name CB )) or resid 229 or (resid 230 through 270 and \ (name N or name CA or name C or name O or name CB )) or resid 271 or (resid 272 \ through 273 and (name N or name CA or name C or name O or name CB )) or (resid \ 274 through 293 and (name N or name CA or name C or name O or name CB )) or resi \ d 294 or (resid 295 through 298 and (name N or name CA or name C or name O or na \ me CB )) or resid 299 or (resid 300 and (name N or name CA or name C or name O o \ r name CB )) or resid 301 or (resid 302 through 313 and (name N or name CA or na \ me C or name O or name CB )) or resid 314 through 315 or (resid 316 through 325 \ and (name N or name CA or name C or name O or name CB )) or (resid 326 and (name \ N or name CA or name C or name O or name CB or name OXT)))) } ncs_group { reference = (chain 'G' and ((resid 1043 through 1053 and (name N or name CA or name C or nam \ e O or name CB )) or resid 1054 or (resid 1055 and (name N or name CA or name C \ or name O or name CB )) or resid 1056 or (resid 1057 through 1062 and (name N or \ name CA or name C or name O or name CB )) or resid 1063 or (resid 1064 through \ 1066 and (name N or name CA or name C or name O or name CB )) or resid 1067 thro \ ugh 1208 or resid 1220 through 1382 or resid 1385 through 1396 or (resid 1397 th \ rough 1416 and (name N or name CA or name C or name O or name CB )) or resid 141 \ 7 through 1692)) selection = (chain 'g' and (resid 1043 through 1082 or resid 1119 through 1121 or (resid 112 \ 2 through 1138 and (name N or name CA or name C or name O or name CB )) or resid \ 1139 through 1183 or resid 1191 through 1398 or resid 1415 through 1521 or resi \ d 1523 or (resid 1524 through 1537 and (name N or name CA or name C or name O or \ name CB )) or resid 1538 through 1556 or resid 1559 through 1569 or (resid 1572 \ through 1585 and (name N or name CA or name C or name O or name CB )) or (resid \ 1591 through 1599 and (name N or name CA or name C or name O or name CB )) or r \ esid 1600 or (resid 1601 through 1605 and (name N or name CA or name C or name O \ or name CB )) or (resid 1612 through 1617 and (name N or name CA or name C or n \ ame O or name CB )) or resid 1618 or (resid 1619 through 1634 and (name N or nam \ e CA or name C or name O or name CB )) or (resid 1640 and (name N or name CA or \ name C or name O or name CB )) or resid 1641 or (resid 1642 through 1663 and (na \ me N or name CA or name C or name O or name CB )) or (resid 1667 through 1692 an \ d (name N or name CA or name C or name O or name CB )))) } ncs_group { reference = (chain 'H' and (resid 6 through 162 or resid 178 through 304)) selection = (chain 'h' and ((resid 6 through 14 and (name N or name CA or name C or name O o \ r name CB )) or resid 15 through 304)) } ncs_group { reference = (chain 'I' and (resid 143 through 181 or resid 200 through 298 or resid 316 thro \ ugh 371 or resid 413 through 458 or resid 471 through 727 or resid 731 through 8 \ 27 or resid 830 through 903)) selection = (chain 'i' and (resid 143 through 298 or resid 316 through 622 or resid 627 thro \ ugh 903)) } ncs_group { reference = (chain 'K' and (resid 60 through 140 or resid 147 through 174 or resid 176 or re \ sid 182 through 213 or resid 222 through 329 or resid 340 through 502 or resid 5 \ 10 through 563 or resid 567 through 636 or resid 645 through 659 or resid 663 th \ rough 738)) selection = (chain 'L' and (resid 60 through 140 or resid 147 through 174 or resid 181 throu \ gh 540 or resid 549 through 563 or resid 567 through 636 or resid 645 through 65 \ 9 or resid 663 through 738)) selection = (chain 'M' and (resid 60 through 140 or resid 147 through 174 or resid 176 or re \ sid 182 through 213 or resid 222 through 329 or resid 340 through 502 or resid 5 \ 10 through 540 or resid 549 through 563 or resid 567 through 636 or resid 645 th \ rough 659 or resid 663 through 738)) selection = (chain 'N' and (resid 60 through 140 or resid 147 through 174 or resid 176 or re \ sid 182 through 329 or resid 340 through 502 or resid 510 through 540 or resid 5 \ 49 through 563 or resid 567 through 636 or resid 645 through 659 or resid 663 th \ rough 738)) selection = (chain 'O' and (resid 60 through 140 or resid 147 through 174 or resid 176 or re \ sid 182 through 213 or resid 222 through 329 or resid 340 through 502 or resid 5 \ 10 through 540 or resid 549 through 738)) } ncs_group { reference = chain 'S' selection = chain 's' } 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.090 Extract box with map and model: 30.430 Check model and map are aligned: 1.230 Set scattering table: 0.760 Process input model: 288.720 Find NCS groups from input model: 8.170 Set up NCS constraints: 0.560 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:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 337.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5116 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 1.602 117109 Z= 0.508 Angle : 0.979 52.288 161214 Z= 0.668 Chirality : 0.048 0.438 20574 Planarity : 0.004 0.103 22056 Dihedral : 9.931 89.204 31374 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.99 % Favored : 93.80 % Rotamer: Outliers : 3.73 % Allowed : 5.98 % Favored : 90.29 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 1.46 % Cis-general : 0.00 % Twisted Proline : 0.73 % 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: -2.13 (0.05), residues: 18634 helix: -0.98 (0.04), residues: 10793 sheet: -0.76 (0.11), residues: 1925 loop : -2.19 (0.07), residues: 5916 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP B 167 HIS 0.007 0.001 HIS g1467 PHE 0.036 0.002 PHE e 907 TYR 0.046 0.002 TYR E1290 ARG 0.007 0.001 ARG f 74 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 37268 Ramachandran restraints generated. 18634 Oldfield, 0 Emsley, 18634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 37268 Ramachandran restraints generated. 18634 Oldfield, 0 Emsley, 18634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1114 residues out of total 16917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 193 poor density : 921 time to evaluate : 9.966 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1227 VAL cc_start: 0.5439 (OUTLIER) cc_final: 0.4824 (p) REVERT: B 140 MET cc_start: 0.4982 (mtt) cc_final: 0.4698 (mtt) REVERT: B 194 PHE cc_start: 0.7025 (t80) cc_final: 0.6753 (t80) REVERT: B 217 GLU cc_start: 0.7257 (tp30) cc_final: 0.6667 (tm-30) REVERT: B 496 PHE cc_start: 0.7447 (OUTLIER) cc_final: 0.7201 (m-80) REVERT: B 545 MET cc_start: 0.7103 (mtt) cc_final: 0.6878 (mtm) REVERT: B 546 TYR cc_start: 0.7638 (OUTLIER) cc_final: 0.7433 (p90) REVERT: C 101 PHE cc_start: 0.7863 (m-80) cc_final: 0.7648 (m-80) REVERT: C 112 VAL cc_start: 0.9073 (OUTLIER) cc_final: 0.8711 (p) REVERT: C 238 MET cc_start: 0.7685 (mmm) cc_final: 0.7211 (mmp) REVERT: D 27 MET cc_start: 0.6667 (ptm) cc_final: 0.6454 (ptt) REVERT: D 190 SER cc_start: 0.8647 (m) cc_final: 0.8303 (t) REVERT: D 318 VAL cc_start: 0.9109 (OUTLIER) cc_final: 0.8814 (t) REVERT: E 926 PHE cc_start: 0.7196 (m-10) cc_final: 0.6987 (m-10) REVERT: E 997 THR cc_start: 0.7060 (OUTLIER) cc_final: 0.6814 (m) REVERT: E 1250 GLN cc_start: 0.6558 (OUTLIER) cc_final: 0.6055 (pp30) REVERT: E 1301 TYR cc_start: 0.5485 (OUTLIER) cc_final: 0.5131 (m-10) REVERT: E 1376 LEU cc_start: 0.4891 (tp) cc_final: 0.4630 (tt) REVERT: G 1053 HIS cc_start: 0.7538 (m90) cc_final: 0.7064 (m170) REVERT: G 1275 LEU cc_start: 0.7103 (tp) cc_final: 0.6729 (tp) REVERT: G 1312 GLN cc_start: 0.7755 (OUTLIER) cc_final: 0.7302 (tm-30) REVERT: G 1505 ILE cc_start: 0.8626 (OUTLIER) cc_final: 0.7933 (mt) REVERT: H 42 VAL cc_start: 0.9143 (OUTLIER) cc_final: 0.8916 (p) REVERT: H 178 TYR cc_start: 0.7782 (m-80) cc_final: 0.7342 (m-80) REVERT: H 235 GLN cc_start: 0.8248 (tp40) cc_final: 0.7854 (tp40) REVERT: W 1238 MET cc_start: 0.8772 (ttp) cc_final: 0.8562 (ttm) REVERT: W 1314 MET cc_start: 0.7894 (mmm) cc_final: 0.7650 (mmt) REVERT: W 1364 MET cc_start: 0.8732 (mtp) cc_final: 0.8427 (mtm) REVERT: a 1287 LEU cc_start: 0.8074 (OUTLIER) cc_final: 0.7838 (tt) REVERT: b 100 GLN cc_start: 0.7593 (tp40) cc_final: 0.7144 (tm-30) REVERT: b 128 GLN cc_start: 0.6701 (tp40) cc_final: 0.6365 (mp10) REVERT: c 48 TRP cc_start: 0.7859 (m100) cc_final: 0.7583 (m100) REVERT: c 78 VAL cc_start: 0.8579 (OUTLIER) cc_final: 0.8370 (m) REVERT: c 83 PHE cc_start: 0.7991 (OUTLIER) cc_final: 0.6262 (m-80) REVERT: c 86 LYS cc_start: 0.7740 (mttt) cc_final: 0.7304 (mmmt) REVERT: c 121 TYR cc_start: 0.7904 (p90) cc_final: 0.7663 (p90) REVERT: c 122 HIS cc_start: 0.4650 (OUTLIER) cc_final: 0.4404 (p-80) REVERT: c 147 ASP cc_start: 0.7848 (OUTLIER) cc_final: 0.7205 (p0) REVERT: c 199 LYS cc_start: 0.8097 (tttt) cc_final: 0.7875 (mmmt) REVERT: c 238 MET cc_start: 0.8876 (mmm) cc_final: 0.8587 (mtm) REVERT: d 27 MET cc_start: 0.6614 (ptt) cc_final: 0.6267 (ptt) REVERT: e 1407 LEU cc_start: 0.8841 (OUTLIER) cc_final: 0.8353 (tp) REVERT: e 1428 LEU cc_start: 0.7436 (tt) cc_final: 0.7189 (mt) REVERT: f 237 MET cc_start: 0.8529 (mmm) cc_final: 0.8285 (mmm) REVERT: f 256 MET cc_start: 0.7301 (tpp) cc_final: 0.7086 (mmm) REVERT: g 1077 ASN cc_start: 0.6132 (t0) cc_final: 0.5855 (t0) outliers start: 193 outliers final: 41 residues processed: 1087 average time/residue: 0.8991 time to fit residues: 1733.8863 Evaluate side-chains 736 residues out of total 16917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 678 time to evaluate : 9.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1227 VAL Chi-restraints excluded: chain B residue 148 GLU Chi-restraints excluded: chain B residue 496 PHE Chi-restraints excluded: chain B residue 546 TYR Chi-restraints excluded: chain B residue 580 LEU Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain E residue 997 THR Chi-restraints excluded: chain E residue 1078 LEU Chi-restraints excluded: chain E residue 1085 TYR Chi-restraints excluded: chain E residue 1107 VAL Chi-restraints excluded: chain E residue 1178 LEU Chi-restraints excluded: chain E residue 1234 LEU Chi-restraints excluded: chain E residue 1235 THR Chi-restraints excluded: chain E residue 1250 GLN Chi-restraints excluded: chain E residue 1301 TYR Chi-restraints excluded: chain G residue 1065 PHE Chi-restraints excluded: chain G residue 1168 VAL Chi-restraints excluded: chain G residue 1287 LEU Chi-restraints excluded: chain G residue 1312 GLN Chi-restraints excluded: chain G residue 1426 LEU Chi-restraints excluded: chain G residue 1505 ILE Chi-restraints excluded: chain G residue 1513 LEU Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain H residue 162 VAL Chi-restraints excluded: chain S residue 128 TYR Chi-restraints excluded: chain S residue 137 TRP Chi-restraints excluded: chain W residue 1088 PHE Chi-restraints excluded: chain W residue 1114 TYR Chi-restraints excluded: chain s residue 122 PHE Chi-restraints excluded: chain s residue 137 TRP Chi-restraints excluded: chain a residue 1247 ILE Chi-restraints excluded: chain a residue 1287 LEU Chi-restraints excluded: chain b residue 67 VAL Chi-restraints excluded: chain c residue 78 VAL Chi-restraints excluded: chain c residue 83 PHE Chi-restraints excluded: chain c residue 122 HIS Chi-restraints excluded: chain c residue 123 VAL Chi-restraints excluded: chain c residue 147 ASP Chi-restraints excluded: chain c residue 183 ILE Chi-restraints excluded: chain c residue 260 GLU Chi-restraints excluded: chain c residue 337 ILE Chi-restraints excluded: chain e residue 898 CYS Chi-restraints excluded: chain e residue 902 VAL Chi-restraints excluded: chain e residue 933 VAL Chi-restraints excluded: chain e residue 957 TYR Chi-restraints excluded: chain e residue 1260 TRP Chi-restraints excluded: chain e residue 1407 LEU Chi-restraints excluded: chain f residue 119 VAL Chi-restraints excluded: chain f residue 190 ILE Chi-restraints excluded: chain g residue 1072 VAL Chi-restraints excluded: chain g residue 1292 VAL Chi-restraints excluded: chain g residue 1435 CYS Chi-restraints excluded: chain g residue 1608 CYS Chi-restraints excluded: chain h residue 42 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1859 random chunks: chunk 1569 optimal weight: 0.9990 chunk 1409 optimal weight: 1.9990 chunk 781 optimal weight: 0.9990 chunk 481 optimal weight: 0.6980 chunk 950 optimal weight: 50.0000 chunk 752 optimal weight: 0.0970 chunk 1457 optimal weight: 0.1980 chunk 563 optimal weight: 8.9990 chunk 885 optimal weight: 30.0000 chunk 1084 optimal weight: 9.9990 chunk 1688 optimal weight: 6.9990 overall best weight: 0.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1206 GLN A1231 HIS A1268 ASN ** A1272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 83 GLN ** B 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 257 GLN B 304 HIS C 113 ASN C 114 GLN C 122 HIS C 273 HIS D 56 HIS D 192 ASN D 273 GLN ** E1008 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1025 GLN E1083 HIS ** E1125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1228 GLN E1318 ASN E1398 GLN E1416 GLN G1053 HIS G1150 ASN G1165 ASN G1172 HIS G1180 ASN G1220 ASN G1290 GLN G1370 GLN G1416 GLN G1431 GLN G1471 HIS G1477 HIS G1499 HIS G1515 ASN ** H 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 142 GLN W1204 HIS W1372 ASN ** a1268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 22 HIS b 97 GLN b 257 GLN c 114 GLN c 151 ASN d 152 GLN d 268 ASN d 276 ASN d 278 ASN d 280 GLN e 869 ASN e 920 HIS e1008 HIS e1054 HIS e1083 HIS ** e1195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e1228 GLN e1249 GLN e1318 ASN ** g1083 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g1165 ASN g1180 ASN g1220 ASN g1290 GLN g1309 ASN ** g1347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g1370 GLN g1477 HIS g1515 ASN ** h 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 261 ASN Total number of N/Q/H flips: 63 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5113 moved from start: 0.1589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.059 117109 Z= 0.143 Angle : 0.481 11.173 161214 Z= 0.271 Chirality : 0.038 0.208 20574 Planarity : 0.003 0.080 22056 Dihedral : 4.802 79.050 20186 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.85 % Favored : 96.09 % Rotamer: Outliers : 2.16 % Allowed : 9.53 % Favored : 88.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.00 % Twisted Proline : 0.29 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.06), residues: 18636 helix: 1.22 (0.05), residues: 10944 sheet: -0.21 (0.11), residues: 1969 loop : -1.69 (0.08), residues: 5723 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP B 167 HIS 0.011 0.001 HIS H 266 PHE 0.058 0.001 PHE G1325 TYR 0.020 0.001 TYR E1290 ARG 0.007 0.000 ARG G1283 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 37272 Ramachandran restraints generated. 18636 Oldfield, 0 Emsley, 18636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 37272 Ramachandran restraints generated. 18636 Oldfield, 0 Emsley, 18636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 840 residues out of total 16917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 728 time to evaluate : 9.970 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: B 116 MET cc_start: 0.6835 (mtt) cc_final: 0.6583 (mtp) REVERT: B 194 PHE cc_start: 0.6625 (t80) cc_final: 0.6411 (t80) REVERT: B 207 MET cc_start: 0.6737 (mtm) cc_final: 0.6465 (mtm) REVERT: B 214 LEU cc_start: 0.7517 (OUTLIER) cc_final: 0.7301 (mt) REVERT: B 217 GLU cc_start: 0.7236 (tp30) cc_final: 0.6618 (tm-30) REVERT: B 252 PHE cc_start: 0.6528 (t80) cc_final: 0.6300 (t80) REVERT: B 496 PHE cc_start: 0.7328 (OUTLIER) cc_final: 0.7098 (m-80) REVERT: B 545 MET cc_start: 0.7469 (mtt) cc_final: 0.7232 (mtm) REVERT: C 112 VAL cc_start: 0.9140 (OUTLIER) cc_final: 0.8748 (p) REVERT: C 127 MET cc_start: 0.3377 (mtm) cc_final: 0.3151 (mtp) REVERT: D 18 VAL cc_start: 0.7365 (OUTLIER) cc_final: 0.7157 (p) REVERT: D 190 SER cc_start: 0.8604 (m) cc_final: 0.8229 (t) REVERT: E 1250 GLN cc_start: 0.6255 (OUTLIER) cc_final: 0.5955 (pp30) REVERT: E 1287 MET cc_start: 0.6605 (tpp) cc_final: 0.6298 (mmm) REVERT: E 1301 TYR cc_start: 0.5576 (OUTLIER) cc_final: 0.5087 (m-80) REVERT: E 1376 LEU cc_start: 0.4802 (tp) cc_final: 0.4502 (tt) REVERT: G 1049 LYS cc_start: 0.6729 (mmmt) cc_final: 0.6381 (mmmt) REVERT: G 1275 LEU cc_start: 0.6795 (tp) cc_final: 0.6453 (tp) REVERT: H 42 VAL cc_start: 0.9085 (OUTLIER) cc_final: 0.8811 (p) REVERT: H 178 TYR cc_start: 0.7741 (m-80) cc_final: 0.7306 (m-80) REVERT: H 236 ASP cc_start: 0.6972 (OUTLIER) cc_final: 0.6626 (p0) REVERT: W 1081 TYR cc_start: 0.7283 (t80) cc_final: 0.6883 (t80) REVERT: W 1314 MET cc_start: 0.7940 (mmm) cc_final: 0.7524 (mmt) REVERT: W 1364 MET cc_start: 0.8598 (mtp) cc_final: 0.8189 (mtm) REVERT: a 1287 LEU cc_start: 0.8413 (OUTLIER) cc_final: 0.8161 (tt) REVERT: b 131 ILE cc_start: 0.8152 (tp) cc_final: 0.7901 (pt) REVERT: b 259 TRP cc_start: 0.6610 (t60) cc_final: 0.6362 (t60) REVERT: c 48 TRP cc_start: 0.7836 (m100) cc_final: 0.7516 (m-10) REVERT: c 78 VAL cc_start: 0.8657 (OUTLIER) cc_final: 0.8417 (m) REVERT: c 86 LYS cc_start: 0.7588 (mttt) cc_final: 0.7220 (mmmt) REVERT: c 122 HIS cc_start: 0.4694 (OUTLIER) cc_final: 0.4122 (p-80) REVERT: c 199 LYS cc_start: 0.8167 (tttt) cc_final: 0.7939 (mmmt) REVERT: c 238 MET cc_start: 0.8760 (mmm) cc_final: 0.8407 (mtm) REVERT: d 27 MET cc_start: 0.6518 (ptt) cc_final: 0.6301 (ptt) REVERT: e 773 MET cc_start: 0.7647 (tpt) cc_final: 0.7150 (tpt) REVERT: e 1096 MET cc_start: 0.7453 (mmp) cc_final: 0.7173 (mmm) REVERT: e 1407 LEU cc_start: 0.8831 (OUTLIER) cc_final: 0.8446 (tp) REVERT: e 1428 LEU cc_start: 0.7705 (tt) cc_final: 0.7331 (mt) REVERT: f 190 ILE cc_start: 0.7900 (OUTLIER) cc_final: 0.7609 (mt) REVERT: f 256 MET cc_start: 0.7192 (tpp) cc_final: 0.6970 (mmm) REVERT: g 1311 LEU cc_start: 0.6646 (tp) cc_final: 0.6420 (tp) REVERT: g 1361 MET cc_start: 0.7552 (OUTLIER) cc_final: 0.7286 (mmt) outliers start: 112 outliers final: 52 residues processed: 819 average time/residue: 0.9003 time to fit residues: 1326.6882 Evaluate side-chains 727 residues out of total 16917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 661 time to evaluate : 10.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1238 VAL Chi-restraints excluded: chain B residue 148 GLU Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 496 PHE Chi-restraints excluded: chain B residue 546 TYR Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain E residue 1078 LEU Chi-restraints excluded: chain E residue 1107 VAL Chi-restraints excluded: chain E residue 1178 LEU Chi-restraints excluded: chain E residue 1198 THR Chi-restraints excluded: chain E residue 1215 VAL Chi-restraints excluded: chain E residue 1234 LEU Chi-restraints excluded: chain E residue 1250 GLN Chi-restraints excluded: chain E residue 1301 TYR Chi-restraints excluded: chain G residue 1159 CYS Chi-restraints excluded: chain G residue 1206 TRP Chi-restraints excluded: chain G residue 1283 ARG Chi-restraints excluded: chain G residue 1426 LEU Chi-restraints excluded: chain G residue 1443 VAL Chi-restraints excluded: chain G residue 1566 LEU Chi-restraints excluded: chain H residue 15 MET Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain H residue 162 VAL Chi-restraints excluded: chain H residue 236 ASP Chi-restraints excluded: chain S residue 110 LEU Chi-restraints excluded: chain S residue 122 PHE Chi-restraints excluded: chain S residue 137 TRP Chi-restraints excluded: chain W residue 1114 TYR Chi-restraints excluded: chain s residue 137 TRP Chi-restraints excluded: chain a residue 1227 VAL Chi-restraints excluded: chain a residue 1247 ILE Chi-restraints excluded: chain a residue 1287 LEU Chi-restraints excluded: chain b residue 168 VAL Chi-restraints excluded: chain b residue 170 LEU Chi-restraints excluded: chain b residue 306 LEU Chi-restraints excluded: chain b residue 318 LYS Chi-restraints excluded: chain c residue 78 VAL Chi-restraints excluded: chain c residue 112 VAL Chi-restraints excluded: chain c residue 122 HIS Chi-restraints excluded: chain c residue 123 VAL Chi-restraints excluded: chain c residue 337 ILE Chi-restraints excluded: chain d residue 102 HIS Chi-restraints excluded: chain d residue 194 MET Chi-restraints excluded: chain e residue 882 CYS Chi-restraints excluded: chain e residue 898 CYS Chi-restraints excluded: chain e residue 957 TYR Chi-restraints excluded: chain e residue 970 LEU Chi-restraints excluded: chain e residue 1260 TRP Chi-restraints excluded: chain e residue 1306 ILE Chi-restraints excluded: chain e residue 1324 TYR Chi-restraints excluded: chain e residue 1328 ASP Chi-restraints excluded: chain e residue 1407 LEU Chi-restraints excluded: chain f residue 119 VAL Chi-restraints excluded: chain f residue 190 ILE Chi-restraints excluded: chain f residue 280 ILE Chi-restraints excluded: chain g residue 1081 VAL Chi-restraints excluded: chain g residue 1205 LEU Chi-restraints excluded: chain g residue 1361 MET Chi-restraints excluded: chain g residue 1365 THR Chi-restraints excluded: chain g residue 1419 VAL Chi-restraints excluded: chain g residue 1520 VAL Chi-restraints excluded: chain g residue 1608 CYS Chi-restraints excluded: chain g residue 1651 VAL Chi-restraints excluded: chain h residue 42 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1859 random chunks: chunk 938 optimal weight: 8.9990 chunk 523 optimal weight: 2.9990 chunk 1405 optimal weight: 10.0000 chunk 1149 optimal weight: 80.0000 chunk 465 optimal weight: 1.9990 chunk 1691 optimal weight: 1.9990 chunk 1826 optimal weight: 30.0000 chunk 1506 optimal weight: 3.9990 chunk 1677 optimal weight: 3.9990 chunk 576 optimal weight: 30.0000 chunk 1356 optimal weight: 0.7980 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 191 HIS ** B 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 416 GLN ** B 640 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G1416 GLN ** G1461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G1471 HIS H 17 HIS ** a1268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 266 HIS b 416 GLN c 228 HIS ** c 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e1008 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e1125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e1194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e1195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e1228 GLN e1266 ASN e1399 HIS f 198 HIS ** g1083 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g1315 HIS ** g1347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g1499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 250 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5245 moved from start: 0.2352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 117109 Z= 0.211 Angle : 0.499 10.870 161214 Z= 0.278 Chirality : 0.039 0.243 20574 Planarity : 0.003 0.082 22056 Dihedral : 4.342 78.995 20144 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.38 % Favored : 95.57 % Rotamer: Outliers : 2.55 % Allowed : 10.31 % Favored : 87.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.00 % Twisted Proline : 0.15 % 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: 1.11 (0.06), residues: 18636 helix: 1.95 (0.05), residues: 10979 sheet: 0.01 (0.11), residues: 1981 loop : -1.45 (0.08), residues: 5676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 167 HIS 0.010 0.002 HIS G1053 PHE 0.027 0.002 PHE g1532 TYR 0.026 0.002 TYR f 272 ARG 0.011 0.001 ARG A1204 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 37272 Ramachandran restraints generated. 18636 Oldfield, 0 Emsley, 18636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 37272 Ramachandran restraints generated. 18636 Oldfield, 0 Emsley, 18636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 825 residues out of total 16917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 693 time to evaluate : 10.211 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 116 MET cc_start: 0.7105 (mtt) cc_final: 0.6847 (mtm) REVERT: B 207 MET cc_start: 0.5594 (mtm) cc_final: 0.5375 (mtm) REVERT: B 214 LEU cc_start: 0.7647 (OUTLIER) cc_final: 0.7418 (mt) REVERT: B 217 GLU cc_start: 0.6960 (tp30) cc_final: 0.6508 (tm-30) REVERT: B 252 PHE cc_start: 0.6699 (t80) cc_final: 0.6272 (t80) REVERT: B 496 PHE cc_start: 0.7572 (OUTLIER) cc_final: 0.7091 (m-80) REVERT: B 545 MET cc_start: 0.7809 (mtt) cc_final: 0.7558 (mtm) REVERT: C 89 ILE cc_start: 0.8495 (mt) cc_final: 0.8286 (tp) REVERT: C 127 MET cc_start: 0.4176 (mtm) cc_final: 0.3973 (mtp) REVERT: D 190 SER cc_start: 0.8606 (m) cc_final: 0.8290 (t) REVERT: E 988 ASP cc_start: 0.6841 (OUTLIER) cc_final: 0.6636 (m-30) REVERT: E 1250 GLN cc_start: 0.6416 (OUTLIER) cc_final: 0.5971 (pp30) REVERT: E 1287 MET cc_start: 0.6828 (tpp) cc_final: 0.6626 (mmm) REVERT: G 1049 LYS cc_start: 0.6909 (mmmt) cc_final: 0.6628 (mmmt) REVERT: G 1171 ILE cc_start: 0.8029 (pt) cc_final: 0.7624 (mp) REVERT: G 1275 LEU cc_start: 0.7010 (tp) cc_final: 0.6684 (tp) REVERT: G 1279 SER cc_start: 0.5895 (m) cc_final: 0.5443 (p) REVERT: G 1398 GLU cc_start: 0.3737 (pm20) cc_final: 0.3460 (pp20) REVERT: H 42 VAL cc_start: 0.9099 (OUTLIER) cc_final: 0.8836 (p) REVERT: H 178 TYR cc_start: 0.7963 (m-80) cc_final: 0.7622 (m-80) REVERT: H 235 GLN cc_start: 0.8030 (tp40) cc_final: 0.7628 (tp40) REVERT: W 1237 ARG cc_start: 0.5920 (mtp-110) cc_final: 0.5307 (mtm180) REVERT: W 1364 MET cc_start: 0.8410 (mtp) cc_final: 0.8026 (mtm) REVERT: a 1237 GLU cc_start: 0.8008 (mm-30) cc_final: 0.7698 (mm-30) REVERT: b 562 MET cc_start: 0.8248 (mmm) cc_final: 0.7933 (mmm) REVERT: c 48 TRP cc_start: 0.8009 (m100) cc_final: 0.7479 (m100) REVERT: c 122 HIS cc_start: 0.5045 (OUTLIER) cc_final: 0.4250 (p-80) REVERT: e 1407 LEU cc_start: 0.8861 (OUTLIER) cc_final: 0.8406 (tp) REVERT: e 1428 LEU cc_start: 0.7840 (tt) cc_final: 0.7414 (mt) REVERT: f 256 MET cc_start: 0.7291 (tpp) cc_final: 0.7008 (mmm) REVERT: g 1154 ASP cc_start: 0.4964 (OUTLIER) cc_final: 0.4698 (p0) REVERT: h 20 GLN cc_start: 0.4215 (OUTLIER) cc_final: 0.3877 (tt0) outliers start: 132 outliers final: 68 residues processed: 806 average time/residue: 0.9472 time to fit residues: 1383.9639 Evaluate side-chains 720 residues out of total 16917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 643 time to evaluate : 8.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 148 GLU Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 240 MET Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain B residue 496 PHE Chi-restraints excluded: chain B residue 546 TYR Chi-restraints excluded: chain B residue 559 LEU Chi-restraints excluded: chain C residue 10 VAL Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain D residue 161 CYS Chi-restraints excluded: chain E residue 988 ASP Chi-restraints excluded: chain E residue 1078 LEU Chi-restraints excluded: chain E residue 1107 VAL Chi-restraints excluded: chain E residue 1198 THR Chi-restraints excluded: chain E residue 1215 VAL Chi-restraints excluded: chain E residue 1234 LEU Chi-restraints excluded: chain E residue 1250 GLN Chi-restraints excluded: chain G residue 1050 SER Chi-restraints excluded: chain G residue 1082 HIS Chi-restraints excluded: chain G residue 1159 CYS Chi-restraints excluded: chain G residue 1182 SER Chi-restraints excluded: chain G residue 1283 ARG Chi-restraints excluded: chain G residue 1426 LEU Chi-restraints excluded: chain G residue 1443 VAL Chi-restraints excluded: chain G residue 1444 THR Chi-restraints excluded: chain G residue 1566 LEU Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain H residue 162 VAL Chi-restraints excluded: chain H residue 225 LEU Chi-restraints excluded: chain H residue 236 ASP Chi-restraints excluded: chain H residue 272 THR Chi-restraints excluded: chain H residue 282 ASP Chi-restraints excluded: chain S residue 122 PHE Chi-restraints excluded: chain S residue 135 VAL Chi-restraints excluded: chain S residue 137 TRP Chi-restraints excluded: chain W residue 1094 VAL Chi-restraints excluded: chain W residue 1114 TYR Chi-restraints excluded: chain s residue 137 TRP Chi-restraints excluded: chain a residue 1227 VAL Chi-restraints excluded: chain a residue 1247 ILE Chi-restraints excluded: chain a residue 1287 LEU Chi-restraints excluded: chain b residue 161 LEU Chi-restraints excluded: chain b residue 168 VAL Chi-restraints excluded: chain b residue 306 LEU Chi-restraints excluded: chain b residue 314 HIS Chi-restraints excluded: chain b residue 502 ASP Chi-restraints excluded: chain b residue 546 TYR Chi-restraints excluded: chain c residue 112 VAL Chi-restraints excluded: chain c residue 122 HIS Chi-restraints excluded: chain c residue 123 VAL Chi-restraints excluded: chain c residue 236 ASP Chi-restraints excluded: chain d residue 194 MET Chi-restraints excluded: chain e residue 800 LEU Chi-restraints excluded: chain e residue 898 CYS Chi-restraints excluded: chain e residue 957 TYR Chi-restraints excluded: chain e residue 970 LEU Chi-restraints excluded: chain e residue 1260 TRP Chi-restraints excluded: chain e residue 1306 ILE Chi-restraints excluded: chain e residue 1324 TYR Chi-restraints excluded: chain e residue 1328 ASP Chi-restraints excluded: chain e residue 1407 LEU Chi-restraints excluded: chain f residue 119 VAL Chi-restraints excluded: chain g residue 1081 VAL Chi-restraints excluded: chain g residue 1154 ASP Chi-restraints excluded: chain g residue 1205 LEU Chi-restraints excluded: chain g residue 1260 VAL Chi-restraints excluded: chain g residue 1285 SER Chi-restraints excluded: chain g residue 1365 THR Chi-restraints excluded: chain g residue 1419 VAL Chi-restraints excluded: chain g residue 1520 VAL Chi-restraints excluded: chain g residue 1539 VAL Chi-restraints excluded: chain h residue 12 HIS Chi-restraints excluded: chain h residue 20 GLN Chi-restraints excluded: chain h residue 42 VAL Chi-restraints excluded: chain h residue 266 HIS Chi-restraints excluded: chain h residue 282 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1859 random chunks: chunk 1670 optimal weight: 3.9990 chunk 1271 optimal weight: 9.9990 chunk 877 optimal weight: 20.0000 chunk 187 optimal weight: 0.9980 chunk 807 optimal weight: 0.9990 chunk 1135 optimal weight: 0.8980 chunk 1697 optimal weight: 4.9990 chunk 1796 optimal weight: 50.0000 chunk 886 optimal weight: 10.0000 chunk 1608 optimal weight: 4.9990 chunk 484 optimal weight: 0.8980 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 412 HIS ** E1008 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1302 HIS G1471 HIS b 374 HIS c 68 GLN c 126 ASN e1008 HIS e1125 ASN ** e1194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e1195 ASN ** f 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 147 HIS ** g1083 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g1256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g1347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5230 moved from start: 0.2649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 117109 Z= 0.150 Angle : 0.434 13.519 161214 Z= 0.240 Chirality : 0.038 0.603 20574 Planarity : 0.003 0.077 22056 Dihedral : 4.081 75.983 20132 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.66 % Favored : 96.31 % Rotamer: Outliers : 2.20 % Allowed : 11.29 % Favored : 86.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.00 % Twisted Proline : 0.15 % 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: 1.62 (0.06), residues: 18636 helix: 2.40 (0.05), residues: 10996 sheet: 0.14 (0.11), residues: 1984 loop : -1.33 (0.08), residues: 5656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP e1262 HIS 0.010 0.001 HIS G1053 PHE 0.029 0.001 PHE E1097 TYR 0.019 0.001 TYR f 272 ARG 0.007 0.000 ARG s 118 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 37272 Ramachandran restraints generated. 18636 Oldfield, 0 Emsley, 18636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 37272 Ramachandran restraints generated. 18636 Oldfield, 0 Emsley, 18636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 777 residues out of total 16917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 663 time to evaluate : 9.753 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 207 MET cc_start: 0.5677 (mtm) cc_final: 0.5422 (mtm) REVERT: B 214 LEU cc_start: 0.7675 (OUTLIER) cc_final: 0.7430 (mt) REVERT: B 217 GLU cc_start: 0.6917 (tp30) cc_final: 0.6535 (tm-30) REVERT: B 238 MET cc_start: 0.7769 (ttt) cc_final: 0.7429 (ttt) REVERT: B 252 PHE cc_start: 0.6708 (t80) cc_final: 0.6330 (t80) REVERT: B 496 PHE cc_start: 0.7380 (OUTLIER) cc_final: 0.7032 (m-80) REVERT: B 545 MET cc_start: 0.7794 (mtt) cc_final: 0.7538 (mtm) REVERT: C 78 VAL cc_start: 0.8445 (OUTLIER) cc_final: 0.8195 (p) REVERT: C 112 VAL cc_start: 0.9167 (OUTLIER) cc_final: 0.8896 (p) REVERT: D 190 SER cc_start: 0.8637 (m) cc_final: 0.8322 (t) REVERT: E 1136 TRP cc_start: 0.6251 (t60) cc_final: 0.6023 (t-100) REVERT: E 1287 MET cc_start: 0.6820 (tpp) cc_final: 0.6583 (mmm) REVERT: E 1301 TYR cc_start: 0.5542 (m-80) cc_final: 0.5176 (m-10) REVERT: G 1275 LEU cc_start: 0.6927 (tp) cc_final: 0.6498 (tp) REVERT: G 1279 SER cc_start: 0.6024 (m) cc_final: 0.5524 (p) REVERT: G 1312 GLN cc_start: 0.7896 (OUTLIER) cc_final: 0.7226 (tm-30) REVERT: H 42 VAL cc_start: 0.9100 (OUTLIER) cc_final: 0.8833 (p) REVERT: W 1237 ARG cc_start: 0.5862 (mtp-110) cc_final: 0.5361 (mtm110) REVERT: W 1364 MET cc_start: 0.8335 (mtp) cc_final: 0.7983 (mtm) REVERT: s 124 MET cc_start: 0.6963 (tpp) cc_final: 0.6620 (tpt) REVERT: a 1287 LEU cc_start: 0.8631 (OUTLIER) cc_final: 0.8383 (tt) REVERT: b 259 TRP cc_start: 0.6762 (t60) cc_final: 0.6317 (t60) REVERT: b 409 PHE cc_start: 0.6916 (OUTLIER) cc_final: 0.6201 (t80) REVERT: c 48 TRP cc_start: 0.8015 (m100) cc_final: 0.7470 (m100) REVERT: c 83 PHE cc_start: 0.8053 (OUTLIER) cc_final: 0.6362 (m-80) REVERT: c 122 HIS cc_start: 0.4975 (OUTLIER) cc_final: 0.4236 (p-80) REVERT: e 1407 LEU cc_start: 0.8852 (OUTLIER) cc_final: 0.8418 (tp) REVERT: e 1428 LEU cc_start: 0.7871 (tt) cc_final: 0.7417 (mt) REVERT: f 117 TYR cc_start: 0.7947 (OUTLIER) cc_final: 0.7643 (p90) REVERT: g 1356 VAL cc_start: 0.5988 (t) cc_final: 0.5660 (t) REVERT: g 1539 VAL cc_start: 0.8307 (OUTLIER) cc_final: 0.7718 (p) outliers start: 114 outliers final: 68 residues processed: 752 average time/residue: 0.8726 time to fit residues: 1194.6807 Evaluate side-chains 717 residues out of total 16917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 636 time to evaluate : 10.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 148 GLU Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 240 MET Chi-restraints excluded: chain B residue 299 MET Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain B residue 496 PHE Chi-restraints excluded: chain B residue 546 TYR Chi-restraints excluded: chain B residue 559 LEU Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 153 PHE Chi-restraints excluded: chain E residue 923 LEU Chi-restraints excluded: chain E residue 1076 TYR Chi-restraints excluded: chain E residue 1078 LEU Chi-restraints excluded: chain E residue 1085 TYR Chi-restraints excluded: chain E residue 1107 VAL Chi-restraints excluded: chain E residue 1178 LEU Chi-restraints excluded: chain E residue 1198 THR Chi-restraints excluded: chain E residue 1215 VAL Chi-restraints excluded: chain E residue 1234 LEU Chi-restraints excluded: chain E residue 1280 THR Chi-restraints excluded: chain E residue 1379 PHE Chi-restraints excluded: chain G residue 1050 SER Chi-restraints excluded: chain G residue 1159 CYS Chi-restraints excluded: chain G residue 1312 GLN Chi-restraints excluded: chain G residue 1327 LEU Chi-restraints excluded: chain G residue 1426 LEU Chi-restraints excluded: chain G residue 1429 GLU Chi-restraints excluded: chain G residue 1443 VAL Chi-restraints excluded: chain G residue 1566 LEU Chi-restraints excluded: chain H residue 15 MET Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain H residue 162 VAL Chi-restraints excluded: chain H residue 223 ILE Chi-restraints excluded: chain H residue 225 LEU Chi-restraints excluded: chain H residue 272 THR Chi-restraints excluded: chain H residue 282 ASP Chi-restraints excluded: chain S residue 122 PHE Chi-restraints excluded: chain S residue 137 TRP Chi-restraints excluded: chain W residue 1114 TYR Chi-restraints excluded: chain W residue 1230 MET Chi-restraints excluded: chain s residue 137 TRP Chi-restraints excluded: chain a residue 1247 ILE Chi-restraints excluded: chain a residue 1287 LEU Chi-restraints excluded: chain b residue 161 LEU Chi-restraints excluded: chain b residue 168 VAL Chi-restraints excluded: chain b residue 170 LEU Chi-restraints excluded: chain b residue 306 LEU Chi-restraints excluded: chain b residue 314 HIS Chi-restraints excluded: chain b residue 318 LYS Chi-restraints excluded: chain b residue 409 PHE Chi-restraints excluded: chain b residue 502 ASP Chi-restraints excluded: chain b residue 588 VAL Chi-restraints excluded: chain c residue 83 PHE Chi-restraints excluded: chain c residue 112 VAL Chi-restraints excluded: chain c residue 122 HIS Chi-restraints excluded: chain c residue 123 VAL Chi-restraints excluded: chain c residue 264 VAL Chi-restraints excluded: chain c residue 337 ILE Chi-restraints excluded: chain d residue 159 ILE Chi-restraints excluded: chain d residue 194 MET Chi-restraints excluded: chain e residue 898 CYS Chi-restraints excluded: chain e residue 957 TYR Chi-restraints excluded: chain e residue 970 LEU Chi-restraints excluded: chain e residue 1260 TRP Chi-restraints excluded: chain e residue 1287 MET Chi-restraints excluded: chain e residue 1324 TYR Chi-restraints excluded: chain e residue 1328 ASP Chi-restraints excluded: chain e residue 1407 LEU Chi-restraints excluded: chain f residue 117 TYR Chi-restraints excluded: chain g residue 1081 VAL Chi-restraints excluded: chain g residue 1205 LEU Chi-restraints excluded: chain g residue 1313 VAL Chi-restraints excluded: chain g residue 1419 VAL Chi-restraints excluded: chain g residue 1490 TRP Chi-restraints excluded: chain g residue 1520 VAL Chi-restraints excluded: chain g residue 1539 VAL Chi-restraints excluded: chain h residue 12 HIS Chi-restraints excluded: chain h residue 42 VAL Chi-restraints excluded: chain h residue 213 TRP Chi-restraints excluded: chain h residue 266 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1859 random chunks: chunk 1496 optimal weight: 0.9980 chunk 1020 optimal weight: 0.5980 chunk 26 optimal weight: 30.0000 chunk 1337 optimal weight: 30.0000 chunk 741 optimal weight: 30.0000 chunk 1533 optimal weight: 0.7980 chunk 1242 optimal weight: 5.9990 chunk 2 optimal weight: 30.0000 chunk 917 optimal weight: 1.9990 chunk 1612 optimal weight: 9.9990 chunk 453 optimal weight: 30.0000 overall best weight: 2.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 640 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 103 HIS ** E1008 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G1471 HIS a1226 ASN b 40 GLN b 97 GLN b 357 GLN e 796 HIS e 834 HIS ** e1194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g1256 HIS ** g1347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g1467 HIS ** h 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5272 moved from start: 0.2980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 117109 Z= 0.181 Angle : 0.440 11.245 161214 Z= 0.244 Chirality : 0.038 0.255 20574 Planarity : 0.003 0.078 22056 Dihedral : 3.990 76.457 20128 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.25 % Favored : 95.72 % Rotamer: Outliers : 2.55 % Allowed : 11.66 % Favored : 85.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.00 % Twisted Proline : 0.15 % 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: 1.85 (0.06), residues: 18636 helix: 2.58 (0.05), residues: 10989 sheet: 0.20 (0.12), residues: 1991 loop : -1.23 (0.08), residues: 5656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP E1262 HIS 0.007 0.001 HIS G1504 PHE 0.022 0.001 PHE B 371 TYR 0.022 0.001 TYR f 272 ARG 0.007 0.001 ARG e 892 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 37272 Ramachandran restraints generated. 18636 Oldfield, 0 Emsley, 18636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 37272 Ramachandran restraints generated. 18636 Oldfield, 0 Emsley, 18636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 788 residues out of total 16917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 656 time to evaluate : 10.059 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 214 LEU cc_start: 0.7712 (OUTLIER) cc_final: 0.7487 (mt) REVERT: B 217 GLU cc_start: 0.6922 (tp30) cc_final: 0.6592 (tm-30) REVERT: B 252 PHE cc_start: 0.6710 (t80) cc_final: 0.6331 (t80) REVERT: B 496 PHE cc_start: 0.7613 (OUTLIER) cc_final: 0.7205 (m-80) REVERT: B 545 MET cc_start: 0.7870 (mtt) cc_final: 0.7620 (mtm) REVERT: C 78 VAL cc_start: 0.8672 (OUTLIER) cc_final: 0.8409 (p) REVERT: C 112 VAL cc_start: 0.9178 (OUTLIER) cc_final: 0.8930 (p) REVERT: D 190 SER cc_start: 0.8674 (m) cc_final: 0.8365 (t) REVERT: E 1136 TRP cc_start: 0.6028 (t60) cc_final: 0.5675 (t60) REVERT: E 1301 TYR cc_start: 0.5672 (m-80) cc_final: 0.5224 (m-80) REVERT: G 1275 LEU cc_start: 0.7160 (tp) cc_final: 0.6753 (tp) REVERT: G 1279 SER cc_start: 0.6067 (m) cc_final: 0.5653 (p) REVERT: G 1502 HIS cc_start: 0.6050 (t-90) cc_final: 0.5579 (t70) REVERT: H 42 VAL cc_start: 0.9089 (OUTLIER) cc_final: 0.8804 (p) REVERT: W 1237 ARG cc_start: 0.5953 (mtp-110) cc_final: 0.5437 (mtm110) REVERT: W 1364 MET cc_start: 0.8314 (mtp) cc_final: 0.7972 (mtm) REVERT: b 114 GLU cc_start: 0.6586 (tp30) cc_final: 0.6385 (tp30) REVERT: b 409 PHE cc_start: 0.7014 (OUTLIER) cc_final: 0.6246 (t80) REVERT: c 48 TRP cc_start: 0.7865 (m100) cc_final: 0.7489 (m100) REVERT: c 83 PHE cc_start: 0.8032 (OUTLIER) cc_final: 0.6416 (m-80) REVERT: c 122 HIS cc_start: 0.5262 (OUTLIER) cc_final: 0.4428 (p-80) REVERT: c 156 GLU cc_start: 0.6996 (tp30) cc_final: 0.6759 (tp30) REVERT: d 126 MET cc_start: 0.7051 (mtp) cc_final: 0.6816 (mtp) REVERT: e 821 GLU cc_start: 0.8443 (OUTLIER) cc_final: 0.8151 (mt-10) REVERT: e 1407 LEU cc_start: 0.8867 (OUTLIER) cc_final: 0.8417 (tp) REVERT: e 1428 LEU cc_start: 0.7951 (tt) cc_final: 0.7507 (mt) REVERT: g 1256 HIS cc_start: 0.5019 (OUTLIER) cc_final: 0.4725 (p90) REVERT: g 1356 VAL cc_start: 0.6276 (t) cc_final: 0.6009 (t) REVERT: g 1429 GLU cc_start: 0.6481 (OUTLIER) cc_final: 0.6235 (pm20) REVERT: g 1539 VAL cc_start: 0.8322 (OUTLIER) cc_final: 0.7770 (p) REVERT: h 20 GLN cc_start: 0.4182 (OUTLIER) cc_final: 0.3921 (tt0) outliers start: 132 outliers final: 85 residues processed: 758 average time/residue: 0.8584 time to fit residues: 1187.7776 Evaluate side-chains 732 residues out of total 16917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 633 time to evaluate : 9.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1287 LEU Chi-restraints excluded: chain B residue 148 GLU Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 299 MET Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain B residue 496 PHE Chi-restraints excluded: chain B residue 546 TYR Chi-restraints excluded: chain B residue 559 LEU Chi-restraints excluded: chain C residue 10 VAL Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 153 PHE Chi-restraints excluded: chain C residue 172 MET Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain E residue 923 LEU Chi-restraints excluded: chain E residue 1036 LEU Chi-restraints excluded: chain E residue 1076 TYR Chi-restraints excluded: chain E residue 1078 LEU Chi-restraints excluded: chain E residue 1085 TYR Chi-restraints excluded: chain E residue 1107 VAL Chi-restraints excluded: chain E residue 1178 LEU Chi-restraints excluded: chain E residue 1198 THR Chi-restraints excluded: chain E residue 1215 VAL Chi-restraints excluded: chain E residue 1234 LEU Chi-restraints excluded: chain E residue 1280 THR Chi-restraints excluded: chain E residue 1379 PHE Chi-restraints excluded: chain G residue 1050 SER Chi-restraints excluded: chain G residue 1082 HIS Chi-restraints excluded: chain G residue 1159 CYS Chi-restraints excluded: chain G residue 1182 SER Chi-restraints excluded: chain G residue 1327 LEU Chi-restraints excluded: chain G residue 1429 GLU Chi-restraints excluded: chain G residue 1443 VAL Chi-restraints excluded: chain G residue 1566 LEU Chi-restraints excluded: chain H residue 15 MET Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain H residue 162 VAL Chi-restraints excluded: chain H residue 223 ILE Chi-restraints excluded: chain H residue 225 LEU Chi-restraints excluded: chain H residue 272 THR Chi-restraints excluded: chain S residue 122 PHE Chi-restraints excluded: chain S residue 137 TRP Chi-restraints excluded: chain W residue 1094 VAL Chi-restraints excluded: chain W residue 1114 TYR Chi-restraints excluded: chain W residue 1164 HIS Chi-restraints excluded: chain W residue 1230 MET Chi-restraints excluded: chain s residue 137 TRP Chi-restraints excluded: chain a residue 1247 ILE Chi-restraints excluded: chain a residue 1287 LEU Chi-restraints excluded: chain b residue 121 GLU Chi-restraints excluded: chain b residue 161 LEU Chi-restraints excluded: chain b residue 168 VAL Chi-restraints excluded: chain b residue 170 LEU Chi-restraints excluded: chain b residue 306 LEU Chi-restraints excluded: chain b residue 314 HIS Chi-restraints excluded: chain b residue 409 PHE Chi-restraints excluded: chain b residue 437 MET Chi-restraints excluded: chain b residue 502 ASP Chi-restraints excluded: chain c residue 83 PHE Chi-restraints excluded: chain c residue 112 VAL Chi-restraints excluded: chain c residue 122 HIS Chi-restraints excluded: chain c residue 123 VAL Chi-restraints excluded: chain c residue 351 LEU Chi-restraints excluded: chain d residue 159 ILE Chi-restraints excluded: chain d residue 194 MET Chi-restraints excluded: chain d residue 225 ILE Chi-restraints excluded: chain e residue 821 GLU Chi-restraints excluded: chain e residue 898 CYS Chi-restraints excluded: chain e residue 957 TYR Chi-restraints excluded: chain e residue 970 LEU Chi-restraints excluded: chain e residue 1260 TRP Chi-restraints excluded: chain e residue 1287 MET Chi-restraints excluded: chain e residue 1328 ASP Chi-restraints excluded: chain e residue 1407 LEU Chi-restraints excluded: chain f residue 22 VAL Chi-restraints excluded: chain g residue 1081 VAL Chi-restraints excluded: chain g residue 1154 ASP Chi-restraints excluded: chain g residue 1191 VAL Chi-restraints excluded: chain g residue 1205 LEU Chi-restraints excluded: chain g residue 1256 HIS Chi-restraints excluded: chain g residue 1260 VAL Chi-restraints excluded: chain g residue 1297 MET Chi-restraints excluded: chain g residue 1313 VAL Chi-restraints excluded: chain g residue 1353 THR Chi-restraints excluded: chain g residue 1419 VAL Chi-restraints excluded: chain g residue 1429 GLU Chi-restraints excluded: chain g residue 1435 CYS Chi-restraints excluded: chain g residue 1490 TRP Chi-restraints excluded: chain g residue 1520 VAL Chi-restraints excluded: chain g residue 1539 VAL Chi-restraints excluded: chain h residue 12 HIS Chi-restraints excluded: chain h residue 20 GLN Chi-restraints excluded: chain h residue 42 VAL Chi-restraints excluded: chain h residue 103 ASP Chi-restraints excluded: chain h residue 213 TRP Chi-restraints excluded: chain h residue 266 HIS Chi-restraints excluded: chain h residue 282 ASP Chi-restraints excluded: chain h residue 295 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1859 random chunks: chunk 604 optimal weight: 30.0000 chunk 1618 optimal weight: 0.9990 chunk 355 optimal weight: 50.0000 chunk 1055 optimal weight: 40.0000 chunk 443 optimal weight: 30.0000 chunk 1798 optimal weight: 80.0000 chunk 1493 optimal weight: 20.0000 chunk 832 optimal weight: 9.9990 chunk 149 optimal weight: 20.0000 chunk 594 optimal weight: 50.0000 chunk 944 optimal weight: 10.0000 overall best weight: 12.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1249 GLN ** B 640 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 218 HIS C 228 HIS C 285 HIS D 178 HIS D 236 HIS E 959 ASN E 992 GLN ** E1302 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1303 HIS G1161 HIS G1180 ASN ** G1256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G1471 HIS H 67 HIS a1231 HIS b 412 HIS ** c 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 285 HIS ** c 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 793 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 869 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 901 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 911 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e1009 ASN ** e1194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e1367 GLN ** f 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g1282 HIS ** g1347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g1499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g1570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5560 moved from start: 0.4192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.247 117109 Z= 0.842 Angle : 0.988 28.477 161214 Z= 0.561 Chirality : 0.056 0.782 20574 Planarity : 0.007 0.115 22056 Dihedral : 5.877 73.417 20126 Min Nonbonded Distance : 1.780 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.98 % Favored : 92.90 % Rotamer: Outliers : 3.73 % Allowed : 12.62 % Favored : 83.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.00 % Twisted Proline : 0.15 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.06), residues: 18636 helix: 0.69 (0.05), residues: 10904 sheet: -0.60 (0.11), residues: 1953 loop : -1.86 (0.08), residues: 5779 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.005 TRP b 167 HIS 0.049 0.005 HIS g1256 PHE 0.056 0.004 PHE c 9 TYR 0.062 0.005 TYR g1140 ARG 0.022 0.002 ARG g1243 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 37272 Ramachandran restraints generated. 18636 Oldfield, 0 Emsley, 18636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 37272 Ramachandran restraints generated. 18636 Oldfield, 0 Emsley, 18636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 847 residues out of total 16917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 193 poor density : 654 time to evaluate : 10.133 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 214 LEU cc_start: 0.8139 (OUTLIER) cc_final: 0.7882 (mt) REVERT: B 571 PHE cc_start: 0.8400 (OUTLIER) cc_final: 0.7982 (t80) REVERT: B 599 MET cc_start: 0.6257 (OUTLIER) cc_final: 0.5945 (ttp) REVERT: D 215 LEU cc_start: 0.8695 (tp) cc_final: 0.8464 (tt) REVERT: E 1076 TYR cc_start: 0.8631 (OUTLIER) cc_final: 0.8053 (t80) REVERT: E 1287 MET cc_start: 0.7038 (tpp) cc_final: 0.6730 (mmm) REVERT: G 1053 HIS cc_start: 0.7978 (m-70) cc_final: 0.7608 (m-70) REVERT: G 1155 ARG cc_start: 0.6829 (OUTLIER) cc_final: 0.6442 (tpt170) REVERT: G 1279 SER cc_start: 0.7108 (m) cc_final: 0.6580 (p) REVERT: G 1307 ASP cc_start: 0.8302 (m-30) cc_final: 0.7670 (p0) REVERT: G 1312 GLN cc_start: 0.7891 (OUTLIER) cc_final: 0.7163 (tm-30) REVERT: G 1502 HIS cc_start: 0.6546 (t-90) cc_final: 0.6065 (t70) REVERT: H 34 ASP cc_start: 0.8581 (OUTLIER) cc_final: 0.8176 (p0) REVERT: H 213 TRP cc_start: 0.7680 (m-90) cc_final: 0.7224 (m-90) REVERT: H 282 ASP cc_start: 0.7910 (OUTLIER) cc_final: 0.7573 (p0) REVERT: S 145 LEU cc_start: 0.8868 (OUTLIER) cc_final: 0.8652 (mm) REVERT: W 1364 MET cc_start: 0.8490 (mtp) cc_final: 0.8213 (mtm) REVERT: s 120 ARG cc_start: 0.6050 (OUTLIER) cc_final: 0.5693 (ptp-170) REVERT: b 358 VAL cc_start: 0.8559 (t) cc_final: 0.8183 (p) REVERT: b 409 PHE cc_start: 0.7434 (OUTLIER) cc_final: 0.6609 (t80) REVERT: b 562 MET cc_start: 0.8612 (mmm) cc_final: 0.8316 (mmm) REVERT: c 83 PHE cc_start: 0.8275 (OUTLIER) cc_final: 0.7227 (m-80) REVERT: c 122 HIS cc_start: 0.6699 (OUTLIER) cc_final: 0.5613 (p90) REVERT: c 127 MET cc_start: 0.3989 (mtm) cc_final: 0.2437 (ptt) REVERT: c 156 GLU cc_start: 0.7013 (tp30) cc_final: 0.6751 (tp30) REVERT: c 227 GLN cc_start: 0.7645 (OUTLIER) cc_final: 0.7011 (mp-120) REVERT: e 821 GLU cc_start: 0.8444 (OUTLIER) cc_final: 0.8031 (mt-10) REVERT: e 954 ARG cc_start: 0.7570 (OUTLIER) cc_final: 0.6894 (ptt90) REVERT: e 1076 TYR cc_start: 0.8233 (OUTLIER) cc_final: 0.7441 (t80) REVERT: e 1300 LEU cc_start: 0.6100 (OUTLIER) cc_final: 0.5713 (mt) REVERT: e 1333 LEU cc_start: 0.7535 (OUTLIER) cc_final: 0.7222 (mt) REVERT: e 1422 THR cc_start: 0.5660 (OUTLIER) cc_final: 0.5355 (m) REVERT: e 1428 LEU cc_start: 0.7925 (tt) cc_final: 0.7625 (mt) REVERT: f 237 MET cc_start: 0.8462 (mmm) cc_final: 0.7957 (mmt) REVERT: g 1429 GLU cc_start: 0.6917 (OUTLIER) cc_final: 0.6671 (pm20) REVERT: h 20 GLN cc_start: 0.4565 (OUTLIER) cc_final: 0.4141 (tt0) REVERT: h 266 HIS cc_start: 0.6708 (OUTLIER) cc_final: 0.4265 (m90) outliers start: 193 outliers final: 114 residues processed: 812 average time/residue: 0.8790 time to fit residues: 1296.8501 Evaluate side-chains 761 residues out of total 16917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 624 time to evaluate : 9.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1299 LEU Chi-restraints excluded: chain B residue 148 GLU Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 351 PHE Chi-restraints excluded: chain B residue 546 TYR Chi-restraints excluded: chain B residue 571 PHE Chi-restraints excluded: chain B residue 599 MET Chi-restraints excluded: chain C residue 10 VAL Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 89 ILE Chi-restraints excluded: chain C residue 153 PHE Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 44 ASN Chi-restraints excluded: chain D residue 161 CYS Chi-restraints excluded: chain D residue 194 MET Chi-restraints excluded: chain D residue 268 ASN Chi-restraints excluded: chain D residue 299 ASP Chi-restraints excluded: chain E residue 923 LEU Chi-restraints excluded: chain E residue 1036 LEU Chi-restraints excluded: chain E residue 1046 VAL Chi-restraints excluded: chain E residue 1076 TYR Chi-restraints excluded: chain E residue 1078 LEU Chi-restraints excluded: chain E residue 1085 TYR Chi-restraints excluded: chain E residue 1107 VAL Chi-restraints excluded: chain E residue 1178 LEU Chi-restraints excluded: chain E residue 1194 HIS Chi-restraints excluded: chain E residue 1198 THR Chi-restraints excluded: chain E residue 1215 VAL Chi-restraints excluded: chain E residue 1224 ILE Chi-restraints excluded: chain E residue 1234 LEU Chi-restraints excluded: chain E residue 1235 THR Chi-restraints excluded: chain E residue 1280 THR Chi-restraints excluded: chain E residue 1306 ILE Chi-restraints excluded: chain E residue 1353 VAL Chi-restraints excluded: chain G residue 1050 SER Chi-restraints excluded: chain G residue 1062 MET Chi-restraints excluded: chain G residue 1082 HIS Chi-restraints excluded: chain G residue 1155 ARG Chi-restraints excluded: chain G residue 1159 CYS Chi-restraints excluded: chain G residue 1173 ASP Chi-restraints excluded: chain G residue 1182 SER Chi-restraints excluded: chain G residue 1206 TRP Chi-restraints excluded: chain G residue 1222 TYR Chi-restraints excluded: chain G residue 1281 ASP Chi-restraints excluded: chain G residue 1309 ASN Chi-restraints excluded: chain G residue 1312 GLN Chi-restraints excluded: chain G residue 1429 GLU Chi-restraints excluded: chain G residue 1443 VAL Chi-restraints excluded: chain G residue 1444 THR Chi-restraints excluded: chain G residue 1566 LEU Chi-restraints excluded: chain H residue 21 MET Chi-restraints excluded: chain H residue 34 ASP Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain H residue 103 ASP Chi-restraints excluded: chain H residue 162 VAL Chi-restraints excluded: chain H residue 225 LEU Chi-restraints excluded: chain H residue 272 THR Chi-restraints excluded: chain H residue 282 ASP Chi-restraints excluded: chain S residue 118 ARG Chi-restraints excluded: chain S residue 122 PHE Chi-restraints excluded: chain S residue 135 VAL Chi-restraints excluded: chain S residue 137 TRP Chi-restraints excluded: chain S residue 145 LEU Chi-restraints excluded: chain W residue 1094 VAL Chi-restraints excluded: chain W residue 1168 VAL Chi-restraints excluded: chain W residue 1338 VAL Chi-restraints excluded: chain s residue 112 SER Chi-restraints excluded: chain s residue 120 ARG Chi-restraints excluded: chain s residue 122 PHE Chi-restraints excluded: chain s residue 137 TRP Chi-restraints excluded: chain a residue 1227 VAL Chi-restraints excluded: chain a residue 1287 LEU Chi-restraints excluded: chain b residue 67 VAL Chi-restraints excluded: chain b residue 113 MET Chi-restraints excluded: chain b residue 118 THR Chi-restraints excluded: chain b residue 121 GLU Chi-restraints excluded: chain b residue 161 LEU Chi-restraints excluded: chain b residue 168 VAL Chi-restraints excluded: chain b residue 170 LEU Chi-restraints excluded: chain b residue 306 LEU Chi-restraints excluded: chain b residue 314 HIS Chi-restraints excluded: chain b residue 409 PHE Chi-restraints excluded: chain b residue 437 MET Chi-restraints excluded: chain b residue 496 PHE Chi-restraints excluded: chain b residue 502 ASP Chi-restraints excluded: chain c residue 83 PHE Chi-restraints excluded: chain c residue 112 VAL Chi-restraints excluded: chain c residue 122 HIS Chi-restraints excluded: chain c residue 123 VAL Chi-restraints excluded: chain c residue 171 THR Chi-restraints excluded: chain c residue 227 GLN Chi-restraints excluded: chain c residue 236 ASP Chi-restraints excluded: chain c residue 348 VAL Chi-restraints excluded: chain c residue 351 LEU Chi-restraints excluded: chain d residue 102 HIS Chi-restraints excluded: chain d residue 159 ILE Chi-restraints excluded: chain d residue 225 ILE Chi-restraints excluded: chain e residue 821 GLU Chi-restraints excluded: chain e residue 902 VAL Chi-restraints excluded: chain e residue 936 GLU Chi-restraints excluded: chain e residue 954 ARG Chi-restraints excluded: chain e residue 957 TYR Chi-restraints excluded: chain e residue 970 LEU Chi-restraints excluded: chain e residue 1076 TYR Chi-restraints excluded: chain e residue 1219 LEU Chi-restraints excluded: chain e residue 1260 TRP Chi-restraints excluded: chain e residue 1300 LEU Chi-restraints excluded: chain e residue 1306 ILE Chi-restraints excluded: chain e residue 1324 TYR Chi-restraints excluded: chain e residue 1328 ASP Chi-restraints excluded: chain e residue 1333 LEU Chi-restraints excluded: chain e residue 1407 LEU Chi-restraints excluded: chain e residue 1422 THR Chi-restraints excluded: chain f residue 21 VAL Chi-restraints excluded: chain f residue 22 VAL Chi-restraints excluded: chain g residue 1154 ASP Chi-restraints excluded: chain g residue 1205 LEU Chi-restraints excluded: chain g residue 1260 VAL Chi-restraints excluded: chain g residue 1282 HIS Chi-restraints excluded: chain g residue 1419 VAL Chi-restraints excluded: chain g residue 1429 GLU Chi-restraints excluded: chain g residue 1435 CYS Chi-restraints excluded: chain g residue 1437 LEU Chi-restraints excluded: chain g residue 1489 LEU Chi-restraints excluded: chain g residue 1490 TRP Chi-restraints excluded: chain g residue 1514 LEU Chi-restraints excluded: chain g residue 1520 VAL Chi-restraints excluded: chain g residue 1539 VAL Chi-restraints excluded: chain g residue 1627 VAL Chi-restraints excluded: chain g residue 1681 ASN Chi-restraints excluded: chain h residue 12 HIS Chi-restraints excluded: chain h residue 20 GLN Chi-restraints excluded: chain h residue 42 VAL Chi-restraints excluded: chain h residue 107 ASN Chi-restraints excluded: chain h residue 266 HIS Chi-restraints excluded: chain h residue 282 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1859 random chunks: chunk 1734 optimal weight: 30.0000 chunk 202 optimal weight: 2.9990 chunk 1024 optimal weight: 0.7980 chunk 1313 optimal weight: 20.0000 chunk 1017 optimal weight: 30.0000 chunk 1514 optimal weight: 0.9980 chunk 1004 optimal weight: 40.0000 chunk 1791 optimal weight: 9.9990 chunk 1121 optimal weight: 20.0000 chunk 1092 optimal weight: 50.0000 chunk 827 optimal weight: 7.9990 overall best weight: 4.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 128 GLN ** B 640 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 959 ASN ** E1125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G1256 HIS G1309 ASN G1416 GLN s 142 GLN c 120 HIS c 151 ASN ** c 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 793 ASN ** e 901 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 911 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e1009 ASN ** e1194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g1124 HIS ** g1309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g1347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g1559 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5443 moved from start: 0.4161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.140 117109 Z= 0.344 Angle : 0.589 13.083 161214 Z= 0.330 Chirality : 0.042 0.461 20574 Planarity : 0.004 0.084 22056 Dihedral : 4.929 74.478 20119 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.25 % Favored : 94.73 % Rotamer: Outliers : 3.13 % Allowed : 13.88 % Favored : 83.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.00 % Twisted Proline : 0.15 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.06), residues: 18636 helix: 1.46 (0.05), residues: 10943 sheet: -0.51 (0.11), residues: 1973 loop : -1.69 (0.08), residues: 5720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP e1262 HIS 0.013 0.002 HIS A1304 PHE 0.032 0.002 PHE B 305 TYR 0.032 0.002 TYR f 272 ARG 0.016 0.001 ARG A1204 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 37272 Ramachandran restraints generated. 18636 Oldfield, 0 Emsley, 18636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 37272 Ramachandran restraints generated. 18636 Oldfield, 0 Emsley, 18636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 806 residues out of total 16917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 162 poor density : 644 time to evaluate : 10.225 Fit side-chains REVERT: B 53 PHE cc_start: 0.6172 (m-10) cc_final: 0.5908 (m-10) REVERT: B 140 MET cc_start: 0.5854 (mtt) cc_final: 0.5647 (mtt) REVERT: B 214 LEU cc_start: 0.7989 (OUTLIER) cc_final: 0.7738 (mt) REVERT: B 371 PHE cc_start: 0.7405 (t80) cc_final: 0.7103 (t80) REVERT: B 571 PHE cc_start: 0.8306 (OUTLIER) cc_final: 0.7891 (t80) REVERT: C 99 THR cc_start: 0.8360 (OUTLIER) cc_final: 0.8101 (p) REVERT: D 285 SER cc_start: 0.8099 (t) cc_final: 0.7423 (m) REVERT: E 1042 LEU cc_start: 0.6365 (OUTLIER) cc_final: 0.6086 (mt) REVERT: G 1053 HIS cc_start: 0.7919 (m-70) cc_final: 0.7616 (m170) REVERT: G 1279 SER cc_start: 0.6836 (m) cc_final: 0.6342 (p) REVERT: G 1312 GLN cc_start: 0.7830 (OUTLIER) cc_final: 0.7031 (tm-30) REVERT: G 1468 LEU cc_start: 0.6099 (tt) cc_final: 0.5897 (tt) REVERT: G 1502 HIS cc_start: 0.6248 (t-90) cc_final: 0.5787 (t70) REVERT: H 42 VAL cc_start: 0.9070 (OUTLIER) cc_final: 0.8808 (p) REVERT: H 235 GLN cc_start: 0.8427 (tm-30) cc_final: 0.8210 (tm-30) REVERT: W 1197 GLU cc_start: 0.8524 (OUTLIER) cc_final: 0.7853 (mt-10) REVERT: W 1364 MET cc_start: 0.8328 (mtp) cc_final: 0.8045 (mtm) REVERT: s 120 ARG cc_start: 0.5949 (OUTLIER) cc_final: 0.5479 (ptp-170) REVERT: b 351 PHE cc_start: 0.8382 (m-80) cc_final: 0.8095 (m-80) REVERT: b 362 PHE cc_start: 0.6482 (OUTLIER) cc_final: 0.6211 (t80) REVERT: b 409 PHE cc_start: 0.7231 (OUTLIER) cc_final: 0.6375 (t80) REVERT: c 83 PHE cc_start: 0.8251 (OUTLIER) cc_final: 0.7286 (m-80) REVERT: c 122 HIS cc_start: 0.6247 (OUTLIER) cc_final: 0.5406 (p-80) REVERT: c 127 MET cc_start: 0.3904 (mtm) cc_final: 0.2167 (ptp) REVERT: e 773 MET cc_start: 0.7946 (tpt) cc_final: 0.7301 (tpt) REVERT: e 793 ASN cc_start: 0.6028 (OUTLIER) cc_final: 0.5759 (t0) REVERT: e 821 GLU cc_start: 0.8391 (OUTLIER) cc_final: 0.7961 (mt-10) REVERT: e 954 ARG cc_start: 0.7383 (OUTLIER) cc_final: 0.6794 (ptt90) REVERT: e 1300 LEU cc_start: 0.5598 (OUTLIER) cc_final: 0.5371 (mt) REVERT: e 1324 TYR cc_start: 0.7862 (OUTLIER) cc_final: 0.7379 (m-80) REVERT: e 1327 MET cc_start: 0.7215 (mtp) cc_final: 0.6827 (mtm) REVERT: e 1333 LEU cc_start: 0.7285 (OUTLIER) cc_final: 0.6931 (mt) REVERT: e 1428 LEU cc_start: 0.7938 (tt) cc_final: 0.7604 (mt) REVERT: g 1429 GLU cc_start: 0.6971 (OUTLIER) cc_final: 0.6729 (pm20) REVERT: g 1430 ARG cc_start: 0.7583 (OUTLIER) cc_final: 0.6749 (mtm180) REVERT: g 1539 VAL cc_start: 0.8655 (OUTLIER) cc_final: 0.8269 (p) REVERT: h 20 GLN cc_start: 0.4426 (OUTLIER) cc_final: 0.3789 (tt0) REVERT: h 42 VAL cc_start: 0.7074 (OUTLIER) cc_final: 0.6834 (p) REVERT: h 96 THR cc_start: 0.7569 (OUTLIER) cc_final: 0.7102 (p) REVERT: h 266 HIS cc_start: 0.5777 (OUTLIER) cc_final: 0.4380 (m90) outliers start: 162 outliers final: 104 residues processed: 776 average time/residue: 0.8618 time to fit residues: 1218.9808 Evaluate side-chains 759 residues out of total 16917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 630 time to evaluate : 10.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 148 GLU Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain B residue 546 TYR Chi-restraints excluded: chain B residue 559 LEU Chi-restraints excluded: chain B residue 571 PHE Chi-restraints excluded: chain C residue 10 VAL Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 153 PHE Chi-restraints excluded: chain C residue 172 MET Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 44 ASN Chi-restraints excluded: chain D residue 161 CYS Chi-restraints excluded: chain D residue 190 SER Chi-restraints excluded: chain D residue 194 MET Chi-restraints excluded: chain D residue 299 ASP Chi-restraints excluded: chain E residue 923 LEU Chi-restraints excluded: chain E residue 1036 LEU Chi-restraints excluded: chain E residue 1042 LEU Chi-restraints excluded: chain E residue 1076 TYR Chi-restraints excluded: chain E residue 1078 LEU Chi-restraints excluded: chain E residue 1084 ILE Chi-restraints excluded: chain E residue 1085 TYR Chi-restraints excluded: chain E residue 1107 VAL Chi-restraints excluded: chain E residue 1130 ILE Chi-restraints excluded: chain E residue 1178 LEU Chi-restraints excluded: chain E residue 1198 THR Chi-restraints excluded: chain E residue 1215 VAL Chi-restraints excluded: chain E residue 1235 THR Chi-restraints excluded: chain E residue 1280 THR Chi-restraints excluded: chain G residue 1050 SER Chi-restraints excluded: chain G residue 1082 HIS Chi-restraints excluded: chain G residue 1159 CYS Chi-restraints excluded: chain G residue 1182 SER Chi-restraints excluded: chain G residue 1222 TYR Chi-restraints excluded: chain G residue 1283 ARG Chi-restraints excluded: chain G residue 1312 GLN Chi-restraints excluded: chain G residue 1429 GLU Chi-restraints excluded: chain G residue 1444 THR Chi-restraints excluded: chain G residue 1513 LEU Chi-restraints excluded: chain G residue 1566 LEU Chi-restraints excluded: chain H residue 15 MET Chi-restraints excluded: chain H residue 21 MET Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain H residue 60 VAL Chi-restraints excluded: chain H residue 162 VAL Chi-restraints excluded: chain H residue 223 ILE Chi-restraints excluded: chain H residue 225 LEU Chi-restraints excluded: chain H residue 272 THR Chi-restraints excluded: chain S residue 118 ARG Chi-restraints excluded: chain S residue 122 PHE Chi-restraints excluded: chain S residue 135 VAL Chi-restraints excluded: chain S residue 137 TRP Chi-restraints excluded: chain W residue 1094 VAL Chi-restraints excluded: chain W residue 1197 GLU Chi-restraints excluded: chain s residue 120 ARG Chi-restraints excluded: chain s residue 122 PHE Chi-restraints excluded: chain s residue 137 TRP Chi-restraints excluded: chain s residue 142 GLN Chi-restraints excluded: chain a residue 1227 VAL Chi-restraints excluded: chain a residue 1287 LEU Chi-restraints excluded: chain b residue 67 VAL Chi-restraints excluded: chain b residue 113 MET Chi-restraints excluded: chain b residue 121 GLU Chi-restraints excluded: chain b residue 124 ARG Chi-restraints excluded: chain b residue 161 LEU Chi-restraints excluded: chain b residue 168 VAL Chi-restraints excluded: chain b residue 170 LEU Chi-restraints excluded: chain b residue 306 LEU Chi-restraints excluded: chain b residue 314 HIS Chi-restraints excluded: chain b residue 318 LYS Chi-restraints excluded: chain b residue 343 LEU Chi-restraints excluded: chain b residue 362 PHE Chi-restraints excluded: chain b residue 409 PHE Chi-restraints excluded: chain b residue 442 LEU Chi-restraints excluded: chain b residue 502 ASP Chi-restraints excluded: chain c residue 83 PHE Chi-restraints excluded: chain c residue 112 VAL Chi-restraints excluded: chain c residue 122 HIS Chi-restraints excluded: chain c residue 123 VAL Chi-restraints excluded: chain c residue 171 THR Chi-restraints excluded: chain c residue 197 LEU Chi-restraints excluded: chain c residue 235 GLN Chi-restraints excluded: chain c residue 351 LEU Chi-restraints excluded: chain d residue 64 THR Chi-restraints excluded: chain d residue 159 ILE Chi-restraints excluded: chain d residue 225 ILE Chi-restraints excluded: chain e residue 793 ASN Chi-restraints excluded: chain e residue 800 LEU Chi-restraints excluded: chain e residue 821 GLU Chi-restraints excluded: chain e residue 902 VAL Chi-restraints excluded: chain e residue 954 ARG Chi-restraints excluded: chain e residue 957 TYR Chi-restraints excluded: chain e residue 970 LEU Chi-restraints excluded: chain e residue 1260 TRP Chi-restraints excluded: chain e residue 1300 LEU Chi-restraints excluded: chain e residue 1306 ILE Chi-restraints excluded: chain e residue 1324 TYR Chi-restraints excluded: chain e residue 1328 ASP Chi-restraints excluded: chain e residue 1333 LEU Chi-restraints excluded: chain e residue 1407 LEU Chi-restraints excluded: chain f residue 21 VAL Chi-restraints excluded: chain f residue 22 VAL Chi-restraints excluded: chain f residue 136 GLU Chi-restraints excluded: chain g residue 1081 VAL Chi-restraints excluded: chain g residue 1154 ASP Chi-restraints excluded: chain g residue 1193 LYS Chi-restraints excluded: chain g residue 1205 LEU Chi-restraints excluded: chain g residue 1297 MET Chi-restraints excluded: chain g residue 1353 THR Chi-restraints excluded: chain g residue 1419 VAL Chi-restraints excluded: chain g residue 1429 GLU Chi-restraints excluded: chain g residue 1430 ARG Chi-restraints excluded: chain g residue 1435 CYS Chi-restraints excluded: chain g residue 1443 VAL Chi-restraints excluded: chain g residue 1490 TRP Chi-restraints excluded: chain g residue 1520 VAL Chi-restraints excluded: chain g residue 1539 VAL Chi-restraints excluded: chain h residue 12 HIS Chi-restraints excluded: chain h residue 20 GLN Chi-restraints excluded: chain h residue 42 VAL Chi-restraints excluded: chain h residue 96 THR Chi-restraints excluded: chain h residue 107 ASN Chi-restraints excluded: chain h residue 137 ASP Chi-restraints excluded: chain h residue 266 HIS Chi-restraints excluded: chain h residue 282 ASP Chi-restraints excluded: chain h residue 295 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1859 random chunks: chunk 1108 optimal weight: 0.6980 chunk 715 optimal weight: 50.0000 chunk 1070 optimal weight: 50.0000 chunk 539 optimal weight: 0.8980 chunk 352 optimal weight: 50.0000 chunk 347 optimal weight: 0.0470 chunk 1139 optimal weight: 5.9990 chunk 1220 optimal weight: 20.0000 chunk 885 optimal weight: 20.0000 chunk 166 optimal weight: 7.9990 chunk 1408 optimal weight: 0.9990 overall best weight: 1.7282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 640 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G1180 ASN ** a1268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 200 GLN ** d 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 125 HIS ** e1194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e1266 ASN e1367 GLN ** f 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g1309 ASN ** g1347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5366 moved from start: 0.4166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.067 117109 Z= 0.171 Angle : 0.475 10.984 161214 Z= 0.262 Chirality : 0.039 0.301 20574 Planarity : 0.003 0.082 22056 Dihedral : 4.309 74.193 20117 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.93 % Favored : 95.05 % Rotamer: Outliers : 2.30 % Allowed : 14.94 % Favored : 82.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.00 % Twisted Proline : 0.15 % 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: 1.27 (0.06), residues: 18636 helix: 2.18 (0.05), residues: 10972 sheet: -0.25 (0.12), residues: 1969 loop : -1.49 (0.08), residues: 5695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP e1262 HIS 0.009 0.001 HIS A1304 PHE 0.022 0.001 PHE s 122 TYR 0.039 0.001 TYR B 35 ARG 0.012 0.001 ARG s 120 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 37272 Ramachandran restraints generated. 18636 Oldfield, 0 Emsley, 18636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 37272 Ramachandran restraints generated. 18636 Oldfield, 0 Emsley, 18636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 763 residues out of total 16917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 644 time to evaluate : 10.257 Fit side-chains revert: symmetry clash REVERT: B 214 LEU cc_start: 0.7851 (OUTLIER) cc_final: 0.7637 (mt) REVERT: B 371 PHE cc_start: 0.7308 (t80) cc_final: 0.7079 (t80) REVERT: C 78 VAL cc_start: 0.8700 (OUTLIER) cc_final: 0.8439 (p) REVERT: C 99 THR cc_start: 0.8425 (OUTLIER) cc_final: 0.8205 (p) REVERT: D 285 SER cc_start: 0.8008 (t) cc_final: 0.7400 (m) REVERT: E 1301 TYR cc_start: 0.5967 (m-80) cc_final: 0.5553 (m-80) REVERT: G 1053 HIS cc_start: 0.7935 (m-70) cc_final: 0.7708 (m170) REVERT: G 1279 SER cc_start: 0.6621 (m) cc_final: 0.6167 (p) REVERT: G 1312 GLN cc_start: 0.8011 (OUTLIER) cc_final: 0.7153 (tm-30) REVERT: G 1468 LEU cc_start: 0.6106 (tt) cc_final: 0.5892 (tt) REVERT: G 1502 HIS cc_start: 0.6327 (t-90) cc_final: 0.5870 (t70) REVERT: H 42 VAL cc_start: 0.9055 (OUTLIER) cc_final: 0.8797 (p) REVERT: H 235 GLN cc_start: 0.8236 (tm-30) cc_final: 0.7969 (tm-30) REVERT: W 1197 GLU cc_start: 0.8387 (OUTLIER) cc_final: 0.7661 (mt-10) REVERT: W 1237 ARG cc_start: 0.5886 (mtp-110) cc_final: 0.5341 (mtm180) REVERT: W 1364 MET cc_start: 0.8236 (mtp) cc_final: 0.8004 (mtm) REVERT: s 141 LYS cc_start: 0.7166 (tptp) cc_final: 0.6812 (tmtt) REVERT: b 351 PHE cc_start: 0.8324 (m-80) cc_final: 0.8039 (m-80) REVERT: b 409 PHE cc_start: 0.7135 (OUTLIER) cc_final: 0.6338 (t80) REVERT: b 562 MET cc_start: 0.8505 (mmm) cc_final: 0.8209 (mmm) REVERT: c 83 PHE cc_start: 0.8261 (OUTLIER) cc_final: 0.7221 (m-80) REVERT: c 122 HIS cc_start: 0.6051 (OUTLIER) cc_final: 0.5207 (p-80) REVERT: c 127 MET cc_start: 0.2818 (mtm) cc_final: 0.1181 (ptp) REVERT: e 821 GLU cc_start: 0.8477 (OUTLIER) cc_final: 0.8049 (mt-10) REVERT: e 934 GLU cc_start: 0.6513 (OUTLIER) cc_final: 0.6205 (pm20) REVERT: e 1076 TYR cc_start: 0.7984 (OUTLIER) cc_final: 0.7335 (t80) REVERT: e 1428 LEU cc_start: 0.7862 (tt) cc_final: 0.7481 (mt) REVERT: g 1122 LYS cc_start: 0.3236 (OUTLIER) cc_final: 0.1476 (mmtm) REVERT: g 1356 VAL cc_start: 0.6307 (t) cc_final: 0.5962 (t) REVERT: g 1430 ARG cc_start: 0.7544 (OUTLIER) cc_final: 0.6956 (mtm180) REVERT: h 20 GLN cc_start: 0.4194 (OUTLIER) cc_final: 0.3702 (tt0) REVERT: h 42 VAL cc_start: 0.7038 (OUTLIER) cc_final: 0.6812 (p) REVERT: h 96 THR cc_start: 0.7519 (OUTLIER) cc_final: 0.7154 (p) REVERT: h 266 HIS cc_start: 0.5134 (OUTLIER) cc_final: 0.4034 (m90) outliers start: 119 outliers final: 76 residues processed: 740 average time/residue: 0.8964 time to fit residues: 1207.5970 Evaluate side-chains 719 residues out of total 16917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 625 time to evaluate : 9.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 148 GLU Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 546 TYR Chi-restraints excluded: chain B residue 559 LEU Chi-restraints excluded: chain C residue 10 VAL Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 153 PHE Chi-restraints excluded: chain C residue 172 MET Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 161 CYS Chi-restraints excluded: chain E residue 923 LEU Chi-restraints excluded: chain E residue 968 VAL Chi-restraints excluded: chain E residue 1036 LEU Chi-restraints excluded: chain E residue 1076 TYR Chi-restraints excluded: chain E residue 1078 LEU Chi-restraints excluded: chain E residue 1107 VAL Chi-restraints excluded: chain E residue 1178 LEU Chi-restraints excluded: chain E residue 1198 THR Chi-restraints excluded: chain E residue 1215 VAL Chi-restraints excluded: chain G residue 1050 SER Chi-restraints excluded: chain G residue 1159 CYS Chi-restraints excluded: chain G residue 1222 TYR Chi-restraints excluded: chain G residue 1283 ARG Chi-restraints excluded: chain G residue 1312 GLN Chi-restraints excluded: chain G residue 1444 THR Chi-restraints excluded: chain G residue 1513 LEU Chi-restraints excluded: chain G residue 1566 LEU Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain H residue 162 VAL Chi-restraints excluded: chain H residue 223 ILE Chi-restraints excluded: chain H residue 225 LEU Chi-restraints excluded: chain S residue 118 ARG Chi-restraints excluded: chain S residue 122 PHE Chi-restraints excluded: chain S residue 135 VAL Chi-restraints excluded: chain S residue 137 TRP Chi-restraints excluded: chain W residue 1094 VAL Chi-restraints excluded: chain W residue 1114 TYR Chi-restraints excluded: chain W residue 1197 GLU Chi-restraints excluded: chain s residue 122 PHE Chi-restraints excluded: chain s residue 137 TRP Chi-restraints excluded: chain a residue 1227 VAL Chi-restraints excluded: chain a residue 1247 ILE Chi-restraints excluded: chain a residue 1287 LEU Chi-restraints excluded: chain b residue 121 GLU Chi-restraints excluded: chain b residue 124 ARG Chi-restraints excluded: chain b residue 161 LEU Chi-restraints excluded: chain b residue 168 VAL Chi-restraints excluded: chain b residue 170 LEU Chi-restraints excluded: chain b residue 306 LEU Chi-restraints excluded: chain b residue 314 HIS Chi-restraints excluded: chain b residue 318 LYS Chi-restraints excluded: chain b residue 409 PHE Chi-restraints excluded: chain b residue 496 PHE Chi-restraints excluded: chain b residue 502 ASP Chi-restraints excluded: chain c residue 83 PHE Chi-restraints excluded: chain c residue 112 VAL Chi-restraints excluded: chain c residue 122 HIS Chi-restraints excluded: chain c residue 123 VAL Chi-restraints excluded: chain c residue 197 LEU Chi-restraints excluded: chain c residue 351 LEU Chi-restraints excluded: chain d residue 3 VAL Chi-restraints excluded: chain d residue 18 VAL Chi-restraints excluded: chain d residue 159 ILE Chi-restraints excluded: chain d residue 225 ILE Chi-restraints excluded: chain e residue 821 GLU Chi-restraints excluded: chain e residue 934 GLU Chi-restraints excluded: chain e residue 957 TYR Chi-restraints excluded: chain e residue 970 LEU Chi-restraints excluded: chain e residue 1076 TYR Chi-restraints excluded: chain e residue 1260 TRP Chi-restraints excluded: chain e residue 1306 ILE Chi-restraints excluded: chain e residue 1328 ASP Chi-restraints excluded: chain e residue 1374 SER Chi-restraints excluded: chain e residue 1407 LEU Chi-restraints excluded: chain f residue 136 GLU Chi-restraints excluded: chain g residue 1081 VAL Chi-restraints excluded: chain g residue 1122 LYS Chi-restraints excluded: chain g residue 1154 ASP Chi-restraints excluded: chain g residue 1297 MET Chi-restraints excluded: chain g residue 1353 THR Chi-restraints excluded: chain g residue 1419 VAL Chi-restraints excluded: chain g residue 1430 ARG Chi-restraints excluded: chain g residue 1490 TRP Chi-restraints excluded: chain g residue 1519 VAL Chi-restraints excluded: chain g residue 1520 VAL Chi-restraints excluded: chain h residue 12 HIS Chi-restraints excluded: chain h residue 20 GLN Chi-restraints excluded: chain h residue 42 VAL Chi-restraints excluded: chain h residue 96 THR Chi-restraints excluded: chain h residue 137 ASP Chi-restraints excluded: chain h residue 266 HIS Chi-restraints excluded: chain h residue 282 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1859 random chunks: chunk 1629 optimal weight: 2.9990 chunk 1716 optimal weight: 7.9990 chunk 1566 optimal weight: 0.2980 chunk 1669 optimal weight: 3.9990 chunk 1004 optimal weight: 40.0000 chunk 727 optimal weight: 30.0000 chunk 1311 optimal weight: 40.0000 chunk 512 optimal weight: 10.0000 chunk 1508 optimal weight: 7.9990 chunk 1579 optimal weight: 1.9990 chunk 1663 optimal weight: 7.9990 overall best weight: 3.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1304 HIS ** B 640 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a1268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 152 GLN ** e 901 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e1194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g1347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5408 moved from start: 0.4295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.106 117109 Z= 0.266 Angle : 0.521 11.200 161214 Z= 0.289 Chirality : 0.040 0.453 20574 Planarity : 0.004 0.084 22056 Dihedral : 4.375 74.388 20117 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.39 % Favored : 94.59 % Rotamer: Outliers : 2.51 % Allowed : 14.88 % Favored : 82.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.00 % Twisted Proline : 0.15 % 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: 1.27 (0.06), residues: 18636 helix: 2.18 (0.05), residues: 10990 sheet: -0.30 (0.12), residues: 2000 loop : -1.49 (0.08), residues: 5646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP e1262 HIS 0.014 0.002 HIS A1304 PHE 0.033 0.002 PHE B 305 TYR 0.034 0.002 TYR B 35 ARG 0.012 0.001 ARG s 120 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 37272 Ramachandran restraints generated. 18636 Oldfield, 0 Emsley, 18636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 37272 Ramachandran restraints generated. 18636 Oldfield, 0 Emsley, 18636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 768 residues out of total 16917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 638 time to evaluate : 10.011 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 214 LEU cc_start: 0.7958 (OUTLIER) cc_final: 0.7716 (mt) REVERT: B 371 PHE cc_start: 0.7407 (t80) cc_final: 0.7184 (t80) REVERT: C 99 THR cc_start: 0.8442 (OUTLIER) cc_final: 0.8232 (p) REVERT: C 112 VAL cc_start: 0.9187 (OUTLIER) cc_final: 0.8925 (p) REVERT: G 1053 HIS cc_start: 0.7980 (m-70) cc_final: 0.7699 (m170) REVERT: G 1279 SER cc_start: 0.6796 (m) cc_final: 0.6300 (p) REVERT: G 1312 GLN cc_start: 0.8006 (OUTLIER) cc_final: 0.7145 (tm-30) REVERT: H 42 VAL cc_start: 0.9087 (OUTLIER) cc_final: 0.8822 (p) REVERT: H 235 GLN cc_start: 0.8280 (tm-30) cc_final: 0.8005 (tm-30) REVERT: W 1197 GLU cc_start: 0.8443 (OUTLIER) cc_final: 0.7703 (mt-10) REVERT: W 1364 MET cc_start: 0.8293 (mtp) cc_final: 0.8061 (mtm) REVERT: s 120 ARG cc_start: 0.6340 (OUTLIER) cc_final: 0.5903 (ptp-170) REVERT: b 259 TRP cc_start: 0.7527 (t60) cc_final: 0.7121 (t60) REVERT: b 351 PHE cc_start: 0.8330 (m-80) cc_final: 0.8066 (m-80) REVERT: b 409 PHE cc_start: 0.7194 (OUTLIER) cc_final: 0.6376 (t80) REVERT: c 83 PHE cc_start: 0.8334 (OUTLIER) cc_final: 0.7363 (m-80) REVERT: c 122 HIS cc_start: 0.6217 (OUTLIER) cc_final: 0.5325 (p-80) REVERT: c 127 MET cc_start: 0.2816 (mtm) cc_final: 0.1320 (ptp) REVERT: e 821 GLU cc_start: 0.8468 (OUTLIER) cc_final: 0.8046 (mt-10) REVERT: e 954 ARG cc_start: 0.7369 (OUTLIER) cc_final: 0.6973 (ptp90) REVERT: e 1076 TYR cc_start: 0.8054 (OUTLIER) cc_final: 0.7360 (t80) REVERT: e 1128 ARG cc_start: 0.7206 (OUTLIER) cc_final: 0.6005 (ppt170) REVERT: e 1300 LEU cc_start: 0.5589 (OUTLIER) cc_final: 0.5383 (mt) REVERT: e 1428 LEU cc_start: 0.7962 (tt) cc_final: 0.7588 (mt) REVERT: g 1122 LYS cc_start: 0.3287 (OUTLIER) cc_final: 0.1641 (mmtm) REVERT: g 1356 VAL cc_start: 0.6848 (t) cc_final: 0.6527 (t) REVERT: g 1430 ARG cc_start: 0.7563 (OUTLIER) cc_final: 0.6485 (mtm180) REVERT: g 1539 VAL cc_start: 0.8594 (m) cc_final: 0.8193 (p) REVERT: h 20 GLN cc_start: 0.4311 (OUTLIER) cc_final: 0.3820 (tt0) REVERT: h 42 VAL cc_start: 0.6994 (OUTLIER) cc_final: 0.6767 (p) REVERT: h 96 THR cc_start: 0.7445 (OUTLIER) cc_final: 0.6958 (p) REVERT: h 266 HIS cc_start: 0.5412 (OUTLIER) cc_final: 0.4269 (m90) outliers start: 130 outliers final: 95 residues processed: 743 average time/residue: 0.9276 time to fit residues: 1262.4721 Evaluate side-chains 747 residues out of total 16917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 631 time to evaluate : 10.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 148 GLU Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 546 TYR Chi-restraints excluded: chain B residue 559 LEU Chi-restraints excluded: chain C residue 10 VAL Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 153 PHE Chi-restraints excluded: chain C residue 172 MET Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 161 CYS Chi-restraints excluded: chain D residue 190 SER Chi-restraints excluded: chain E residue 923 LEU Chi-restraints excluded: chain E residue 1036 LEU Chi-restraints excluded: chain E residue 1076 TYR Chi-restraints excluded: chain E residue 1078 LEU Chi-restraints excluded: chain E residue 1084 ILE Chi-restraints excluded: chain E residue 1107 VAL Chi-restraints excluded: chain E residue 1178 LEU Chi-restraints excluded: chain E residue 1198 THR Chi-restraints excluded: chain E residue 1215 VAL Chi-restraints excluded: chain E residue 1280 THR Chi-restraints excluded: chain G residue 1050 SER Chi-restraints excluded: chain G residue 1062 MET Chi-restraints excluded: chain G residue 1159 CYS Chi-restraints excluded: chain G residue 1222 TYR Chi-restraints excluded: chain G residue 1283 ARG Chi-restraints excluded: chain G residue 1312 GLN Chi-restraints excluded: chain G residue 1429 GLU Chi-restraints excluded: chain G residue 1444 THR Chi-restraints excluded: chain G residue 1513 LEU Chi-restraints excluded: chain G residue 1566 LEU Chi-restraints excluded: chain H residue 21 MET Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain H residue 60 VAL Chi-restraints excluded: chain H residue 162 VAL Chi-restraints excluded: chain H residue 223 ILE Chi-restraints excluded: chain H residue 225 LEU Chi-restraints excluded: chain H residue 245 ASP Chi-restraints excluded: chain S residue 118 ARG Chi-restraints excluded: chain S residue 122 PHE Chi-restraints excluded: chain S residue 135 VAL Chi-restraints excluded: chain S residue 137 TRP Chi-restraints excluded: chain W residue 1094 VAL Chi-restraints excluded: chain W residue 1197 GLU Chi-restraints excluded: chain s residue 120 ARG Chi-restraints excluded: chain s residue 122 PHE Chi-restraints excluded: chain s residue 137 TRP Chi-restraints excluded: chain a residue 1227 VAL Chi-restraints excluded: chain a residue 1247 ILE Chi-restraints excluded: chain a residue 1287 LEU Chi-restraints excluded: chain b residue 67 VAL Chi-restraints excluded: chain b residue 121 GLU Chi-restraints excluded: chain b residue 124 ARG Chi-restraints excluded: chain b residue 161 LEU Chi-restraints excluded: chain b residue 168 VAL Chi-restraints excluded: chain b residue 170 LEU Chi-restraints excluded: chain b residue 306 LEU Chi-restraints excluded: chain b residue 314 HIS Chi-restraints excluded: chain b residue 318 LYS Chi-restraints excluded: chain b residue 409 PHE Chi-restraints excluded: chain b residue 496 PHE Chi-restraints excluded: chain b residue 502 ASP Chi-restraints excluded: chain c residue 83 PHE Chi-restraints excluded: chain c residue 112 VAL Chi-restraints excluded: chain c residue 122 HIS Chi-restraints excluded: chain c residue 123 VAL Chi-restraints excluded: chain c residue 197 LEU Chi-restraints excluded: chain c residue 235 GLN Chi-restraints excluded: chain c residue 236 ASP Chi-restraints excluded: chain c residue 264 VAL Chi-restraints excluded: chain c residue 351 LEU Chi-restraints excluded: chain d residue 3 VAL Chi-restraints excluded: chain d residue 18 VAL Chi-restraints excluded: chain d residue 159 ILE Chi-restraints excluded: chain d residue 225 ILE Chi-restraints excluded: chain e residue 785 VAL Chi-restraints excluded: chain e residue 821 GLU Chi-restraints excluded: chain e residue 902 VAL Chi-restraints excluded: chain e residue 954 ARG Chi-restraints excluded: chain e residue 957 TYR Chi-restraints excluded: chain e residue 970 LEU Chi-restraints excluded: chain e residue 1076 TYR Chi-restraints excluded: chain e residue 1128 ARG Chi-restraints excluded: chain e residue 1260 TRP Chi-restraints excluded: chain e residue 1300 LEU Chi-restraints excluded: chain e residue 1306 ILE Chi-restraints excluded: chain e residue 1324 TYR Chi-restraints excluded: chain e residue 1328 ASP Chi-restraints excluded: chain e residue 1407 LEU Chi-restraints excluded: chain f residue 22 VAL Chi-restraints excluded: chain f residue 136 GLU Chi-restraints excluded: chain g residue 1081 VAL Chi-restraints excluded: chain g residue 1122 LYS Chi-restraints excluded: chain g residue 1154 ASP Chi-restraints excluded: chain g residue 1297 MET Chi-restraints excluded: chain g residue 1353 THR Chi-restraints excluded: chain g residue 1419 VAL Chi-restraints excluded: chain g residue 1430 ARG Chi-restraints excluded: chain g residue 1435 CYS Chi-restraints excluded: chain g residue 1490 TRP Chi-restraints excluded: chain g residue 1520 VAL Chi-restraints excluded: chain h residue 12 HIS Chi-restraints excluded: chain h residue 20 GLN Chi-restraints excluded: chain h residue 42 VAL Chi-restraints excluded: chain h residue 83 VAL Chi-restraints excluded: chain h residue 96 THR Chi-restraints excluded: chain h residue 137 ASP Chi-restraints excluded: chain h residue 213 TRP Chi-restraints excluded: chain h residue 266 HIS Chi-restraints excluded: chain h residue 282 ASP Chi-restraints excluded: chain h residue 295 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1859 random chunks: chunk 1096 optimal weight: 0.0570 chunk 1765 optimal weight: 40.0000 chunk 1077 optimal weight: 10.0000 chunk 837 optimal weight: 30.0000 chunk 1227 optimal weight: 20.0000 chunk 1852 optimal weight: 30.0000 chunk 1704 optimal weight: 4.9990 chunk 1474 optimal weight: 9.9990 chunk 153 optimal weight: 6.9990 chunk 1139 optimal weight: 3.9990 chunk 904 optimal weight: 0.6980 overall best weight: 3.3504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 640 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a1268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e1194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g1347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5404 moved from start: 0.4478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.102 117109 Z= 0.252 Angle : 0.512 16.275 161214 Z= 0.282 Chirality : 0.040 0.427 20574 Planarity : 0.003 0.085 22056 Dihedral : 4.330 75.302 20117 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.26 % Favored : 94.71 % Rotamer: Outliers : 2.39 % Allowed : 15.07 % Favored : 82.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.00 % Twisted Proline : 0.15 % 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: 1.37 (0.06), residues: 18636 helix: 2.26 (0.05), residues: 11000 sheet: -0.26 (0.12), residues: 1979 loop : -1.45 (0.08), residues: 5657 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP g1235 HIS 0.011 0.001 HIS B 117 PHE 0.029 0.002 PHE B 305 TYR 0.028 0.002 TYR f 272 ARG 0.011 0.001 ARG s 120 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 37272 Ramachandran restraints generated. 18636 Oldfield, 0 Emsley, 18636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 37272 Ramachandran restraints generated. 18636 Oldfield, 0 Emsley, 18636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 759 residues out of total 16917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 635 time to evaluate : 10.245 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 214 LEU cc_start: 0.7959 (OUTLIER) cc_final: 0.7699 (mt) REVERT: C 99 THR cc_start: 0.8441 (OUTLIER) cc_final: 0.8234 (p) REVERT: C 112 VAL cc_start: 0.9181 (OUTLIER) cc_final: 0.8925 (p) REVERT: G 1053 HIS cc_start: 0.7976 (m-70) cc_final: 0.7713 (m170) REVERT: G 1279 SER cc_start: 0.7147 (m) cc_final: 0.6637 (p) REVERT: G 1312 GLN cc_start: 0.8050 (OUTLIER) cc_final: 0.7184 (tm-30) REVERT: H 42 VAL cc_start: 0.9092 (OUTLIER) cc_final: 0.8836 (p) REVERT: H 235 GLN cc_start: 0.8399 (tm-30) cc_final: 0.8099 (tm-30) REVERT: W 1197 GLU cc_start: 0.8423 (OUTLIER) cc_final: 0.7662 (mt-10) REVERT: W 1237 ARG cc_start: 0.6063 (mtp-110) cc_final: 0.5570 (mtm180) REVERT: W 1364 MET cc_start: 0.8281 (mtp) cc_final: 0.8044 (mtm) REVERT: s 120 ARG cc_start: 0.6327 (OUTLIER) cc_final: 0.5898 (ptp-170) REVERT: s 141 LYS cc_start: 0.7426 (tptp) cc_final: 0.7106 (tmtt) REVERT: b 114 GLU cc_start: 0.6746 (tp30) cc_final: 0.6359 (tp30) REVERT: b 259 TRP cc_start: 0.7502 (t60) cc_final: 0.7080 (t60) REVERT: b 409 PHE cc_start: 0.7165 (OUTLIER) cc_final: 0.6335 (t80) REVERT: b 562 MET cc_start: 0.8520 (mmm) cc_final: 0.8146 (mmm) REVERT: c 83 PHE cc_start: 0.8333 (OUTLIER) cc_final: 0.7514 (m-80) REVERT: c 127 MET cc_start: 0.2735 (mtm) cc_final: 0.1251 (ptp) REVERT: e 773 MET cc_start: 0.8289 (tpt) cc_final: 0.7915 (mmm) REVERT: e 821 GLU cc_start: 0.8463 (OUTLIER) cc_final: 0.8050 (mt-10) REVERT: e 954 ARG cc_start: 0.7394 (OUTLIER) cc_final: 0.6999 (ptp90) REVERT: e 1076 TYR cc_start: 0.7909 (OUTLIER) cc_final: 0.7297 (t80) REVERT: e 1128 ARG cc_start: 0.7162 (OUTLIER) cc_final: 0.5807 (ppt170) REVERT: e 1300 LEU cc_start: 0.5319 (OUTLIER) cc_final: 0.5115 (mt) REVERT: e 1428 LEU cc_start: 0.7987 (tt) cc_final: 0.7557 (mt) REVERT: g 1122 LYS cc_start: 0.3172 (OUTLIER) cc_final: 0.0628 (mmmt) REVERT: g 1356 VAL cc_start: 0.6665 (t) cc_final: 0.6337 (t) REVERT: g 1430 ARG cc_start: 0.7615 (OUTLIER) cc_final: 0.6576 (mtm180) REVERT: g 1539 VAL cc_start: 0.8611 (m) cc_final: 0.8233 (p) REVERT: h 20 GLN cc_start: 0.4225 (OUTLIER) cc_final: 0.3875 (tt0) REVERT: h 21 MET cc_start: 0.7251 (tpp) cc_final: 0.6819 (tpp) REVERT: h 42 VAL cc_start: 0.7045 (OUTLIER) cc_final: 0.6845 (p) REVERT: h 96 THR cc_start: 0.7499 (OUTLIER) cc_final: 0.7009 (p) REVERT: h 266 HIS cc_start: 0.5296 (OUTLIER) cc_final: 0.4064 (m90) outliers start: 124 outliers final: 93 residues processed: 737 average time/residue: 0.9541 time to fit residues: 1278.5777 Evaluate side-chains 742 residues out of total 16917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 629 time to evaluate : 9.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 148 GLU Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 546 TYR Chi-restraints excluded: chain B residue 559 LEU Chi-restraints excluded: chain C residue 10 VAL Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 153 PHE Chi-restraints excluded: chain C residue 172 MET Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 161 CYS Chi-restraints excluded: chain D residue 190 SER Chi-restraints excluded: chain D residue 299 ASP Chi-restraints excluded: chain E residue 923 LEU Chi-restraints excluded: chain E residue 968 VAL Chi-restraints excluded: chain E residue 1036 LEU Chi-restraints excluded: chain E residue 1076 TYR Chi-restraints excluded: chain E residue 1078 LEU Chi-restraints excluded: chain E residue 1107 VAL Chi-restraints excluded: chain E residue 1178 LEU Chi-restraints excluded: chain E residue 1198 THR Chi-restraints excluded: chain E residue 1215 VAL Chi-restraints excluded: chain E residue 1280 THR Chi-restraints excluded: chain G residue 1050 SER Chi-restraints excluded: chain G residue 1159 CYS Chi-restraints excluded: chain G residue 1222 TYR Chi-restraints excluded: chain G residue 1283 ARG Chi-restraints excluded: chain G residue 1312 GLN Chi-restraints excluded: chain G residue 1429 GLU Chi-restraints excluded: chain G residue 1444 THR Chi-restraints excluded: chain G residue 1513 LEU Chi-restraints excluded: chain G residue 1566 LEU Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain H residue 60 VAL Chi-restraints excluded: chain H residue 162 VAL Chi-restraints excluded: chain H residue 223 ILE Chi-restraints excluded: chain H residue 225 LEU Chi-restraints excluded: chain H residue 245 ASP Chi-restraints excluded: chain S residue 118 ARG Chi-restraints excluded: chain S residue 122 PHE Chi-restraints excluded: chain S residue 135 VAL Chi-restraints excluded: chain S residue 137 TRP Chi-restraints excluded: chain W residue 1094 VAL Chi-restraints excluded: chain W residue 1197 GLU Chi-restraints excluded: chain s residue 120 ARG Chi-restraints excluded: chain s residue 122 PHE Chi-restraints excluded: chain s residue 137 TRP Chi-restraints excluded: chain a residue 1227 VAL Chi-restraints excluded: chain a residue 1247 ILE Chi-restraints excluded: chain a residue 1287 LEU Chi-restraints excluded: chain b residue 67 VAL Chi-restraints excluded: chain b residue 121 GLU Chi-restraints excluded: chain b residue 124 ARG Chi-restraints excluded: chain b residue 161 LEU Chi-restraints excluded: chain b residue 168 VAL Chi-restraints excluded: chain b residue 170 LEU Chi-restraints excluded: chain b residue 306 LEU Chi-restraints excluded: chain b residue 314 HIS Chi-restraints excluded: chain b residue 409 PHE Chi-restraints excluded: chain b residue 496 PHE Chi-restraints excluded: chain b residue 502 ASP Chi-restraints excluded: chain c residue 83 PHE Chi-restraints excluded: chain c residue 112 VAL Chi-restraints excluded: chain c residue 122 HIS Chi-restraints excluded: chain c residue 123 VAL Chi-restraints excluded: chain c residue 197 LEU Chi-restraints excluded: chain c residue 235 GLN Chi-restraints excluded: chain c residue 236 ASP Chi-restraints excluded: chain c residue 264 VAL Chi-restraints excluded: chain c residue 351 LEU Chi-restraints excluded: chain d residue 3 VAL Chi-restraints excluded: chain d residue 18 VAL Chi-restraints excluded: chain d residue 159 ILE Chi-restraints excluded: chain d residue 225 ILE Chi-restraints excluded: chain e residue 785 VAL Chi-restraints excluded: chain e residue 821 GLU Chi-restraints excluded: chain e residue 902 VAL Chi-restraints excluded: chain e residue 954 ARG Chi-restraints excluded: chain e residue 957 TYR Chi-restraints excluded: chain e residue 970 LEU Chi-restraints excluded: chain e residue 1076 TYR Chi-restraints excluded: chain e residue 1128 ARG Chi-restraints excluded: chain e residue 1260 TRP Chi-restraints excluded: chain e residue 1300 LEU Chi-restraints excluded: chain e residue 1306 ILE Chi-restraints excluded: chain e residue 1324 TYR Chi-restraints excluded: chain e residue 1328 ASP Chi-restraints excluded: chain e residue 1407 LEU Chi-restraints excluded: chain f residue 22 VAL Chi-restraints excluded: chain f residue 136 GLU Chi-restraints excluded: chain g residue 1081 VAL Chi-restraints excluded: chain g residue 1122 LYS Chi-restraints excluded: chain g residue 1154 ASP Chi-restraints excluded: chain g residue 1224 ARG Chi-restraints excluded: chain g residue 1297 MET Chi-restraints excluded: chain g residue 1311 LEU Chi-restraints excluded: chain g residue 1419 VAL Chi-restraints excluded: chain g residue 1430 ARG Chi-restraints excluded: chain g residue 1490 TRP Chi-restraints excluded: chain g residue 1520 VAL Chi-restraints excluded: chain h residue 12 HIS Chi-restraints excluded: chain h residue 20 GLN Chi-restraints excluded: chain h residue 42 VAL Chi-restraints excluded: chain h residue 83 VAL Chi-restraints excluded: chain h residue 96 THR Chi-restraints excluded: chain h residue 137 ASP Chi-restraints excluded: chain h residue 213 TRP Chi-restraints excluded: chain h residue 266 HIS Chi-restraints excluded: chain h residue 282 ASP Chi-restraints excluded: chain h residue 295 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1859 random chunks: chunk 1171 optimal weight: 2.9990 chunk 1570 optimal weight: 6.9990 chunk 451 optimal weight: 20.0000 chunk 1359 optimal weight: 7.9990 chunk 217 optimal weight: 0.9990 chunk 409 optimal weight: 3.9990 chunk 1477 optimal weight: 9.9990 chunk 618 optimal weight: 40.0000 chunk 1516 optimal weight: 8.9990 chunk 187 optimal weight: 0.7980 chunk 272 optimal weight: 7.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 97 GLN ** B 640 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 122 HIS ** E1125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a1268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 152 GLN ** e 901 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e1194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g1347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.136635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.118164 restraints weight = 521563.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.113948 restraints weight = 473580.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.114258 restraints weight = 397398.911| |-----------------------------------------------------------------------------| r_work (final): 0.3808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6641 moved from start: 0.4578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.101 117109 Z= 0.245 Angle : 0.508 11.188 161214 Z= 0.280 Chirality : 0.040 0.433 20574 Planarity : 0.003 0.085 22056 Dihedral : 4.289 75.743 20117 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.34 % Favored : 94.63 % Rotamer: Outliers : 2.55 % Allowed : 14.82 % Favored : 82.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.00 % Twisted Proline : 0.15 % 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: 1.43 (0.06), residues: 18636 helix: 2.30 (0.05), residues: 11010 sheet: -0.24 (0.12), residues: 1984 loop : -1.44 (0.08), residues: 5642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP g1235 HIS 0.009 0.001 HIS G1504 PHE 0.031 0.002 PHE B 371 TYR 0.028 0.002 TYR f 272 ARG 0.011 0.001 ARG s 120 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 24395.91 seconds wall clock time: 423 minutes 59.69 seconds (25439.69 seconds total)