Starting phenix.real_space_refine on Mon Mar 25 15:43:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nkx_12449/03_2024/7nkx_12449_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nkx_12449/03_2024/7nkx_12449.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nkx_12449/03_2024/7nkx_12449.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nkx_12449/03_2024/7nkx_12449.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nkx_12449/03_2024/7nkx_12449_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nkx_12449/03_2024/7nkx_12449_updated.pdb" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.001 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: 9 Type Number sf(0) Gaussians Zn 8 6.06 5 P 284 5.49 5 Mg 1 5.21 5 S 228 5.16 5 Be 1 3.05 5 C 30462 2.51 5 N 8819 2.21 5 O 9914 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 28": "NH1" <-> "NH2" Residue "A GLU 39": "OE1" <-> "OE2" Residue "A ASP 62": "OD1" <-> "OD2" Residue "A ARG 63": "NH1" <-> "NH2" Residue "A GLU 76": "OE1" <-> "OE2" Residue "A PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 104": "OE1" <-> "OE2" Residue "A ASP 116": "OD1" <-> "OD2" Residue "A GLU 117": "OE1" <-> "OE2" Residue "A ASP 130": "OD1" <-> "OD2" Residue "A ASP 157": "OD1" <-> "OD2" Residue "A GLU 206": "OE1" <-> "OE2" Residue "A PHE 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 218": "OD1" <-> "OD2" Residue "A GLU 226": "OE1" <-> "OE2" Residue "A PHE 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 254": "OE1" <-> "OE2" Residue "A GLU 259": "OE1" <-> "OE2" Residue "A PHE 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 277": "OE1" <-> "OE2" Residue "A GLU 291": "OE1" <-> "OE2" Residue "A PHE 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 356": "OD1" <-> "OD2" Residue "A GLU 360": "OE1" <-> "OE2" Residue "A ASP 408": "OD1" <-> "OD2" Residue "A ASP 414": "OD1" <-> "OD2" Residue "A ASP 423": "OD1" <-> "OD2" Residue "A TYR 428": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 438": "OD1" <-> "OD2" Residue "A PHE 444": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 465": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 478": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 495": "OE1" <-> "OE2" Residue "A GLU 496": "OE1" <-> "OE2" Residue "A GLU 542": "OE1" <-> "OE2" Residue "A ASP 544": "OD1" <-> "OD2" Residue "A TYR 551": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 555": "OD1" <-> "OD2" Residue "A ASP 557": "OD1" <-> "OD2" Residue "A ASP 592": "OD1" <-> "OD2" Residue "A GLU 593": "OE1" <-> "OE2" Residue "A ASP 609": "OD1" <-> "OD2" Residue "A GLU 618": "OE1" <-> "OE2" Residue "A GLU 636": "OE1" <-> "OE2" Residue "A PHE 646": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 655": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 662": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 672": "OD1" <-> "OD2" Residue "A GLU 678": "OE1" <-> "OE2" Residue "A GLU 685": "OE1" <-> "OE2" Residue "A ASP 692": "OD1" <-> "OD2" Residue "A GLU 696": "OE1" <-> "OE2" Residue "A GLU 715": "OE1" <-> "OE2" Residue "A ASP 716": "OD1" <-> "OD2" Residue "A PHE 755": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 779": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 787": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 801": "OE1" <-> "OE2" Residue "A TYR 804": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 812": "OE1" <-> "OE2" Residue "A PHE 813": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 814": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 833": "OE1" <-> "OE2" Residue "A TYR 852": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 853": "OD1" <-> "OD2" Residue "A GLU 870": "OE1" <-> "OE2" Residue "A ASP 871": "OD1" <-> "OD2" Residue "A ASP 874": "OD1" <-> "OD2" Residue "A GLU 894": "OE1" <-> "OE2" Residue "A ASP 905": "OD1" <-> "OD2" Residue "A ASP 909": "OD1" <-> "OD2" Residue "A GLU 914": "OE1" <-> "OE2" Residue "A GLU 918": "OE1" <-> "OE2" Residue "A ASP 922": "OD1" <-> "OD2" Residue "A GLU 931": "OE1" <-> "OE2" Residue "A TYR 933": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 939": "OD1" <-> "OD2" Residue "A GLU 945": "OE1" <-> "OE2" Residue "A PHE 947": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 951": "OE1" <-> "OE2" Residue "A PHE 971": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 980": "OD1" <-> "OD2" Residue "A ASP 992": "OD1" <-> "OD2" Residue "A GLU 995": "OE1" <-> "OE2" Residue "A GLU 1005": "OE1" <-> "OE2" Residue "A PHE 1018": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1035": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1042": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1050": "OE1" <-> "OE2" Residue "A PHE 1053": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1062": "OE1" <-> "OE2" Residue "A TYR 1119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1121": "OE1" <-> "OE2" Residue "A ASP 1127": "OD1" <-> "OD2" Residue "A GLU 1129": "OE1" <-> "OE2" Residue "A GLU 1139": "OE1" <-> "OE2" Residue "A TYR 1154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1157": "OD1" <-> "OD2" Residue "A GLU 1165": "OE1" <-> "OE2" Residue "A ASP 1166": "OD1" <-> "OD2" Residue "A GLU 1168": "OE1" <-> "OE2" Residue "A GLU 1196": "OE1" <-> "OE2" Residue "A ASP 1198": "OD1" <-> "OD2" Residue "A GLU 1214": "OE1" <-> "OE2" Residue "A PHE 1225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1230": "OE1" <-> "OE2" Residue "A GLU 1255": "OE1" <-> "OE2" Residue "A GLU 1277": "OE1" <-> "OE2" Residue "A GLU 1280": "OE1" <-> "OE2" Residue "A ASP 1288": "OD1" <-> "OD2" Residue "A TYR 1298": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1315": "OE1" <-> "OE2" Residue "A GLU 1342": "OE1" <-> "OE2" Residue "A ASP 1373": "OD1" <-> "OD2" Residue "A PHE 1389": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1403": "OE1" <-> "OE2" Residue "A GLU 1404": "OE1" <-> "OE2" Residue "A PHE 1410": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1411": "OE1" <-> "OE2" Residue "A GLU 1417": "OE1" <-> "OE2" Residue "A ASP 1419": "OD1" <-> "OD2" Residue "A ASP 1420": "OD1" <-> "OD2" Residue "A ASP 1442": "OD1" <-> "OD2" Residue "A ASP 1446": "OD1" <-> "OD2" Residue "A GLU 1447": "OE1" <-> "OE2" Residue "A GLU 1448": "OE1" <-> "OE2" Residue "B GLU 21": "OE1" <-> "OE2" Residue "B GLU 28": "OE1" <-> "OE2" Residue "B ASP 29": "OD1" <-> "OD2" Residue "B PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 40": "OE1" <-> "OE2" Residue "B PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 61": "OD1" <-> "OD2" Residue "B GLU 104": "OE1" <-> "OE2" Residue "B ASP 131": "OD1" <-> "OD2" Residue "B TYR 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 183": "OE1" <-> "OE2" Residue "B TYR 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 194": "OE1" <-> "OE2" Residue "B PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 209": "OE1" <-> "OE2" Residue "B PHE 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 239": "OE1" <-> "OE2" Residue "B GLU 245": "OE1" <-> "OE2" Residue "B TYR 259": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 296": "OE1" <-> "OE2" Residue "B ASP 307": "OD1" <-> "OD2" Residue "B GLU 312": "OE1" <-> "OE2" Residue "B ASP 326": "OD1" <-> "OD2" Residue "B GLU 328": "OE1" <-> "OE2" Residue "B ARG 336": "NH1" <-> "NH2" Residue "B ARG 337": "NH1" <-> "NH2" Residue "B ASP 354": "OD1" <-> "OD2" Residue "B GLU 359": "OE1" <-> "OE2" Residue "B PHE 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 368": "OE1" <-> "OE2" Residue "B PHE 370": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 394": "OD1" <-> "OD2" Residue "B PHE 401": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 407": "OD1" <-> "OD2" Residue "B PHE 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 476": "NH1" <-> "NH2" Residue "B TYR 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 505": "OD1" <-> "OD2" Residue "B GLU 526": "OE1" <-> "OE2" Residue "B PHE 557": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 598": "OE1" <-> "OE2" Residue "B GLU 612": "OE1" <-> "OE2" Residue "B ASP 618": "OD1" <-> "OD2" Residue "B GLU 623": "OE1" <-> "OE2" Residue "B ASP 629": "OD1" <-> "OD2" Residue "B GLU 641": "OE1" <-> "OE2" Residue "B ASP 642": "OD1" <-> "OD2" Residue "B ASP 643": "OD1" <-> "OD2" Residue "B GLU 644": "OE1" <-> "OE2" Residue "B GLU 678": "OE1" <-> "OE2" Residue "B GLU 687": "OE1" <-> "OE2" Residue "B GLU 691": "OE1" <-> "OE2" Residue "B GLU 699": "OE1" <-> "OE2" Residue "B PHE 738": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 760": "OD1" <-> "OD2" Residue "B TYR 785": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 811": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 833": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 837": "OD1" <-> "OD2" Residue "B ASP 847": "OD1" <-> "OD2" Residue "B PHE 851": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 855": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 856": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 863": "OE1" <-> "OE2" Residue "B TYR 866": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 874": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 875": "OE1" <-> "OE2" Residue "B ASP 891": "OD1" <-> "OD2" Residue "B ASP 895": "OD1" <-> "OD2" Residue "B ASP 896": "OD1" <-> "OD2" Residue "B ASP 909": "OD1" <-> "OD2" Residue "B ARG 935": "NH1" <-> "NH2" Residue "B ASP 936": "OD1" <-> "OD2" Residue "B GLU 945": "OE1" <-> "OE2" Residue "B ASP 950": "OD1" <-> "OD2" Residue "B ASP 959": "OD1" <-> "OD2" Residue "B TYR 994": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 998": "OD1" <-> "OD2" Residue "B PHE 1001": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1004": "OE1" <-> "OE2" Residue "B GLU 1041": "OE1" <-> "OE2" Residue "B ASP 1049": "OD1" <-> "OD2" Residue "B GLU 1053": "OE1" <-> "OE2" Residue "B GLU 1061": "OE1" <-> "OE2" Residue "B PHE 1086": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1092": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1101": "OD1" <-> "OD2" Residue "B ASP 1125": "OD1" <-> "OD2" Residue "B PHE 1130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1136": "OD1" <-> "OD2" Residue "B GLU 1149": "OE1" <-> "OE2" Residue "B GLU 1153": "OE1" <-> "OE2" Residue "B PHE 1158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1181": "OE1" <-> "OE2" Residue "B ASP 1186": "OD1" <-> "OD2" Residue "B ASP 1190": "OD1" <-> "OD2" Residue "B TYR 1192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1206": "OE1" <-> "OE2" Residue "B ASP 1223": "OD1" <-> "OD2" Residue "C ASP 16": "OD1" <-> "OD2" Residue "C PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 26": "OD1" <-> "OD2" Residue "C GLU 40": "OE1" <-> "OE2" Residue "C GLU 50": "OE1" <-> "OE2" Residue "C GLU 52": "OE1" <-> "OE2" Residue "C ASP 76": "OD1" <-> "OD2" Residue "C ASP 85": "OD1" <-> "OD2" Residue "C GLU 89": "OE1" <-> "OE2" Residue "C ASP 90": "OD1" <-> "OD2" Residue "C PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 166": "OE1" <-> "OE2" Residue "C PHE 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 181": "OD1" <-> "OD2" Residue "C ASP 190": "OD1" <-> "OD2" Residue "C TYR 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 196": "OD1" <-> "OD2" Residue "C GLU 200": "OE1" <-> "OE2" Residue "C GLU 208": "OE1" <-> "OE2" Residue "C TYR 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 210": "OE1" <-> "OE2" Residue "C ASP 217": "OD1" <-> "OD2" Residue "C PHE 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 220": "OD1" <-> "OD2" Residue "C TYR 229": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 233": "OE1" <-> "OE2" Residue "C ASP 241": "OD1" <-> "OD2" Residue "C ASP 249": "OD1" <-> "OD2" Residue "C ASP 266": "OD1" <-> "OD2" Residue "E ASP 2": "OD1" <-> "OD2" Residue "E PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 33": "OE1" <-> "OE2" Residue "E GLU 34": "OE1" <-> "OE2" Residue "E GLU 40": "OE1" <-> "OE2" Residue "E ASP 41": "OD1" <-> "OD2" Residue "E ASP 48": "OD1" <-> "OD2" Residue "E PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 84": "OD1" <-> "OD2" Residue "E PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 148": "OE1" <-> "OE2" Residue "E ASP 159": "OD1" <-> "OD2" Residue "E TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 194": "OE1" <-> "OE2" Residue "E TYR 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 89": "OE1" <-> "OE2" Residue "F PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 110": "OD1" <-> "OD2" Residue "F GLU 114": "OE1" <-> "OE2" Residue "F ASP 140": "OD1" <-> "OD2" Residue "F GLU 144": "OE1" <-> "OE2" Residue "F ASP 145": "OD1" <-> "OD2" Residue "F GLU 149": "OE1" <-> "OE2" Residue "F GLU 150": "OE1" <-> "OE2" Residue "H ASP 16": "OD1" <-> "OD2" Residue "H ASP 34": "OD1" <-> "OD2" Residue "H ASP 41": "OD1" <-> "OD2" Residue "H PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 86": "OD1" <-> "OD2" Residue "H ASP 92": "OD1" <-> "OD2" Residue "H TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 94": "OD1" <-> "OD2" Residue "H TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 105": "OE1" <-> "OE2" Residue "H GLU 106": "OE1" <-> "OE2" Residue "H ASP 110": "OD1" <-> "OD2" Residue "H TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 126": "OE1" <-> "OE2" Residue "H TYR 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 138": "OE1" <-> "OE2" Residue "H ARG 146": "NH1" <-> "NH2" Residue "I PHE 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 18": "OE1" <-> "OE2" Residue "I GLU 36": "OE1" <-> "OE2" Residue "I TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 74": "OE1" <-> "OE2" Residue "I PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 94": "OD1" <-> "OD2" Residue "I PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 16": "OD1" <-> "OD2" Residue "J ASP 28": "OD1" <-> "OD2" Residue "J ASP 31": "OD1" <-> "OD2" Residue "J TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 55": "OD1" <-> "OD2" Residue "J GLU 58": "OE1" <-> "OE2" Residue "J PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 5": "OD1" <-> "OD2" Residue "K PHE 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 8": "OE1" <-> "OE2" Residue "K PHE 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 14": "OE1" <-> "OE2" Residue "K GLU 16": "OE1" <-> "OE2" Residue "K ASP 22": "OD1" <-> "OD2" Residue "K ASP 24": "OD1" <-> "OD2" Residue "K ASP 39": "OD1" <-> "OD2" Residue "K TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 79": "OE1" <-> "OE2" Residue "K TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 82": "OD1" <-> "OD2" Residue "K GLU 106": "OE1" <-> "OE2" Residue "L GLU 33": "OE1" <-> "OE2" Residue "L GLU 68": "OE1" <-> "OE2" Residue "a GLU 59": "OE1" <-> "OE2" Residue "a GLU 73": "OE1" <-> "OE2" Residue "a ASP 81": "OD1" <-> "OD2" Residue "a PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ASP 106": "OD1" <-> "OD2" Residue "a ASP 123": "OD1" <-> "OD2" Residue "a GLU 133": "OE1" <-> "OE2" Residue "b ASP 24": "OD1" <-> "OD2" Residue "b ARG 45": "NH1" <-> "NH2" Residue "b PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 63": "OE1" <-> "OE2" Residue "c TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c GLU 56": "OE1" <-> "OE2" Residue "c GLU 61": "OE1" <-> "OE2" Residue "c ARG 71": "NH1" <-> "NH2" Residue "c ASP 72": "OD1" <-> "OD2" Residue "c ASP 90": "OD1" <-> "OD2" Residue "c GLU 91": "OE1" <-> "OE2" Residue "c GLU 92": "OE1" <-> "OE2" Residue "d GLU 32": "OE1" <-> "OE2" Residue "d TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ASP 48": "OD1" <-> "OD2" Residue "d PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ASP 65": "OD1" <-> "OD2" Residue "d TYR 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e GLU 59": "OE1" <-> "OE2" Residue "e PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e GLU 97": "OE1" <-> "OE2" Residue "e GLU 105": "OE1" <-> "OE2" Residue "f ARG 35": "NH1" <-> "NH2" Residue "f TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f GLU 52": "OE1" <-> "OE2" Residue "f GLU 63": "OE1" <-> "OE2" Residue "f TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g PHE 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g GLU 56": "OE1" <-> "OE2" Residue "g GLU 64": "OE1" <-> "OE2" Residue "g ARG 71": "NH1" <-> "NH2" Residue "g ASP 72": "OD1" <-> "OD2" Residue "h GLU 32": "OE1" <-> "OE2" Residue "h TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h ASP 48": "OD1" <-> "OD2" Residue "h ASP 65": "OD1" <-> "OD2" Residue "h PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h GLU 73": "OE1" <-> "OE2" Residue "h GLU 102": "OE1" <-> "OE2" Residue "h TYR 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ASP 175": "OD1" <-> "OD2" Residue "W ASP 180": "OD1" <-> "OD2" Residue "W ASP 203": "OD1" <-> "OD2" Residue "W GLU 209": "OE1" <-> "OE2" Residue "W GLU 220": "OE1" <-> "OE2" Residue "W GLU 228": "OE1" <-> "OE2" Residue "W GLU 231": "OE1" <-> "OE2" Residue "W GLU 252": "OE1" <-> "OE2" Residue "W ASP 253": "OD1" <-> "OD2" Residue "W ASP 259": "OD1" <-> "OD2" Residue "W TYR 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 265": "OE1" <-> "OE2" Residue "W ASP 266": "OD1" <-> "OD2" Residue "W GLU 268": "OE1" <-> "OE2" Residue "W PHE 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 283": "OE1" <-> "OE2" Residue "W GLU 288": "OE1" <-> "OE2" Residue "W ASP 292": "OD1" <-> "OD2" Residue "W TYR 307": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W TYR 316": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 318": "OE1" <-> "OE2" Residue "W GLU 333": "OE1" <-> "OE2" Residue "W TYR 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 362": "OE1" <-> "OE2" Residue "W GLU 375": "OE1" <-> "OE2" Residue "W PHE 379": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 389": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ASP 401": "OD1" <-> "OD2" Residue "W PHE 420": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ASP 442": "OD1" <-> "OD2" Residue "W PHE 444": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 445": "OE1" <-> "OE2" Residue "W ASP 450": "OD1" <-> "OD2" Residue "W ASP 464": "OD1" <-> "OD2" Residue "W GLU 468": "OE1" <-> "OE2" Residue "W PHE 471": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 485": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 493": "OE1" <-> "OE2" Residue "W TYR 494": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ASP 498": "OD1" <-> "OD2" Residue "W GLU 501": "OE1" <-> "OE2" Residue "W PHE 509": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 514": "OE1" <-> "OE2" Residue "W TYR 526": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 532": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 558": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 564": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 581": "OE1" <-> "OE2" Residue "W ASP 585": "OD1" <-> "OD2" Residue "W ARG 597": "NH1" <-> "NH2" Residue "W ASP 601": "OD1" <-> "OD2" Residue "W GLU 624": "OE1" <-> "OE2" Residue "W TYR 626": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 654": "OE1" <-> "OE2" Residue "W TYR 663": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 684": "OE1" <-> "OE2" Residue "W ASP 710": "OD1" <-> "OD2" Residue "W PHE 717": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ASP 729": "OD1" <-> "OD2" Residue "W ASP 742": "OD1" <-> "OD2" Residue "W PHE 757": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ASP 764": "OD1" <-> "OD2" Residue "W PHE 789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ASP 798": "OD1" <-> "OD2" Residue "W ARG 807": "NH1" <-> "NH2" Residue "W GLU 827": "OE1" <-> "OE2" Residue "Y GLU 4": "OE1" <-> "OE2" Residue "Y GLU 18": "OE1" <-> "OE2" Residue "Y PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 32": "OE1" <-> "OE2" Residue "Y GLU 40": "OE1" <-> "OE2" Residue "Y PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ASP 67": "OD1" <-> "OD2" Residue "Y ASP 79": "OD1" <-> "OD2" Residue "Y GLU 88": "OE1" <-> "OE2" Residue "Y ASP 97": "OD1" <-> "OD2" Residue "Z PHE 326": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z TYR 336": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 338": "OE1" <-> "OE2" Residue "Z PHE 348": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ASP 354": "OD1" <-> "OD2" Residue "Z TYR 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ASP 821": "OD1" <-> "OD2" Residue "Z GLU 854": "OE1" <-> "OE2" Residue "Z TYR 858": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 860": "OE1" <-> "OE2" Residue "D ARG 13": "NH1" <-> "NH2" Residue "D GLU 19": "OE1" <-> "OE2" Residue "D GLU 20": "OE1" <-> "OE2" Residue "D GLU 32": "OE1" <-> "OE2" Residue "D PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 45": "OE1" <-> "OE2" Residue "D GLU 65": "OE1" <-> "OE2" Residue "D PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 120": "OE1" <-> "OE2" Residue "D GLU 124": "OE1" <-> "OE2" Residue "D ASP 127": "OD1" <-> "OD2" Residue "D GLU 131": "OE1" <-> "OE2" Residue "D PHE 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 158": "OE1" <-> "OE2" Residue "D PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 176": "OE1" <-> "OE2" Residue "D ASP 186": "OD1" <-> "OD2" Residue "D GLU 206": "OE1" <-> "OE2" Residue "G ASP 6": "OD1" <-> "OD2" Residue "G TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 32": "OE1" <-> "OE2" Residue "G GLU 35": "OE1" <-> "OE2" Residue "G TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 50": "OD1" <-> "OD2" Residue "G ASP 52": "OD1" <-> "OD2" Residue "G ASP 65": "OD1" <-> "OD2" Residue "G TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 85": "OE1" <-> "OE2" Residue "G PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 100": "OE1" <-> "OE2" Residue "G PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 148": "OE1" <-> "OE2" Residue "G ASP 166": "OD1" <-> "OD2" Time to flip residues: 0.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 49720 Number of models: 1 Model: "" Number of chains: 33 Chain: "A" Number of atoms: 11086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1409, 11086 Classifications: {'peptide': 1409} Link IDs: {'PTRANS': 65, 'TRANS': 1343} Chain breaks: 4 Chain: "B" Number of atoms: 8865 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1116, 8865 Classifications: {'peptide': 1116} Link IDs: {'PTRANS': 50, 'TRANS': 1065} Chain breaks: 6 Chain: "C" Number of atoms: 2086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 2086 Classifications: {'peptide': 265} Link IDs: {'PTRANS': 11, 'TRANS': 253} Chain: "E" Number of atoms: 1752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1752 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 201} Chain: "F" Number of atoms: 705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 705 Classifications: {'peptide': 87} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 80} Chain: "H" Number of atoms: 1068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1068 Classifications: {'peptide': 133} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 128} Chain breaks: 1 Chain: "I" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 971 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 5, 'TRANS': 113} Chain: "J" Number of atoms: 532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 532 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 2, 'TRANS': 62} Chain: "K" Number of atoms: 920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 920 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 5, 'TRANS': 109} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 1 Chain: "L" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 351 Classifications: {'peptide': 44} Link IDs: {'TRANS': 43} Chain: "a" Number of atoms: 620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 620 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 2, 'TRANS': 73} Chain: "b" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 638 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "c" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 795 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 5, 'TRANS': 97} Chain: "d" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 719 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "e" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 801 Classifications: {'peptide': 97} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "f" Number of atoms: 619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 619 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "g" Number of atoms: 718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 718 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 3, 'TRANS': 89} Chain: "h" Number of atoms: 726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 726 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "T" Number of atoms: 2834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 2834 Classifications: {'DNA': 139} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 138} Chain: "N" Number of atoms: 2640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 2640 Classifications: {'DNA': 128} Link IDs: {'rna3p': 127} Chain breaks: 1 Chain: "W" Number of atoms: 5129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 622, 5129 Classifications: {'peptide': 622} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 21, 'TRANS': 600} Chain breaks: 5 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 3 Chain: "P" Number of atoms: 330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 330 Classifications: {'RNA': 16} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 2, 'rna3p_pur': 3, 'rna3p_pyr': 10} Link IDs: {'rna2p': 3, 'rna3p': 12} Chain: "Y" Number of atoms: 739 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 739 Classifications: {'peptide': 98} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 6, 'TRANS': 91} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "Z" Number of atoms: 1252 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1252 Classifications: {'peptide': 156} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 149} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 1444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1444 Classifications: {'peptide': 180} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 177} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "G" Number of atoms: 1340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1340 Classifications: {'peptide': 171} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 162} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "W" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 31 Unusual residues: {'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 813 SG CYS A 107 118.717 76.599 130.780 1.00 99.16 S ATOM 837 SG CYS A 110 121.434 77.292 131.789 1.00 97.11 S ATOM 1142 SG CYS A 148 117.932 76.324 131.425 1.00104.97 S ATOM 1280 SG CYS A 167 119.834 78.274 133.219 1.00101.18 S ATOM 508 SG CYS A 67 136.300 98.905 91.527 1.00 95.22 S ATOM 530 SG CYS A 70 137.783 96.094 89.858 1.00 92.70 S ATOM 583 SG CYS A 77 135.482 95.997 90.076 1.00 88.47 S ATOM 19469 SG CYS B1163 138.427 82.880 99.315 1.00 95.07 S ATOM 19487 SG CYS B1166 137.302 83.443 100.152 1.00 93.03 S ATOM 19612 SG CYS B1182 139.444 86.236 99.644 1.00 96.27 S ATOM 19631 SG CYS B1185 139.585 83.987 103.104 1.00101.41 S ATOM 20598 SG CYS C 86 116.738 102.449 26.266 1.00 83.86 S ATOM 20615 SG CYS C 88 116.761 104.782 26.532 1.00 97.69 S ATOM 20648 SG CYS C 92 115.352 104.864 25.238 1.00 87.26 S ATOM 20671 SG CYS C 95 113.048 103.715 27.502 1.00 75.72 S ATOM 25615 SG CYS I 7 53.520 85.495 131.164 1.00121.79 S ATOM 25640 SG CYS I 10 54.099 88.466 132.302 1.00123.27 S ATOM 25830 SG CYS I 32 55.215 87.058 133.669 1.00125.89 S ATOM 26157 SG CYS I 75 38.852 70.855 91.435 1.00 94.12 S ATOM 26179 SG CYS I 78 36.022 72.658 90.196 1.00 95.85 S ATOM 26395 SG CYS I 103 39.375 74.401 89.966 1.00 88.67 S ATOM 26415 SG CYS I 106 38.252 73.946 92.963 1.00 91.71 S ATOM 26587 SG CYS J 7 86.604 90.616 38.849 1.00 61.19 S ATOM 26610 SG CYS J 10 86.914 89.255 35.771 1.00 62.03 S ATOM 26890 SG CYS J 45 85.149 87.863 38.130 1.00 62.83 S ATOM 26896 SG CYS J 46 84.077 90.386 35.783 1.00 62.09 S ATOM 28028 SG CYS L 31 95.246 127.898 58.936 1.00 90.48 S ATOM 28048 SG CYS L 34 93.716 130.774 58.605 1.00 90.22 S ATOM 28152 SG CYS L 48 96.703 131.339 59.039 1.00 94.13 S ATOM 28175 SG CYS L 51 93.378 130.767 60.397 1.00 94.25 S Time building chain proxies: 25.50, per 1000 atoms: 0.51 Number of scatterers: 49720 At special positions: 0 Unit cell: (198.45, 171.15, 236.25, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 9 Type Number sf(0) Zn 8 29.99 S 228 16.00 P 284 15.00 Mg 1 11.99 F 3 9.00 O 9914 8.00 N 8819 7.00 C 30462 6.00 Be 1 4.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 22.61 Conformation dependent library (CDL) restraints added in 7.9 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1801 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 167 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 148 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 107 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 110 " pdb=" ZN A1802 " pdb="ZN ZN A1802 " - pdb=" NE2 HIS A 80 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 70 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 67 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 77 " pdb=" ZN B1301 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1166 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1182 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1163 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1185 " pdb=" ZN C 401 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 95 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 86 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 88 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 92 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 7 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 32 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 10 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 103 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 106 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 75 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 78 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 45 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 46 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 7 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 10 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 48 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 51 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 31 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 34 " Number of angles added : 39 10846 Ramachandran restraints generated. 5423 Oldfield, 0 Emsley, 5423 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10342 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 197 helices and 43 sheets defined 38.2% alpha, 11.5% beta 92 base pairs and 234 stacking pairs defined. Time for finding SS restraints: 22.48 Creating SS restraints... Processing helix chain 'A' and resid 24 through 30 Processing helix chain 'A' and resid 43 through 45 No H-bonds generated for 'chain 'A' and resid 43 through 45' Processing helix chain 'A' and resid 73 through 76 No H-bonds generated for 'chain 'A' and resid 73 through 76' Processing helix chain 'A' and resid 93 through 105 removed outlier: 4.826A pdb=" N ALA A 97 " --> pdb=" O GLY A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 126 Processing helix chain 'A' and resid 131 through 144 removed outlier: 4.458A pdb=" N THR A 144 " --> pdb=" O THR A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 213 Processing helix chain 'A' and resid 216 through 221 Processing helix chain 'A' and resid 231 through 234 Processing helix chain 'A' and resid 244 through 246 No H-bonds generated for 'chain 'A' and resid 244 through 246' Processing helix chain 'A' and resid 261 through 281 Processing helix chain 'A' and resid 288 through 304 Processing helix chain 'A' and resid 325 through 329 Processing helix chain 'A' and resid 335 through 339 Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 385 through 394 Processing helix chain 'A' and resid 452 through 454 No H-bonds generated for 'chain 'A' and resid 452 through 454' Processing helix chain 'A' and resid 472 through 478 removed outlier: 4.138A pdb=" N SER A 476 " --> pdb=" O SER A 473 " (cutoff:3.500A) Proline residue: A 477 - end of helix Processing helix chain 'A' and resid 495 through 503 Processing helix chain 'A' and resid 507 through 510 No H-bonds generated for 'chain 'A' and resid 507 through 510' Processing helix chain 'A' and resid 526 through 535 Processing helix chain 'A' and resid 543 through 552 Processing helix chain 'A' and resid 574 through 580 removed outlier: 3.821A pdb=" N VAL A 580 " --> pdb=" O GLN A 576 " (cutoff:3.500A) Processing helix chain 'A' and resid 619 through 622 No H-bonds generated for 'chain 'A' and resid 619 through 622' Processing helix chain 'A' and resid 629 through 636 Processing helix chain 'A' and resid 639 through 660 Processing helix chain 'A' and resid 666 through 668 No H-bonds generated for 'chain 'A' and resid 666 through 668' Processing helix chain 'A' and resid 673 through 698 Processing helix chain 'A' and resid 710 through 736 Processing helix chain 'A' and resid 742 through 749 Processing helix chain 'A' and resid 755 through 762 Processing helix chain 'A' and resid 810 through 845 removed outlier: 3.918A pdb=" N ALA A 832 " --> pdb=" O ALA A 828 " (cutoff:3.500A) Processing helix chain 'A' and resid 868 through 870 No H-bonds generated for 'chain 'A' and resid 868 through 870' Processing helix chain 'A' and resid 875 through 877 No H-bonds generated for 'chain 'A' and resid 875 through 877' Processing helix chain 'A' and resid 890 through 897 Processing helix chain 'A' and resid 916 through 919 No H-bonds generated for 'chain 'A' and resid 916 through 919' Processing helix chain 'A' and resid 923 through 946 Processing helix chain 'A' and resid 960 through 971 Processing helix chain 'A' and resid 983 through 996 Processing helix chain 'A' and resid 1005 through 1014 Processing helix chain 'A' and resid 1016 through 1025 Processing helix chain 'A' and resid 1028 through 1033 Processing helix chain 'A' and resid 1039 through 1056 Processing helix chain 'A' and resid 1064 through 1078 Proline residue: A1075 - end of helix removed outlier: 3.673A pdb=" N GLN A1078 " --> pdb=" O GLU A1074 " (cutoff:3.500A) Processing helix chain 'A' and resid 1098 through 1105 Processing helix chain 'A' and resid 1122 through 1124 No H-bonds generated for 'chain 'A' and resid 1122 through 1124' Processing helix chain 'A' and resid 1129 through 1138 Processing helix chain 'A' and resid 1143 through 1146 No H-bonds generated for 'chain 'A' and resid 1143 through 1146' Processing helix chain 'A' and resid 1166 through 1174 removed outlier: 3.558A pdb=" N GLN A1171 " --> pdb=" O GLU A1168 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N LEU A1172 " --> pdb=" O ILE A1169 " (cutoff:3.500A) Processing helix chain 'A' and resid 1199 through 1205 Processing helix chain 'A' and resid 1209 through 1219 Processing helix chain 'A' and resid 1256 through 1269 removed outlier: 4.228A pdb=" N LYS A1261 " --> pdb=" O ASP A1257 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N LYS A1262 " --> pdb=" O HIS A1258 " (cutoff:3.500A) Processing helix chain 'A' and resid 1313 through 1318 removed outlier: 4.131A pdb=" N THR A1318 " --> pdb=" O SER A1314 " (cutoff:3.500A) Processing helix chain 'A' and resid 1332 through 1339 Processing helix chain 'A' and resid 1341 through 1359 removed outlier: 4.566A pdb=" N ASP A1359 " --> pdb=" O VAL A1355 " (cutoff:3.500A) Processing helix chain 'A' and resid 1365 through 1374 Processing helix chain 'A' and resid 1389 through 1391 No H-bonds generated for 'chain 'A' and resid 1389 through 1391' Processing helix chain 'A' and resid 1396 through 1401 removed outlier: 3.552A pdb=" N SER A1401 " --> pdb=" O LEU A1397 " (cutoff:3.500A) Processing helix chain 'A' and resid 1406 through 1415 Processing helix chain 'A' and resid 1424 through 1430 Processing helix chain 'A' and resid 1447 through 1453 Processing helix chain 'B' and resid 29 through 40 Processing helix chain 'B' and resid 45 through 65 removed outlier: 4.864A pdb=" N LEU B 59 " --> pdb=" O VAL B 55 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N GLN B 60 " --> pdb=" O ASP B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 120 Processing helix chain 'B' and resid 186 through 191 Processing helix chain 'B' and resid 282 through 289 Processing helix chain 'B' and resid 295 through 301 Processing helix chain 'B' and resid 308 through 323 Proline residue: B 316 - end of helix removed outlier: 3.551A pdb=" N PHE B 322 " --> pdb=" O VAL B 318 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N VAL B 323 " --> pdb=" O GLU B 319 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 338 Processing helix chain 'B' and resid 349 through 358 Processing helix chain 'B' and resid 372 through 389 Processing helix chain 'B' and resid 409 through 434 Processing helix chain 'B' and resid 450 through 463 removed outlier: 3.624A pdb=" N GLY B 456 " --> pdb=" O THR B 452 " (cutoff:3.500A) Processing helix chain 'B' and resid 488 through 495 Processing helix chain 'B' and resid 516 through 518 No H-bonds generated for 'chain 'B' and resid 516 through 518' Processing helix chain 'B' and resid 552 through 560 Processing helix chain 'B' and resid 593 through 606 Processing helix chain 'B' and resid 655 through 667 Processing helix chain 'B' and resid 681 through 687 Processing helix chain 'B' and resid 697 through 700 removed outlier: 3.509A pdb=" N SER B 700 " --> pdb=" O GLU B 697 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 697 through 700' Processing helix chain 'B' and resid 745 through 748 Processing helix chain 'B' and resid 753 through 755 No H-bonds generated for 'chain 'B' and resid 753 through 755' Processing helix chain 'B' and resid 764 through 776 removed outlier: 4.222A pdb=" N LYS B 775 " --> pdb=" O SER B 771 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N GLN B 776 " --> pdb=" O ALA B 772 " (cutoff:3.500A) Processing helix chain 'B' and resid 807 through 812 removed outlier: 3.677A pdb=" N GLU B 810 " --> pdb=" O ARG B 807 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU B 812 " --> pdb=" O MET B 809 " (cutoff:3.500A) Processing helix chain 'B' and resid 843 through 848 Processing helix chain 'B' and resid 1014 through 1020 Proline residue: B1018 - end of helix Processing helix chain 'B' and resid 1023 through 1038 Processing helix chain 'B' and resid 1052 through 1061 Processing helix chain 'B' and resid 1099 through 1102 No H-bonds generated for 'chain 'B' and resid 1099 through 1102' Processing helix chain 'B' and resid 1132 through 1141 Processing helix chain 'B' and resid 1144 through 1152 Processing helix chain 'B' and resid 1198 through 1210 Processing helix chain 'C' and resid 27 through 39 Processing helix chain 'C' and resid 60 through 68 Processing helix chain 'C' and resid 115 through 117 No H-bonds generated for 'chain 'C' and resid 115 through 117' Processing helix chain 'C' and resid 168 through 170 No H-bonds generated for 'chain 'C' and resid 168 through 170' Processing helix chain 'C' and resid 197 through 200 No H-bonds generated for 'chain 'C' and resid 197 through 200' Processing helix chain 'C' and resid 205 through 209 removed outlier: 3.883A pdb=" N GLU C 208 " --> pdb=" O LYS C 205 " (cutoff:3.500A) Processing helix chain 'C' and resid 240 through 267 removed outlier: 4.212A pdb=" N GLN C 267 " --> pdb=" O THR C 263 " (cutoff:3.500A) Processing helix chain 'E' and resid 5 through 26 Processing helix chain 'E' and resid 32 through 35 No H-bonds generated for 'chain 'E' and resid 32 through 35' Processing helix chain 'E' and resid 39 through 46 Processing helix chain 'E' and resid 55 through 58 No H-bonds generated for 'chain 'E' and resid 55 through 58' Processing helix chain 'E' and resid 66 through 71 Processing helix chain 'E' and resid 90 through 103 Processing helix chain 'E' and resid 118 through 126 Proline residue: E 125 - end of helix Processing helix chain 'E' and resid 137 through 140 No H-bonds generated for 'chain 'E' and resid 137 through 140' Processing helix chain 'E' and resid 158 through 168 Processing helix chain 'E' and resid 183 through 188 Processing helix chain 'F' and resid 87 through 102 Processing helix chain 'F' and resid 117 through 127 Processing helix chain 'H' and resid 129 through 133 removed outlier: 4.464A pdb=" N ASN H 133 " --> pdb=" O ARG H 130 " (cutoff:3.500A) Processing helix chain 'I' and resid 62 through 64 No H-bonds generated for 'chain 'I' and resid 62 through 64' Processing helix chain 'J' and resid 15 through 26 removed outlier: 4.102A pdb=" N TRP J 18 " --> pdb=" O GLY J 15 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N GLU J 19 " --> pdb=" O ASP J 16 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER J 20 " --> pdb=" O LYS J 17 " (cutoff:3.500A) Processing helix chain 'J' and resid 32 through 39 Processing helix chain 'J' and resid 44 through 51 Processing helix chain 'J' and resid 56 through 61 Processing helix chain 'K' and resid 7 through 9 No H-bonds generated for 'chain 'K' and resid 7 through 9' Processing helix chain 'K' and resid 40 through 52 removed outlier: 4.077A pdb=" N LEU K 45 " --> pdb=" O THR K 41 " (cutoff:3.500A) Processing helix chain 'K' and resid 83 through 111 Processing helix chain 'a' and resid 64 through 78 removed outlier: 3.638A pdb=" N ASP a 77 " --> pdb=" O GLU a 73 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N PHE a 78 " --> pdb=" O ILE a 74 " (cutoff:3.500A) Processing helix chain 'a' and resid 86 through 113 Processing helix chain 'a' and resid 121 through 131 Processing helix chain 'b' and resid 25 through 28 Processing helix chain 'b' and resid 31 through 41 Processing helix chain 'b' and resid 48 through 76 removed outlier: 3.805A pdb=" N TYR b 51 " --> pdb=" O GLY b 48 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N GLU b 52 " --> pdb=" O LEU b 49 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU b 58 " --> pdb=" O ARG b 55 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ILE b 66 " --> pdb=" O GLU b 63 " (cutoff:3.500A) Processing helix chain 'b' and resid 83 through 93 Processing helix chain 'c' and resid 17 through 20 No H-bonds generated for 'chain 'c' and resid 17 through 20' Processing helix chain 'c' and resid 27 through 36 Processing helix chain 'c' and resid 45 through 72 removed outlier: 4.494A pdb=" N VAL c 49 " --> pdb=" O ALA c 45 " (cutoff:3.500A) Processing helix chain 'c' and resid 80 through 89 Processing helix chain 'c' and resid 93 through 96 No H-bonds generated for 'chain 'c' and resid 93 through 96' Processing helix chain 'd' and resid 35 through 45 Processing helix chain 'd' and resid 53 through 80 Processing helix chain 'd' and resid 88 through 98 Processing helix chain 'd' and resid 106 through 120 Processing helix chain 'e' and resid 45 through 56 Processing helix chain 'e' and resid 64 through 76 Processing helix chain 'e' and resid 86 through 113 Processing helix chain 'e' and resid 121 through 131 Processing helix chain 'f' and resid 26 through 28 No H-bonds generated for 'chain 'f' and resid 26 through 28' Processing helix chain 'f' and resid 31 through 40 Processing helix chain 'f' and resid 48 through 76 removed outlier: 3.830A pdb=" N ARG f 67 " --> pdb=" O ASN f 64 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL f 70 " --> pdb=" O ARG f 67 " (cutoff:3.500A) Processing helix chain 'f' and resid 83 through 92 Processing helix chain 'g' and resid 17 through 21 Processing helix chain 'g' and resid 27 through 36 Processing helix chain 'g' and resid 45 through 72 removed outlier: 4.165A pdb=" N VAL g 49 " --> pdb=" O ALA g 45 " (cutoff:3.500A) Processing helix chain 'g' and resid 80 through 89 Processing helix chain 'g' and resid 91 through 96 Processing helix chain 'h' and resid 35 through 45 Processing helix chain 'h' and resid 53 through 80 Processing helix chain 'h' and resid 88 through 98 Processing helix chain 'h' and resid 104 through 120 Processing helix chain 'W' and resid 204 through 210 Processing helix chain 'W' and resid 230 through 233 No H-bonds generated for 'chain 'W' and resid 230 through 233' Processing helix chain 'W' and resid 239 through 256 Processing helix chain 'W' and resid 264 through 285 removed outlier: 3.792A pdb=" N HIS W 285 " --> pdb=" O PHE W 281 " (cutoff:3.500A) Processing helix chain 'W' and resid 324 through 330 Processing helix chain 'W' and resid 332 through 342 Processing helix chain 'W' and resid 378 through 393 Processing helix chain 'W' and resid 407 through 420 Processing helix chain 'W' and resid 437 through 447 Processing helix chain 'W' and resid 460 through 470 removed outlier: 3.693A pdb=" N TYR W 469 " --> pdb=" O THR W 465 " (cutoff:3.500A) Processing helix chain 'W' and resid 492 through 497 Processing helix chain 'W' and resid 499 through 504 removed outlier: 3.641A pdb=" N SER W 504 " --> pdb=" O ALA W 500 " (cutoff:3.500A) Processing helix chain 'W' and resid 524 through 531 Processing helix chain 'W' and resid 549 through 559 Processing helix chain 'W' and resid 576 through 593 removed outlier: 3.706A pdb=" N GLU W 581 " --> pdb=" O GLU W 577 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N HIS W 584 " --> pdb=" O GLU W 580 " (cutoff:3.500A) Proline residue: W 592 - end of helix Processing helix chain 'W' and resid 620 through 629 Processing helix chain 'W' and resid 652 through 660 Processing helix chain 'W' and resid 662 through 664 No H-bonds generated for 'chain 'W' and resid 662 through 664' Processing helix chain 'W' and resid 669 through 672 No H-bonds generated for 'chain 'W' and resid 669 through 672' Processing helix chain 'W' and resid 684 through 693 Processing helix chain 'W' and resid 695 through 709 Processing helix chain 'W' and resid 721 through 734 Processing helix chain 'W' and resid 747 through 758 Processing helix chain 'W' and resid 795 through 804 removed outlier: 4.002A pdb=" N ARG W 804 " --> pdb=" O GLN W 800 " (cutoff:3.500A) Processing helix chain 'W' and resid 825 through 840 removed outlier: 3.882A pdb=" N LYS W 835 " --> pdb=" O GLU W 831 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LYS W 836 " --> pdb=" O ARG W 832 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLU W 840 " --> pdb=" O LYS W 836 " (cutoff:3.500A) Processing helix chain 'Y' and resid 16 through 21 Processing helix chain 'Y' and resid 28 through 34 Processing helix chain 'Y' and resid 38 through 41 No H-bonds generated for 'chain 'Y' and resid 38 through 41' Processing helix chain 'Y' and resid 59 through 64 Processing helix chain 'Y' and resid 84 through 89 Processing helix chain 'Z' and resid 297 through 314 Processing helix chain 'Z' and resid 342 through 349 Processing helix chain 'Z' and resid 365 through 371 Proline residue: Z 369 - end of helix Processing helix chain 'Z' and resid 842 through 844 No H-bonds generated for 'chain 'Z' and resid 842 through 844' Processing helix chain 'D' and resid 52 through 75 Processing helix chain 'D' and resid 122 through 133 Processing helix chain 'D' and resid 139 through 150 removed outlier: 3.554A pdb=" N ASN D 150 " --> pdb=" O GLN D 146 " (cutoff:3.500A) Processing helix chain 'D' and resid 157 through 170 removed outlier: 3.635A pdb=" N SER D 169 " --> pdb=" O GLN D 165 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N THR D 170 " --> pdb=" O LEU D 166 " (cutoff:3.500A) Processing helix chain 'D' and resid 174 through 182 Processing helix chain 'D' and resid 188 through 194 Processing helix chain 'D' and resid 204 through 217 Processing helix chain 'G' and resid 20 through 34 removed outlier: 4.265A pdb=" N LYS G 23 " --> pdb=" O PRO G 20 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N TYR G 25 " --> pdb=" O MET G 22 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL G 34 " --> pdb=" O LEU G 31 " (cutoff:3.500A) Processing helix chain 'G' and resid 51 through 53 No H-bonds generated for 'chain 'G' and resid 51 through 53' Processing helix chain 'G' and resid 112 through 114 No H-bonds generated for 'chain 'G' and resid 112 through 114' Processing sheet with id= A, first strand: chain 'A' and resid 82 through 85 Processing sheet with id= B, first strand: chain 'A' and resid 173 through 177 Processing sheet with id= C, first strand: chain 'A' and resid 348 through 352 Processing sheet with id= D, first strand: chain 'A' and resid 353 through 355 removed outlier: 6.648A pdb=" N PHE A 468 " --> pdb=" O SER A 354 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'A' and resid 375 through 379 removed outlier: 3.503A pdb=" N ARG A 434 " --> pdb=" O TYR A 376 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 404 through 406 Processing sheet with id= G, first strand: chain 'A' and resid 588 through 590 removed outlier: 3.571A pdb=" N LEU A 606 " --> pdb=" O PHE A 614 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ILE A 608 " --> pdb=" O ILE A 612 " (cutoff:3.500A) removed outlier: 5.178A pdb=" N ILE A 612 " --> pdb=" O ILE A 608 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 849 through 851 removed outlier: 3.500A pdb=" N THR A 855 " --> pdb=" O HIS A 851 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 879 through 881 Processing sheet with id= J, first strand: chain 'A' and resid 1116 through 1119 Processing sheet with id= K, first strand: chain 'A' and resid 1224 through 1228 removed outlier: 4.244A pdb=" N VAL A1242 " --> pdb=" O TRP A1191 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N TRP A1191 " --> pdb=" O VAL A1242 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 95 through 97 removed outlier: 3.765A pdb=" N GLY B 168 " --> pdb=" O LEU B 128 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N VAL B 130 " --> pdb=" O PHE B 166 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N PHE B 166 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'B' and resid 203 through 205 Processing sheet with id= N, first strand: chain 'B' and resid 498 through 500 removed outlier: 6.080A pdb=" N ALA B 214 " --> pdb=" O ASN B 499 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'B' and resid 224 through 226 removed outlier: 3.503A pdb=" N LEU B 254 " --> pdb=" O ILE B 240 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N SER B 242 " --> pdb=" O SER B 252 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'B' and resid 543 through 545 Processing sheet with id= Q, first strand: chain 'B' and resid 614 through 618 removed outlier: 6.259A pdb=" N ARG B 579 " --> pdb=" O LEU B 624 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N ILE B 626 " --> pdb=" O ARG B 579 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N PHE B 581 " --> pdb=" O ILE B 626 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N VAL B 582 " --> pdb=" O TRP B 586 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N TRP B 586 " --> pdb=" O VAL B 582 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'B' and resid 792 through 796 removed outlier: 5.794A pdb=" N ARG B 969 " --> pdb=" O VAL B 949 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N VAL B 949 " --> pdb=" O ARG B 969 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'B' and resid 990 through 994 removed outlier: 7.252A pdb=" N MET B 839 " --> pdb=" O GLY B 991 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N THR B 993 " --> pdb=" O MET B 839 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N MET B 841 " --> pdb=" O THR B 993 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N PHE B1086 " --> pdb=" O ILE B 827 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'B' and resid 915 through 917 Processing sheet with id= U, first strand: chain 'B' and resid 1158 through 1163 Processing sheet with id= V, first strand: chain 'C' and resid 176 through 180 removed outlier: 3.745A pdb=" N GLU C 12 " --> pdb=" O ASP C 19 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ILE C 21 " --> pdb=" O ILE C 10 " (cutoff:3.500A) removed outlier: 5.424A pdb=" N ILE C 10 " --> pdb=" O ILE C 21 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N SER C 23 " --> pdb=" O VAL C 8 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N VAL C 8 " --> pdb=" O SER C 23 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'C' and resid 96 through 102 removed outlier: 6.077A pdb=" N LYS C 160 " --> pdb=" O ILE C 46 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N ILE C 46 " --> pdb=" O LYS C 160 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N GLY C 162 " --> pdb=" O LEU C 44 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N LEU C 44 " --> pdb=" O GLY C 162 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'C' and resid 111 through 113 removed outlier: 3.643A pdb=" N CYS C 145 " --> pdb=" O VAL C 113 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'E' and resid 60 through 62 removed outlier: 6.703A pdb=" N THR E 107 " --> pdb=" O TRP E 79 " (cutoff:3.500A) removed outlier: 8.160A pdb=" N GLU E 81 " --> pdb=" O THR E 107 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ILE E 109 " --> pdb=" O GLU E 81 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N THR E 131 " --> pdb=" O GLY E 108 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N PHE E 110 " --> pdb=" O THR E 131 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N GLU E 133 " --> pdb=" O PHE E 110 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N TYR E 112 " --> pdb=" O GLU E 133 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N PHE E 135 " --> pdb=" O TYR E 112 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'E' and resid 152 through 155 Processing sheet with id= AA, first strand: chain 'F' and resid 133 through 137 Processing sheet with id= AB, first strand: chain 'H' and resid 100 through 107 removed outlier: 6.909A pdb=" N TYR H 115 " --> pdb=" O TYR H 102 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N PHE H 104 " --> pdb=" O ALA H 113 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N ALA H 113 " --> pdb=" O PHE H 104 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N GLU H 106 " --> pdb=" O LEU H 111 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N LEU H 111 " --> pdb=" O GLU H 106 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N LEU H 122 " --> pdb=" O ASP H 41 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ALA H 29 " --> pdb=" O VAL H 12 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N VAL H 12 " --> pdb=" O ALA H 29 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ILE H 59 " --> pdb=" O LEU H 5 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N ASP H 7 " --> pdb=" O VAL H 57 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N VAL H 57 " --> pdb=" O ASP H 7 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N ILE H 9 " --> pdb=" O LEU H 55 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N LEU H 55 " --> pdb=" O ILE H 9 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA H 140 " --> pdb=" O GLY H 99 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'I' and resid 15 through 19 Processing sheet with id= AD, first strand: chain 'I' and resid 69 through 72 Processing sheet with id= AE, first strand: chain 'K' and resid 19 through 23 Processing sheet with id= AF, first strand: chain 'W' and resid 225 through 228 removed outlier: 3.879A pdb=" N ASN W 184 " --> pdb=" O LEU W 214 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N LYS W 216 " --> pdb=" O VAL W 182 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N VAL W 182 " --> pdb=" O LYS W 216 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'W' and resid 292 through 295 removed outlier: 3.741A pdb=" N ASP W 292 " --> pdb=" O LEU W 308 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL W 309 " --> pdb=" O THR W 320 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N THR W 320 " --> pdb=" O VAL W 309 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'W' and resid 536 through 539 Processing sheet with id= AI, first strand: chain 'W' and resid 610 through 616 removed outlier: 3.623A pdb=" N VAL W 786 " --> pdb=" O MET W 815 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'W' and resid 287 through 290 removed outlier: 6.885A pdb=" N LYS W 310 " --> pdb=" O GLU W 288 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'Y' and resid 49 through 52 Processing sheet with id= AL, first strand: chain 'Z' and resid 360 through 362 removed outlier: 3.941A pdb=" N SER Z 324 " --> pdb=" O GLU Z 338 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'Z' and resid 845 through 847 removed outlier: 7.057A pdb=" N THR Z 828 " --> pdb=" O LYS Z 820 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'D' and resid 36 through 38 Processing sheet with id= AO, first strand: chain 'G' and resid 3 through 13 removed outlier: 6.971A pdb=" N PHE G 79 " --> pdb=" O ILE G 45 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N ILE G 45 " --> pdb=" O PHE G 79 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'G' and resid 142 through 146 removed outlier: 6.912A pdb=" N GLU G 100 " --> pdb=" O VAL G 92 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N CYS G 94 " --> pdb=" O GLY G 98 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N GLY G 98 " --> pdb=" O CYS G 94 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N PHE G 99 " --> pdb=" O VAL G 110 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N VAL G 110 " --> pdb=" O PHE G 99 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N LYS G 107 " --> pdb=" O ILE G 157 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA G 159 " --> pdb=" O LYS G 107 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N SER G 156 " --> pdb=" O GLN G 153 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N SER G 162 " --> pdb=" O ILE G 147 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N ILE G 147 " --> pdb=" O SER G 162 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'G' and resid 120 through 122 1655 hydrogen bonds defined for protein. 4563 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 233 hydrogen bonds 466 hydrogen bond angles 0 basepair planarities 92 basepair parallelities 234 stacking parallelities Total time for adding SS restraints: 30.23 Time building geometry restraints manager: 24.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 9953 1.33 - 1.45: 13164 1.45 - 1.58: 27129 1.58 - 1.70: 564 1.70 - 1.82: 370 Bond restraints: 51180 Sorted by residual: bond pdb=" BE BEF W1502 " pdb=" F2 BEF W1502 " ideal model delta sigma weight residual 1.476 1.565 -0.089 2.00e-02 2.50e+03 2.00e+01 bond pdb=" CG ARG F 136 " pdb=" CD ARG F 136 " ideal model delta sigma weight residual 1.520 1.394 0.126 3.00e-02 1.11e+03 1.76e+01 bond pdb=" CG ARG I 91 " pdb=" CD ARG I 91 " ideal model delta sigma weight residual 1.520 1.416 0.104 3.00e-02 1.11e+03 1.21e+01 bond pdb=" BE BEF W1502 " pdb=" F3 BEF W1502 " ideal model delta sigma weight residual 1.476 1.543 -0.067 2.00e-02 2.50e+03 1.14e+01 bond pdb=" CD LYS K 62 " pdb=" CE LYS K 62 " ideal model delta sigma weight residual 1.520 1.421 0.099 3.00e-02 1.11e+03 1.09e+01 ... (remaining 51175 not shown) Histogram of bond angle deviations from ideal: 95.24 - 103.42: 825 103.42 - 111.61: 23077 111.61 - 119.79: 23111 119.79 - 127.98: 22485 127.98 - 136.16: 802 Bond angle restraints: 70300 Sorted by residual: angle pdb=" CG ARG E 167 " pdb=" CD ARG E 167 " pdb=" NE ARG E 167 " ideal model delta sigma weight residual 112.00 96.67 15.33 2.20e+00 2.07e-01 4.86e+01 angle pdb=" CA ARG G 60 " pdb=" CB ARG G 60 " pdb=" CG ARG G 60 " ideal model delta sigma weight residual 114.10 126.54 -12.44 2.00e+00 2.50e-01 3.87e+01 angle pdb=" N GLY B1121 " pdb=" CA GLY B1121 " pdb=" C GLY B1121 " ideal model delta sigma weight residual 112.48 119.46 -6.98 1.21e+00 6.83e-01 3.33e+01 angle pdb=" CG ARG A 857 " pdb=" CD ARG A 857 " pdb=" NE ARG A 857 " ideal model delta sigma weight residual 112.00 124.49 -12.49 2.20e+00 2.07e-01 3.22e+01 angle pdb=" CB ARG e 129 " pdb=" CG ARG e 129 " pdb=" CD ARG e 129 " ideal model delta sigma weight residual 111.30 124.07 -12.77 2.30e+00 1.89e-01 3.08e+01 ... (remaining 70295 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.77: 28863 35.77 - 71.53: 1613 71.53 - 107.30: 67 107.30 - 143.06: 2 143.06 - 178.83: 5 Dihedral angle restraints: 30550 sinusoidal: 14573 harmonic: 15977 Sorted by residual: dihedral pdb=" CA ILE a 62 " pdb=" C ILE a 62 " pdb=" N ARG a 63 " pdb=" CA ARG a 63 " ideal model delta harmonic sigma weight residual -180.00 -145.89 -34.11 0 5.00e+00 4.00e-02 4.65e+01 dihedral pdb=" CA GLU h 102 " pdb=" C GLU h 102 " pdb=" N LEU h 103 " pdb=" CA LEU h 103 " ideal model delta harmonic sigma weight residual 180.00 146.75 33.25 0 5.00e+00 4.00e-02 4.42e+01 dihedral pdb=" CA ASP C 90 " pdb=" C ASP C 90 " pdb=" N HIS C 91 " pdb=" CA HIS C 91 " ideal model delta harmonic sigma weight residual 180.00 -147.08 -32.92 0 5.00e+00 4.00e-02 4.33e+01 ... (remaining 30547 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 6633 0.076 - 0.152: 1151 0.152 - 0.228: 114 0.228 - 0.304: 17 0.304 - 0.380: 5 Chirality restraints: 7920 Sorted by residual: chirality pdb=" CA GLU C 166 " pdb=" N GLU C 166 " pdb=" C GLU C 166 " pdb=" CB GLU C 166 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.61e+00 chirality pdb=" CB ILE d 51 " pdb=" CA ILE d 51 " pdb=" CG1 ILE d 51 " pdb=" CG2 ILE d 51 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.34 2.00e-01 2.50e+01 2.87e+00 chirality pdb=" CA PRO G 15 " pdb=" N PRO G 15 " pdb=" C PRO G 15 " pdb=" CB PRO G 15 " both_signs ideal model delta sigma weight residual False 2.72 2.41 0.31 2.00e-01 2.50e+01 2.37e+00 ... (remaining 7917 not shown) Planarity restraints: 8063 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 233 " -0.042 2.00e-02 2.50e+03 3.28e-02 2.69e+01 pdb=" CG TRP A 233 " 0.087 2.00e-02 2.50e+03 pdb=" CD1 TRP A 233 " -0.035 2.00e-02 2.50e+03 pdb=" CD2 TRP A 233 " 0.007 2.00e-02 2.50e+03 pdb=" NE1 TRP A 233 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP A 233 " 0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP A 233 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 233 " -0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 233 " -0.009 2.00e-02 2.50e+03 pdb=" CH2 TRP A 233 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B1129 " -0.120 9.50e-02 1.11e+02 6.82e-02 2.38e+01 pdb=" NE ARG B1129 " 0.034 2.00e-02 2.50e+03 pdb=" CZ ARG B1129 " -0.080 2.00e-02 2.50e+03 pdb=" NH1 ARG B1129 " 0.029 2.00e-02 2.50e+03 pdb=" NH2 ARG B1129 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B1001 " 0.035 2.00e-02 2.50e+03 3.47e-02 2.10e+01 pdb=" CG PHE B1001 " -0.078 2.00e-02 2.50e+03 pdb=" CD1 PHE B1001 " 0.003 2.00e-02 2.50e+03 pdb=" CD2 PHE B1001 " 0.027 2.00e-02 2.50e+03 pdb=" CE1 PHE B1001 " 0.015 2.00e-02 2.50e+03 pdb=" CE2 PHE B1001 " -0.008 2.00e-02 2.50e+03 pdb=" CZ PHE B1001 " 0.007 2.00e-02 2.50e+03 ... (remaining 8060 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 493 2.54 - 3.13: 39828 3.13 - 3.72: 81746 3.72 - 4.31: 113705 4.31 - 4.90: 181976 Nonbonded interactions: 417748 Sorted by model distance: nonbonded pdb=" OD1 ASP W 701 " pdb=" OH TYR W 730 " model vdw 1.950 2.440 nonbonded pdb=" O3' U P 46 " pdb="MG MG A1803 " model vdw 1.954 2.170 nonbonded pdb=" OH TYR A1328 " pdb=" OE2 GLU A1351 " model vdw 1.959 2.440 nonbonded pdb=" OG1 THR B 971 " pdb=" OE1 GLU C 61 " model vdw 1.975 2.440 nonbonded pdb=" OP1 DG N 21 " pdb=" OG SER W 523 " model vdw 2.001 2.440 ... (remaining 417743 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 'b' and resid 25 through 102) selection = chain 'f' } ncs_group { reference = (chain 'c' and resid 16 through 108) selection = chain 'g' } ncs_group { reference = chain 'd' selection = (chain 'h' and resid 30 through 121) } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.590 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: 0.050 Extract box with map and model: 16.440 Check model and map are aligned: 0.750 Set scattering table: 0.490 Process input model: 162.410 Find NCS groups from input model: 1.610 Set up NCS constraints: 0.290 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:13.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 198.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7398 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 : 0.008 0.126 51180 Z= 0.501 Angle : 1.167 15.746 70300 Z= 0.630 Chirality : 0.058 0.380 7920 Planarity : 0.006 0.068 8063 Dihedral : 19.719 178.827 20208 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 0.10 % Allowed : 1.58 % Favored : 98.32 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -0.66 (0.11), residues: 5423 helix: 0.46 (0.11), residues: 2227 sheet: -1.01 (0.19), residues: 681 loop : -1.03 (0.12), residues: 2515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.087 0.004 TRP A 233 HIS 0.030 0.003 HIS c 82 PHE 0.078 0.005 PHE B1001 TYR 0.077 0.004 TYR h 80 ARG 0.081 0.004 ARG B1129 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10846 Ramachandran restraints generated. 5423 Oldfield, 0 Emsley, 5423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10846 Ramachandran restraints generated. 5423 Oldfield, 0 Emsley, 5423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 708 residues out of total 4824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 703 time to evaluate : 5.892 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "SER W 635 " (corrupted residue). Skipping it. REVERT: A 317 LYS cc_start: 0.8119 (pptt) cc_final: 0.7563 (tmtt) REVERT: A 780 VAL cc_start: 0.8388 (t) cc_final: 0.8078 (m) REVERT: A 826 ASP cc_start: 0.6812 (m-30) cc_final: 0.6203 (t0) REVERT: A 873 MET cc_start: 0.7561 (mmp) cc_final: 0.7147 (mmp) REVERT: A 934 LYS cc_start: 0.8329 (mptt) cc_final: 0.7897 (mmtm) REVERT: A 1167 GLU cc_start: 0.6466 (mm-30) cc_final: 0.6210 (pm20) REVERT: B 206 ASN cc_start: 0.6982 (OUTLIER) cc_final: 0.6745 (t0) REVERT: B 328 GLU cc_start: 0.7757 (mp0) cc_final: 0.7393 (mm-30) REVERT: B 531 GLN cc_start: 0.6989 (mm-40) cc_final: 0.6782 (pp30) REVERT: B 1138 MET cc_start: 0.8008 (mmm) cc_final: 0.7765 (mmm) REVERT: F 99 LEU cc_start: 0.8763 (mt) cc_final: 0.8444 (mt) REVERT: H 77 ARG cc_start: 0.6081 (ttt-90) cc_final: 0.5775 (ttt-90) REVERT: I 22 ASN cc_start: 0.7528 (m-40) cc_final: 0.7234 (p0) REVERT: I 83 ASN cc_start: 0.7441 (m110) cc_final: 0.7218 (m-40) REVERT: J 26 GLN cc_start: 0.7682 (tt0) cc_final: 0.7431 (tt0) REVERT: J 42 LYS cc_start: 0.8041 (ttpt) cc_final: 0.7784 (tttm) REVERT: L 37 LYS cc_start: 0.8473 (mtpp) cc_final: 0.8259 (mtmt) REVERT: a 61 LEU cc_start: 0.7496 (mp) cc_final: 0.7080 (mt) REVERT: b 59 LYS cc_start: 0.8224 (tptt) cc_final: 0.6785 (tptt) REVERT: b 74 GLU cc_start: 0.7558 (tm-30) cc_final: 0.7116 (tp30) REVERT: b 79 LYS cc_start: 0.8245 (mtmm) cc_final: 0.7948 (mtpm) REVERT: b 93 GLN cc_start: 0.7967 (mp-120) cc_final: 0.7730 (mp10) REVERT: c 41 GLU cc_start: 0.7869 (mm-30) cc_final: 0.7555 (mp0) REVERT: d 56 MET cc_start: 0.7714 (mmm) cc_final: 0.7398 (tpt) REVERT: d 68 GLU cc_start: 0.7943 (tp30) cc_final: 0.7703 (tp30) REVERT: e 77 ASP cc_start: 0.8110 (m-30) cc_final: 0.7714 (t0) REVERT: e 106 ASP cc_start: 0.7918 (m-30) cc_final: 0.7717 (m-30) REVERT: f 52 GLU cc_start: 0.7580 (tp30) cc_final: 0.7269 (tm-30) REVERT: f 77 LYS cc_start: 0.8670 (mptt) cc_final: 0.8404 (mppt) REVERT: g 42 ARG cc_start: 0.7033 (mtm-85) cc_final: 0.6811 (mtm-85) REVERT: g 89 ASN cc_start: 0.8315 (m110) cc_final: 0.8038 (m110) REVERT: g 102 ILE cc_start: 0.8812 (mm) cc_final: 0.8570 (tp) REVERT: h 85 THR cc_start: 0.8700 (t) cc_final: 0.8450 (t) REVERT: h 90 GLU cc_start: 0.8151 (mm-30) cc_final: 0.7817 (mp0) REVERT: h 92 GLN cc_start: 0.8312 (tp40) cc_final: 0.8050 (mm110) REVERT: h 102 GLU cc_start: 0.5665 (tm-30) cc_final: 0.5438 (tm-30) REVERT: h 105 LYS cc_start: 0.8152 (mmmt) cc_final: 0.7827 (mmmm) REVERT: W 203 ASP cc_start: 0.7486 (m-30) cc_final: 0.7091 (m-30) REVERT: W 239 LEU cc_start: 0.7668 (tp) cc_final: 0.7396 (tm) REVERT: W 247 LYS cc_start: 0.7578 (tppt) cc_final: 0.7375 (tppt) REVERT: W 255 GLN cc_start: 0.7454 (mp10) cc_final: 0.7025 (tm-30) REVERT: W 291 ILE cc_start: 0.7656 (mt) cc_final: 0.7357 (mm) REVERT: W 334 GLN cc_start: 0.7131 (tp40) cc_final: 0.6837 (tp40) REVERT: W 522 GLU cc_start: 0.8184 (tp30) cc_final: 0.7976 (tp30) REVERT: W 550 LYS cc_start: 0.8998 (tmtt) cc_final: 0.8477 (mmmt) REVERT: W 723 MET cc_start: 0.8859 (tpp) cc_final: 0.8622 (tpt) REVERT: W 766 VAL cc_start: 0.8194 (t) cc_final: 0.7982 (m) REVERT: Y 39 MET cc_start: 0.1198 (tpt) cc_final: 0.0857 (tmm) REVERT: Z 346 GLU cc_start: 0.1303 (mm-30) cc_final: -0.0561 (pt0) REVERT: G 14 HIS cc_start: 0.7435 (t-90) cc_final: 0.7204 (t-90) REVERT: G 69 GLU cc_start: 0.6698 (tp30) cc_final: 0.6231 (mm-30) REVERT: G 79 PHE cc_start: 0.4144 (t80) cc_final: 0.3779 (t80) outliers start: 5 outliers final: 6 residues processed: 707 average time/residue: 1.7046 time to fit residues: 1490.0787 Evaluate side-chains 553 residues out of total 4824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 546 time to evaluate : 5.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 206 ASN Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain I residue 11 ASN Chi-restraints excluded: chain a residue 112 ILE Chi-restraints excluded: chain g residue 62 ILE Chi-restraints excluded: chain W residue 389 PHE Chi-restraints excluded: chain W residue 635 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 566 random chunks: chunk 477 optimal weight: 4.9990 chunk 429 optimal weight: 7.9990 chunk 238 optimal weight: 1.9990 chunk 146 optimal weight: 0.6980 chunk 289 optimal weight: 0.0770 chunk 229 optimal weight: 0.7980 chunk 443 optimal weight: 2.9990 chunk 171 optimal weight: 2.9990 chunk 269 optimal weight: 0.0870 chunk 330 optimal weight: 0.8980 chunk 513 optimal weight: 5.9990 overall best weight: 0.5116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 445 ASN ** A 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 611 GLN A 768 GLN A1070 GLN A1218 GLN B 587 HIS B 763 GLN B 767 ASN B 862 GLN B1076 HIS B1179 GLN B1195 HIS B1205 GLN ** C 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 188 HIS H 21 ASN ** H 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 2 ASN ** K 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 25 ASN b 64 ASN ** c 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 81 ASN d 106 HIS f 93 GLN ** g 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 177 HIS ** W 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 224 HIS W 244 ASN W 323 ASN ** W 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 579 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 810 GLN Z 366 GLN D 9 GLN D 31 GLN D 173 HIS G 158 HIS Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7368 moved from start: 0.1461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 51180 Z= 0.218 Angle : 0.675 10.543 70300 Z= 0.359 Chirality : 0.044 0.219 7920 Planarity : 0.005 0.059 8063 Dihedral : 19.249 175.904 9193 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 1.97 % Allowed : 12.76 % Favored : 85.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.14 (0.11), residues: 5423 helix: 0.94 (0.11), residues: 2230 sheet: -0.69 (0.19), residues: 699 loop : -0.81 (0.12), residues: 2494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 233 HIS 0.007 0.001 HIS G 158 PHE 0.023 0.002 PHE A 252 TYR 0.029 0.002 TYR h 80 ARG 0.010 0.001 ARG G 60 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10846 Ramachandran restraints generated. 5423 Oldfield, 0 Emsley, 5423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10846 Ramachandran restraints generated. 5423 Oldfield, 0 Emsley, 5423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 706 residues out of total 4824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 611 time to evaluate : 5.492 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 317 LYS cc_start: 0.8184 (pptt) cc_final: 0.7613 (tmtt) REVERT: A 806 ARG cc_start: 0.6399 (tpt170) cc_final: 0.6197 (tpt170) REVERT: A 826 ASP cc_start: 0.6726 (m-30) cc_final: 0.6115 (t0) REVERT: A 849 MET cc_start: 0.8091 (OUTLIER) cc_final: 0.7840 (ttp) REVERT: A 934 LYS cc_start: 0.8293 (mptt) cc_final: 0.7790 (mppt) REVERT: A 1167 GLU cc_start: 0.6368 (mm-30) cc_final: 0.5847 (pm20) REVERT: A 1308 THR cc_start: 0.8720 (m) cc_final: 0.8477 (p) REVERT: B 206 ASN cc_start: 0.6991 (OUTLIER) cc_final: 0.6573 (t0) REVERT: B 572 HIS cc_start: 0.6737 (OUTLIER) cc_final: 0.6502 (p-80) REVERT: B 885 MET cc_start: 0.8169 (mtp) cc_final: 0.7952 (mtp) REVERT: B 1082 MET cc_start: 0.8266 (tpp) cc_final: 0.8019 (tpp) REVERT: B 1129 ARG cc_start: 0.6579 (OUTLIER) cc_final: 0.5245 (ptm160) REVERT: E 54 GLN cc_start: 0.6517 (mp10) cc_final: 0.6093 (mp-120) REVERT: E 74 ASP cc_start: 0.7607 (t70) cc_final: 0.7370 (t0) REVERT: E 85 GLU cc_start: 0.7305 (OUTLIER) cc_final: 0.7091 (mp0) REVERT: F 114 GLU cc_start: 0.7118 (mm-30) cc_final: 0.6723 (mm-30) REVERT: F 119 ARG cc_start: 0.7849 (tpp80) cc_final: 0.7438 (mmm-85) REVERT: H 77 ARG cc_start: 0.6304 (ttt-90) cc_final: 0.6104 (ttt-90) REVERT: I 25 LEU cc_start: 0.4583 (mt) cc_final: 0.4293 (mp) REVERT: I 26 LEU cc_start: 0.6787 (tt) cc_final: 0.6550 (tm) REVERT: J 29 GLU cc_start: 0.7799 (OUTLIER) cc_final: 0.7576 (mt-10) REVERT: J 42 LYS cc_start: 0.7786 (ttpt) cc_final: 0.7543 (tttm) REVERT: a 64 LYS cc_start: 0.7354 (OUTLIER) cc_final: 0.6866 (mppt) REVERT: a 73 GLU cc_start: 0.7729 (pt0) cc_final: 0.7248 (pt0) REVERT: a 97 GLU cc_start: 0.6923 (OUTLIER) cc_final: 0.6591 (mm-30) REVERT: a 123 ASP cc_start: 0.7657 (m-30) cc_final: 0.7290 (m-30) REVERT: b 26 ILE cc_start: 0.8926 (tp) cc_final: 0.8628 (tp) REVERT: b 44 LYS cc_start: 0.8461 (tptt) cc_final: 0.8137 (tttm) REVERT: b 68 ASP cc_start: 0.7796 (m-30) cc_final: 0.7591 (m-30) REVERT: b 74 GLU cc_start: 0.7648 (tm-30) cc_final: 0.7231 (tp30) REVERT: b 79 LYS cc_start: 0.8112 (mtmm) cc_final: 0.7840 (mtpm) REVERT: c 41 GLU cc_start: 0.7781 (mm-30) cc_final: 0.7437 (mp0) REVERT: c 56 GLU cc_start: 0.8362 (tt0) cc_final: 0.8153 (tt0) REVERT: d 56 MET cc_start: 0.7896 (mmm) cc_final: 0.7561 (tpt) REVERT: d 59 MET cc_start: 0.7824 (tpp) cc_final: 0.7501 (tpt) REVERT: e 68 GLN cc_start: 0.8158 (OUTLIER) cc_final: 0.7743 (tp40) REVERT: e 77 ASP cc_start: 0.8120 (m-30) cc_final: 0.7746 (t0) REVERT: e 115 LYS cc_start: 0.7974 (pttt) cc_final: 0.7526 (ptpp) REVERT: e 123 ASP cc_start: 0.7482 (m-30) cc_final: 0.7241 (m-30) REVERT: e 125 GLN cc_start: 0.8520 (mt0) cc_final: 0.8223 (mt0) REVERT: e 129 ARG cc_start: 0.7728 (ptm-80) cc_final: 0.7416 (ttt90) REVERT: f 52 GLU cc_start: 0.7649 (tp30) cc_final: 0.7407 (tm-30) REVERT: f 77 LYS cc_start: 0.8633 (mptt) cc_final: 0.8337 (mppt) REVERT: f 95 ARG cc_start: 0.7563 (mtp85) cc_final: 0.7357 (mtt90) REVERT: g 24 GLN cc_start: 0.7558 (mm-40) cc_final: 0.6977 (mp10) REVERT: g 35 ARG cc_start: 0.7645 (mtm110) cc_final: 0.7131 (mtm110) REVERT: g 42 ARG cc_start: 0.6898 (mtm-85) cc_final: 0.6552 (mtm-85) REVERT: g 89 ASN cc_start: 0.8396 (m110) cc_final: 0.8074 (m110) REVERT: g 94 ASN cc_start: 0.8140 (t0) cc_final: 0.7895 (t0) REVERT: g 99 ARG cc_start: 0.6398 (tpt170) cc_final: 0.5499 (tpt170) REVERT: h 68 GLU cc_start: 0.7744 (mm-30) cc_final: 0.7517 (mm-30) REVERT: h 73 GLU cc_start: 0.7697 (tp30) cc_final: 0.7342 (tm-30) REVERT: h 105 LYS cc_start: 0.8160 (mmmt) cc_final: 0.7810 (mmmm) REVERT: h 110 GLU cc_start: 0.7690 (mt-10) cc_final: 0.7438 (mt-10) REVERT: W 177 HIS cc_start: 0.5966 (OUTLIER) cc_final: 0.4977 (p90) REVERT: W 226 THR cc_start: 0.7497 (m) cc_final: 0.7173 (p) REVERT: W 239 LEU cc_start: 0.7707 (tp) cc_final: 0.7469 (tm) REVERT: W 291 ILE cc_start: 0.7855 (mt) cc_final: 0.7577 (mm) REVERT: W 334 GLN cc_start: 0.7573 (tp40) cc_final: 0.7117 (tp40) REVERT: W 437 MET cc_start: 0.7667 (ttt) cc_final: 0.7428 (ttp) REVERT: Y 39 MET cc_start: 0.1362 (tpt) cc_final: 0.0838 (tmm) REVERT: Z 315 MET cc_start: 0.1339 (tpp) cc_final: 0.0696 (mmm) REVERT: Z 346 GLU cc_start: 0.1834 (mm-30) cc_final: -0.0228 (pt0) REVERT: Z 367 GLU cc_start: 0.3212 (tp30) cc_final: 0.3008 (tp30) REVERT: D 1 MET cc_start: 0.5631 (OUTLIER) cc_final: 0.4962 (ttm) REVERT: G 69 GLU cc_start: 0.6899 (tp30) cc_final: 0.6315 (mm-30) REVERT: G 79 PHE cc_start: 0.4511 (t80) cc_final: 0.4122 (t80) REVERT: G 106 MET cc_start: 0.3153 (ptp) cc_final: 0.2573 (ptt) outliers start: 95 outliers final: 32 residues processed: 653 average time/residue: 1.6264 time to fit residues: 1327.7389 Evaluate side-chains 584 residues out of total 4824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 541 time to evaluate : 5.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 HIS Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain A residue 693 VAL Chi-restraints excluded: chain A residue 708 MET Chi-restraints excluded: chain A residue 754 SER Chi-restraints excluded: chain A residue 849 MET Chi-restraints excluded: chain A residue 923 LEU Chi-restraints excluded: chain A residue 927 VAL Chi-restraints excluded: chain A residue 988 LEU Chi-restraints excluded: chain A residue 1124 HIS Chi-restraints excluded: chain B residue 206 ASN Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 572 HIS Chi-restraints excluded: chain B residue 578 THR Chi-restraints excluded: chain B residue 780 VAL Chi-restraints excluded: chain B residue 889 THR Chi-restraints excluded: chain B residue 1129 ARG Chi-restraints excluded: chain C residue 137 LYS Chi-restraints excluded: chain C residue 207 CYS Chi-restraints excluded: chain E residue 85 GLU Chi-restraints excluded: chain H residue 39 THR Chi-restraints excluded: chain H residue 112 ILE Chi-restraints excluded: chain I residue 64 SER Chi-restraints excluded: chain J residue 29 GLU Chi-restraints excluded: chain L residue 55 ILE Chi-restraints excluded: chain a residue 64 LYS Chi-restraints excluded: chain a residue 87 SER Chi-restraints excluded: chain a residue 97 GLU Chi-restraints excluded: chain a residue 122 LYS Chi-restraints excluded: chain b residue 85 ASP Chi-restraints excluded: chain c residue 79 ILE Chi-restraints excluded: chain e residue 68 GLN Chi-restraints excluded: chain e residue 80 THR Chi-restraints excluded: chain f residue 92 ARG Chi-restraints excluded: chain g residue 79 ILE Chi-restraints excluded: chain g residue 100 VAL Chi-restraints excluded: chain h residue 54 LYS Chi-restraints excluded: chain W residue 177 HIS Chi-restraints excluded: chain W residue 249 PHE Chi-restraints excluded: chain W residue 389 PHE Chi-restraints excluded: chain W residue 541 THR Chi-restraints excluded: chain Z residue 830 GLU Chi-restraints excluded: chain D residue 1 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 566 random chunks: chunk 285 optimal weight: 7.9990 chunk 159 optimal weight: 7.9990 chunk 427 optimal weight: 2.9990 chunk 349 optimal weight: 0.2980 chunk 141 optimal weight: 0.9990 chunk 514 optimal weight: 20.0000 chunk 556 optimal weight: 6.9990 chunk 458 optimal weight: 9.9990 chunk 510 optimal weight: 20.0000 chunk 175 optimal weight: 2.9990 chunk 413 optimal weight: 0.8980 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 768 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 851 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 357 GLN E 113 GLN H 21 ASN ** H 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 2 ASN ** K 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 75 HIS ** c 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 46 HIS ** d 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 81 ASN h 60 ASN h 92 GLN ** W 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 244 ASN W 323 ASN W 425 ASN ** W 579 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 653 ASN D 143 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7464 moved from start: 0.1906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 51180 Z= 0.291 Angle : 0.644 9.092 70300 Z= 0.343 Chirality : 0.043 0.213 7920 Planarity : 0.005 0.060 8063 Dihedral : 19.492 175.006 9184 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 14.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 3.05 % Allowed : 16.45 % Favored : 80.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.11), residues: 5423 helix: 1.02 (0.11), residues: 2222 sheet: -0.70 (0.18), residues: 722 loop : -0.72 (0.13), residues: 2479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 233 HIS 0.039 0.001 HIS W 177 PHE 0.029 0.002 PHE G 121 TYR 0.024 0.002 TYR h 80 ARG 0.011 0.001 ARG e 83 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10846 Ramachandran restraints generated. 5423 Oldfield, 0 Emsley, 5423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10846 Ramachandran restraints generated. 5423 Oldfield, 0 Emsley, 5423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 741 residues out of total 4824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 594 time to evaluate : 5.444 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 GLU cc_start: 0.8094 (OUTLIER) cc_final: 0.7765 (mp0) REVERT: A 317 LYS cc_start: 0.8257 (pptt) cc_final: 0.7572 (tmtt) REVERT: A 450 LEU cc_start: 0.8490 (mm) cc_final: 0.8241 (mp) REVERT: A 826 ASP cc_start: 0.6863 (m-30) cc_final: 0.6235 (t0) REVERT: A 857 ARG cc_start: 0.7794 (OUTLIER) cc_final: 0.7300 (mtp85) REVERT: A 1167 GLU cc_start: 0.6673 (mm-30) cc_final: 0.6313 (pm20) REVERT: A 1308 THR cc_start: 0.8706 (m) cc_final: 0.8502 (p) REVERT: B 101 MET cc_start: 0.7640 (OUTLIER) cc_final: 0.7403 (mtm) REVERT: B 206 ASN cc_start: 0.7378 (OUTLIER) cc_final: 0.6913 (t0) REVERT: B 662 MET cc_start: 0.7807 (mtt) cc_final: 0.7489 (mtp) REVERT: B 868 MET cc_start: 0.6916 (tpp) cc_final: 0.6682 (tpt) REVERT: B 887 HIS cc_start: 0.7206 (m-70) cc_final: 0.6985 (m90) REVERT: B 1021 MET cc_start: 0.8309 (OUTLIER) cc_final: 0.7489 (mpp) REVERT: B 1037 LEU cc_start: 0.8175 (OUTLIER) cc_final: 0.7913 (mp) REVERT: B 1129 ARG cc_start: 0.7288 (OUTLIER) cc_final: 0.6174 (ptm-80) REVERT: B 1149 GLU cc_start: 0.7905 (tm-30) cc_final: 0.7689 (pp20) REVERT: C 221 TYR cc_start: 0.7433 (OUTLIER) cc_final: 0.6640 (m-10) REVERT: E 54 GLN cc_start: 0.6432 (mp10) cc_final: 0.6138 (mp-120) REVERT: E 74 ASP cc_start: 0.7710 (t70) cc_final: 0.7431 (t0) REVERT: E 85 GLU cc_start: 0.7450 (OUTLIER) cc_final: 0.7231 (mt-10) REVERT: F 119 ARG cc_start: 0.7928 (tpp80) cc_final: 0.7527 (mmm-85) REVERT: I 74 GLU cc_start: 0.7408 (tp30) cc_final: 0.7194 (tp30) REVERT: J 42 LYS cc_start: 0.7978 (ttpt) cc_final: 0.7701 (tttm) REVERT: J 58 GLU cc_start: 0.7750 (mm-30) cc_final: 0.7543 (mm-30) REVERT: a 64 LYS cc_start: 0.7931 (OUTLIER) cc_final: 0.7330 (mppt) REVERT: a 123 ASP cc_start: 0.7627 (m-30) cc_final: 0.7361 (m-30) REVERT: b 78 ARG cc_start: 0.6051 (tpm170) cc_final: 0.3904 (ttp-110) REVERT: b 79 LYS cc_start: 0.8244 (mtmm) cc_final: 0.7931 (mtpm) REVERT: b 93 GLN cc_start: 0.8138 (OUTLIER) cc_final: 0.7909 (mp10) REVERT: c 41 GLU cc_start: 0.7793 (mm-30) cc_final: 0.7467 (mp0) REVERT: c 88 ARG cc_start: 0.8212 (mmt-90) cc_final: 0.7911 (mmt-90) REVERT: d 56 MET cc_start: 0.8005 (mmm) cc_final: 0.7632 (tpt) REVERT: e 68 GLN cc_start: 0.8319 (OUTLIER) cc_final: 0.7897 (tp40) REVERT: e 77 ASP cc_start: 0.8154 (m-30) cc_final: 0.7737 (t0) REVERT: e 115 LYS cc_start: 0.8307 (pttt) cc_final: 0.7696 (ptpp) REVERT: e 116 ARG cc_start: 0.4917 (OUTLIER) cc_final: 0.3824 (tpp80) REVERT: e 125 GLN cc_start: 0.8647 (mt0) cc_final: 0.8360 (mt0) REVERT: e 129 ARG cc_start: 0.7840 (ptm-80) cc_final: 0.7613 (ttt90) REVERT: f 52 GLU cc_start: 0.7664 (tp30) cc_final: 0.7416 (tm-30) REVERT: f 63 GLU cc_start: 0.8061 (OUTLIER) cc_final: 0.7834 (mp0) REVERT: f 77 LYS cc_start: 0.8650 (mptt) cc_final: 0.8304 (mppt) REVERT: g 24 GLN cc_start: 0.7614 (mm-40) cc_final: 0.7010 (mp10) REVERT: g 27 VAL cc_start: 0.8741 (t) cc_final: 0.8481 (p) REVERT: g 35 ARG cc_start: 0.7739 (mtm110) cc_final: 0.7205 (mtm110) REVERT: g 89 ASN cc_start: 0.8469 (m110) cc_final: 0.8154 (m110) REVERT: g 94 ASN cc_start: 0.8260 (t0) cc_final: 0.8006 (t0) REVERT: g 99 ARG cc_start: 0.6611 (tpt170) cc_final: 0.6372 (ttt90) REVERT: h 68 GLU cc_start: 0.7791 (mm-30) cc_final: 0.7186 (mm-30) REVERT: h 73 GLU cc_start: 0.7693 (tp30) cc_final: 0.7488 (tm-30) REVERT: h 90 GLU cc_start: 0.8421 (mp0) cc_final: 0.7922 (mp0) REVERT: h 102 GLU cc_start: 0.6134 (tm-30) cc_final: 0.5877 (tm-30) REVERT: h 105 LYS cc_start: 0.8259 (mmmt) cc_final: 0.8028 (mmmm) REVERT: h 110 GLU cc_start: 0.7948 (mt-10) cc_final: 0.7660 (mt-10) REVERT: W 226 THR cc_start: 0.7662 (m) cc_final: 0.7305 (p) REVERT: W 239 LEU cc_start: 0.7753 (tp) cc_final: 0.7530 (tm) REVERT: W 291 ILE cc_start: 0.8051 (mt) cc_final: 0.7800 (mm) REVERT: W 334 GLN cc_start: 0.7586 (tp40) cc_final: 0.7132 (tp40) REVERT: W 375 GLU cc_start: 0.6563 (OUTLIER) cc_final: 0.5539 (tm-30) REVERT: W 522 GLU cc_start: 0.8060 (tp30) cc_final: 0.7805 (tp30) REVERT: W 548 ASN cc_start: 0.8605 (m110) cc_final: 0.8236 (t0) REVERT: W 550 LYS cc_start: 0.8877 (tptt) cc_final: 0.8582 (tptt) REVERT: W 587 HIS cc_start: 0.6345 (OUTLIER) cc_final: 0.5992 (m-70) REVERT: W 600 LYS cc_start: 0.8830 (mmmm) cc_final: 0.8614 (tppt) REVERT: W 723 MET cc_start: 0.8872 (tpp) cc_final: 0.8607 (tpt) REVERT: W 772 ARG cc_start: 0.6466 (ppt90) cc_final: 0.4905 (pmm-80) REVERT: Y 39 MET cc_start: 0.1514 (tpt) cc_final: 0.1035 (tmm) REVERT: Z 315 MET cc_start: 0.0989 (tpp) cc_final: 0.0325 (mmm) REVERT: Z 346 GLU cc_start: 0.2113 (mm-30) cc_final: 0.0111 (pt0) REVERT: D 1 MET cc_start: 0.5853 (OUTLIER) cc_final: 0.5146 (ttm) REVERT: G 106 MET cc_start: 0.3230 (OUTLIER) cc_final: 0.2865 (ptp) REVERT: G 121 PHE cc_start: 0.5920 (t80) cc_final: 0.5300 (t80) outliers start: 147 outliers final: 57 residues processed: 676 average time/residue: 1.6260 time to fit residues: 1375.5201 Evaluate side-chains 612 residues out of total 4824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 537 time to evaluate : 5.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 CYS Chi-restraints excluded: chain A residue 117 GLU Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 419 LYS Chi-restraints excluded: chain A residue 437 MET Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain A residue 693 VAL Chi-restraints excluded: chain A residue 754 SER Chi-restraints excluded: chain A residue 849 MET Chi-restraints excluded: chain A residue 857 ARG Chi-restraints excluded: chain A residue 927 VAL Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 988 LEU Chi-restraints excluded: chain A residue 1071 SER Chi-restraints excluded: chain A residue 1118 VAL Chi-restraints excluded: chain A residue 1209 MET Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 206 ASN Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 578 THR Chi-restraints excluded: chain B residue 705 MET Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 780 VAL Chi-restraints excluded: chain B residue 1021 MET Chi-restraints excluded: chain B residue 1037 LEU Chi-restraints excluded: chain B residue 1065 GLN Chi-restraints excluded: chain B residue 1129 ARG Chi-restraints excluded: chain C residue 137 LYS Chi-restraints excluded: chain C residue 166 GLU Chi-restraints excluded: chain C residue 207 CYS Chi-restraints excluded: chain C residue 221 TYR Chi-restraints excluded: chain C residue 258 ILE Chi-restraints excluded: chain E residue 41 ASP Chi-restraints excluded: chain E residue 85 GLU Chi-restraints excluded: chain H residue 5 LEU Chi-restraints excluded: chain H residue 39 THR Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 112 ILE Chi-restraints excluded: chain K residue 31 VAL Chi-restraints excluded: chain K residue 103 THR Chi-restraints excluded: chain L residue 55 ILE Chi-restraints excluded: chain a residue 64 LYS Chi-restraints excluded: chain a residue 86 SER Chi-restraints excluded: chain b residue 85 ASP Chi-restraints excluded: chain b residue 93 GLN Chi-restraints excluded: chain c residue 59 THR Chi-restraints excluded: chain c residue 79 ILE Chi-restraints excluded: chain d residue 39 TYR Chi-restraints excluded: chain d residue 87 THR Chi-restraints excluded: chain e residue 46 VAL Chi-restraints excluded: chain e residue 68 GLN Chi-restraints excluded: chain e residue 80 THR Chi-restraints excluded: chain e residue 116 ARG Chi-restraints excluded: chain e residue 124 ILE Chi-restraints excluded: chain f residue 63 GLU Chi-restraints excluded: chain f residue 92 ARG Chi-restraints excluded: chain g residue 62 ILE Chi-restraints excluded: chain g residue 79 ILE Chi-restraints excluded: chain g residue 100 VAL Chi-restraints excluded: chain h residue 92 GLN Chi-restraints excluded: chain W residue 249 PHE Chi-restraints excluded: chain W residue 256 VAL Chi-restraints excluded: chain W residue 375 GLU Chi-restraints excluded: chain W residue 389 PHE Chi-restraints excluded: chain W residue 436 THR Chi-restraints excluded: chain W residue 534 VAL Chi-restraints excluded: chain W residue 541 THR Chi-restraints excluded: chain W residue 587 HIS Chi-restraints excluded: chain Y residue 33 GLU Chi-restraints excluded: chain Z residue 287 ILE Chi-restraints excluded: chain Z residue 857 THR Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain G residue 106 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 566 random chunks: chunk 508 optimal weight: 10.0000 chunk 387 optimal weight: 2.9990 chunk 267 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 245 optimal weight: 0.9990 chunk 345 optimal weight: 2.9990 chunk 516 optimal weight: 7.9990 chunk 547 optimal weight: 8.9990 chunk 269 optimal weight: 0.9980 chunk 489 optimal weight: 2.9990 chunk 147 optimal weight: 4.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 287 HIS ** A 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 654 ASN ** A 768 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 802 ASN A 851 HIS A1008 GLN A1171 GLN A1265 ASN B 449 ASN B1178 ASN C 195 GLN H 21 ASN H 33 GLN ** H 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 87 GLN ** I 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 2 ASN ** K 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 81 ASN h 60 ASN W 177 HIS ** W 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 244 ASN W 323 ASN ** W 579 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7501 moved from start: 0.2345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 51180 Z= 0.298 Angle : 0.634 9.372 70300 Z= 0.338 Chirality : 0.043 0.218 7920 Planarity : 0.005 0.063 8063 Dihedral : 19.641 175.347 9184 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 14.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 3.51 % Allowed : 19.09 % Favored : 77.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.11), residues: 5423 helix: 1.03 (0.11), residues: 2216 sheet: -0.64 (0.19), residues: 717 loop : -0.75 (0.13), residues: 2490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP W 391 HIS 0.009 0.001 HIS A 399 PHE 0.027 0.002 PHE A 252 TYR 0.025 0.002 TYR A1298 ARG 0.008 0.001 ARG e 83 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10846 Ramachandran restraints generated. 5423 Oldfield, 0 Emsley, 5423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10846 Ramachandran restraints generated. 5423 Oldfield, 0 Emsley, 5423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 749 residues out of total 4824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 169 poor density : 580 time to evaluate : 5.409 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 317 LYS cc_start: 0.8350 (pptt) cc_final: 0.7720 (tttt) REVERT: A 450 LEU cc_start: 0.8571 (mm) cc_final: 0.8319 (mp) REVERT: A 780 VAL cc_start: 0.8462 (t) cc_final: 0.8086 (m) REVERT: A 826 ASP cc_start: 0.6928 (m-30) cc_final: 0.6340 (t0) REVERT: A 857 ARG cc_start: 0.7800 (OUTLIER) cc_final: 0.7385 (mtp85) REVERT: B 101 MET cc_start: 0.7703 (OUTLIER) cc_final: 0.7381 (mtm) REVERT: B 206 ASN cc_start: 0.7672 (t0) cc_final: 0.7098 (t0) REVERT: B 662 MET cc_start: 0.7905 (mtt) cc_final: 0.7597 (mtp) REVERT: B 1021 MET cc_start: 0.8281 (OUTLIER) cc_final: 0.7517 (mpp) REVERT: B 1120 GLU cc_start: 0.5956 (mm-30) cc_final: 0.5540 (mm-30) REVERT: B 1129 ARG cc_start: 0.7348 (OUTLIER) cc_final: 0.6865 (ptm160) REVERT: B 1149 GLU cc_start: 0.7943 (tm-30) cc_final: 0.7670 (pp20) REVERT: B 1163 CYS cc_start: 0.7290 (OUTLIER) cc_final: 0.7000 (p) REVERT: C 221 TYR cc_start: 0.7498 (OUTLIER) cc_final: 0.6723 (m-10) REVERT: E 54 GLN cc_start: 0.6519 (mp10) cc_final: 0.6239 (mp-120) REVERT: E 74 ASP cc_start: 0.7716 (t70) cc_final: 0.7451 (t0) REVERT: E 85 GLU cc_start: 0.7472 (OUTLIER) cc_final: 0.7253 (mt-10) REVERT: F 114 GLU cc_start: 0.6819 (mm-30) cc_final: 0.6332 (mm-30) REVERT: F 119 ARG cc_start: 0.7884 (tpp80) cc_final: 0.7527 (mmm-85) REVERT: H 62 SER cc_start: 0.7640 (t) cc_final: 0.7292 (m) REVERT: J 26 GLN cc_start: 0.7821 (tm-30) cc_final: 0.7615 (pp30) REVERT: J 42 LYS cc_start: 0.8004 (ttpt) cc_final: 0.7708 (tttm) REVERT: a 64 LYS cc_start: 0.8114 (OUTLIER) cc_final: 0.7497 (mppt) REVERT: a 123 ASP cc_start: 0.7669 (m-30) cc_final: 0.7424 (m-30) REVERT: b 49 LEU cc_start: 0.8748 (mt) cc_final: 0.8376 (mt) REVERT: b 74 GLU cc_start: 0.7746 (tp30) cc_final: 0.7420 (tp30) REVERT: b 78 ARG cc_start: 0.6208 (OUTLIER) cc_final: 0.4113 (ttp80) REVERT: b 79 LYS cc_start: 0.8303 (mtmm) cc_final: 0.7976 (mtpm) REVERT: c 36 LYS cc_start: 0.7282 (ptpt) cc_final: 0.7052 (ptpt) REVERT: c 41 GLU cc_start: 0.7787 (mm-30) cc_final: 0.7486 (mp0) REVERT: c 88 ARG cc_start: 0.8241 (mmt-90) cc_final: 0.7931 (mmt-90) REVERT: d 56 MET cc_start: 0.8162 (mmm) cc_final: 0.7626 (tpt) REVERT: d 117 LYS cc_start: 0.8560 (OUTLIER) cc_final: 0.8106 (ptmt) REVERT: e 68 GLN cc_start: 0.8319 (OUTLIER) cc_final: 0.7892 (tp40) REVERT: e 77 ASP cc_start: 0.8187 (m-30) cc_final: 0.7758 (t0) REVERT: e 109 LEU cc_start: 0.8853 (tp) cc_final: 0.8618 (tp) REVERT: e 115 LYS cc_start: 0.8318 (pttt) cc_final: 0.7668 (ptpp) REVERT: e 125 GLN cc_start: 0.8712 (mt0) cc_final: 0.8438 (mt0) REVERT: e 131 ARG cc_start: 0.7899 (mmm-85) cc_final: 0.7581 (mmm-85) REVERT: f 77 LYS cc_start: 0.8655 (mptt) cc_final: 0.8282 (mppt) REVERT: g 24 GLN cc_start: 0.7668 (mm-40) cc_final: 0.7137 (mp10) REVERT: g 27 VAL cc_start: 0.8746 (t) cc_final: 0.8487 (p) REVERT: g 29 ARG cc_start: 0.8686 (OUTLIER) cc_final: 0.7914 (ttm-80) REVERT: g 35 ARG cc_start: 0.7794 (mtm110) cc_final: 0.7371 (mtm110) REVERT: g 36 LYS cc_start: 0.8027 (mmtm) cc_final: 0.7716 (ttpt) REVERT: g 89 ASN cc_start: 0.8541 (m110) cc_final: 0.8244 (m110) REVERT: g 94 ASN cc_start: 0.8221 (t0) cc_final: 0.8017 (t0) REVERT: g 99 ARG cc_start: 0.6649 (tpt170) cc_final: 0.6403 (ttt90) REVERT: h 68 GLU cc_start: 0.7810 (mm-30) cc_final: 0.7183 (mm-30) REVERT: h 73 GLU cc_start: 0.7718 (tp30) cc_final: 0.7516 (tm-30) REVERT: h 90 GLU cc_start: 0.8525 (mp0) cc_final: 0.7999 (mp0) REVERT: h 92 GLN cc_start: 0.8304 (mm-40) cc_final: 0.8013 (mm110) REVERT: h 105 LYS cc_start: 0.8339 (mmmt) cc_final: 0.8125 (mmmm) REVERT: h 110 GLU cc_start: 0.8012 (mt-10) cc_final: 0.7713 (mt-10) REVERT: W 226 THR cc_start: 0.7695 (m) cc_final: 0.7302 (p) REVERT: W 318 GLU cc_start: 0.6389 (tp30) cc_final: 0.5792 (tp30) REVERT: W 334 GLN cc_start: 0.7593 (tp40) cc_final: 0.7187 (tp40) REVERT: W 407 LYS cc_start: 0.7615 (OUTLIER) cc_final: 0.7405 (mtmp) REVERT: W 457 MET cc_start: 0.7867 (mtm) cc_final: 0.7596 (mtm) REVERT: W 548 ASN cc_start: 0.8659 (m110) cc_final: 0.8217 (t0) REVERT: W 550 LYS cc_start: 0.8795 (tptt) cc_final: 0.8457 (tptt) REVERT: W 723 MET cc_start: 0.8915 (tpp) cc_final: 0.8662 (tpt) REVERT: W 772 ARG cc_start: 0.6556 (ppt90) cc_final: 0.5560 (pmm-80) REVERT: Y 39 MET cc_start: 0.1633 (tpt) cc_final: 0.1073 (tmm) REVERT: Z 315 MET cc_start: 0.1046 (tpp) cc_final: 0.0303 (mmm) REVERT: Z 346 GLU cc_start: 0.2403 (mm-30) cc_final: 0.0222 (pt0) REVERT: Z 367 GLU cc_start: 0.3674 (tp30) cc_final: 0.3303 (tp30) REVERT: G 106 MET cc_start: 0.3258 (OUTLIER) cc_final: 0.2858 (ptp) outliers start: 169 outliers final: 84 residues processed: 690 average time/residue: 1.5894 time to fit residues: 1378.9580 Evaluate side-chains 626 residues out of total 4824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 528 time to evaluate : 5.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 CYS Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 437 MET Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain A residue 652 VAL Chi-restraints excluded: chain A residue 693 VAL Chi-restraints excluded: chain A residue 754 SER Chi-restraints excluded: chain A residue 849 MET Chi-restraints excluded: chain A residue 857 ARG Chi-restraints excluded: chain A residue 925 LEU Chi-restraints excluded: chain A residue 927 VAL Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 988 LEU Chi-restraints excluded: chain A residue 1071 SER Chi-restraints excluded: chain A residue 1118 VAL Chi-restraints excluded: chain A residue 1209 MET Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 517 THR Chi-restraints excluded: chain B residue 578 THR Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 741 CYS Chi-restraints excluded: chain B residue 764 SER Chi-restraints excluded: chain B residue 780 VAL Chi-restraints excluded: chain B residue 889 THR Chi-restraints excluded: chain B residue 1021 MET Chi-restraints excluded: chain B residue 1065 GLN Chi-restraints excluded: chain B residue 1099 VAL Chi-restraints excluded: chain B residue 1129 ARG Chi-restraints excluded: chain B residue 1163 CYS Chi-restraints excluded: chain C residue 93 ASP Chi-restraints excluded: chain C residue 137 LYS Chi-restraints excluded: chain C residue 166 GLU Chi-restraints excluded: chain C residue 207 CYS Chi-restraints excluded: chain C residue 221 TYR Chi-restraints excluded: chain C residue 258 ILE Chi-restraints excluded: chain E residue 85 GLU Chi-restraints excluded: chain H residue 39 THR Chi-restraints excluded: chain H residue 54 SER Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 112 ILE Chi-restraints excluded: chain I residue 55 THR Chi-restraints excluded: chain K residue 31 VAL Chi-restraints excluded: chain K residue 94 ILE Chi-restraints excluded: chain K residue 103 THR Chi-restraints excluded: chain L residue 31 CYS Chi-restraints excluded: chain L residue 35 SER Chi-restraints excluded: chain L residue 50 ASP Chi-restraints excluded: chain L residue 55 ILE Chi-restraints excluded: chain a residue 61 LEU Chi-restraints excluded: chain a residue 64 LYS Chi-restraints excluded: chain a residue 86 SER Chi-restraints excluded: chain a residue 87 SER Chi-restraints excluded: chain a residue 112 ILE Chi-restraints excluded: chain b residue 60 VAL Chi-restraints excluded: chain b residue 78 ARG Chi-restraints excluded: chain c residue 59 THR Chi-restraints excluded: chain d residue 39 TYR Chi-restraints excluded: chain d residue 87 THR Chi-restraints excluded: chain d residue 103 LEU Chi-restraints excluded: chain d residue 113 LYS Chi-restraints excluded: chain d residue 117 LYS Chi-restraints excluded: chain e residue 46 VAL Chi-restraints excluded: chain e residue 68 GLN Chi-restraints excluded: chain e residue 80 THR Chi-restraints excluded: chain e residue 116 ARG Chi-restraints excluded: chain e residue 117 VAL Chi-restraints excluded: chain e residue 124 ILE Chi-restraints excluded: chain f residue 92 ARG Chi-restraints excluded: chain g residue 29 ARG Chi-restraints excluded: chain g residue 62 ILE Chi-restraints excluded: chain g residue 79 ILE Chi-restraints excluded: chain g residue 100 VAL Chi-restraints excluded: chain h residue 87 THR Chi-restraints excluded: chain W residue 203 ASP Chi-restraints excluded: chain W residue 204 LEU Chi-restraints excluded: chain W residue 225 ASN Chi-restraints excluded: chain W residue 249 PHE Chi-restraints excluded: chain W residue 256 VAL Chi-restraints excluded: chain W residue 389 PHE Chi-restraints excluded: chain W residue 407 LYS Chi-restraints excluded: chain W residue 488 LEU Chi-restraints excluded: chain W residue 534 VAL Chi-restraints excluded: chain W residue 541 THR Chi-restraints excluded: chain W residue 606 LEU Chi-restraints excluded: chain W residue 655 LEU Chi-restraints excluded: chain W residue 701 ASP Chi-restraints excluded: chain Y residue 33 GLU Chi-restraints excluded: chain Z residue 287 ILE Chi-restraints excluded: chain Z residue 830 GLU Chi-restraints excluded: chain Z residue 857 THR Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain G residue 87 VAL Chi-restraints excluded: chain G residue 106 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 566 random chunks: chunk 455 optimal weight: 3.9990 chunk 310 optimal weight: 2.9990 chunk 7 optimal weight: 4.9990 chunk 407 optimal weight: 0.8980 chunk 225 optimal weight: 1.9990 chunk 466 optimal weight: 5.9990 chunk 378 optimal weight: 3.9990 chunk 0 optimal weight: 8.9990 chunk 279 optimal weight: 2.9990 chunk 491 optimal weight: 0.9990 chunk 138 optimal weight: 4.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 HIS ** A 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 768 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 ASN E 113 GLN H 21 ASN ** H 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 87 GLN K 2 ASN ** K 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 104 GLN ** d 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 60 ASN ** h 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 177 HIS ** W 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 244 ASN W 323 ASN ** W 579 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7535 moved from start: 0.2731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 51180 Z= 0.318 Angle : 0.646 9.167 70300 Z= 0.343 Chirality : 0.043 0.253 7920 Planarity : 0.005 0.060 8063 Dihedral : 19.824 175.655 9182 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 15.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 4.13 % Allowed : 20.52 % Favored : 75.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.11), residues: 5423 helix: 0.96 (0.11), residues: 2207 sheet: -0.67 (0.19), residues: 693 loop : -0.77 (0.12), residues: 2523 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP W 391 HIS 0.009 0.001 HIS A 399 PHE 0.026 0.002 PHE A 252 TYR 0.024 0.002 TYR H 20 ARG 0.012 0.001 ARG e 129 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10846 Ramachandran restraints generated. 5423 Oldfield, 0 Emsley, 5423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10846 Ramachandran restraints generated. 5423 Oldfield, 0 Emsley, 5423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 772 residues out of total 4824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 199 poor density : 573 time to evaluate : 5.452 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 317 LYS cc_start: 0.8383 (pptt) cc_final: 0.7765 (tttt) REVERT: A 497 THR cc_start: 0.8890 (OUTLIER) cc_final: 0.8539 (p) REVERT: A 826 ASP cc_start: 0.6960 (m-30) cc_final: 0.6437 (t0) REVERT: A 857 ARG cc_start: 0.8035 (OUTLIER) cc_final: 0.7791 (mtp85) REVERT: A 919 ILE cc_start: 0.8380 (mm) cc_final: 0.8085 (pp) REVERT: A 934 LYS cc_start: 0.8319 (OUTLIER) cc_final: 0.7770 (mppt) REVERT: A 1218 GLN cc_start: 0.7922 (OUTLIER) cc_final: 0.7457 (tm130) REVERT: B 101 MET cc_start: 0.7715 (OUTLIER) cc_final: 0.7365 (mtm) REVERT: B 206 ASN cc_start: 0.7809 (t0) cc_final: 0.7191 (t0) REVERT: B 662 MET cc_start: 0.7944 (mtt) cc_final: 0.7656 (mtp) REVERT: B 760 ASP cc_start: 0.8462 (OUTLIER) cc_final: 0.8204 (p0) REVERT: B 1021 MET cc_start: 0.8330 (OUTLIER) cc_final: 0.7568 (mpp) REVERT: B 1120 GLU cc_start: 0.5979 (mm-30) cc_final: 0.5598 (mm-30) REVERT: B 1163 CYS cc_start: 0.7356 (OUTLIER) cc_final: 0.7082 (p) REVERT: C 221 TYR cc_start: 0.7574 (OUTLIER) cc_final: 0.6888 (m-10) REVERT: E 54 GLN cc_start: 0.6561 (mp10) cc_final: 0.6344 (mp-120) REVERT: E 85 GLU cc_start: 0.7495 (OUTLIER) cc_final: 0.7268 (mt-10) REVERT: F 114 GLU cc_start: 0.6973 (mm-30) cc_final: 0.6732 (mm-30) REVERT: F 119 ARG cc_start: 0.7871 (tpp80) cc_final: 0.7567 (mmm-85) REVERT: H 62 SER cc_start: 0.7991 (t) cc_final: 0.7645 (m) REVERT: I 82 GLU cc_start: 0.7257 (pm20) cc_final: 0.6883 (pp20) REVERT: K 26 LYS cc_start: 0.7207 (OUTLIER) cc_final: 0.6851 (tttp) REVERT: a 64 LYS cc_start: 0.8233 (OUTLIER) cc_final: 0.7547 (mppt) REVERT: a 90 MET cc_start: 0.7969 (mmm) cc_final: 0.7702 (mmp) REVERT: a 123 ASP cc_start: 0.7749 (m-30) cc_final: 0.7520 (m-30) REVERT: b 78 ARG cc_start: 0.6300 (OUTLIER) cc_final: 0.4377 (ttp80) REVERT: b 79 LYS cc_start: 0.8385 (mtmm) cc_final: 0.8111 (mtpm) REVERT: b 93 GLN cc_start: 0.8151 (OUTLIER) cc_final: 0.7914 (mp10) REVERT: c 25 PHE cc_start: 0.7860 (OUTLIER) cc_final: 0.6302 (m-80) REVERT: c 41 GLU cc_start: 0.7785 (mm-30) cc_final: 0.7490 (mp0) REVERT: c 88 ARG cc_start: 0.8269 (mmt-90) cc_final: 0.7940 (mmt-90) REVERT: d 56 MET cc_start: 0.8263 (mmm) cc_final: 0.7674 (tpt) REVERT: d 82 LYS cc_start: 0.8699 (OUTLIER) cc_final: 0.8471 (mppt) REVERT: e 68 GLN cc_start: 0.8317 (OUTLIER) cc_final: 0.7874 (tp-100) REVERT: e 77 ASP cc_start: 0.8150 (m-30) cc_final: 0.7773 (t0) REVERT: e 83 ARG cc_start: 0.6068 (OUTLIER) cc_final: 0.5836 (tpt170) REVERT: e 109 LEU cc_start: 0.8807 (tp) cc_final: 0.8534 (tp) REVERT: e 115 LYS cc_start: 0.8264 (pttt) cc_final: 0.7616 (ptpp) REVERT: e 116 ARG cc_start: 0.5675 (OUTLIER) cc_final: 0.4863 (ttp80) REVERT: e 129 ARG cc_start: 0.7824 (ttt90) cc_final: 0.7579 (mtp85) REVERT: f 77 LYS cc_start: 0.8687 (mptt) cc_final: 0.8270 (mppt) REVERT: f 79 LYS cc_start: 0.6938 (pttt) cc_final: 0.6696 (pttt) REVERT: g 24 GLN cc_start: 0.7651 (mm-40) cc_final: 0.7083 (mp10) REVERT: g 27 VAL cc_start: 0.8743 (t) cc_final: 0.8494 (p) REVERT: g 29 ARG cc_start: 0.8673 (OUTLIER) cc_final: 0.8226 (ptp-110) REVERT: g 36 LYS cc_start: 0.8126 (mmtm) cc_final: 0.7887 (ttpt) REVERT: g 89 ASN cc_start: 0.8573 (m110) cc_final: 0.8221 (m110) REVERT: g 94 ASN cc_start: 0.8369 (t0) cc_final: 0.8093 (t0) REVERT: g 99 ARG cc_start: 0.6700 (tpt170) cc_final: 0.6404 (ttt90) REVERT: h 68 GLU cc_start: 0.7797 (mm-30) cc_final: 0.7164 (mm-30) REVERT: h 90 GLU cc_start: 0.8521 (mp0) cc_final: 0.7896 (mp0) REVERT: h 105 LYS cc_start: 0.8344 (mmmt) cc_final: 0.8136 (mmmm) REVERT: h 110 GLU cc_start: 0.8061 (mt-10) cc_final: 0.7818 (mt-10) REVERT: W 177 HIS cc_start: 0.5974 (OUTLIER) cc_final: 0.4238 (p90) REVERT: W 208 LYS cc_start: 0.6852 (ttpt) cc_final: 0.6353 (tptp) REVERT: W 226 THR cc_start: 0.7784 (m) cc_final: 0.7558 (p) REVERT: W 334 GLN cc_start: 0.7638 (tp40) cc_final: 0.7199 (tp40) REVERT: W 550 LYS cc_start: 0.8781 (tptt) cc_final: 0.8569 (tptt) REVERT: W 551 GLU cc_start: 0.7626 (mp0) cc_final: 0.7390 (mp0) REVERT: W 723 MET cc_start: 0.8953 (tpp) cc_final: 0.8700 (tpt) REVERT: W 802 MET cc_start: 0.8220 (ttm) cc_final: 0.8010 (ttp) REVERT: Z 315 MET cc_start: 0.1034 (tpp) cc_final: 0.0322 (mmm) REVERT: Z 346 GLU cc_start: 0.2464 (mm-30) cc_final: 0.0379 (pt0) REVERT: Z 367 GLU cc_start: 0.3700 (tp30) cc_final: 0.3338 (tp30) REVERT: D 147 TYR cc_start: 0.4324 (t80) cc_final: 0.4108 (t80) REVERT: G 106 MET cc_start: 0.2861 (ptp) cc_final: 0.2420 (ptp) outliers start: 199 outliers final: 95 residues processed: 709 average time/residue: 1.6017 time to fit residues: 1425.3380 Evaluate side-chains 645 residues out of total 4824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 529 time to evaluate : 5.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 CYS Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 437 MET Chi-restraints excluded: chain A residue 497 THR Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain A residue 693 VAL Chi-restraints excluded: chain A residue 708 MET Chi-restraints excluded: chain A residue 754 SER Chi-restraints excluded: chain A residue 849 MET Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain A residue 857 ARG Chi-restraints excluded: chain A residue 927 VAL Chi-restraints excluded: chain A residue 934 LYS Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 988 LEU Chi-restraints excluded: chain A residue 1071 SER Chi-restraints excluded: chain A residue 1118 VAL Chi-restraints excluded: chain A residue 1124 HIS Chi-restraints excluded: chain A residue 1209 MET Chi-restraints excluded: chain A residue 1218 GLN Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 517 THR Chi-restraints excluded: chain B residue 578 THR Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 741 CYS Chi-restraints excluded: chain B residue 760 ASP Chi-restraints excluded: chain B residue 764 SER Chi-restraints excluded: chain B residue 780 VAL Chi-restraints excluded: chain B residue 797 TYR Chi-restraints excluded: chain B residue 889 THR Chi-restraints excluded: chain B residue 1021 MET Chi-restraints excluded: chain B residue 1065 GLN Chi-restraints excluded: chain B residue 1163 CYS Chi-restraints excluded: chain B residue 1176 ASN Chi-restraints excluded: chain C residue 93 ASP Chi-restraints excluded: chain C residue 137 LYS Chi-restraints excluded: chain C residue 166 GLU Chi-restraints excluded: chain C residue 207 CYS Chi-restraints excluded: chain C residue 221 TYR Chi-restraints excluded: chain C residue 258 ILE Chi-restraints excluded: chain E residue 85 GLU Chi-restraints excluded: chain E residue 214 CYS Chi-restraints excluded: chain H residue 5 LEU Chi-restraints excluded: chain H residue 39 THR Chi-restraints excluded: chain H residue 54 SER Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 92 ASP Chi-restraints excluded: chain H residue 112 ILE Chi-restraints excluded: chain I residue 55 THR Chi-restraints excluded: chain K residue 26 LYS Chi-restraints excluded: chain K residue 94 ILE Chi-restraints excluded: chain K residue 103 THR Chi-restraints excluded: chain L residue 31 CYS Chi-restraints excluded: chain L residue 35 SER Chi-restraints excluded: chain L residue 50 ASP Chi-restraints excluded: chain L residue 55 ILE Chi-restraints excluded: chain a residue 64 LYS Chi-restraints excluded: chain a residue 86 SER Chi-restraints excluded: chain a residue 87 SER Chi-restraints excluded: chain a residue 112 ILE Chi-restraints excluded: chain b residue 60 VAL Chi-restraints excluded: chain b residue 68 ASP Chi-restraints excluded: chain b residue 78 ARG Chi-restraints excluded: chain b residue 93 GLN Chi-restraints excluded: chain c residue 25 PHE Chi-restraints excluded: chain c residue 59 THR Chi-restraints excluded: chain c residue 74 LYS Chi-restraints excluded: chain c residue 114 VAL Chi-restraints excluded: chain d residue 51 ILE Chi-restraints excluded: chain d residue 82 LYS Chi-restraints excluded: chain d residue 87 THR Chi-restraints excluded: chain d residue 103 LEU Chi-restraints excluded: chain d residue 113 LYS Chi-restraints excluded: chain e residue 42 ARG Chi-restraints excluded: chain e residue 46 VAL Chi-restraints excluded: chain e residue 68 GLN Chi-restraints excluded: chain e residue 80 THR Chi-restraints excluded: chain e residue 83 ARG Chi-restraints excluded: chain e residue 116 ARG Chi-restraints excluded: chain e residue 124 ILE Chi-restraints excluded: chain f residue 92 ARG Chi-restraints excluded: chain g residue 29 ARG Chi-restraints excluded: chain g residue 62 ILE Chi-restraints excluded: chain g residue 100 VAL Chi-restraints excluded: chain h residue 87 THR Chi-restraints excluded: chain h residue 92 GLN Chi-restraints excluded: chain W residue 177 HIS Chi-restraints excluded: chain W residue 203 ASP Chi-restraints excluded: chain W residue 204 LEU Chi-restraints excluded: chain W residue 225 ASN Chi-restraints excluded: chain W residue 249 PHE Chi-restraints excluded: chain W residue 256 VAL Chi-restraints excluded: chain W residue 389 PHE Chi-restraints excluded: chain W residue 408 THR Chi-restraints excluded: chain W residue 436 THR Chi-restraints excluded: chain W residue 452 ASN Chi-restraints excluded: chain W residue 488 LEU Chi-restraints excluded: chain W residue 534 VAL Chi-restraints excluded: chain W residue 541 THR Chi-restraints excluded: chain W residue 655 LEU Chi-restraints excluded: chain W residue 701 ASP Chi-restraints excluded: chain W residue 733 ILE Chi-restraints excluded: chain Y residue 33 GLU Chi-restraints excluded: chain Z residue 287 ILE Chi-restraints excluded: chain Z residue 812 TYR Chi-restraints excluded: chain Z residue 830 GLU Chi-restraints excluded: chain Z residue 846 THR Chi-restraints excluded: chain Z residue 857 THR Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain G residue 87 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 566 random chunks: chunk 184 optimal weight: 2.9990 chunk 492 optimal weight: 5.9990 chunk 108 optimal weight: 4.9990 chunk 321 optimal weight: 10.0000 chunk 135 optimal weight: 7.9990 chunk 547 optimal weight: 9.9990 chunk 454 optimal weight: 10.0000 chunk 253 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 181 optimal weight: 3.9990 chunk 287 optimal weight: 0.1980 overall best weight: 2.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 768 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1009 ASN ** A1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 513 GLN C 24 ASN E 113 GLN H 21 ASN I 87 GLN ** K 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 104 GLN ** d 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 244 ASN W 323 ASN ** W 579 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 633 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.2970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 51180 Z= 0.325 Angle : 0.651 11.343 70300 Z= 0.344 Chirality : 0.043 0.227 7920 Planarity : 0.005 0.064 8063 Dihedral : 19.893 175.657 9182 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 15.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 4.05 % Allowed : 22.26 % Favored : 73.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.15 (0.11), residues: 5423 helix: 0.90 (0.11), residues: 2211 sheet: -0.68 (0.19), residues: 684 loop : -0.77 (0.12), residues: 2528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP W 391 HIS 0.030 0.001 HIS W 177 PHE 0.025 0.002 PHE A 252 TYR 0.026 0.002 TYR h 80 ARG 0.011 0.001 ARG c 17 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10846 Ramachandran restraints generated. 5423 Oldfield, 0 Emsley, 5423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10846 Ramachandran restraints generated. 5423 Oldfield, 0 Emsley, 5423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 738 residues out of total 4824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 195 poor density : 543 time to evaluate : 5.500 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 317 LYS cc_start: 0.8398 (pptt) cc_final: 0.7784 (tttt) REVERT: A 443 LEU cc_start: 0.8857 (OUTLIER) cc_final: 0.8552 (tt) REVERT: A 488 ASN cc_start: 0.8405 (m-40) cc_final: 0.8202 (m-40) REVERT: A 497 THR cc_start: 0.8844 (OUTLIER) cc_final: 0.8615 (p) REVERT: A 780 VAL cc_start: 0.8596 (t) cc_final: 0.8227 (m) REVERT: A 826 ASP cc_start: 0.6970 (m-30) cc_final: 0.6471 (t0) REVERT: A 857 ARG cc_start: 0.8093 (OUTLIER) cc_final: 0.7832 (mtp85) REVERT: A 919 ILE cc_start: 0.8431 (mm) cc_final: 0.8101 (pp) REVERT: A 934 LYS cc_start: 0.8325 (OUTLIER) cc_final: 0.7748 (mppt) REVERT: A 1218 GLN cc_start: 0.7907 (OUTLIER) cc_final: 0.7451 (tm130) REVERT: B 101 MET cc_start: 0.7666 (OUTLIER) cc_final: 0.7289 (mtm) REVERT: B 206 ASN cc_start: 0.7878 (t0) cc_final: 0.7249 (t0) REVERT: B 632 ARG cc_start: 0.7848 (OUTLIER) cc_final: 0.7570 (mtm110) REVERT: B 662 MET cc_start: 0.7951 (mtt) cc_final: 0.7628 (mtp) REVERT: B 760 ASP cc_start: 0.8435 (OUTLIER) cc_final: 0.8218 (p0) REVERT: B 1021 MET cc_start: 0.8313 (OUTLIER) cc_final: 0.7545 (mpp) REVERT: B 1163 CYS cc_start: 0.7374 (OUTLIER) cc_final: 0.7073 (p) REVERT: C 61 GLU cc_start: 0.6371 (tm-30) cc_final: 0.6149 (tm-30) REVERT: C 149 LYS cc_start: 0.7577 (ptmm) cc_final: 0.7271 (tttm) REVERT: C 221 TYR cc_start: 0.7602 (OUTLIER) cc_final: 0.6900 (m-10) REVERT: E 54 GLN cc_start: 0.6585 (mp10) cc_final: 0.6353 (mp-120) REVERT: E 85 GLU cc_start: 0.7526 (OUTLIER) cc_final: 0.7302 (mt-10) REVERT: F 114 GLU cc_start: 0.7093 (mm-30) cc_final: 0.6857 (mm-30) REVERT: F 119 ARG cc_start: 0.7825 (tpp80) cc_final: 0.7527 (mmm-85) REVERT: H 62 SER cc_start: 0.7974 (t) cc_final: 0.7645 (m) REVERT: I 82 GLU cc_start: 0.7266 (pm20) cc_final: 0.6958 (pp20) REVERT: K 26 LYS cc_start: 0.7377 (OUTLIER) cc_final: 0.6968 (tttp) REVERT: a 64 LYS cc_start: 0.8291 (OUTLIER) cc_final: 0.7616 (mppt) REVERT: a 90 MET cc_start: 0.7942 (mmm) cc_final: 0.7666 (mmp) REVERT: a 123 ASP cc_start: 0.7811 (m-30) cc_final: 0.7600 (m-30) REVERT: b 74 GLU cc_start: 0.7859 (tp30) cc_final: 0.7564 (tp30) REVERT: b 78 ARG cc_start: 0.6271 (OUTLIER) cc_final: 0.4679 (ttm110) REVERT: b 79 LYS cc_start: 0.8461 (mtmm) cc_final: 0.8188 (mtpm) REVERT: c 25 PHE cc_start: 0.7916 (OUTLIER) cc_final: 0.6397 (m-80) REVERT: c 41 GLU cc_start: 0.7775 (mm-30) cc_final: 0.7501 (mp0) REVERT: c 88 ARG cc_start: 0.8256 (mmt-90) cc_final: 0.7905 (mmt-90) REVERT: d 56 MET cc_start: 0.8285 (mmm) cc_final: 0.7740 (tpt) REVERT: d 82 LYS cc_start: 0.8690 (OUTLIER) cc_final: 0.8455 (mppt) REVERT: d 117 LYS cc_start: 0.8578 (OUTLIER) cc_final: 0.8135 (ptmt) REVERT: e 68 GLN cc_start: 0.8320 (OUTLIER) cc_final: 0.7921 (tp-100) REVERT: e 77 ASP cc_start: 0.8148 (m-30) cc_final: 0.7785 (t0) REVERT: e 109 LEU cc_start: 0.8829 (tp) cc_final: 0.8563 (tp) REVERT: e 115 LYS cc_start: 0.8216 (pttt) cc_final: 0.7581 (ptpp) REVERT: e 116 ARG cc_start: 0.5542 (OUTLIER) cc_final: 0.4577 (ttp80) REVERT: e 129 ARG cc_start: 0.7987 (ttt90) cc_final: 0.7658 (mtp85) REVERT: e 131 ARG cc_start: 0.8032 (mmm-85) cc_final: 0.7825 (mmm-85) REVERT: f 77 LYS cc_start: 0.8668 (mptt) cc_final: 0.8247 (mppt) REVERT: g 24 GLN cc_start: 0.7670 (mm-40) cc_final: 0.7111 (mp10) REVERT: g 27 VAL cc_start: 0.8735 (t) cc_final: 0.8489 (p) REVERT: g 29 ARG cc_start: 0.8662 (OUTLIER) cc_final: 0.8217 (ptp-110) REVERT: g 35 ARG cc_start: 0.7850 (mtm110) cc_final: 0.7387 (mtm110) REVERT: g 36 LYS cc_start: 0.8132 (mmtm) cc_final: 0.7865 (ttpt) REVERT: g 89 ASN cc_start: 0.8620 (m110) cc_final: 0.8266 (m110) REVERT: g 94 ASN cc_start: 0.8382 (t0) cc_final: 0.8116 (t0) REVERT: g 99 ARG cc_start: 0.6722 (tpt170) cc_final: 0.6419 (ttt90) REVERT: h 68 GLU cc_start: 0.7811 (mm-30) cc_final: 0.7175 (mm-30) REVERT: h 80 TYR cc_start: 0.6916 (m-80) cc_final: 0.6628 (m-80) REVERT: h 90 GLU cc_start: 0.8508 (mp0) cc_final: 0.7874 (mp0) REVERT: h 110 GLU cc_start: 0.8098 (mt-10) cc_final: 0.7868 (mt-10) REVERT: W 208 LYS cc_start: 0.6895 (ttpt) cc_final: 0.6392 (tptp) REVERT: W 226 THR cc_start: 0.7803 (m) cc_final: 0.7566 (p) REVERT: W 334 GLN cc_start: 0.7663 (tp40) cc_final: 0.7271 (tp40) REVERT: W 550 LYS cc_start: 0.8752 (tptt) cc_final: 0.8501 (tptt) REVERT: W 551 GLU cc_start: 0.7568 (mp0) cc_final: 0.7218 (mp0) REVERT: W 701 ASP cc_start: 0.8035 (OUTLIER) cc_final: 0.7665 (m-30) REVERT: W 723 MET cc_start: 0.8933 (tpp) cc_final: 0.8684 (tpt) REVERT: W 802 MET cc_start: 0.8216 (ttm) cc_final: 0.7994 (ttp) REVERT: Z 315 MET cc_start: 0.1127 (tpp) cc_final: 0.0343 (mmm) REVERT: Z 346 GLU cc_start: 0.2472 (mm-30) cc_final: 0.0281 (pt0) REVERT: Z 367 GLU cc_start: 0.3932 (tp30) cc_final: 0.3616 (tp30) REVERT: G 106 MET cc_start: 0.2702 (OUTLIER) cc_final: 0.2180 (ptp) outliers start: 195 outliers final: 103 residues processed: 680 average time/residue: 1.6306 time to fit residues: 1387.6929 Evaluate side-chains 645 residues out of total 4824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 519 time to evaluate : 4.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 CYS Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 437 MET Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 497 THR Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain A residue 693 VAL Chi-restraints excluded: chain A residue 708 MET Chi-restraints excluded: chain A residue 754 SER Chi-restraints excluded: chain A residue 849 MET Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain A residue 857 ARG Chi-restraints excluded: chain A residue 878 ILE Chi-restraints excluded: chain A residue 927 VAL Chi-restraints excluded: chain A residue 934 LYS Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 988 LEU Chi-restraints excluded: chain A residue 1071 SER Chi-restraints excluded: chain A residue 1118 VAL Chi-restraints excluded: chain A residue 1124 HIS Chi-restraints excluded: chain A residue 1218 GLN Chi-restraints excluded: chain A residue 1229 SER Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 517 THR Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 578 THR Chi-restraints excluded: chain B residue 632 ARG Chi-restraints excluded: chain B residue 741 CYS Chi-restraints excluded: chain B residue 760 ASP Chi-restraints excluded: chain B residue 764 SER Chi-restraints excluded: chain B residue 780 VAL Chi-restraints excluded: chain B residue 797 TYR Chi-restraints excluded: chain B residue 889 THR Chi-restraints excluded: chain B residue 1021 MET Chi-restraints excluded: chain B residue 1065 GLN Chi-restraints excluded: chain B residue 1163 CYS Chi-restraints excluded: chain B residue 1176 ASN Chi-restraints excluded: chain C residue 93 ASP Chi-restraints excluded: chain C residue 137 LYS Chi-restraints excluded: chain C residue 166 GLU Chi-restraints excluded: chain C residue 207 CYS Chi-restraints excluded: chain C residue 221 TYR Chi-restraints excluded: chain C residue 258 ILE Chi-restraints excluded: chain E residue 85 GLU Chi-restraints excluded: chain E residue 214 CYS Chi-restraints excluded: chain F residue 99 LEU Chi-restraints excluded: chain H residue 5 LEU Chi-restraints excluded: chain H residue 39 THR Chi-restraints excluded: chain H residue 54 SER Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 92 ASP Chi-restraints excluded: chain I residue 55 THR Chi-restraints excluded: chain K residue 26 LYS Chi-restraints excluded: chain K residue 31 VAL Chi-restraints excluded: chain K residue 103 THR Chi-restraints excluded: chain L residue 31 CYS Chi-restraints excluded: chain L residue 35 SER Chi-restraints excluded: chain L residue 50 ASP Chi-restraints excluded: chain L residue 55 ILE Chi-restraints excluded: chain L residue 68 GLU Chi-restraints excluded: chain a residue 64 LYS Chi-restraints excluded: chain a residue 86 SER Chi-restraints excluded: chain a residue 87 SER Chi-restraints excluded: chain a residue 112 ILE Chi-restraints excluded: chain b residue 60 VAL Chi-restraints excluded: chain b residue 78 ARG Chi-restraints excluded: chain b residue 85 ASP Chi-restraints excluded: chain c residue 25 PHE Chi-restraints excluded: chain c residue 59 THR Chi-restraints excluded: chain c residue 114 VAL Chi-restraints excluded: chain d residue 51 ILE Chi-restraints excluded: chain d residue 82 LYS Chi-restraints excluded: chain d residue 87 THR Chi-restraints excluded: chain d residue 103 LEU Chi-restraints excluded: chain d residue 113 LYS Chi-restraints excluded: chain d residue 117 LYS Chi-restraints excluded: chain e residue 42 ARG Chi-restraints excluded: chain e residue 46 VAL Chi-restraints excluded: chain e residue 68 GLN Chi-restraints excluded: chain e residue 80 THR Chi-restraints excluded: chain e residue 116 ARG Chi-restraints excluded: chain e residue 117 VAL Chi-restraints excluded: chain e residue 124 ILE Chi-restraints excluded: chain g residue 29 ARG Chi-restraints excluded: chain g residue 62 ILE Chi-restraints excluded: chain g residue 79 ILE Chi-restraints excluded: chain g residue 90 ASP Chi-restraints excluded: chain g residue 100 VAL Chi-restraints excluded: chain h residue 87 THR Chi-restraints excluded: chain W residue 203 ASP Chi-restraints excluded: chain W residue 204 LEU Chi-restraints excluded: chain W residue 225 ASN Chi-restraints excluded: chain W residue 249 PHE Chi-restraints excluded: chain W residue 256 VAL Chi-restraints excluded: chain W residue 389 PHE Chi-restraints excluded: chain W residue 408 THR Chi-restraints excluded: chain W residue 436 THR Chi-restraints excluded: chain W residue 452 ASN Chi-restraints excluded: chain W residue 488 LEU Chi-restraints excluded: chain W residue 534 VAL Chi-restraints excluded: chain W residue 541 THR Chi-restraints excluded: chain W residue 548 ASN Chi-restraints excluded: chain W residue 587 HIS Chi-restraints excluded: chain W residue 606 LEU Chi-restraints excluded: chain W residue 620 ASP Chi-restraints excluded: chain W residue 655 LEU Chi-restraints excluded: chain W residue 701 ASP Chi-restraints excluded: chain W residue 707 LEU Chi-restraints excluded: chain W residue 733 ILE Chi-restraints excluded: chain W residue 837 MET Chi-restraints excluded: chain Y residue 33 GLU Chi-restraints excluded: chain Z residue 286 THR Chi-restraints excluded: chain Z residue 287 ILE Chi-restraints excluded: chain Z residue 812 TYR Chi-restraints excluded: chain Z residue 846 THR Chi-restraints excluded: chain Z residue 857 THR Chi-restraints excluded: chain G residue 87 VAL Chi-restraints excluded: chain G residue 106 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 566 random chunks: chunk 527 optimal weight: 10.0000 chunk 61 optimal weight: 2.9990 chunk 312 optimal weight: 0.9980 chunk 399 optimal weight: 0.2980 chunk 309 optimal weight: 5.9990 chunk 460 optimal weight: 2.9990 chunk 305 optimal weight: 2.9990 chunk 545 optimal weight: 10.0000 chunk 341 optimal weight: 0.9990 chunk 332 optimal weight: 1.9990 chunk 251 optimal weight: 3.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 768 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 21 ASN I 87 GLN ** K 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 104 GLN ** d 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 177 HIS ** W 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 244 ASN W 323 ASN ** W 579 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 633 ASN W 812 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.3098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 51180 Z= 0.264 Angle : 0.629 9.683 70300 Z= 0.332 Chirality : 0.042 0.318 7920 Planarity : 0.004 0.054 8063 Dihedral : 19.897 175.528 9182 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 15.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 3.82 % Allowed : 23.53 % Favored : 72.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.11), residues: 5423 helix: 0.99 (0.11), residues: 2206 sheet: -0.59 (0.19), residues: 687 loop : -0.73 (0.13), residues: 2530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP W 391 HIS 0.008 0.001 HIS A 399 PHE 0.019 0.002 PHE K 71 TYR 0.025 0.001 TYR H 20 ARG 0.009 0.001 ARG c 17 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10846 Ramachandran restraints generated. 5423 Oldfield, 0 Emsley, 5423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10846 Ramachandran restraints generated. 5423 Oldfield, 0 Emsley, 5423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 731 residues out of total 4824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 184 poor density : 547 time to evaluate : 5.536 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 PHE cc_start: 0.8767 (OUTLIER) cc_final: 0.7736 (m-80) REVERT: A 317 LYS cc_start: 0.8430 (pptt) cc_final: 0.7790 (tttt) REVERT: A 443 LEU cc_start: 0.8821 (OUTLIER) cc_final: 0.8544 (tt) REVERT: A 497 THR cc_start: 0.8825 (OUTLIER) cc_final: 0.8597 (p) REVERT: A 780 VAL cc_start: 0.8570 (t) cc_final: 0.8250 (m) REVERT: A 826 ASP cc_start: 0.7007 (m-30) cc_final: 0.6478 (t0) REVERT: A 857 ARG cc_start: 0.8072 (OUTLIER) cc_final: 0.7817 (mtp85) REVERT: A 919 ILE cc_start: 0.8415 (mm) cc_final: 0.8151 (pp) REVERT: A 934 LYS cc_start: 0.8317 (OUTLIER) cc_final: 0.7728 (mppt) REVERT: A 1218 GLN cc_start: 0.7896 (OUTLIER) cc_final: 0.7461 (tm130) REVERT: B 101 MET cc_start: 0.7660 (OUTLIER) cc_final: 0.7251 (mtm) REVERT: B 206 ASN cc_start: 0.7915 (t0) cc_final: 0.7246 (t0) REVERT: B 563 MET cc_start: 0.7824 (tmm) cc_final: 0.7547 (ttt) REVERT: B 632 ARG cc_start: 0.7771 (OUTLIER) cc_final: 0.7535 (mtm110) REVERT: B 662 MET cc_start: 0.7943 (mtt) cc_final: 0.7623 (mtp) REVERT: B 1021 MET cc_start: 0.8248 (OUTLIER) cc_final: 0.7454 (mpp) REVERT: B 1163 CYS cc_start: 0.7358 (OUTLIER) cc_final: 0.7068 (p) REVERT: C 137 LYS cc_start: 0.8216 (OUTLIER) cc_final: 0.8013 (ptmt) REVERT: C 221 TYR cc_start: 0.7566 (OUTLIER) cc_final: 0.6861 (m-10) REVERT: C 227 THR cc_start: 0.7936 (OUTLIER) cc_final: 0.7728 (p) REVERT: E 85 GLU cc_start: 0.7505 (OUTLIER) cc_final: 0.7262 (mt-10) REVERT: H 62 SER cc_start: 0.7917 (t) cc_final: 0.7611 (m) REVERT: I 61 ASP cc_start: 0.5692 (p0) cc_final: 0.5447 (p0) REVERT: I 82 GLU cc_start: 0.7204 (pm20) cc_final: 0.6936 (pp20) REVERT: K 26 LYS cc_start: 0.7388 (OUTLIER) cc_final: 0.7112 (tttp) REVERT: K 70 ARG cc_start: 0.8471 (ptp90) cc_final: 0.7360 (ptp90) REVERT: a 64 LYS cc_start: 0.8324 (OUTLIER) cc_final: 0.7620 (mppt) REVERT: a 90 MET cc_start: 0.7954 (mmm) cc_final: 0.7656 (mmp) REVERT: a 123 ASP cc_start: 0.7718 (m-30) cc_final: 0.7501 (m-30) REVERT: b 74 GLU cc_start: 0.7729 (tp30) cc_final: 0.7433 (tp30) REVERT: b 78 ARG cc_start: 0.6208 (OUTLIER) cc_final: 0.4537 (ttp80) REVERT: b 79 LYS cc_start: 0.8443 (mtmm) cc_final: 0.8187 (mtpm) REVERT: c 25 PHE cc_start: 0.7913 (OUTLIER) cc_final: 0.6404 (m-80) REVERT: c 41 GLU cc_start: 0.7752 (mm-30) cc_final: 0.7489 (mp0) REVERT: c 88 ARG cc_start: 0.8262 (mmt-90) cc_final: 0.7916 (mmt-90) REVERT: d 117 LYS cc_start: 0.8540 (OUTLIER) cc_final: 0.8130 (ptmt) REVERT: e 42 ARG cc_start: 0.7642 (OUTLIER) cc_final: 0.6957 (ptp90) REVERT: e 68 GLN cc_start: 0.8296 (OUTLIER) cc_final: 0.7910 (tp-100) REVERT: e 77 ASP cc_start: 0.8108 (m-30) cc_final: 0.7749 (t0) REVERT: e 109 LEU cc_start: 0.8780 (tp) cc_final: 0.8534 (tp) REVERT: e 115 LYS cc_start: 0.8218 (pttt) cc_final: 0.7597 (ptpp) REVERT: e 116 ARG cc_start: 0.5495 (OUTLIER) cc_final: 0.4931 (ttm110) REVERT: f 77 LYS cc_start: 0.8583 (mptt) cc_final: 0.8222 (mptp) REVERT: g 24 GLN cc_start: 0.7600 (mm-40) cc_final: 0.7047 (mp10) REVERT: g 27 VAL cc_start: 0.8718 (t) cc_final: 0.8463 (p) REVERT: g 29 ARG cc_start: 0.8626 (OUTLIER) cc_final: 0.8178 (ptp-110) REVERT: g 35 ARG cc_start: 0.7873 (mtm110) cc_final: 0.7395 (mtm110) REVERT: g 36 LYS cc_start: 0.8148 (mmtm) cc_final: 0.7869 (ttpt) REVERT: g 89 ASN cc_start: 0.8620 (m110) cc_final: 0.8236 (m110) REVERT: g 94 ASN cc_start: 0.8352 (t0) cc_final: 0.8126 (t0) REVERT: h 68 GLU cc_start: 0.7780 (mm-30) cc_final: 0.7112 (mm-30) REVERT: h 90 GLU cc_start: 0.8466 (mp0) cc_final: 0.7900 (mp0) REVERT: W 177 HIS cc_start: 0.6297 (OUTLIER) cc_final: 0.4663 (p90) REVERT: W 226 THR cc_start: 0.7775 (m) cc_final: 0.7533 (p) REVERT: W 244 ASN cc_start: 0.7958 (m-40) cc_final: 0.7608 (m110) REVERT: W 334 GLN cc_start: 0.7583 (tp40) cc_final: 0.7232 (tp40) REVERT: W 550 LYS cc_start: 0.8698 (tptt) cc_final: 0.8453 (tptt) REVERT: W 551 GLU cc_start: 0.7540 (mp0) cc_final: 0.7159 (mp0) REVERT: W 701 ASP cc_start: 0.7899 (OUTLIER) cc_final: 0.7315 (m-30) REVERT: W 723 MET cc_start: 0.8920 (tpp) cc_final: 0.8678 (tpt) REVERT: W 802 MET cc_start: 0.8192 (ttm) cc_final: 0.7980 (ttp) REVERT: Z 315 MET cc_start: 0.1044 (tpp) cc_final: 0.0289 (mmm) REVERT: Z 346 GLU cc_start: 0.2427 (mm-30) cc_final: 0.0280 (pt0) REVERT: Z 367 GLU cc_start: 0.4039 (tp30) cc_final: 0.3727 (tp30) REVERT: G 106 MET cc_start: 0.1925 (ptp) cc_final: 0.1593 (ptp) outliers start: 184 outliers final: 94 residues processed: 678 average time/residue: 1.6587 time to fit residues: 1414.6297 Evaluate side-chains 633 residues out of total 4824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 514 time to evaluate : 5.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 107 CYS Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 437 MET Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 497 THR Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 693 VAL Chi-restraints excluded: chain A residue 754 SER Chi-restraints excluded: chain A residue 849 MET Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain A residue 857 ARG Chi-restraints excluded: chain A residue 878 ILE Chi-restraints excluded: chain A residue 927 VAL Chi-restraints excluded: chain A residue 934 LYS Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 988 LEU Chi-restraints excluded: chain A residue 1071 SER Chi-restraints excluded: chain A residue 1118 VAL Chi-restraints excluded: chain A residue 1124 HIS Chi-restraints excluded: chain A residue 1218 GLN Chi-restraints excluded: chain A residue 1229 SER Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 517 THR Chi-restraints excluded: chain B residue 561 TRP Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 632 ARG Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 741 CYS Chi-restraints excluded: chain B residue 764 SER Chi-restraints excluded: chain B residue 797 TYR Chi-restraints excluded: chain B residue 889 THR Chi-restraints excluded: chain B residue 1021 MET Chi-restraints excluded: chain B residue 1065 GLN Chi-restraints excluded: chain B residue 1115 THR Chi-restraints excluded: chain B residue 1163 CYS Chi-restraints excluded: chain B residue 1176 ASN Chi-restraints excluded: chain C residue 93 ASP Chi-restraints excluded: chain C residue 137 LYS Chi-restraints excluded: chain C residue 166 GLU Chi-restraints excluded: chain C residue 207 CYS Chi-restraints excluded: chain C residue 221 TYR Chi-restraints excluded: chain C residue 227 THR Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 258 ILE Chi-restraints excluded: chain E residue 85 GLU Chi-restraints excluded: chain E residue 214 CYS Chi-restraints excluded: chain F residue 99 LEU Chi-restraints excluded: chain H residue 5 LEU Chi-restraints excluded: chain H residue 39 THR Chi-restraints excluded: chain H residue 54 SER Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 92 ASP Chi-restraints excluded: chain H residue 117 SER Chi-restraints excluded: chain I residue 55 THR Chi-restraints excluded: chain K residue 26 LYS Chi-restraints excluded: chain K residue 31 VAL Chi-restraints excluded: chain L residue 50 ASP Chi-restraints excluded: chain L residue 55 ILE Chi-restraints excluded: chain a residue 64 LYS Chi-restraints excluded: chain a residue 86 SER Chi-restraints excluded: chain b residue 78 ARG Chi-restraints excluded: chain b residue 85 ASP Chi-restraints excluded: chain c residue 25 PHE Chi-restraints excluded: chain c residue 59 THR Chi-restraints excluded: chain c residue 76 THR Chi-restraints excluded: chain c residue 114 VAL Chi-restraints excluded: chain d residue 54 LYS Chi-restraints excluded: chain d residue 87 THR Chi-restraints excluded: chain d residue 103 LEU Chi-restraints excluded: chain d residue 113 LYS Chi-restraints excluded: chain d residue 117 LYS Chi-restraints excluded: chain e residue 42 ARG Chi-restraints excluded: chain e residue 46 VAL Chi-restraints excluded: chain e residue 68 GLN Chi-restraints excluded: chain e residue 80 THR Chi-restraints excluded: chain e residue 116 ARG Chi-restraints excluded: chain e residue 124 ILE Chi-restraints excluded: chain f residue 25 ASN Chi-restraints excluded: chain g residue 29 ARG Chi-restraints excluded: chain g residue 62 ILE Chi-restraints excluded: chain g residue 79 ILE Chi-restraints excluded: chain g residue 100 VAL Chi-restraints excluded: chain h residue 87 THR Chi-restraints excluded: chain W residue 177 HIS Chi-restraints excluded: chain W residue 203 ASP Chi-restraints excluded: chain W residue 204 LEU Chi-restraints excluded: chain W residue 225 ASN Chi-restraints excluded: chain W residue 249 PHE Chi-restraints excluded: chain W residue 256 VAL Chi-restraints excluded: chain W residue 389 PHE Chi-restraints excluded: chain W residue 452 ASN Chi-restraints excluded: chain W residue 488 LEU Chi-restraints excluded: chain W residue 534 VAL Chi-restraints excluded: chain W residue 541 THR Chi-restraints excluded: chain W residue 548 ASN Chi-restraints excluded: chain W residue 701 ASP Chi-restraints excluded: chain W residue 707 LEU Chi-restraints excluded: chain W residue 733 ILE Chi-restraints excluded: chain W residue 837 MET Chi-restraints excluded: chain Y residue 33 GLU Chi-restraints excluded: chain Z residue 287 ILE Chi-restraints excluded: chain Z residue 812 TYR Chi-restraints excluded: chain Z residue 833 SER Chi-restraints excluded: chain Z residue 846 THR Chi-restraints excluded: chain G residue 9 LEU Chi-restraints excluded: chain G residue 87 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 566 random chunks: chunk 337 optimal weight: 2.9990 chunk 217 optimal weight: 0.4980 chunk 325 optimal weight: 3.9990 chunk 164 optimal weight: 5.9990 chunk 107 optimal weight: 0.6980 chunk 105 optimal weight: 3.9990 chunk 346 optimal weight: 0.9990 chunk 371 optimal weight: 6.9990 chunk 269 optimal weight: 1.9990 chunk 50 optimal weight: 0.6980 chunk 428 optimal weight: 5.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 768 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1078 GLN ** A1124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 357 GLN E 61 GLN H 21 ASN ** K 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 89 ASN ** a 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 104 GLN d 60 ASN ** h 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 177 HIS ** W 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 323 ASN ** W 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 579 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 812 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.3198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 51180 Z= 0.225 Angle : 0.630 9.805 70300 Z= 0.330 Chirality : 0.041 0.247 7920 Planarity : 0.004 0.054 8063 Dihedral : 19.854 175.483 9182 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 15.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 3.53 % Allowed : 24.21 % Favored : 72.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.12), residues: 5423 helix: 1.10 (0.11), residues: 2200 sheet: -0.59 (0.19), residues: 693 loop : -0.66 (0.13), residues: 2530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP W 391 HIS 0.014 0.001 HIS W 177 PHE 0.018 0.002 PHE A 228 TYR 0.025 0.001 TYR H 20 ARG 0.010 0.001 ARG H 19 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10846 Ramachandran restraints generated. 5423 Oldfield, 0 Emsley, 5423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10846 Ramachandran restraints generated. 5423 Oldfield, 0 Emsley, 5423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 705 residues out of total 4824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 170 poor density : 535 time to evaluate : 5.601 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 PHE cc_start: 0.8764 (OUTLIER) cc_final: 0.7824 (m-80) REVERT: A 317 LYS cc_start: 0.8465 (pptt) cc_final: 0.7773 (tttt) REVERT: A 443 LEU cc_start: 0.8757 (OUTLIER) cc_final: 0.8496 (tt) REVERT: A 497 THR cc_start: 0.8752 (OUTLIER) cc_final: 0.8510 (p) REVERT: A 780 VAL cc_start: 0.8519 (t) cc_final: 0.8182 (m) REVERT: A 826 ASP cc_start: 0.7020 (m-30) cc_final: 0.6483 (t0) REVERT: A 919 ILE cc_start: 0.8438 (mm) cc_final: 0.8168 (pp) REVERT: A 934 LYS cc_start: 0.8308 (OUTLIER) cc_final: 0.7698 (mppt) REVERT: A 1218 GLN cc_start: 0.7880 (OUTLIER) cc_final: 0.7463 (tm130) REVERT: B 101 MET cc_start: 0.7658 (OUTLIER) cc_final: 0.7225 (mtm) REVERT: B 206 ASN cc_start: 0.7857 (t0) cc_final: 0.7204 (t0) REVERT: B 561 TRP cc_start: 0.7986 (OUTLIER) cc_final: 0.7214 (t60) REVERT: B 567 GLU cc_start: 0.7902 (mp0) cc_final: 0.7639 (mp0) REVERT: B 662 MET cc_start: 0.7866 (mtt) cc_final: 0.7543 (mtp) REVERT: B 760 ASP cc_start: 0.8364 (OUTLIER) cc_final: 0.8093 (p0) REVERT: B 1021 MET cc_start: 0.8220 (OUTLIER) cc_final: 0.7416 (mpp) REVERT: B 1120 GLU cc_start: 0.6204 (OUTLIER) cc_final: 0.5973 (mt-10) REVERT: B 1163 CYS cc_start: 0.7340 (OUTLIER) cc_final: 0.7053 (p) REVERT: C 75 MET cc_start: 0.7771 (tpp) cc_final: 0.7526 (tpt) REVERT: C 137 LYS cc_start: 0.8205 (OUTLIER) cc_final: 0.7997 (ptmt) REVERT: C 221 TYR cc_start: 0.7498 (OUTLIER) cc_final: 0.6725 (m-10) REVERT: C 227 THR cc_start: 0.7898 (OUTLIER) cc_final: 0.7680 (p) REVERT: E 85 GLU cc_start: 0.7388 (OUTLIER) cc_final: 0.7178 (mt-10) REVERT: H 62 SER cc_start: 0.7880 (t) cc_final: 0.7591 (m) REVERT: I 61 ASP cc_start: 0.5604 (p0) cc_final: 0.5357 (p0) REVERT: K 26 LYS cc_start: 0.7358 (OUTLIER) cc_final: 0.7044 (tttp) REVERT: K 70 ARG cc_start: 0.8470 (ptp90) cc_final: 0.7325 (ptp90) REVERT: K 108 GLU cc_start: 0.7938 (tp30) cc_final: 0.7700 (tp30) REVERT: L 54 ARG cc_start: 0.7335 (OUTLIER) cc_final: 0.7050 (ptm160) REVERT: a 64 LYS cc_start: 0.8304 (OUTLIER) cc_final: 0.7643 (mppt) REVERT: a 83 ARG cc_start: 0.6360 (tpt170) cc_final: 0.5212 (ttt180) REVERT: a 90 MET cc_start: 0.7892 (mmm) cc_final: 0.7657 (mmp) REVERT: a 93 GLN cc_start: 0.7310 (tt0) cc_final: 0.7082 (tt0) REVERT: a 123 ASP cc_start: 0.7704 (m-30) cc_final: 0.7494 (m-30) REVERT: b 74 GLU cc_start: 0.7719 (tp30) cc_final: 0.7411 (tp30) REVERT: b 78 ARG cc_start: 0.6032 (OUTLIER) cc_final: 0.4376 (ttp80) REVERT: b 79 LYS cc_start: 0.8406 (mtmm) cc_final: 0.8155 (mtpm) REVERT: c 25 PHE cc_start: 0.7907 (OUTLIER) cc_final: 0.6465 (m-80) REVERT: c 41 GLU cc_start: 0.7742 (mm-30) cc_final: 0.7480 (mp0) REVERT: c 56 GLU cc_start: 0.8261 (tt0) cc_final: 0.8043 (tt0) REVERT: c 88 ARG cc_start: 0.8272 (mmt-90) cc_final: 0.7912 (mmt-90) REVERT: c 104 GLN cc_start: 0.7876 (pm20) cc_final: 0.7605 (pm20) REVERT: d 56 MET cc_start: 0.8339 (tpp) cc_final: 0.7642 (tpt) REVERT: d 117 LYS cc_start: 0.8497 (OUTLIER) cc_final: 0.8119 (ptmt) REVERT: e 42 ARG cc_start: 0.7677 (OUTLIER) cc_final: 0.5862 (ptt-90) REVERT: e 68 GLN cc_start: 0.8289 (OUTLIER) cc_final: 0.7904 (tp-100) REVERT: e 77 ASP cc_start: 0.8097 (m-30) cc_final: 0.7729 (t0) REVERT: e 109 LEU cc_start: 0.8748 (tp) cc_final: 0.8488 (tp) REVERT: e 115 LYS cc_start: 0.8187 (pttt) cc_final: 0.7585 (ptpp) REVERT: e 116 ARG cc_start: 0.5401 (OUTLIER) cc_final: 0.5035 (ttm110) REVERT: e 125 GLN cc_start: 0.8667 (mt0) cc_final: 0.8441 (mt0) REVERT: f 77 LYS cc_start: 0.8521 (mptt) cc_final: 0.8184 (mptp) REVERT: g 24 GLN cc_start: 0.7599 (mm-40) cc_final: 0.7059 (mp10) REVERT: g 29 ARG cc_start: 0.8653 (OUTLIER) cc_final: 0.8140 (ptp-110) REVERT: g 33 LEU cc_start: 0.8289 (OUTLIER) cc_final: 0.7767 (mp) REVERT: g 35 ARG cc_start: 0.7891 (mtm110) cc_final: 0.7439 (mtm110) REVERT: g 36 LYS cc_start: 0.8142 (mmtm) cc_final: 0.7862 (ttpt) REVERT: g 89 ASN cc_start: 0.8665 (m110) cc_final: 0.8285 (m110) REVERT: g 94 ASN cc_start: 0.8328 (t0) cc_final: 0.8127 (t0) REVERT: h 68 GLU cc_start: 0.7701 (mm-30) cc_final: 0.7075 (mm-30) REVERT: h 90 GLU cc_start: 0.8440 (mp0) cc_final: 0.7863 (mp0) REVERT: W 177 HIS cc_start: 0.6352 (OUTLIER) cc_final: 0.4913 (p90) REVERT: W 226 THR cc_start: 0.7796 (m) cc_final: 0.7550 (p) REVERT: W 244 ASN cc_start: 0.7756 (m-40) cc_final: 0.7193 (m110) REVERT: W 334 GLN cc_start: 0.7521 (tp40) cc_final: 0.7201 (tp-100) REVERT: W 346 ILE cc_start: 0.8366 (tp) cc_final: 0.8024 (pp) REVERT: W 550 LYS cc_start: 0.8680 (tptt) cc_final: 0.8444 (tptt) REVERT: W 551 GLU cc_start: 0.7520 (mp0) cc_final: 0.7207 (mp0) REVERT: W 701 ASP cc_start: 0.7888 (OUTLIER) cc_final: 0.7336 (m-30) REVERT: W 723 MET cc_start: 0.8925 (tpp) cc_final: 0.8692 (tpt) REVERT: W 802 MET cc_start: 0.8176 (ttm) cc_final: 0.7972 (ttp) REVERT: W 837 MET cc_start: 0.8034 (mmp) cc_final: 0.7695 (mpp) REVERT: Z 315 MET cc_start: 0.1002 (tpp) cc_final: 0.0304 (mmm) REVERT: Z 346 GLU cc_start: 0.2384 (mm-30) cc_final: 0.0281 (pt0) REVERT: Z 367 GLU cc_start: 0.4174 (tp30) cc_final: 0.3900 (tp30) REVERT: D 1 MET cc_start: 0.5848 (ttt) cc_final: 0.5542 (ttp) outliers start: 170 outliers final: 84 residues processed: 662 average time/residue: 1.6479 time to fit residues: 1373.2362 Evaluate side-chains 628 residues out of total 4824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 516 time to evaluate : 5.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 107 CYS Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 437 MET Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 497 THR Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 693 VAL Chi-restraints excluded: chain A residue 754 SER Chi-restraints excluded: chain A residue 849 MET Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain A residue 878 ILE Chi-restraints excluded: chain A residue 927 VAL Chi-restraints excluded: chain A residue 934 LYS Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 1071 SER Chi-restraints excluded: chain A residue 1118 VAL Chi-restraints excluded: chain A residue 1218 GLN Chi-restraints excluded: chain A residue 1229 SER Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 517 THR Chi-restraints excluded: chain B residue 561 TRP Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 741 CYS Chi-restraints excluded: chain B residue 760 ASP Chi-restraints excluded: chain B residue 764 SER Chi-restraints excluded: chain B residue 780 VAL Chi-restraints excluded: chain B residue 797 TYR Chi-restraints excluded: chain B residue 889 THR Chi-restraints excluded: chain B residue 1021 MET Chi-restraints excluded: chain B residue 1065 GLN Chi-restraints excluded: chain B residue 1115 THR Chi-restraints excluded: chain B residue 1120 GLU Chi-restraints excluded: chain B residue 1163 CYS Chi-restraints excluded: chain B residue 1176 ASN Chi-restraints excluded: chain C residue 93 ASP Chi-restraints excluded: chain C residue 137 LYS Chi-restraints excluded: chain C residue 166 GLU Chi-restraints excluded: chain C residue 207 CYS Chi-restraints excluded: chain C residue 221 TYR Chi-restraints excluded: chain C residue 227 THR Chi-restraints excluded: chain C residue 258 ILE Chi-restraints excluded: chain E residue 85 GLU Chi-restraints excluded: chain F residue 99 LEU Chi-restraints excluded: chain H residue 5 LEU Chi-restraints excluded: chain H residue 38 LEU Chi-restraints excluded: chain H residue 39 THR Chi-restraints excluded: chain H residue 54 SER Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 92 ASP Chi-restraints excluded: chain I residue 55 THR Chi-restraints excluded: chain K residue 26 LYS Chi-restraints excluded: chain K residue 31 VAL Chi-restraints excluded: chain L residue 54 ARG Chi-restraints excluded: chain a residue 64 LYS Chi-restraints excluded: chain a residue 86 SER Chi-restraints excluded: chain b residue 78 ARG Chi-restraints excluded: chain b residue 85 ASP Chi-restraints excluded: chain c residue 25 PHE Chi-restraints excluded: chain c residue 59 THR Chi-restraints excluded: chain c residue 76 THR Chi-restraints excluded: chain c residue 114 VAL Chi-restraints excluded: chain d residue 87 THR Chi-restraints excluded: chain d residue 103 LEU Chi-restraints excluded: chain d residue 117 LYS Chi-restraints excluded: chain e residue 42 ARG Chi-restraints excluded: chain e residue 46 VAL Chi-restraints excluded: chain e residue 68 GLN Chi-restraints excluded: chain e residue 116 ARG Chi-restraints excluded: chain e residue 124 ILE Chi-restraints excluded: chain g residue 29 ARG Chi-restraints excluded: chain g residue 33 LEU Chi-restraints excluded: chain g residue 62 ILE Chi-restraints excluded: chain g residue 79 ILE Chi-restraints excluded: chain g residue 100 VAL Chi-restraints excluded: chain h residue 87 THR Chi-restraints excluded: chain W residue 177 HIS Chi-restraints excluded: chain W residue 203 ASP Chi-restraints excluded: chain W residue 204 LEU Chi-restraints excluded: chain W residue 249 PHE Chi-restraints excluded: chain W residue 256 VAL Chi-restraints excluded: chain W residue 389 PHE Chi-restraints excluded: chain W residue 408 THR Chi-restraints excluded: chain W residue 436 THR Chi-restraints excluded: chain W residue 488 LEU Chi-restraints excluded: chain W residue 534 VAL Chi-restraints excluded: chain W residue 541 THR Chi-restraints excluded: chain W residue 548 ASN Chi-restraints excluded: chain W residue 655 LEU Chi-restraints excluded: chain W residue 701 ASP Chi-restraints excluded: chain W residue 707 LEU Chi-restraints excluded: chain W residue 733 ILE Chi-restraints excluded: chain W residue 753 SER Chi-restraints excluded: chain Y residue 33 GLU Chi-restraints excluded: chain Z residue 286 THR Chi-restraints excluded: chain Z residue 287 ILE Chi-restraints excluded: chain Z residue 812 TYR Chi-restraints excluded: chain Z residue 846 THR Chi-restraints excluded: chain G residue 3 PHE Chi-restraints excluded: chain G residue 9 LEU Chi-restraints excluded: chain G residue 87 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 566 random chunks: chunk 496 optimal weight: 5.9990 chunk 522 optimal weight: 4.9990 chunk 476 optimal weight: 3.9990 chunk 508 optimal weight: 8.9990 chunk 305 optimal weight: 2.9990 chunk 221 optimal weight: 5.9990 chunk 399 optimal weight: 0.9980 chunk 156 optimal weight: 0.0670 chunk 459 optimal weight: 2.9990 chunk 480 optimal weight: 7.9990 chunk 506 optimal weight: 9.9990 overall best weight: 2.2124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 768 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 865 GLN ** A1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 113 GLN H 21 ASN ** H 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 89 ASN ** a 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 25 ASN ** h 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 323 ASN ** W 574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 579 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 633 ASN D 9 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.3384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 51180 Z= 0.351 Angle : 0.686 10.656 70300 Z= 0.361 Chirality : 0.044 0.223 7920 Planarity : 0.005 0.057 8063 Dihedral : 20.005 175.715 9182 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 17.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 3.26 % Allowed : 24.88 % Favored : 71.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.11), residues: 5423 helix: 0.90 (0.11), residues: 2195 sheet: -0.63 (0.19), residues: 719 loop : -0.73 (0.13), residues: 2509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP Y 63 HIS 0.017 0.001 HIS W 177 PHE 0.023 0.002 PHE A 252 TYR 0.026 0.002 TYR h 80 ARG 0.014 0.001 ARG c 17 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10846 Ramachandran restraints generated. 5423 Oldfield, 0 Emsley, 5423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10846 Ramachandran restraints generated. 5423 Oldfield, 0 Emsley, 5423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 692 residues out of total 4824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 157 poor density : 535 time to evaluate : 5.208 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 PHE cc_start: 0.8804 (OUTLIER) cc_final: 0.7626 (m-80) REVERT: A 317 LYS cc_start: 0.8478 (pptt) cc_final: 0.7832 (tttt) REVERT: A 443 LEU cc_start: 0.8808 (OUTLIER) cc_final: 0.8565 (tt) REVERT: A 497 THR cc_start: 0.8819 (OUTLIER) cc_final: 0.8591 (p) REVERT: A 780 VAL cc_start: 0.8572 (t) cc_final: 0.8217 (m) REVERT: A 826 ASP cc_start: 0.7084 (m-30) cc_final: 0.6575 (t0) REVERT: A 919 ILE cc_start: 0.8472 (mm) cc_final: 0.8226 (pp) REVERT: A 1218 GLN cc_start: 0.7936 (OUTLIER) cc_final: 0.7508 (tm130) REVERT: B 101 MET cc_start: 0.7691 (OUTLIER) cc_final: 0.7281 (mtm) REVERT: B 206 ASN cc_start: 0.7967 (t0) cc_final: 0.7341 (t0) REVERT: B 563 MET cc_start: 0.8009 (tmm) cc_final: 0.7420 (ttt) REVERT: B 632 ARG cc_start: 0.7807 (OUTLIER) cc_final: 0.7547 (mtm110) REVERT: B 662 MET cc_start: 0.7920 (mtt) cc_final: 0.7592 (mtp) REVERT: B 904 ARG cc_start: 0.7806 (OUTLIER) cc_final: 0.7606 (ptm160) REVERT: B 1021 MET cc_start: 0.8254 (OUTLIER) cc_final: 0.7578 (mpp) REVERT: B 1163 CYS cc_start: 0.7395 (OUTLIER) cc_final: 0.7098 (p) REVERT: B 1210 MET cc_start: 0.7619 (OUTLIER) cc_final: 0.6427 (tmm) REVERT: C 61 GLU cc_start: 0.6404 (tm-30) cc_final: 0.6161 (tm-30) REVERT: C 137 LYS cc_start: 0.8240 (OUTLIER) cc_final: 0.8039 (ptmt) REVERT: C 221 TYR cc_start: 0.7613 (OUTLIER) cc_final: 0.6987 (m-10) REVERT: C 227 THR cc_start: 0.8028 (OUTLIER) cc_final: 0.7802 (p) REVERT: E 85 GLU cc_start: 0.7538 (OUTLIER) cc_final: 0.7308 (mt-10) REVERT: H 62 SER cc_start: 0.8020 (t) cc_final: 0.7636 (m) REVERT: I 36 GLU cc_start: 0.7203 (tp30) cc_final: 0.6777 (tp30) REVERT: I 82 GLU cc_start: 0.7345 (pm20) cc_final: 0.6816 (pp20) REVERT: K 26 LYS cc_start: 0.7517 (OUTLIER) cc_final: 0.7166 (tttp) REVERT: K 70 ARG cc_start: 0.8529 (ptp90) cc_final: 0.7378 (ptp90) REVERT: L 54 ARG cc_start: 0.7325 (OUTLIER) cc_final: 0.7040 (ptm160) REVERT: a 83 ARG cc_start: 0.6730 (tpt170) cc_final: 0.5732 (ttt180) REVERT: b 74 GLU cc_start: 0.7854 (tp30) cc_final: 0.7524 (tp30) REVERT: b 78 ARG cc_start: 0.6129 (OUTLIER) cc_final: 0.4542 (ttp80) REVERT: b 79 LYS cc_start: 0.8469 (mtmm) cc_final: 0.8189 (mtpm) REVERT: c 25 PHE cc_start: 0.7901 (OUTLIER) cc_final: 0.6413 (m-80) REVERT: c 41 GLU cc_start: 0.7830 (mm-30) cc_final: 0.7526 (mp0) REVERT: c 88 ARG cc_start: 0.8292 (mmt-90) cc_final: 0.7927 (mmt-90) REVERT: d 117 LYS cc_start: 0.8551 (OUTLIER) cc_final: 0.8140 (ptmt) REVERT: e 42 ARG cc_start: 0.7745 (OUTLIER) cc_final: 0.5744 (ptt-90) REVERT: e 68 GLN cc_start: 0.8332 (OUTLIER) cc_final: 0.7921 (tp-100) REVERT: e 77 ASP cc_start: 0.8082 (m-30) cc_final: 0.7725 (t0) REVERT: e 109 LEU cc_start: 0.8804 (tp) cc_final: 0.8526 (tp) REVERT: e 115 LYS cc_start: 0.8188 (pttt) cc_final: 0.7557 (ptpp) REVERT: e 116 ARG cc_start: 0.5851 (OUTLIER) cc_final: 0.5548 (ttm110) REVERT: f 77 LYS cc_start: 0.8538 (mptt) cc_final: 0.8115 (mppt) REVERT: f 79 LYS cc_start: 0.6625 (pttt) cc_final: 0.6394 (pttt) REVERT: g 24 GLN cc_start: 0.7653 (mm-40) cc_final: 0.7097 (mp10) REVERT: g 27 VAL cc_start: 0.8744 (t) cc_final: 0.8510 (p) REVERT: g 29 ARG cc_start: 0.8625 (ttm-80) cc_final: 0.8202 (ptp-110) REVERT: g 35 ARG cc_start: 0.7915 (mtm110) cc_final: 0.7396 (mtm110) REVERT: g 36 LYS cc_start: 0.8148 (mmtm) cc_final: 0.7895 (ttpt) REVERT: g 89 ASN cc_start: 0.8678 (m110) cc_final: 0.8240 (m110) REVERT: h 68 GLU cc_start: 0.7775 (mm-30) cc_final: 0.7138 (mm-30) REVERT: h 90 GLU cc_start: 0.8438 (mp0) cc_final: 0.7848 (mp0) REVERT: W 177 HIS cc_start: 0.5916 (OUTLIER) cc_final: 0.4207 (p-80) REVERT: W 207 CYS cc_start: 0.7913 (p) cc_final: 0.7674 (p) REVERT: W 244 ASN cc_start: 0.7819 (m-40) cc_final: 0.7321 (m110) REVERT: W 334 GLN cc_start: 0.7634 (tp40) cc_final: 0.7284 (tp40) REVERT: W 346 ILE cc_start: 0.8474 (tp) cc_final: 0.8147 (pp) REVERT: W 548 ASN cc_start: 0.8599 (OUTLIER) cc_final: 0.8176 (t0) REVERT: W 550 LYS cc_start: 0.8706 (tptt) cc_final: 0.8350 (tptt) REVERT: W 551 GLU cc_start: 0.7514 (mp0) cc_final: 0.7243 (mp0) REVERT: W 701 ASP cc_start: 0.7964 (OUTLIER) cc_final: 0.7548 (m-30) REVERT: W 723 MET cc_start: 0.8934 (tpp) cc_final: 0.8681 (tpt) REVERT: W 802 MET cc_start: 0.8212 (ttm) cc_final: 0.8006 (ttp) REVERT: Z 315 MET cc_start: 0.0888 (tpp) cc_final: 0.0255 (mmm) REVERT: Z 346 GLU cc_start: 0.2351 (mm-30) cc_final: 0.0270 (pt0) REVERT: D 1 MET cc_start: 0.5803 (ttt) cc_final: 0.5559 (ttp) outliers start: 157 outliers final: 89 residues processed: 654 average time/residue: 1.6620 time to fit residues: 1368.3635 Evaluate side-chains 626 residues out of total 4824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 512 time to evaluate : 5.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 107 CYS Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 437 MET Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 497 THR Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 693 VAL Chi-restraints excluded: chain A residue 708 MET Chi-restraints excluded: chain A residue 754 SER Chi-restraints excluded: chain A residue 849 MET Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain A residue 878 ILE Chi-restraints excluded: chain A residue 927 VAL Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 1071 SER Chi-restraints excluded: chain A residue 1118 VAL Chi-restraints excluded: chain A residue 1218 GLN Chi-restraints excluded: chain A residue 1229 SER Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 310 MET Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 517 THR Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 589 VAL Chi-restraints excluded: chain B residue 632 ARG Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 741 CYS Chi-restraints excluded: chain B residue 764 SER Chi-restraints excluded: chain B residue 780 VAL Chi-restraints excluded: chain B residue 797 TYR Chi-restraints excluded: chain B residue 889 THR Chi-restraints excluded: chain B residue 904 ARG Chi-restraints excluded: chain B residue 1021 MET Chi-restraints excluded: chain B residue 1065 GLN Chi-restraints excluded: chain B residue 1163 CYS Chi-restraints excluded: chain B residue 1176 ASN Chi-restraints excluded: chain B residue 1210 MET Chi-restraints excluded: chain C residue 93 ASP Chi-restraints excluded: chain C residue 137 LYS Chi-restraints excluded: chain C residue 166 GLU Chi-restraints excluded: chain C residue 207 CYS Chi-restraints excluded: chain C residue 221 TYR Chi-restraints excluded: chain C residue 227 THR Chi-restraints excluded: chain C residue 258 ILE Chi-restraints excluded: chain E residue 85 GLU Chi-restraints excluded: chain E residue 214 CYS Chi-restraints excluded: chain F residue 99 LEU Chi-restraints excluded: chain H residue 5 LEU Chi-restraints excluded: chain H residue 39 THR Chi-restraints excluded: chain H residue 54 SER Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 92 ASP Chi-restraints excluded: chain I residue 55 THR Chi-restraints excluded: chain K residue 26 LYS Chi-restraints excluded: chain K residue 31 VAL Chi-restraints excluded: chain K residue 103 THR Chi-restraints excluded: chain L residue 31 CYS Chi-restraints excluded: chain L residue 50 ASP Chi-restraints excluded: chain L residue 54 ARG Chi-restraints excluded: chain a residue 86 SER Chi-restraints excluded: chain a residue 87 SER Chi-restraints excluded: chain b residue 78 ARG Chi-restraints excluded: chain b residue 85 ASP Chi-restraints excluded: chain c residue 25 PHE Chi-restraints excluded: chain c residue 59 THR Chi-restraints excluded: chain c residue 74 LYS Chi-restraints excluded: chain c residue 76 THR Chi-restraints excluded: chain c residue 114 VAL Chi-restraints excluded: chain d residue 87 THR Chi-restraints excluded: chain d residue 103 LEU Chi-restraints excluded: chain d residue 117 LYS Chi-restraints excluded: chain e residue 42 ARG Chi-restraints excluded: chain e residue 46 VAL Chi-restraints excluded: chain e residue 68 GLN Chi-restraints excluded: chain e residue 80 THR Chi-restraints excluded: chain e residue 116 ARG Chi-restraints excluded: chain e residue 124 ILE Chi-restraints excluded: chain f residue 25 ASN Chi-restraints excluded: chain g residue 62 ILE Chi-restraints excluded: chain g residue 100 VAL Chi-restraints excluded: chain W residue 177 HIS Chi-restraints excluded: chain W residue 203 ASP Chi-restraints excluded: chain W residue 204 LEU Chi-restraints excluded: chain W residue 249 PHE Chi-restraints excluded: chain W residue 256 VAL Chi-restraints excluded: chain W residue 408 THR Chi-restraints excluded: chain W residue 436 THR Chi-restraints excluded: chain W residue 534 VAL Chi-restraints excluded: chain W residue 541 THR Chi-restraints excluded: chain W residue 548 ASN Chi-restraints excluded: chain W residue 620 ASP Chi-restraints excluded: chain W residue 701 ASP Chi-restraints excluded: chain W residue 707 LEU Chi-restraints excluded: chain W residue 715 LEU Chi-restraints excluded: chain W residue 733 ILE Chi-restraints excluded: chain W residue 753 SER Chi-restraints excluded: chain Y residue 33 GLU Chi-restraints excluded: chain Z residue 286 THR Chi-restraints excluded: chain Z residue 287 ILE Chi-restraints excluded: chain Z residue 812 TYR Chi-restraints excluded: chain Z residue 833 SER Chi-restraints excluded: chain Z residue 846 THR Chi-restraints excluded: chain Z residue 857 THR Chi-restraints excluded: chain G residue 6 ASP Chi-restraints excluded: chain G residue 9 LEU Chi-restraints excluded: chain G residue 87 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 566 random chunks: chunk 333 optimal weight: 2.9990 chunk 537 optimal weight: 9.9990 chunk 328 optimal weight: 0.8980 chunk 255 optimal weight: 0.4980 chunk 373 optimal weight: 0.6980 chunk 563 optimal weight: 9.9990 chunk 518 optimal weight: 8.9990 chunk 449 optimal weight: 7.9990 chunk 46 optimal weight: 0.0010 chunk 346 optimal weight: 1.9990 chunk 275 optimal weight: 0.8980 overall best weight: 0.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 768 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 518 HIS E 61 GLN H 21 ASN I 87 GLN J 26 GLN ** K 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 89 ASN ** c 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 104 GLN h 92 GLN W 177 HIS ** W 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 323 ASN W 334 GLN ** W 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 579 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 9 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7496 moved from start: 0.3448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 51180 Z= 0.205 Angle : 0.650 11.174 70300 Z= 0.338 Chirality : 0.041 0.191 7920 Planarity : 0.004 0.073 8063 Dihedral : 19.888 174.928 9180 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 15.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 2.51 % Allowed : 25.93 % Favored : 71.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.12), residues: 5423 helix: 1.08 (0.11), residues: 2194 sheet: -0.58 (0.19), residues: 710 loop : -0.65 (0.13), residues: 2519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP W 391 HIS 0.007 0.001 HIS B 572 PHE 0.035 0.002 PHE W 389 TYR 0.034 0.001 TYR h 80 ARG 0.014 0.001 ARG H 19 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10846 Ramachandran restraints generated. 5423 Oldfield, 0 Emsley, 5423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10846 Ramachandran restraints generated. 5423 Oldfield, 0 Emsley, 5423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 666 residues out of total 4824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 545 time to evaluate : 5.704 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 PHE cc_start: 0.8745 (OUTLIER) cc_final: 0.7638 (m-80) REVERT: A 317 LYS cc_start: 0.8436 (pptt) cc_final: 0.7772 (tttt) REVERT: A 412 ARG cc_start: 0.7164 (ppt170) cc_final: 0.6956 (ppt170) REVERT: A 443 LEU cc_start: 0.8708 (OUTLIER) cc_final: 0.8467 (tt) REVERT: A 497 THR cc_start: 0.8800 (OUTLIER) cc_final: 0.8565 (p) REVERT: A 780 VAL cc_start: 0.8467 (t) cc_final: 0.8181 (m) REVERT: A 826 ASP cc_start: 0.7059 (m-30) cc_final: 0.6500 (t0) REVERT: A 919 ILE cc_start: 0.8438 (mm) cc_final: 0.8225 (pp) REVERT: A 1218 GLN cc_start: 0.7877 (OUTLIER) cc_final: 0.7475 (tm130) REVERT: B 101 MET cc_start: 0.7651 (OUTLIER) cc_final: 0.7181 (mtm) REVERT: B 206 ASN cc_start: 0.7895 (t0) cc_final: 0.7255 (t0) REVERT: B 563 MET cc_start: 0.7945 (tmm) cc_final: 0.7424 (ttt) REVERT: B 662 MET cc_start: 0.7840 (mtt) cc_final: 0.7516 (mtp) REVERT: B 705 MET cc_start: 0.8506 (mmt) cc_final: 0.8029 (tpt) REVERT: B 1021 MET cc_start: 0.8130 (OUTLIER) cc_final: 0.7280 (mpp) REVERT: B 1163 CYS cc_start: 0.7346 (OUTLIER) cc_final: 0.7056 (p) REVERT: B 1210 MET cc_start: 0.7396 (OUTLIER) cc_final: 0.6998 (ttt) REVERT: C 84 ARG cc_start: 0.7782 (mtm-85) cc_final: 0.7470 (ptt-90) REVERT: C 137 LYS cc_start: 0.8238 (OUTLIER) cc_final: 0.7884 (pttt) REVERT: C 227 THR cc_start: 0.7879 (OUTLIER) cc_final: 0.7661 (p) REVERT: C 265 MET cc_start: 0.7789 (ppp) cc_final: 0.7071 (pp-130) REVERT: E 85 GLU cc_start: 0.7383 (OUTLIER) cc_final: 0.7171 (mt-10) REVERT: F 119 ARG cc_start: 0.7620 (tpp80) cc_final: 0.7401 (tpp80) REVERT: H 62 SER cc_start: 0.7883 (t) cc_final: 0.7546 (m) REVERT: I 36 GLU cc_start: 0.6965 (tp30) cc_final: 0.6559 (tp30) REVERT: I 82 GLU cc_start: 0.7371 (pm20) cc_final: 0.6785 (pp20) REVERT: K 26 LYS cc_start: 0.7368 (OUTLIER) cc_final: 0.7044 (tttp) REVERT: K 70 ARG cc_start: 0.8457 (ptp90) cc_final: 0.7323 (ptp90) REVERT: L 68 GLU cc_start: 0.7379 (pm20) cc_final: 0.7133 (mp0) REVERT: a 83 ARG cc_start: 0.6495 (tpt170) cc_final: 0.5492 (ttt180) REVERT: b 74 GLU cc_start: 0.7726 (tp30) cc_final: 0.7317 (tp30) REVERT: b 78 ARG cc_start: 0.5905 (OUTLIER) cc_final: 0.4426 (ttp80) REVERT: b 79 LYS cc_start: 0.8279 (mtmm) cc_final: 0.8034 (mtpm) REVERT: c 25 PHE cc_start: 0.7874 (OUTLIER) cc_final: 0.6448 (m-80) REVERT: c 41 GLU cc_start: 0.7793 (mm-30) cc_final: 0.7466 (mp0) REVERT: c 88 ARG cc_start: 0.8296 (mmt-90) cc_final: 0.7930 (mmt-90) REVERT: d 56 MET cc_start: 0.8281 (tpp) cc_final: 0.7559 (tpt) REVERT: d 117 LYS cc_start: 0.8444 (OUTLIER) cc_final: 0.8080 (ptmt) REVERT: e 77 ASP cc_start: 0.8032 (m-30) cc_final: 0.7682 (t0) REVERT: e 109 LEU cc_start: 0.8726 (tp) cc_final: 0.8436 (tp) REVERT: e 115 LYS cc_start: 0.8051 (pttt) cc_final: 0.7556 (ptpp) REVERT: e 116 ARG cc_start: 0.5211 (OUTLIER) cc_final: 0.4906 (ttp80) REVERT: e 125 GLN cc_start: 0.8628 (mt0) cc_final: 0.8368 (mt0) REVERT: g 24 GLN cc_start: 0.7596 (mm-40) cc_final: 0.7064 (mp10) REVERT: g 35 ARG cc_start: 0.7901 (mtm110) cc_final: 0.7451 (mtm110) REVERT: g 36 LYS cc_start: 0.8107 (mmtm) cc_final: 0.7864 (pttt) REVERT: g 89 ASN cc_start: 0.8681 (m110) cc_final: 0.8268 (m110) REVERT: h 68 GLU cc_start: 0.7674 (mm-30) cc_final: 0.7057 (mm-30) REVERT: h 90 GLU cc_start: 0.8355 (mp0) cc_final: 0.7794 (mp0) REVERT: h 92 GLN cc_start: 0.8037 (OUTLIER) cc_final: 0.7769 (tp40) REVERT: W 177 HIS cc_start: 0.6198 (OUTLIER) cc_final: 0.4676 (p90) REVERT: W 207 CYS cc_start: 0.7887 (p) cc_final: 0.7653 (p) REVERT: W 244 ASN cc_start: 0.7779 (m-40) cc_final: 0.7291 (m110) REVERT: W 247 LYS cc_start: 0.7242 (mmmt) cc_final: 0.6694 (mtmm) REVERT: W 334 GLN cc_start: 0.7482 (tp-100) cc_final: 0.7148 (tp40) REVERT: W 346 ILE cc_start: 0.8308 (tp) cc_final: 0.7991 (pp) REVERT: W 548 ASN cc_start: 0.8602 (OUTLIER) cc_final: 0.8206 (t0) REVERT: W 550 LYS cc_start: 0.8617 (tptt) cc_final: 0.8278 (tptt) REVERT: W 551 GLU cc_start: 0.7478 (mp0) cc_final: 0.7197 (mp0) REVERT: W 701 ASP cc_start: 0.7789 (OUTLIER) cc_final: 0.7438 (m-30) REVERT: W 723 MET cc_start: 0.8893 (tpp) cc_final: 0.8674 (tpt) REVERT: W 781 MET cc_start: 0.5322 (mmm) cc_final: 0.4791 (mmm) REVERT: Y 52 MET cc_start: 0.0875 (mtm) cc_final: 0.0412 (mpp) REVERT: Z 315 MET cc_start: 0.0927 (tpp) cc_final: 0.0309 (mmm) REVERT: Z 346 GLU cc_start: 0.2284 (mm-30) cc_final: 0.0242 (pt0) REVERT: Z 367 GLU cc_start: 0.3518 (tp30) cc_final: 0.3262 (tp30) outliers start: 121 outliers final: 71 residues processed: 630 average time/residue: 1.7616 time to fit residues: 1402.6201 Evaluate side-chains 607 residues out of total 4824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 516 time to evaluate : 5.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 497 THR Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 693 VAL Chi-restraints excluded: chain A residue 754 SER Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain A residue 878 ILE Chi-restraints excluded: chain A residue 927 VAL Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 1071 SER Chi-restraints excluded: chain A residue 1218 GLN Chi-restraints excluded: chain A residue 1229 SER Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 517 THR Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 589 VAL Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 741 CYS Chi-restraints excluded: chain B residue 764 SER Chi-restraints excluded: chain B residue 780 VAL Chi-restraints excluded: chain B residue 797 TYR Chi-restraints excluded: chain B residue 889 THR Chi-restraints excluded: chain B residue 1021 MET Chi-restraints excluded: chain B residue 1065 GLN Chi-restraints excluded: chain B residue 1163 CYS Chi-restraints excluded: chain B residue 1210 MET Chi-restraints excluded: chain C residue 93 ASP Chi-restraints excluded: chain C residue 137 LYS Chi-restraints excluded: chain C residue 166 GLU Chi-restraints excluded: chain C residue 207 CYS Chi-restraints excluded: chain C residue 227 THR Chi-restraints excluded: chain C residue 258 ILE Chi-restraints excluded: chain E residue 85 GLU Chi-restraints excluded: chain E residue 214 CYS Chi-restraints excluded: chain F residue 99 LEU Chi-restraints excluded: chain H residue 5 LEU Chi-restraints excluded: chain H residue 39 THR Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 92 ASP Chi-restraints excluded: chain H residue 117 SER Chi-restraints excluded: chain I residue 55 THR Chi-restraints excluded: chain J residue 55 ASP Chi-restraints excluded: chain K residue 26 LYS Chi-restraints excluded: chain K residue 31 VAL Chi-restraints excluded: chain b residue 78 ARG Chi-restraints excluded: chain b residue 85 ASP Chi-restraints excluded: chain c residue 25 PHE Chi-restraints excluded: chain c residue 76 THR Chi-restraints excluded: chain c residue 114 VAL Chi-restraints excluded: chain d residue 87 THR Chi-restraints excluded: chain d residue 117 LYS Chi-restraints excluded: chain e residue 42 ARG Chi-restraints excluded: chain e residue 46 VAL Chi-restraints excluded: chain e residue 116 ARG Chi-restraints excluded: chain e residue 117 VAL Chi-restraints excluded: chain e residue 124 ILE Chi-restraints excluded: chain g residue 62 ILE Chi-restraints excluded: chain g residue 100 VAL Chi-restraints excluded: chain h residue 87 THR Chi-restraints excluded: chain h residue 92 GLN Chi-restraints excluded: chain W residue 177 HIS Chi-restraints excluded: chain W residue 204 LEU Chi-restraints excluded: chain W residue 249 PHE Chi-restraints excluded: chain W residue 256 VAL Chi-restraints excluded: chain W residue 323 ASN Chi-restraints excluded: chain W residue 408 THR Chi-restraints excluded: chain W residue 436 THR Chi-restraints excluded: chain W residue 534 VAL Chi-restraints excluded: chain W residue 541 THR Chi-restraints excluded: chain W residue 548 ASN Chi-restraints excluded: chain W residue 701 ASP Chi-restraints excluded: chain W residue 707 LEU Chi-restraints excluded: chain W residue 733 ILE Chi-restraints excluded: chain W residue 753 SER Chi-restraints excluded: chain Y residue 33 GLU Chi-restraints excluded: chain Z residue 286 THR Chi-restraints excluded: chain Z residue 287 ILE Chi-restraints excluded: chain Z residue 812 TYR Chi-restraints excluded: chain Z residue 833 SER Chi-restraints excluded: chain G residue 9 LEU Chi-restraints excluded: chain G residue 87 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 566 random chunks: chunk 356 optimal weight: 7.9990 chunk 478 optimal weight: 6.9990 chunk 137 optimal weight: 5.9990 chunk 414 optimal weight: 3.9990 chunk 66 optimal weight: 5.9990 chunk 124 optimal weight: 0.9990 chunk 449 optimal weight: 9.9990 chunk 188 optimal weight: 4.9990 chunk 461 optimal weight: 5.9990 chunk 56 optimal weight: 4.9990 chunk 82 optimal weight: 1.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 768 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1015 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 ASN E 113 GLN H 21 ASN J 26 GLN ** K 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 89 ASN a 93 GLN b 25 ASN ** c 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 104 GLN f 25 ASN ** g 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 81 ASN ** h 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 177 HIS ** W 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 323 ASN ** W 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 579 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 633 ASN D 9 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.110172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.083000 restraints weight = 117685.911| |-----------------------------------------------------------------------------| r_work (start): 0.3499 rms_B_bonded: 3.09 r_work: 0.3345 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.3660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.078 51180 Z= 0.489 Angle : 0.775 12.303 70300 Z= 0.406 Chirality : 0.048 0.325 7920 Planarity : 0.005 0.070 8063 Dihedral : 20.181 175.641 9180 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 18.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 2.99 % Allowed : 25.91 % Favored : 71.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.11), residues: 5423 helix: 0.66 (0.11), residues: 2187 sheet: -0.75 (0.19), residues: 709 loop : -0.78 (0.13), residues: 2527 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP Y 63 HIS 0.012 0.002 HIS A 399 PHE 0.030 0.003 PHE W 176 TYR 0.043 0.002 TYR b 88 ARG 0.016 0.001 ARG c 17 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 20506.26 seconds wall clock time: 362 minutes 51.99 seconds (21771.99 seconds total)