Starting phenix.real_space_refine on Sat Apr 13 19:12:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i03_35093/04_2024/8i03_35093_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i03_35093/04_2024/8i03_35093.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i03_35093/04_2024/8i03_35093.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i03_35093/04_2024/8i03_35093.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i03_35093/04_2024/8i03_35093_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i03_35093/04_2024/8i03_35093_updated.pdb" } resolution = 3.2 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= 0.003 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: 7 Type Number sf(0) Gaussians K 4 8.98 5 Zn 2 6.06 5 P 4 5.49 5 S 148 5.16 5 C 18642 2.51 5 N 5059 2.21 5 O 5571 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 514": "OE1" <-> "OE2" Residue "A GLU 516": "OE1" <-> "OE2" Residue "A PHE 517": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 531": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 533": "OE1" <-> "OE2" Residue "A PHE 534": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 539": "OE1" <-> "OE2" Residue "A TYR 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 544": "OE1" <-> "OE2" Residue "A ASP 547": "OD1" <-> "OD2" Residue "A GLU 553": "OE1" <-> "OE2" Residue "A TYR 556": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 575": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 607": "OE1" <-> "OE2" Residue "A PHE 630": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 649": "OE1" <-> "OE2" Residue "A GLU 658": "OE1" <-> "OE2" Residue "A ARG 659": "NH1" <-> "NH2" Residue "A TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 662": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 663": "OD1" <-> "OD2" Residue "A PHE 672": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 688": "OE1" <-> "OE2" Residue "A GLU 719": "OE1" <-> "OE2" Residue "A GLU 726": "OE1" <-> "OE2" Residue "A ASP 763": "OD1" <-> "OD2" Residue "A GLU 766": "OE1" <-> "OE2" Residue "A PHE 769": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 780": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 792": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 807": "OE1" <-> "OE2" Residue "A GLU 810": "OE1" <-> "OE2" Residue "A TYR 823": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 857": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 861": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 871": "OD1" <-> "OD2" Residue "A PHE 873": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 971": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 975": "OE1" <-> "OE2" Residue "A ASP 984": "OD1" <-> "OD2" Residue "A ASP 986": "OD1" <-> "OD2" Residue "A ASP 992": "OD1" <-> "OD2" Residue "A TYR 1002": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1011": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1014": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1017": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1026": "OE1" <-> "OE2" Residue "A GLU 1031": "OE1" <-> "OE2" Residue "A TYR 1035": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1049": "OE1" <-> "OE2" Residue "A GLU 1058": "OE1" <-> "OE2" Residue "A ARG 1059": "NH1" <-> "NH2" Residue "A PHE 1062": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1068": "OD1" <-> "OD2" Residue "A GLU 1072": "OE1" <-> "OE2" Residue "A PHE 1091": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1110": "OE1" <-> "OE2" Residue "A TYR 1136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1158": "OE1" <-> "OE2" Residue "A ASP 1164": "OD1" <-> "OD2" Residue "A ASP 1171": "OD1" <-> "OD2" Residue "A ASP 1197": "OD1" <-> "OD2" Residue "A GLU 1199": "OE1" <-> "OE2" Residue "A TYR 1203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1215": "OE1" <-> "OE2" Residue "B GLU 410": "OE1" <-> "OE2" Residue "B GLU 411": "OE1" <-> "OE2" Residue "B ARG 419": "NH1" <-> "NH2" Residue "B PHE 428": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 431": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 433": "OE1" <-> "OE2" Residue "B TYR 438": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 439": "NH1" <-> "NH2" Residue "B GLU 440": "OE1" <-> "OE2" Residue "B GLU 447": "OE1" <-> "OE2" Residue "B PHE 452": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 465": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 467": "OE1" <-> "OE2" Residue "B PHE 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 488": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 500": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 505": "OD1" <-> "OD2" Residue "B TYR 547": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 557": "OE1" <-> "OE2" Residue "B TYR 559": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 561": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 580": "OE1" <-> "OE2" Residue "B GLU 612": "OE1" <-> "OE2" Residue "B PHE 622": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 642": "OE1" <-> "OE2" Residue "B ARG 648": "NH1" <-> "NH2" Residue "B GLU 649": "OE1" <-> "OE2" Residue "B PHE 666": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 667": "OD1" <-> "OD2" Residue "B ASP 668": "OD1" <-> "OD2" Residue "B TYR 670": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 677": "OD1" <-> "OD2" Residue "B ARG 679": "NH1" <-> "NH2" Residue "B TYR 683": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 689": "OD1" <-> "OD2" Residue "B ASP 691": "OD1" <-> "OD2" Residue "B ARG 700": "NH1" <-> "NH2" Residue "B PHE 710": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 739": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 836": "OE1" <-> "OE2" Residue "B TYR 844": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 846": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 853": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 856": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 886": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 887": "OE1" <-> "OE2" Residue "B TYR 896": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 903": "NH1" <-> "NH2" Residue "B PHE 913": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 916": "OE1" <-> "OE2" Residue "B GLU 925": "OE1" <-> "OE2" Residue "B TYR 933": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 951": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 952": "OE1" <-> "OE2" Residue "B ASP 954": "OD1" <-> "OD2" Residue "B GLU 964": "OE1" <-> "OE2" Residue "B TYR 968": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 979": "OE1" <-> "OE2" Residue "B GLU 991": "OE1" <-> "OE2" Residue "B GLU 1010": "OE1" <-> "OE2" Residue "B PHE 1016": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1018": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1019": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1030": "OE1" <-> "OE2" Residue "B ASP 1033": "OD1" <-> "OD2" Residue "B TYR 1085": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1089": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1144": "OE1" <-> "OE2" Residue "C PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 46": "OE1" <-> "OE2" Residue "C TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 71": "OE1" <-> "OE2" Residue "C PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 82": "OE1" <-> "OE2" Residue "C PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 143": "OE1" <-> "OE2" Residue "C ASP 152": "OD1" <-> "OD2" Residue "C GLU 159": "OE1" <-> "OE2" Residue "C TYR 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 182": "OE1" <-> "OE2" Residue "C TYR 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 227": "OD1" <-> "OD2" Residue "C ASP 230": "OD1" <-> "OD2" Residue "C GLU 235": "OE1" <-> "OE2" Residue "C PHE 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 252": "OE1" <-> "OE2" Residue "C ASP 266": "OD1" <-> "OD2" Residue "C PHE 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 311": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 312": "OE1" <-> "OE2" Residue "C GLU 319": "OE1" <-> "OE2" Residue "C GLU 320": "OE1" <-> "OE2" Residue "C TYR 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 333": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 337": "OD1" <-> "OD2" Residue "C GLU 348": "OE1" <-> "OE2" Residue "C TYR 355": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 362": "OE1" <-> "OE2" Residue "C GLU 365": "OE1" <-> "OE2" Residue "D TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 14": "OE1" <-> "OE2" Residue "D TYR 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 46": "OE1" <-> "OE2" Residue "D ASP 67": "OD1" <-> "OD2" Residue "D GLU 68": "OE1" <-> "OE2" Residue "D TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 79": "OD1" <-> "OD2" Residue "D GLU 82": "OE1" <-> "OE2" Residue "D ASP 95": "OD1" <-> "OD2" Residue "D ASP 101": "OD1" <-> "OD2" Residue "D TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 120": "OE1" <-> "OE2" Residue "D GLU 143": "OE1" <-> "OE2" Residue "D TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 159": "OE1" <-> "OE2" Residue "D TYR 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 171": "OD1" <-> "OD2" Residue "D ASP 173": "OD1" <-> "OD2" Residue "D GLU 181": "OE1" <-> "OE2" Residue "D GLU 182": "OE1" <-> "OE2" Residue "D TYR 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 200": "OE1" <-> "OE2" Residue "D TYR 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 227": "OD1" <-> "OD2" Residue "D ASP 230": "OD1" <-> "OD2" Residue "D TYR 234": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 235": "OE1" <-> "OE2" Residue "D PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 252": "OE1" <-> "OE2" Residue "D PHE 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 288": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 311": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 312": "OE1" <-> "OE2" Residue "D GLU 319": "OE1" <-> "OE2" Residue "D GLU 320": "OE1" <-> "OE2" Residue "D GLU 323": "OE1" <-> "OE2" Residue "D TYR 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 333": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 337": "OD1" <-> "OD2" Residue "D GLU 348": "OE1" <-> "OE2" Residue "D TYR 355": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 357": "OD1" <-> "OD2" Residue "D GLU 362": "OE1" <-> "OE2" Residue "D GLU 365": "OE1" <-> "OE2" Residue "E GLU 336": "OE1" <-> "OE2" Residue "E GLU 338": "OE1" <-> "OE2" Residue "E GLU 344": "OE1" <-> "OE2" Residue "E PHE 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 354": "OD1" <-> "OD2" Residue "E GLU 358": "OE1" <-> "OE2" Residue "E ARG 359": "NH1" <-> "NH2" Residue "E ASP 362": "OD1" <-> "OD2" Residue "E GLU 369": "OE1" <-> "OE2" Residue "E TYR 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 395": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 445": "NH1" <-> "NH2" Residue "E TYR 448": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 455": "OE1" <-> "OE2" Residue "E PHE 462": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 469": "OE1" <-> "OE2" Residue "E PHE 473": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 482": "OE1" <-> "OE2" Residue "F GLU 5": "OE1" <-> "OE2" Residue "F GLU 6": "OE1" <-> "OE2" Residue "F ARG 10": "NH1" <-> "NH2" Residue "F PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 25": "OD1" <-> "OD2" Residue "F ARG 35": "NH1" <-> "NH2" Residue "F TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 71": "NH1" <-> "NH2" Residue "F ARG 78": "NH1" <-> "NH2" Residue "F PHE 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 121": "OE1" <-> "OE2" Residue "F TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 134": "OE1" <-> "OE2" Residue "F GLU 139": "OE1" <-> "OE2" Residue "F TYR 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 147": "OE1" <-> "OE2" Residue "F ASP 157": "OD1" <-> "OD2" Residue "F GLU 166": "OE1" <-> "OE2" Residue "F PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 184": "OE1" <-> "OE2" Residue "F GLU 187": "OE1" <-> "OE2" Residue "F PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 208": "NH1" <-> "NH2" Residue "F TYR 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 220": "OE1" <-> "OE2" Residue "F ASP 221": "OD1" <-> "OD2" Residue "F TYR 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 34": "OE1" <-> "OE2" Residue "G GLU 36": "OE1" <-> "OE2" Residue "G GLU 38": "OE1" <-> "OE2" Residue "G GLU 40": "OE1" <-> "OE2" Residue "G ASP 55": "OD1" <-> "OD2" Residue "G GLU 56": "OE1" <-> "OE2" Residue "G GLU 64": "OE1" <-> "OE2" Residue "G ARG 72": "NH1" <-> "NH2" Residue "G PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 81": "OE1" <-> "OE2" Residue "G TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 86": "OE1" <-> "OE2" Residue "G GLU 92": "OE1" <-> "OE2" Residue "G TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 111": "OE1" <-> "OE2" Residue "G TYR 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 118": "OE1" <-> "OE2" Residue "G GLU 233": "OE1" <-> "OE2" Residue "G ARG 236": "NH1" <-> "NH2" Residue "G GLU 237": "OE1" <-> "OE2" Residue "G GLU 241": "OE1" <-> "OE2" Residue "G GLU 249": "OE1" <-> "OE2" Residue "H GLU 7": "OE1" <-> "OE2" Residue "H PHE 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 68": "NH1" <-> "NH2" Residue "H GLU 70": "OE1" <-> "OE2" Residue "H ARG 71": "NH1" <-> "NH2" Residue "H GLU 78": "OE1" <-> "OE2" Residue "H ASP 105": "OD1" <-> "OD2" Residue "H PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 114": "OE1" <-> "OE2" Residue "H TYR 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 168": "NH1" <-> "NH2" Residue "I PHE 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 200": "OE1" <-> "OE2" Residue "I TYR 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 225": "OD1" <-> "OD2" Residue "I GLU 241": "OE1" <-> "OE2" Residue "I ASP 246": "OD1" <-> "OD2" Residue "I TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 296": "OE1" <-> "OE2" Residue "I PHE 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 325": "OE1" <-> "OE2" Residue "I GLU 334": "OE1" <-> "OE2" Residue "I GLU 342": "OE1" <-> "OE2" Residue "I PHE 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 18": "OE1" <-> "OE2" Residue "J GLU 23": "OE1" <-> "OE2" Residue "J GLU 29": "OE1" <-> "OE2" Residue "J PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 50": "OE1" <-> "OE2" Residue "J GLU 61": "OE1" <-> "OE2" Residue "J GLU 72": "OE1" <-> "OE2" Residue "J PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 82": "OD1" <-> "OD2" Residue "J TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 141": "OD1" <-> "OD2" Residue "J ASP 142": "OD1" <-> "OD2" Residue "J TYR 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 159": "OD1" <-> "OD2" Residue "J GLU 171": "OE1" <-> "OE2" Residue "J ASP 206": "OD1" <-> "OD2" Residue "J TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 219": "OE1" <-> "OE2" Residue "J ASP 239": "OD1" <-> "OD2" Residue "J PHE 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 256": "OD1" <-> "OD2" Residue "J TYR 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 263": "OD1" <-> "OD2" Residue "J ASP 268": "OD1" <-> "OD2" Residue "J PHE 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 303": "OD1" <-> "OD2" Residue "J ASP 310": "OD1" <-> "OD2" Residue "J GLU 322": "OE1" <-> "OE2" Residue "J GLU 325": "OE1" <-> "OE2" Residue "J ASP 326": "OD1" <-> "OD2" Residue "J GLU 337": "OE1" <-> "OE2" Residue "J GLU 338": "OE1" <-> "OE2" Residue "J ASP 347": "OD1" <-> "OD2" Residue "J ASP 354": "OD1" <-> "OD2" Residue "J ASP 361": "OD1" <-> "OD2" Residue "J PHE 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 389": "OD1" <-> "OD2" Residue "J GLU 403": "OE1" <-> "OE2" Residue "J ASP 404": "OD1" <-> "OD2" Residue "K GLU 18": "OE1" <-> "OE2" Residue "K GLU 23": "OE1" <-> "OE2" Residue "K GLU 29": "OE1" <-> "OE2" Residue "K PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 50": "OE1" <-> "OE2" Residue "K GLU 61": "OE1" <-> "OE2" Residue "K GLU 72": "OE1" <-> "OE2" Residue "K PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 82": "OD1" <-> "OD2" Residue "K TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 141": "OD1" <-> "OD2" Residue "K ASP 142": "OD1" <-> "OD2" Residue "K TYR 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 159": "OD1" <-> "OD2" Residue "K GLU 171": "OE1" <-> "OE2" Residue "K ASP 206": "OD1" <-> "OD2" Residue "K TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 219": "OE1" <-> "OE2" Residue "K ASP 239": "OD1" <-> "OD2" Residue "K PHE 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 256": "OD1" <-> "OD2" Residue "K TYR 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 263": "OD1" <-> "OD2" Residue "K ASP 268": "OD1" <-> "OD2" Residue "K PHE 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 303": "OD1" <-> "OD2" Residue "K ASP 310": "OD1" <-> "OD2" Residue "K GLU 322": "OE1" <-> "OE2" Residue "K GLU 325": "OE1" <-> "OE2" Residue "K ASP 326": "OD1" <-> "OD2" Residue "K GLU 337": "OE1" <-> "OE2" Residue "K GLU 338": "OE1" <-> "OE2" Residue "K ASP 347": "OD1" <-> "OD2" Residue "K ASP 354": "OD1" <-> "OD2" Residue "K ASP 361": "OD1" <-> "OD2" Residue "K PHE 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 389": "OD1" <-> "OD2" Residue "K GLU 403": "OE1" <-> "OE2" Residue "K ASP 404": "OD1" <-> "OD2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 29430 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 5072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 616, 5072 Classifications: {'peptide': 616} Link IDs: {'PTRANS': 27, 'TRANS': 588} Chain breaks: 2 Chain: "B" Number of atoms: 5305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 639, 5305 Classifications: {'peptide': 639} Link IDs: {'PTRANS': 21, 'TRANS': 617} Chain breaks: 4 Chain: "C" Number of atoms: 2962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2962 Classifications: {'peptide': 370} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 355} Chain: "D" Number of atoms: 2911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 363, 2911 Classifications: {'peptide': 363} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 348} Chain: "E" Number of atoms: 1328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1328 Classifications: {'peptide': 169} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 3, 'TRANS': 165} Chain breaks: 1 Unresolved non-hydrogen bonds: 71 Unresolved non-hydrogen angles: 91 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 2, 'ASN:plan1': 2, 'TYR:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 43 Chain: "F" Number of atoms: 1831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1831 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 10, 'TRANS': 217} Chain: "G" Number of atoms: 1306 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1306 Classifications: {'peptide': 166} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 1, 'TRANS': 164} Chain breaks: 2 Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'HIS:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 24 Chain: "H" Number of atoms: 994 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 994 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 4, 'TRANS': 121} Chain: "I" Number of atoms: 1505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1505 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 11, 'TRANS': 173} Chain: "J" Number of atoms: 3105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3105 Classifications: {'peptide': 388} Link IDs: {'PTRANS': 20, 'TRANS': 367} Chain breaks: 1 Chain: "K" Number of atoms: 3105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3105 Classifications: {'peptide': 388} Link IDs: {'PTRANS': 20, 'TRANS': 367} Chain breaks: 1 Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' K': 2, ' ZN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' K': 2, ' ZN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 15.36, per 1000 atoms: 0.52 Number of scatterers: 29430 At special positions: 0 Unit cell: (113.048, 184.79, 303.273, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 K 4 19.00 S 148 16.00 P 4 15.00 O 5571 8.00 N 5059 7.00 C 18642 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 12.71 Conformation dependent library (CDL) restraints added in 6.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN C 501 " pdb="ZN ZN C 501 " - pdb=" ND1 HIS C 175 " pdb=" ZN D 501 " pdb="ZN ZN D 501 " - pdb=" ND1 HIS D 175 " 7166 Ramachandran restraints generated. 3583 Oldfield, 0 Emsley, 3583 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6944 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 128 helices and 26 sheets defined 45.0% alpha, 11.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.02 Creating SS restraints... Processing helix chain 'A' and resid 512 through 521 Processing helix chain 'A' and resid 532 through 542 Processing helix chain 'A' and resid 548 through 558 removed outlier: 3.782A pdb=" N VAL A 552 " --> pdb=" O LYS A 548 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N GLU A 553 " --> pdb=" O ASN A 549 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N ARG A 554 " --> pdb=" O ALA A 550 " (cutoff:3.500A) Processing helix chain 'A' and resid 563 through 572 removed outlier: 3.625A pdb=" N ASN A 567 " --> pdb=" O GLU A 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 590 through 592 No H-bonds generated for 'chain 'A' and resid 590 through 592' Processing helix chain 'A' and resid 605 through 609 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 647 through 685 removed outlier: 4.106A pdb=" N ILE A 678 " --> pdb=" O GLU A 674 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N HIS A 679 " --> pdb=" O LEU A 675 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ASP A 681 " --> pdb=" O GLN A 677 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N LYS A 685 " --> pdb=" O ASP A 681 " (cutoff:3.500A) Processing helix chain 'A' and resid 690 through 692 No H-bonds generated for 'chain 'A' and resid 690 through 692' Processing helix chain 'A' and resid 705 through 716 Processing helix chain 'A' and resid 721 through 730 Processing helix chain 'A' and resid 732 through 772 Proline residue: A 737 - end of helix removed outlier: 4.618A pdb=" N GLU A 759 " --> pdb=" O ASN A 755 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N LEU A 760 " --> pdb=" O HIS A 756 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N TYR A 770 " --> pdb=" O GLU A 766 " (cutoff:3.500A) removed outlier: 5.800A pdb=" N ARG A 771 " --> pdb=" O LYS A 767 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N SER A 772 " --> pdb=" O ASN A 768 " (cutoff:3.500A) Processing helix chain 'A' and resid 775 through 778 No H-bonds generated for 'chain 'A' and resid 775 through 778' Processing helix chain 'A' and resid 783 through 786 No H-bonds generated for 'chain 'A' and resid 783 through 786' Processing helix chain 'A' and resid 790 through 809 Processing helix chain 'A' and resid 828 through 842 Processing helix chain 'A' and resid 848 through 865 Processing helix chain 'A' and resid 870 through 873 Processing helix chain 'A' and resid 1008 through 1038 removed outlier: 4.770A pdb=" N GLN A1032 " --> pdb=" O LYS A1028 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N MET A1033 " --> pdb=" O ASN A1029 " (cutoff:3.500A) Processing helix chain 'A' and resid 1045 through 1049 Processing helix chain 'A' and resid 1070 through 1083 Processing helix chain 'A' and resid 1088 through 1099 Processing helix chain 'A' and resid 1104 through 1123 removed outlier: 4.058A pdb=" N THR A1108 " --> pdb=" O ARG A1105 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL A1109 " --> pdb=" O LEU A1106 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N GLU A1110 " --> pdb=" O TYR A1107 " (cutoff:3.500A) Processing helix chain 'A' and resid 1127 through 1141 removed outlier: 4.124A pdb=" N GLN A1131 " --> pdb=" O ARG A1127 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N VAL A1141 " --> pdb=" O GLU A1137 " (cutoff:3.500A) Processing helix chain 'A' and resid 1147 through 1161 Processing helix chain 'A' and resid 1197 through 1206 Processing helix chain 'B' and resid 409 through 421 Processing helix chain 'B' and resid 425 through 439 Processing helix chain 'B' and resid 445 through 456 Processing helix chain 'B' and resid 459 through 468 Processing helix chain 'B' and resid 485 through 487 No H-bonds generated for 'chain 'B' and resid 485 through 487' Processing helix chain 'B' and resid 489 through 492 Processing helix chain 'B' and resid 519 through 522 No H-bonds generated for 'chain 'B' and resid 519 through 522' Processing helix chain 'B' and resid 548 through 578 removed outlier: 3.635A pdb=" N VAL B 564 " --> pdb=" O ASP B 560 " (cutoff:3.500A) Processing helix chain 'B' and resid 581 through 584 removed outlier: 4.354A pdb=" N HIS B 584 " --> pdb=" O PRO B 581 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 581 through 584' Processing helix chain 'B' and resid 587 through 608 removed outlier: 3.849A pdb=" N GLN B 592 " --> pdb=" O GLU B 588 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLU B 595 " --> pdb=" O LEU B 591 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N SER B 597 " --> pdb=" O GLU B 593 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N ARG B 599 " --> pdb=" O GLU B 595 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N ILE B 600 " --> pdb=" O ARG B 596 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE B 601 " --> pdb=" O SER B 597 " (cutoff:3.500A) Processing helix chain 'B' and resid 613 through 623 Processing helix chain 'B' and resid 625 through 665 Proline residue: B 630 - end of helix removed outlier: 3.549A pdb=" N GLU B 649 " --> pdb=" O ARG B 645 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N ILE B 653 " --> pdb=" O GLU B 649 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ARG B 655 " --> pdb=" O SER B 651 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N GLN B 656 " --> pdb=" O LYS B 652 " (cutoff:3.500A) Processing helix chain 'B' and resid 670 through 680 Processing helix chain 'B' and resid 683 through 698 Processing helix chain 'B' and resid 718 through 733 removed outlier: 3.779A pdb=" N ASN B 733 " --> pdb=" O ALA B 729 " (cutoff:3.500A) Processing helix chain 'B' and resid 739 through 757 removed outlier: 4.121A pdb=" N GLY B 743 " --> pdb=" O TYR B 739 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N PHE B 756 " --> pdb=" O LEU B 752 " (cutoff:3.500A) Processing helix chain 'B' and resid 838 through 841 No H-bonds generated for 'chain 'B' and resid 838 through 841' Processing helix chain 'B' and resid 850 through 875 Processing helix chain 'B' and resid 885 through 898 removed outlier: 3.635A pdb=" N LYS B 898 " --> pdb=" O GLU B 894 " (cutoff:3.500A) Processing helix chain 'B' and resid 903 through 913 removed outlier: 3.704A pdb=" N LYS B 912 " --> pdb=" O LYS B 908 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N PHE B 913 " --> pdb=" O TYR B 909 " (cutoff:3.500A) Processing helix chain 'B' and resid 916 through 940 removed outlier: 4.723A pdb=" N ILE B 921 " --> pdb=" O THR B 917 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N CYS B 922 " --> pdb=" O CYS B 918 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N SER B 923 " --> pdb=" O TYR B 919 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N ILE B 924 " --> pdb=" O MET B 920 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N GLU B 925 " --> pdb=" O ILE B 921 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N ARG B 926 " --> pdb=" O CYS B 922 " (cutoff:3.500A) Processing helix chain 'B' and resid 942 through 955 removed outlier: 3.707A pdb=" N GLY B 945 " --> pdb=" O PRO B 942 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N GLN B 946 " --> pdb=" O LYS B 943 " (cutoff:3.500A) Processing helix chain 'B' and resid 962 through 975 Processing helix chain 'B' and resid 1012 through 1025 Processing helix chain 'B' and resid 1107 through 1124 Processing helix chain 'B' and resid 1136 through 1144 Processing helix chain 'C' and resid 16 through 18 No H-bonds generated for 'chain 'C' and resid 16 through 18' Processing helix chain 'C' and resid 29 through 41 removed outlier: 4.152A pdb=" N VAL C 40 " --> pdb=" O ASN C 37 " (cutoff:3.500A) Processing helix chain 'C' and resid 44 through 46 No H-bonds generated for 'chain 'C' and resid 44 through 46' Processing helix chain 'C' and resid 58 through 61 No H-bonds generated for 'chain 'C' and resid 58 through 61' Processing helix chain 'C' and resid 67 through 75 Processing helix chain 'C' and resid 80 through 83 removed outlier: 3.828A pdb=" N LYS C 83 " --> pdb=" O THR C 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 80 through 83' Processing helix chain 'C' and resid 85 through 91 removed outlier: 3.562A pdb=" N LEU C 89 " --> pdb=" O GLN C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 123 Processing helix chain 'C' and resid 152 through 162 removed outlier: 3.946A pdb=" N LYS C 162 " --> pdb=" O LEU C 158 " (cutoff:3.500A) Processing helix chain 'C' and resid 178 through 183 Processing helix chain 'C' and resid 214 through 216 No H-bonds generated for 'chain 'C' and resid 214 through 216' Processing helix chain 'C' and resid 231 through 248 Proline residue: C 240 - end of helix Processing helix chain 'C' and resid 275 through 288 removed outlier: 4.103A pdb=" N CYS C 281 " --> pdb=" O GLY C 277 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N VAL C 282 " --> pdb=" O HIS C 278 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N PHE C 288 " --> pdb=" O PHE C 284 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 316 Processing helix chain 'C' and resid 331 through 333 No H-bonds generated for 'chain 'C' and resid 331 through 333' Processing helix chain 'C' and resid 353 through 369 Processing helix chain 'D' and resid 14 through 18 removed outlier: 3.995A pdb=" N GLY D 17 " --> pdb=" O GLU D 14 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 41 removed outlier: 4.417A pdb=" N VAL D 40 " --> pdb=" O ASN D 37 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ASN D 41 " --> pdb=" O LEU D 38 " (cutoff:3.500A) Processing helix chain 'D' and resid 58 through 61 No H-bonds generated for 'chain 'D' and resid 58 through 61' Processing helix chain 'D' and resid 67 through 75 Processing helix chain 'D' and resid 89 through 91 No H-bonds generated for 'chain 'D' and resid 89 through 91' Processing helix chain 'D' and resid 103 through 122 Processing helix chain 'D' and resid 152 through 162 removed outlier: 4.360A pdb=" N LYS D 162 " --> pdb=" O LEU D 158 " (cutoff:3.500A) Processing helix chain 'D' and resid 178 through 183 Processing helix chain 'D' and resid 214 through 216 No H-bonds generated for 'chain 'D' and resid 214 through 216' Processing helix chain 'D' and resid 231 through 248 Proline residue: D 240 - end of helix Processing helix chain 'D' and resid 275 through 288 removed outlier: 4.342A pdb=" N CYS D 281 " --> pdb=" O GLY D 277 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N VAL D 282 " --> pdb=" O HIS D 278 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N PHE D 288 " --> pdb=" O PHE D 284 " (cutoff:3.500A) Processing helix chain 'D' and resid 302 through 317 Processing helix chain 'D' and resid 331 through 334 Processing helix chain 'D' and resid 353 through 366 Processing helix chain 'E' and resid 312 through 342 Processing helix chain 'E' and resid 348 through 422 removed outlier: 3.854A pdb=" N ARG E 359 " --> pdb=" O LEU E 355 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N MET E 372 " --> pdb=" O THR E 368 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LYS E 373 " --> pdb=" O GLU E 369 " (cutoff:3.500A) Processing helix chain 'E' and resid 436 through 459 removed outlier: 3.524A pdb=" N ALA E 451 " --> pdb=" O GLU E 447 " (cutoff:3.500A) Processing helix chain 'E' and resid 473 through 483 Processing helix chain 'F' and resid 2 through 16 Processing helix chain 'F' and resid 43 through 45 No H-bonds generated for 'chain 'F' and resid 43 through 45' Processing helix chain 'F' and resid 87 through 89 No H-bonds generated for 'chain 'F' and resid 87 through 89' Processing helix chain 'F' and resid 97 through 100 No H-bonds generated for 'chain 'F' and resid 97 through 100' Processing helix chain 'F' and resid 107 through 111 Processing helix chain 'F' and resid 114 through 119 Processing helix chain 'F' and resid 125 through 154 removed outlier: 3.682A pdb=" N SER F 130 " --> pdb=" O SER F 126 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ALA F 138 " --> pdb=" O GLU F 134 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLU F 139 " --> pdb=" O ILE F 135 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N HIS F 145 " --> pdb=" O LYS F 141 " (cutoff:3.500A) Processing helix chain 'F' and resid 164 through 167 No H-bonds generated for 'chain 'F' and resid 164 through 167' Processing helix chain 'F' and resid 174 through 218 removed outlier: 3.556A pdb=" N ILE F 193 " --> pdb=" O SER F 189 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASN F 198 " --> pdb=" O ARG F 194 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N GLN F 218 " --> pdb=" O ILE F 214 " (cutoff:3.500A) Processing helix chain 'G' and resid 3 through 5 No H-bonds generated for 'chain 'G' and resid 3 through 5' Processing helix chain 'G' and resid 25 through 44 removed outlier: 3.651A pdb=" N ASN G 44 " --> pdb=" O GLU G 40 " (cutoff:3.500A) Processing helix chain 'G' and resid 50 through 137 removed outlier: 3.678A pdb=" N THR G 73 " --> pdb=" O GLU G 69 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N PHE G 74 " --> pdb=" O ARG G 70 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLU G 86 " --> pdb=" O GLU G 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 233 through 243 removed outlier: 4.259A pdb=" N LYS G 238 " --> pdb=" O ARG G 234 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLY G 243 " --> pdb=" O ALA G 239 " (cutoff:3.500A) Processing helix chain 'G' and resid 249 through 264 Processing helix chain 'H' and resid 10 through 39 removed outlier: 3.982A pdb=" N THR H 16 " --> pdb=" O LEU H 12 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ASP H 17 " --> pdb=" O ASN H 13 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N VAL H 20 " --> pdb=" O THR H 16 " (cutoff:3.500A) Proline residue: H 23 - end of helix removed outlier: 4.486A pdb=" N VAL H 26 " --> pdb=" O VAL H 22 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ILE H 36 " --> pdb=" O SER H 32 " (cutoff:3.500A) Processing helix chain 'H' and resid 41 through 56 Processing helix chain 'H' and resid 65 through 78 removed outlier: 3.653A pdb=" N CYS H 69 " --> pdb=" O GLY H 65 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLU H 70 " --> pdb=" O GLU H 66 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LEU H 72 " --> pdb=" O ARG H 68 " (cutoff:3.500A) Processing helix chain 'H' and resid 80 through 111 removed outlier: 3.735A pdb=" N ASP H 84 " --> pdb=" O LEU H 80 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N SER H 85 " --> pdb=" O PRO H 81 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N TYR H 110 " --> pdb=" O ALA H 106 " (cutoff:3.500A) Processing helix chain 'H' and resid 117 through 119 No H-bonds generated for 'chain 'H' and resid 117 through 119' Processing helix chain 'I' and resid 181 through 186 Proline residue: I 184 - end of helix No H-bonds generated for 'chain 'I' and resid 181 through 186' Processing helix chain 'I' and resid 213 through 215 No H-bonds generated for 'chain 'I' and resid 213 through 215' Processing helix chain 'I' and resid 227 through 229 No H-bonds generated for 'chain 'I' and resid 227 through 229' Processing helix chain 'I' and resid 236 through 239 No H-bonds generated for 'chain 'I' and resid 236 through 239' Processing helix chain 'I' and resid 254 through 260 Processing helix chain 'I' and resid 324 through 327 No H-bonds generated for 'chain 'I' and resid 324 through 327' Processing helix chain 'I' and resid 333 through 343 Processing helix chain 'J' and resid 15 through 35 Processing helix chain 'J' and resid 37 through 39 No H-bonds generated for 'chain 'J' and resid 37 through 39' Processing helix chain 'J' and resid 160 through 165 Processing helix chain 'J' and resid 214 through 216 No H-bonds generated for 'chain 'J' and resid 214 through 216' Processing helix chain 'J' and resid 268 through 270 No H-bonds generated for 'chain 'J' and resid 268 through 270' Processing helix chain 'J' and resid 355 through 357 No H-bonds generated for 'chain 'J' and resid 355 through 357' Processing helix chain 'J' and resid 365 through 367 No H-bonds generated for 'chain 'J' and resid 365 through 367' Processing helix chain 'J' and resid 414 through 417 No H-bonds generated for 'chain 'J' and resid 414 through 417' Processing helix chain 'K' and resid 15 through 35 Processing helix chain 'K' and resid 37 through 39 No H-bonds generated for 'chain 'K' and resid 37 through 39' Processing helix chain 'K' and resid 160 through 165 Processing helix chain 'K' and resid 214 through 216 No H-bonds generated for 'chain 'K' and resid 214 through 216' Processing helix chain 'K' and resid 268 through 270 No H-bonds generated for 'chain 'K' and resid 268 through 270' Processing helix chain 'K' and resid 355 through 357 No H-bonds generated for 'chain 'K' and resid 355 through 357' Processing helix chain 'K' and resid 365 through 367 No H-bonds generated for 'chain 'K' and resid 365 through 367' Processing helix chain 'K' and resid 414 through 417 No H-bonds generated for 'chain 'K' and resid 414 through 417' Processing sheet with id= A, first strand: chain 'A' and resid 600 through 602 Processing sheet with id= B, first strand: chain 'A' and resid 819 through 822 removed outlier: 3.962A pdb=" N LEU A1167 " --> pdb=" O MET A1184 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 710 through 713 Processing sheet with id= D, first strand: chain 'B' and resid 1078 through 1080 Processing sheet with id= E, first strand: chain 'C' and resid 8 through 11 Processing sheet with id= F, first strand: chain 'C' and resid 128 through 131 removed outlier: 6.817A pdb=" N MET C 292 " --> pdb=" O ALA C 129 " (cutoff:3.500A) removed outlier: 8.338A pdb=" N ASN C 131 " --> pdb=" O MET C 292 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N CYS C 294 " --> pdb=" O ASN C 131 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'D' and resid 8 through 11 Processing sheet with id= H, first strand: chain 'D' and resid 128 through 131 removed outlier: 6.611A pdb=" N MET D 292 " --> pdb=" O ALA D 129 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N ASN D 131 " --> pdb=" O MET D 292 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N CYS D 294 " --> pdb=" O ASN D 131 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'F' and resid 64 through 66 Processing sheet with id= J, first strand: chain 'I' and resid 200 through 202 removed outlier: 9.273A pdb=" N TYR I 201 " --> pdb=" O PHE I 219 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N ARG I 221 " --> pdb=" O TYR I 201 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N TYR I 279 " --> pdb=" O ILE I 311 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N ILE I 311 " --> pdb=" O TYR I 279 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N LEU I 281 " --> pdb=" O LEU I 309 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N LEU I 309 " --> pdb=" O LEU I 281 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'J' and resid 62 through 65 Processing sheet with id= L, first strand: chain 'J' and resid 134 through 137 Processing sheet with id= M, first strand: chain 'J' and resid 187 through 192 removed outlier: 7.177A pdb=" N GLY J 203 " --> pdb=" O THR J 188 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N VAL J 190 " --> pdb=" O VAL J 201 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N VAL J 201 " --> pdb=" O VAL J 190 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N TRP J 192 " --> pdb=" O THR J 199 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N THR J 199 " --> pdb=" O TRP J 192 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N ASP J 213 " --> pdb=" O LEU J 226 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N LEU J 226 " --> pdb=" O ASP J 213 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'J' and resid 275 through 278 removed outlier: 3.597A pdb=" N TYR J 258 " --> pdb=" O SER J 254 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASP J 239 " --> pdb=" O VAL J 253 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'J' and resid 306 through 310 removed outlier: 3.680A pdb=" N SER J 286 " --> pdb=" O CYS J 300 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'J' and resid 328 through 333 removed outlier: 6.935A pdb=" N THR J 344 " --> pdb=" O THR J 329 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N ILE J 331 " --> pdb=" O ALA J 342 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ALA J 342 " --> pdb=" O ILE J 331 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N PHE J 333 " --> pdb=" O ILE J 340 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N ILE J 340 " --> pdb=" O PHE J 333 " (cutoff:3.500A) removed outlier: 5.656A pdb=" N ASP J 354 " --> pdb=" O LEU J 374 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N LEU J 374 " --> pdb=" O ASP J 354 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'J' and resid 41 through 48 removed outlier: 6.627A pdb=" N THR J 411 " --> pdb=" O ASP J 42 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ILE J 44 " --> pdb=" O ILE J 409 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ILE J 409 " --> pdb=" O ILE J 44 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N THR J 46 " --> pdb=" O LEU J 407 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N LEU J 407 " --> pdb=" O THR J 46 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ILE J 406 " --> pdb=" O ALA J 402 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'J' and resid 52 through 58 removed outlier: 6.783A pdb=" N GLY J 78 " --> pdb=" O MET J 54 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N LEU J 56 " --> pdb=" O PHE J 76 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N PHE J 76 " --> pdb=" O LEU J 56 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'K' and resid 62 through 65 Processing sheet with id= T, first strand: chain 'K' and resid 134 through 137 Processing sheet with id= U, first strand: chain 'K' and resid 187 through 192 removed outlier: 7.177A pdb=" N GLY K 203 " --> pdb=" O THR K 188 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N VAL K 190 " --> pdb=" O VAL K 201 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N VAL K 201 " --> pdb=" O VAL K 190 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N TRP K 192 " --> pdb=" O THR K 199 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N THR K 199 " --> pdb=" O TRP K 192 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N ASP K 213 " --> pdb=" O LEU K 226 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N LEU K 226 " --> pdb=" O ASP K 213 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'K' and resid 275 through 278 removed outlier: 3.597A pdb=" N TYR K 258 " --> pdb=" O SER K 254 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASP K 239 " --> pdb=" O VAL K 253 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'K' and resid 306 through 310 removed outlier: 3.680A pdb=" N SER K 286 " --> pdb=" O CYS K 300 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'K' and resid 328 through 333 removed outlier: 6.935A pdb=" N THR K 344 " --> pdb=" O THR K 329 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N ILE K 331 " --> pdb=" O ALA K 342 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ALA K 342 " --> pdb=" O ILE K 331 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N PHE K 333 " --> pdb=" O ILE K 340 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N ILE K 340 " --> pdb=" O PHE K 333 " (cutoff:3.500A) removed outlier: 5.657A pdb=" N ASP K 354 " --> pdb=" O LEU K 374 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N LEU K 374 " --> pdb=" O ASP K 354 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'K' and resid 41 through 48 removed outlier: 6.628A pdb=" N THR K 411 " --> pdb=" O ASP K 42 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ILE K 44 " --> pdb=" O ILE K 409 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ILE K 409 " --> pdb=" O ILE K 44 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N THR K 46 " --> pdb=" O LEU K 407 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N LEU K 407 " --> pdb=" O THR K 46 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ILE K 406 " --> pdb=" O ALA K 402 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'K' and resid 52 through 58 removed outlier: 6.784A pdb=" N GLY K 78 " --> pdb=" O MET K 54 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N LEU K 56 " --> pdb=" O PHE K 76 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N PHE K 76 " --> pdb=" O LEU K 56 " (cutoff:3.500A) 1310 hydrogen bonds defined for protein. 3705 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 10.57 Time building geometry restraints manager: 13.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 9400 1.34 - 1.46: 5610 1.46 - 1.58: 14863 1.58 - 1.70: 4 1.70 - 1.82: 216 Bond restraints: 30093 Sorted by residual: bond pdb=" O1P SEP F 22 " pdb=" P SEP F 22 " ideal model delta sigma weight residual 1.610 1.513 0.097 2.00e-02 2.50e+03 2.37e+01 bond pdb=" O1P SEP F 27 " pdb=" P SEP F 27 " ideal model delta sigma weight residual 1.610 1.513 0.097 2.00e-02 2.50e+03 2.34e+01 bond pdb=" O2P SEP F 27 " pdb=" P SEP F 27 " ideal model delta sigma weight residual 1.610 1.514 0.096 2.00e-02 2.50e+03 2.30e+01 bond pdb=" O2P SEP F 24 " pdb=" P SEP F 24 " ideal model delta sigma weight residual 1.610 1.515 0.095 2.00e-02 2.50e+03 2.28e+01 bond pdb=" O3P SEP F 22 " pdb=" P SEP F 22 " ideal model delta sigma weight residual 1.610 1.515 0.095 2.00e-02 2.50e+03 2.27e+01 ... (remaining 30088 not shown) Histogram of bond angle deviations from ideal: 97.78 - 105.10: 498 105.10 - 112.42: 15262 112.42 - 119.73: 10758 119.73 - 127.05: 13844 127.05 - 134.37: 388 Bond angle restraints: 40750 Sorted by residual: angle pdb=" N LYS K 31 " pdb=" CA LYS K 31 " pdb=" CB LYS K 31 " ideal model delta sigma weight residual 110.41 119.62 -9.21 1.68e+00 3.54e-01 3.01e+01 angle pdb=" N LYS J 31 " pdb=" CA LYS J 31 " pdb=" CB LYS J 31 " ideal model delta sigma weight residual 110.41 119.61 -9.20 1.68e+00 3.54e-01 3.00e+01 angle pdb=" C TYR K 30 " pdb=" N LYS K 31 " pdb=" CA LYS K 31 " ideal model delta sigma weight residual 121.58 111.75 9.83 1.95e+00 2.63e-01 2.54e+01 angle pdb=" C TYR J 30 " pdb=" N LYS J 31 " pdb=" CA LYS J 31 " ideal model delta sigma weight residual 121.58 111.78 9.80 1.95e+00 2.63e-01 2.53e+01 angle pdb=" C VAL A 978 " pdb=" CA VAL A 978 " pdb=" CB VAL A 978 " ideal model delta sigma weight residual 111.18 102.60 8.58 1.80e+00 3.09e-01 2.27e+01 ... (remaining 40745 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 15166 17.89 - 35.78: 1906 35.78 - 53.66: 771 53.66 - 71.55: 215 71.55 - 89.44: 51 Dihedral angle restraints: 18109 sinusoidal: 7388 harmonic: 10721 Sorted by residual: dihedral pdb=" CA VAL A 978 " pdb=" C VAL A 978 " pdb=" N ASN A 979 " pdb=" CA ASN A 979 " ideal model delta harmonic sigma weight residual 180.00 125.51 54.49 0 5.00e+00 4.00e-02 1.19e+02 dihedral pdb=" CA GLY F 49 " pdb=" C GLY F 49 " pdb=" N CYS F 50 " pdb=" CA CYS F 50 " ideal model delta harmonic sigma weight residual 180.00 139.17 40.83 0 5.00e+00 4.00e-02 6.67e+01 dihedral pdb=" CA TRP A 977 " pdb=" C TRP A 977 " pdb=" N VAL A 978 " pdb=" CA VAL A 978 " ideal model delta harmonic sigma weight residual 180.00 144.90 35.10 0 5.00e+00 4.00e-02 4.93e+01 ... (remaining 18106 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.101: 4179 0.101 - 0.202: 252 0.202 - 0.303: 2 0.303 - 0.404: 0 0.404 - 0.505: 1 Chirality restraints: 4434 Sorted by residual: chirality pdb=" CB VAL A 978 " pdb=" CA VAL A 978 " pdb=" CG1 VAL A 978 " pdb=" CG2 VAL A 978 " both_signs ideal model delta sigma weight residual False -2.63 -2.12 -0.50 2.00e-01 2.50e+01 6.37e+00 chirality pdb=" CA THR B1093 " pdb=" N THR B1093 " pdb=" C THR B1093 " pdb=" CB THR B1093 " both_signs ideal model delta sigma weight residual False 2.53 2.78 -0.25 2.00e-01 2.50e+01 1.60e+00 chirality pdb=" CA ASN B1092 " pdb=" N ASN B1092 " pdb=" C ASN B1092 " pdb=" CB ASN B1092 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.41e+00 ... (remaining 4431 not shown) Planarity restraints: 5267 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 581 " 0.064 5.00e-02 4.00e+02 9.75e-02 1.52e+01 pdb=" N PRO A 582 " -0.169 5.00e-02 4.00e+02 pdb=" CA PRO A 582 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO A 582 " 0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP J 51 " -0.017 2.00e-02 2.50e+03 1.98e-02 9.80e+00 pdb=" CG TRP J 51 " 0.053 2.00e-02 2.50e+03 pdb=" CD1 TRP J 51 " -0.027 2.00e-02 2.50e+03 pdb=" CD2 TRP J 51 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP J 51 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP J 51 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP J 51 " -0.012 2.00e-02 2.50e+03 pdb=" CZ2 TRP J 51 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP J 51 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP J 51 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP K 51 " 0.017 2.00e-02 2.50e+03 1.96e-02 9.61e+00 pdb=" CG TRP K 51 " -0.052 2.00e-02 2.50e+03 pdb=" CD1 TRP K 51 " 0.027 2.00e-02 2.50e+03 pdb=" CD2 TRP K 51 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP K 51 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP K 51 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP K 51 " 0.012 2.00e-02 2.50e+03 pdb=" CZ2 TRP K 51 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP K 51 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP K 51 " 0.000 2.00e-02 2.50e+03 ... (remaining 5264 not shown) Histogram of nonbonded interaction distances: 1.84 - 2.50: 286 2.50 - 3.16: 25219 3.16 - 3.82: 55665 3.82 - 4.48: 77625 4.48 - 5.14: 128240 Nonbonded interactions: 287035 Sorted by model distance: nonbonded pdb=" O3P SEP F 27 " pdb=" OG SER F 57 " model vdw 1.837 2.440 nonbonded pdb=" OD2 ASP C 173 " pdb="ZN ZN C 501 " model vdw 1.870 2.230 nonbonded pdb=" OD2 ASP D 173 " pdb="ZN ZN D 501 " model vdw 1.962 2.230 nonbonded pdb=" OG SER J 345 " pdb=" OD1 ASP J 347 " model vdw 1.970 2.440 nonbonded pdb=" OG SER K 345 " pdb=" OD1 ASP K 347 " model vdw 1.971 2.440 ... (remaining 287030 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 'C' and (resid 7 through 369 or resid 501 through 503)) selection = chain 'D' } ncs_group { reference = chain 'J' selection = chain 'K' } 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: 2.730 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: 0.020 Extract box with map and model: 11.790 Check model and map are aligned: 0.430 Set scattering table: 0.300 Process input model: 86.930 Find NCS groups from input model: 1.250 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 106.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 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 : 0.010 0.097 30093 Z= 0.665 Angle : 0.900 13.255 40750 Z= 0.506 Chirality : 0.053 0.505 4434 Planarity : 0.005 0.097 5267 Dihedral : 19.655 89.439 11165 Min Nonbonded Distance : 1.837 Molprobity Statistics. All-atom Clashscore : 16.34 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.20 % Favored : 92.74 % Rotamer: Outliers : 15.70 % Allowed : 17.81 % Favored : 66.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.95 (0.12), residues: 3583 helix: -1.15 (0.11), residues: 1689 sheet: -1.39 (0.21), residues: 542 loop : -3.17 (0.13), residues: 1352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.003 TRP J 51 HIS 0.009 0.002 HIS J 183 PHE 0.025 0.002 PHE C 100 TYR 0.032 0.003 TYR K 86 ARG 0.009 0.001 ARG K 266 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7166 Ramachandran restraints generated. 3583 Oldfield, 0 Emsley, 3583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7166 Ramachandran restraints generated. 3583 Oldfield, 0 Emsley, 3583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 834 residues out of total 3269 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 508 poor density : 326 time to evaluate : 3.759 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 854 MET cc_start: 0.7922 (mtm) cc_final: 0.7630 (mtt) REVERT: A 1182 ARG cc_start: 0.6905 (OUTLIER) cc_final: 0.6384 (ptp90) REVERT: B 836 GLU cc_start: 0.0149 (OUTLIER) cc_final: -0.0943 (tm-30) REVERT: B 1039 MET cc_start: 0.7424 (ptt) cc_final: 0.7194 (ptt) REVERT: B 1079 PHE cc_start: 0.6974 (t80) cc_final: 0.6709 (m-80) REVERT: B 1112 LYS cc_start: 0.7155 (mttt) cc_final: 0.6790 (ttmm) REVERT: C 3 PHE cc_start: 0.7793 (t80) cc_final: 0.7489 (t80) REVERT: C 44 LEU cc_start: 0.9280 (OUTLIER) cc_final: 0.8600 (tt) REVERT: C 90 LYS cc_start: 0.9107 (OUTLIER) cc_final: 0.8889 (tptm) REVERT: C 142 ARG cc_start: 0.8577 (mtp-110) cc_final: 0.8370 (mtp-110) REVERT: C 189 ARG cc_start: 0.8639 (OUTLIER) cc_final: 0.7803 (mmp80) REVERT: D 132 TRP cc_start: 0.9093 (OUTLIER) cc_final: 0.8762 (m100) REVERT: D 227 ASP cc_start: 0.8343 (OUTLIER) cc_final: 0.8031 (m-30) REVERT: E 361 ASP cc_start: 0.7700 (t0) cc_final: 0.7380 (t0) REVERT: E 401 ARG cc_start: 0.9072 (OUTLIER) cc_final: 0.7828 (ttp-170) REVERT: F 66 ILE cc_start: 0.8232 (mm) cc_final: 0.7921 (mm) REVERT: F 105 THR cc_start: 0.8887 (p) cc_final: 0.8618 (p) REVERT: F 168 PHE cc_start: 0.8755 (OUTLIER) cc_final: 0.8085 (p90) REVERT: F 227 GLN cc_start: 0.7407 (tp40) cc_final: 0.7190 (tp40) REVERT: G 1 MET cc_start: 0.7540 (ptt) cc_final: 0.7023 (ptt) REVERT: H 79 ILE cc_start: 0.9301 (OUTLIER) cc_final: 0.8952 (mt) REVERT: H 114 GLU cc_start: 0.7827 (OUTLIER) cc_final: 0.7340 (pm20) REVERT: H 115 ILE cc_start: 0.8558 (OUTLIER) cc_final: 0.8095 (tt) REVERT: I 304 GLN cc_start: 0.8496 (OUTLIER) cc_final: 0.7672 (tm-30) REVERT: J 58 TRP cc_start: 0.7353 (m100) cc_final: 0.7002 (m100) REVERT: J 98 LEU cc_start: 0.3831 (OUTLIER) cc_final: 0.3270 (mp) REVERT: J 214 LEU cc_start: 0.6159 (OUTLIER) cc_final: 0.5907 (pt) REVERT: J 265 ARG cc_start: 0.5501 (OUTLIER) cc_final: 0.4513 (tmm-80) REVERT: J 355 LEU cc_start: 0.8178 (OUTLIER) cc_final: 0.7950 (mt) REVERT: J 377 MET cc_start: 0.6654 (OUTLIER) cc_final: 0.6143 (ptm) REVERT: K 18 GLU cc_start: 0.3977 (OUTLIER) cc_final: 0.3100 (tp30) REVERT: K 46 THR cc_start: 0.2883 (OUTLIER) cc_final: 0.2664 (p) REVERT: K 77 LEU cc_start: 0.3938 (OUTLIER) cc_final: 0.3149 (tp) REVERT: K 175 LYS cc_start: 0.4641 (OUTLIER) cc_final: 0.3960 (tttt) REVERT: K 215 ASN cc_start: 0.1927 (OUTLIER) cc_final: 0.1027 (t0) REVERT: K 241 ARG cc_start: 0.1838 (OUTLIER) cc_final: 0.1074 (tpt170) REVERT: K 246 HIS cc_start: 0.1511 (OUTLIER) cc_final: 0.1172 (t-90) REVERT: K 263 ASP cc_start: 0.0061 (OUTLIER) cc_final: -0.0215 (p0) REVERT: K 264 ILE cc_start: -0.0477 (OUTLIER) cc_final: -0.0741 (tt) REVERT: K 265 ARG cc_start: 0.3338 (OUTLIER) cc_final: 0.2500 (mmm160) REVERT: K 311 LEU cc_start: 0.1326 (OUTLIER) cc_final: -0.0063 (tp) REVERT: K 315 ASN cc_start: 0.1504 (OUTLIER) cc_final: 0.0992 (m-40) REVERT: K 345 SER cc_start: 0.0206 (OUTLIER) cc_final: -0.0587 (p) REVERT: K 355 LEU cc_start: -0.0174 (OUTLIER) cc_final: -0.0813 (pp) REVERT: K 388 MET cc_start: 0.2026 (OUTLIER) cc_final: -0.0186 (mmm) REVERT: K 395 ASN cc_start: -0.1052 (OUTLIER) cc_final: -0.1562 (m-40) REVERT: K 416 ILE cc_start: -0.1034 (OUTLIER) cc_final: -0.1260 (pt) outliers start: 508 outliers final: 204 residues processed: 769 average time/residue: 0.4267 time to fit residues: 517.4681 Evaluate side-chains 480 residues out of total 3269 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 239 poor density : 241 time to evaluate : 3.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 522 ARG Chi-restraints excluded: chain A residue 561 SER Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain A residue 587 ARG Chi-restraints excluded: chain A residue 592 GLN Chi-restraints excluded: chain A residue 599 SER Chi-restraints excluded: chain A residue 613 SER Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain A residue 684 LEU Chi-restraints excluded: chain A residue 695 THR Chi-restraints excluded: chain A residue 698 SER Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 706 SER Chi-restraints excluded: chain A residue 731 ASN Chi-restraints excluded: chain A residue 735 THR Chi-restraints excluded: chain A residue 752 SER Chi-restraints excluded: chain A residue 778 VAL Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 830 THR Chi-restraints excluded: chain A residue 851 ASN Chi-restraints excluded: chain A residue 863 SER Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 973 THR Chi-restraints excluded: chain A residue 978 VAL Chi-restraints excluded: chain A residue 983 THR Chi-restraints excluded: chain A residue 1019 THR Chi-restraints excluded: chain A residue 1022 SER Chi-restraints excluded: chain A residue 1033 MET Chi-restraints excluded: chain A residue 1041 VAL Chi-restraints excluded: chain A residue 1043 SER Chi-restraints excluded: chain A residue 1055 HIS Chi-restraints excluded: chain A residue 1060 LEU Chi-restraints excluded: chain A residue 1079 GLU Chi-restraints excluded: chain A residue 1085 GLU Chi-restraints excluded: chain A residue 1102 HIS Chi-restraints excluded: chain A residue 1113 VAL Chi-restraints excluded: chain A residue 1116 ILE Chi-restraints excluded: chain A residue 1117 ILE Chi-restraints excluded: chain A residue 1125 THR Chi-restraints excluded: chain A residue 1176 THR Chi-restraints excluded: chain A residue 1182 ARG Chi-restraints excluded: chain A residue 1193 THR Chi-restraints excluded: chain A residue 1208 TYR Chi-restraints excluded: chain B residue 403 SER Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 416 THR Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain B residue 440 GLU Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain B residue 469 ILE Chi-restraints excluded: chain B residue 473 ASP Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 491 GLU Chi-restraints excluded: chain B residue 492 THR Chi-restraints excluded: chain B residue 496 ILE Chi-restraints excluded: chain B residue 497 SER Chi-restraints excluded: chain B residue 506 SER Chi-restraints excluded: chain B residue 516 ASP Chi-restraints excluded: chain B residue 523 LEU Chi-restraints excluded: chain B residue 529 SER Chi-restraints excluded: chain B residue 537 VAL Chi-restraints excluded: chain B residue 566 ASN Chi-restraints excluded: chain B residue 567 THR Chi-restraints excluded: chain B residue 582 THR Chi-restraints excluded: chain B residue 591 LEU Chi-restraints excluded: chain B residue 619 ASP Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain B residue 653 ILE Chi-restraints excluded: chain B residue 706 LEU Chi-restraints excluded: chain B residue 719 ILE Chi-restraints excluded: chain B residue 738 SER Chi-restraints excluded: chain B residue 741 ASP Chi-restraints excluded: chain B residue 836 GLU Chi-restraints excluded: chain B residue 876 SER Chi-restraints excluded: chain B residue 881 SER Chi-restraints excluded: chain B residue 892 ILE Chi-restraints excluded: chain B residue 917 THR Chi-restraints excluded: chain B residue 937 GLU Chi-restraints excluded: chain B residue 944 LEU Chi-restraints excluded: chain B residue 960 THR Chi-restraints excluded: chain B residue 961 THR Chi-restraints excluded: chain B residue 1034 LEU Chi-restraints excluded: chain B residue 1076 LEU Chi-restraints excluded: chain B residue 1081 SER Chi-restraints excluded: chain B residue 1086 VAL Chi-restraints excluded: chain B residue 1119 ASN Chi-restraints excluded: chain B residue 1136 ASN Chi-restraints excluded: chain B residue 1137 THR Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 90 LYS Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 189 ARG Chi-restraints excluded: chain C residue 201 TYR Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 231 ASP Chi-restraints excluded: chain C residue 233 SER Chi-restraints excluded: chain C residue 243 SER Chi-restraints excluded: chain C residue 303 ARG Chi-restraints excluded: chain C residue 337 ASP Chi-restraints excluded: chain C residue 344 SER Chi-restraints excluded: chain D residue 8 VAL Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 42 TYR Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 57 THR Chi-restraints excluded: chain D residue 60 ASP Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 127 GLU Chi-restraints excluded: chain D residue 132 TRP Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 178 ASP Chi-restraints excluded: chain D residue 180 VAL Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 188 ASP Chi-restraints excluded: chain D residue 192 THR Chi-restraints excluded: chain D residue 194 SER Chi-restraints excluded: chain D residue 213 ILE Chi-restraints excluded: chain D residue 215 THR Chi-restraints excluded: chain D residue 227 ASP Chi-restraints excluded: chain D residue 231 ASP Chi-restraints excluded: chain D residue 233 SER Chi-restraints excluded: chain D residue 236 SER Chi-restraints excluded: chain D residue 260 THR Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 329 ASP Chi-restraints excluded: chain D residue 361 SER Chi-restraints excluded: chain E residue 353 ILE Chi-restraints excluded: chain E residue 366 LEU Chi-restraints excluded: chain E residue 401 ARG Chi-restraints excluded: chain E residue 406 THR Chi-restraints excluded: chain E residue 412 CYS Chi-restraints excluded: chain E residue 415 LEU Chi-restraints excluded: chain E residue 424 ASP Chi-restraints excluded: chain E residue 438 SER Chi-restraints excluded: chain E residue 459 PHE Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 54 SER Chi-restraints excluded: chain F residue 59 ILE Chi-restraints excluded: chain F residue 61 ILE Chi-restraints excluded: chain F residue 75 SER Chi-restraints excluded: chain F residue 151 VAL Chi-restraints excluded: chain F residue 154 LEU Chi-restraints excluded: chain F residue 156 ASP Chi-restraints excluded: chain F residue 168 PHE Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 225 ASN Chi-restraints excluded: chain G residue 31 LYS Chi-restraints excluded: chain G residue 41 SER Chi-restraints excluded: chain G residue 60 SER Chi-restraints excluded: chain G residue 100 THR Chi-restraints excluded: chain G residue 248 THR Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 32 SER Chi-restraints excluded: chain H residue 33 LEU Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 56 LYS Chi-restraints excluded: chain H residue 67 GLU Chi-restraints excluded: chain H residue 79 ILE Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 97 ILE Chi-restraints excluded: chain H residue 101 ILE Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain H residue 114 GLU Chi-restraints excluded: chain H residue 115 ILE Chi-restraints excluded: chain H residue 119 LEU Chi-restraints excluded: chain H residue 125 ASP Chi-restraints excluded: chain I residue 178 ASP Chi-restraints excluded: chain I residue 198 VAL Chi-restraints excluded: chain I residue 204 THR Chi-restraints excluded: chain I residue 256 THR Chi-restraints excluded: chain I residue 261 CYS Chi-restraints excluded: chain I residue 265 SER Chi-restraints excluded: chain I residue 299 SER Chi-restraints excluded: chain I residue 304 GLN Chi-restraints excluded: chain I residue 305 ASP Chi-restraints excluded: chain I residue 332 THR Chi-restraints excluded: chain I residue 346 SER Chi-restraints excluded: chain J residue 47 ARG Chi-restraints excluded: chain J residue 64 ILE Chi-restraints excluded: chain J residue 71 THR Chi-restraints excluded: chain J residue 75 MET Chi-restraints excluded: chain J residue 98 LEU Chi-restraints excluded: chain J residue 123 SER Chi-restraints excluded: chain J residue 142 ASP Chi-restraints excluded: chain J residue 143 SER Chi-restraints excluded: chain J residue 170 SER Chi-restraints excluded: chain J residue 174 LEU Chi-restraints excluded: chain J residue 181 THR Chi-restraints excluded: chain J residue 210 SER Chi-restraints excluded: chain J residue 214 LEU Chi-restraints excluded: chain J residue 229 HIS Chi-restraints excluded: chain J residue 238 SER Chi-restraints excluded: chain J residue 241 ARG Chi-restraints excluded: chain J residue 263 ASP Chi-restraints excluded: chain J residue 265 ARG Chi-restraints excluded: chain J residue 302 THR Chi-restraints excluded: chain J residue 305 THR Chi-restraints excluded: chain J residue 320 THR Chi-restraints excluded: chain J residue 329 THR Chi-restraints excluded: chain J residue 344 THR Chi-restraints excluded: chain J residue 355 LEU Chi-restraints excluded: chain J residue 358 ILE Chi-restraints excluded: chain J residue 377 MET Chi-restraints excluded: chain J residue 395 ASN Chi-restraints excluded: chain J residue 409 ILE Chi-restraints excluded: chain J residue 416 ILE Chi-restraints excluded: chain K residue 18 GLU Chi-restraints excluded: chain K residue 46 THR Chi-restraints excluded: chain K residue 71 THR Chi-restraints excluded: chain K residue 77 LEU Chi-restraints excluded: chain K residue 174 LEU Chi-restraints excluded: chain K residue 175 LYS Chi-restraints excluded: chain K residue 215 ASN Chi-restraints excluded: chain K residue 238 SER Chi-restraints excluded: chain K residue 241 ARG Chi-restraints excluded: chain K residue 246 HIS Chi-restraints excluded: chain K residue 263 ASP Chi-restraints excluded: chain K residue 264 ILE Chi-restraints excluded: chain K residue 265 ARG Chi-restraints excluded: chain K residue 270 SER Chi-restraints excluded: chain K residue 302 THR Chi-restraints excluded: chain K residue 311 LEU Chi-restraints excluded: chain K residue 315 ASN Chi-restraints excluded: chain K residue 320 THR Chi-restraints excluded: chain K residue 329 THR Chi-restraints excluded: chain K residue 343 SER Chi-restraints excluded: chain K residue 345 SER Chi-restraints excluded: chain K residue 355 LEU Chi-restraints excluded: chain K residue 368 GLN Chi-restraints excluded: chain K residue 388 MET Chi-restraints excluded: chain K residue 395 ASN Chi-restraints excluded: chain K residue 400 THR Chi-restraints excluded: chain K residue 416 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 301 optimal weight: 8.9990 chunk 270 optimal weight: 1.9990 chunk 150 optimal weight: 0.5980 chunk 92 optimal weight: 0.8980 chunk 182 optimal weight: 0.6980 chunk 144 optimal weight: 0.6980 chunk 279 optimal weight: 4.9990 chunk 108 optimal weight: 1.9990 chunk 170 optimal weight: 0.9990 chunk 208 optimal weight: 7.9990 chunk 324 optimal weight: 5.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 511 ASN A 665 HIS A 720 HIS A 729 GLN A 803 GLN A 846 HIS ** A 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 882 ASN ** A1142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 421 HIS B 474 ASN B 584 HIS B 663 GLN B 697 GLN B 722 ASN B 888 ASN B 984 ASN B 997 GLN B1036 GLN B1070 HIS B1075 ASN B1114 GLN B1115 ASN C 37 ASN C 88 GLN C 164 HIS ** C 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 350 HIS D 20 HIS ** D 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 164 HIS D 218 ASN D 222 ASN D 369 ASN E 335 ASN E 392 GLN E 414 GLN E 417 ASN F 122 GLN F 198 ASN F 225 ASN H 13 ASN ** H 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 21 ASN J 100 GLN J 121 ASN J 152 HIS ** J 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 280 HIS J 285 HIS J 319 HIS J 324 HIS J 408 GLN K 21 ASN K 121 ASN K 152 HIS K 193 ASN ** K 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 285 HIS K 319 HIS K 324 HIS Total number of N/Q/H flips: 54 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.1709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 30093 Z= 0.183 Angle : 0.597 10.332 40750 Z= 0.312 Chirality : 0.042 0.404 4434 Planarity : 0.004 0.069 5267 Dihedral : 10.535 74.206 4402 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 5.53 % Allowed : 22.63 % Favored : 71.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.13), residues: 3583 helix: 0.51 (0.12), residues: 1675 sheet: -0.67 (0.22), residues: 553 loop : -2.44 (0.15), residues: 1355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 977 HIS 0.004 0.001 HIS C 138 PHE 0.041 0.001 PHE A 836 TYR 0.021 0.001 TYR J 217 ARG 0.006 0.000 ARG K 80 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7166 Ramachandran restraints generated. 3583 Oldfield, 0 Emsley, 3583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7166 Ramachandran restraints generated. 3583 Oldfield, 0 Emsley, 3583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 465 residues out of total 3269 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 179 poor density : 286 time to evaluate : 4.009 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 823 TYR cc_start: 0.7969 (m-80) cc_final: 0.7696 (m-80) REVERT: A 854 MET cc_start: 0.7825 (mtm) cc_final: 0.7583 (mtt) REVERT: A 1182 ARG cc_start: 0.6867 (ttm110) cc_final: 0.6351 (ptp90) REVERT: A 1210 MET cc_start: 0.4481 (pmm) cc_final: 0.4078 (pmm) REVERT: B 465 PHE cc_start: 0.6983 (OUTLIER) cc_final: 0.6574 (t80) REVERT: B 688 ARG cc_start: 0.7811 (ttp-110) cc_final: 0.7559 (mtm-85) REVERT: B 1039 MET cc_start: 0.7296 (ptt) cc_final: 0.7060 (ptt) REVERT: B 1079 PHE cc_start: 0.6818 (t80) cc_final: 0.6388 (m-80) REVERT: B 1112 LYS cc_start: 0.7130 (mttt) cc_final: 0.6595 (ttmm) REVERT: C 3 PHE cc_start: 0.7871 (t80) cc_final: 0.7583 (t80) REVERT: C 44 LEU cc_start: 0.9117 (OUTLIER) cc_final: 0.8524 (tt) REVERT: F 66 ILE cc_start: 0.8073 (OUTLIER) cc_final: 0.7806 (mm) REVERT: F 168 PHE cc_start: 0.8608 (OUTLIER) cc_final: 0.8037 (p90) REVERT: G 1 MET cc_start: 0.7346 (ptt) cc_final: 0.6902 (ptt) REVERT: G 94 TYR cc_start: 0.7664 (t80) cc_final: 0.7395 (t80) REVERT: I 267 LEU cc_start: 0.8108 (mt) cc_final: 0.7897 (mp) REVERT: I 307 ILE cc_start: 0.8605 (OUTLIER) cc_final: 0.8400 (pt) REVERT: J 58 TRP cc_start: 0.7063 (m100) cc_final: 0.6796 (m100) REVERT: J 98 LEU cc_start: 0.3742 (OUTLIER) cc_final: 0.3506 (mp) REVERT: J 384 CYS cc_start: 0.7975 (OUTLIER) cc_final: 0.7386 (p) REVERT: K 18 GLU cc_start: 0.3706 (OUTLIER) cc_final: 0.2972 (mp0) REVERT: K 215 ASN cc_start: 0.2391 (m-40) cc_final: 0.1118 (t0) REVERT: K 241 ARG cc_start: 0.2097 (OUTLIER) cc_final: -0.0018 (ptm160) REVERT: K 246 HIS cc_start: 0.1704 (OUTLIER) cc_final: 0.1151 (t-90) REVERT: K 265 ARG cc_start: 0.3800 (OUTLIER) cc_final: 0.2884 (mmm160) REVERT: K 315 ASN cc_start: 0.1412 (OUTLIER) cc_final: 0.0697 (m-40) REVERT: K 326 ASP cc_start: 0.2014 (OUTLIER) cc_final: 0.1122 (p0) REVERT: K 330 LYS cc_start: 0.0679 (OUTLIER) cc_final: -0.1210 (ttpp) REVERT: K 388 MET cc_start: 0.1318 (ptt) cc_final: 0.1027 (mtp) outliers start: 179 outliers final: 103 residues processed: 447 average time/residue: 0.4337 time to fit residues: 310.9514 Evaluate side-chains 343 residues out of total 3269 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 226 time to evaluate : 3.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain A residue 684 LEU Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 706 SER Chi-restraints excluded: chain A residue 731 ASN Chi-restraints excluded: chain A residue 735 THR Chi-restraints excluded: chain A residue 747 ASP Chi-restraints excluded: chain A residue 973 THR Chi-restraints excluded: chain A residue 1033 MET Chi-restraints excluded: chain A residue 1055 HIS Chi-restraints excluded: chain A residue 1079 GLU Chi-restraints excluded: chain A residue 1113 VAL Chi-restraints excluded: chain A residue 1125 THR Chi-restraints excluded: chain A residue 1158 GLU Chi-restraints excluded: chain A residue 1193 THR Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 416 THR Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain B residue 440 GLU Chi-restraints excluded: chain B residue 465 PHE Chi-restraints excluded: chain B residue 473 ASP Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 491 GLU Chi-restraints excluded: chain B residue 516 ASP Chi-restraints excluded: chain B residue 538 LYS Chi-restraints excluded: chain B residue 575 LEU Chi-restraints excluded: chain B residue 582 THR Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain B residue 742 LYS Chi-restraints excluded: chain B residue 761 LEU Chi-restraints excluded: chain B residue 938 ILE Chi-restraints excluded: chain B residue 940 LEU Chi-restraints excluded: chain B residue 944 LEU Chi-restraints excluded: chain B residue 960 THR Chi-restraints excluded: chain B residue 1120 TRP Chi-restraints excluded: chain B residue 1137 THR Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 231 ASP Chi-restraints excluded: chain C residue 347 MET Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 127 GLU Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 178 ASP Chi-restraints excluded: chain D residue 180 VAL Chi-restraints excluded: chain D residue 192 THR Chi-restraints excluded: chain D residue 231 ASP Chi-restraints excluded: chain D residue 329 ASP Chi-restraints excluded: chain E residue 364 VAL Chi-restraints excluded: chain E residue 366 LEU Chi-restraints excluded: chain E residue 416 LEU Chi-restraints excluded: chain E residue 422 VAL Chi-restraints excluded: chain E residue 424 ASP Chi-restraints excluded: chain F residue 59 ILE Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain F residue 119 ILE Chi-restraints excluded: chain F residue 154 LEU Chi-restraints excluded: chain F residue 156 ASP Chi-restraints excluded: chain F residue 168 PHE Chi-restraints excluded: chain F residue 225 ASN Chi-restraints excluded: chain G residue 42 ILE Chi-restraints excluded: chain G residue 248 THR Chi-restraints excluded: chain H residue 42 ASP Chi-restraints excluded: chain H residue 67 GLU Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 97 ILE Chi-restraints excluded: chain H residue 101 ILE Chi-restraints excluded: chain H residue 115 ILE Chi-restraints excluded: chain H residue 130 MET Chi-restraints excluded: chain I residue 178 ASP Chi-restraints excluded: chain I residue 198 VAL Chi-restraints excluded: chain I residue 204 THR Chi-restraints excluded: chain I residue 216 ILE Chi-restraints excluded: chain I residue 251 ASP Chi-restraints excluded: chain I residue 258 LEU Chi-restraints excluded: chain I residue 307 ILE Chi-restraints excluded: chain J residue 64 ILE Chi-restraints excluded: chain J residue 71 THR Chi-restraints excluded: chain J residue 98 LEU Chi-restraints excluded: chain J residue 142 ASP Chi-restraints excluded: chain J residue 170 SER Chi-restraints excluded: chain J residue 174 LEU Chi-restraints excluded: chain J residue 181 THR Chi-restraints excluded: chain J residue 302 THR Chi-restraints excluded: chain J residue 305 THR Chi-restraints excluded: chain J residue 316 GLN Chi-restraints excluded: chain J residue 320 THR Chi-restraints excluded: chain J residue 329 THR Chi-restraints excluded: chain J residue 344 THR Chi-restraints excluded: chain J residue 358 ILE Chi-restraints excluded: chain J residue 361 ASP Chi-restraints excluded: chain J residue 382 THR Chi-restraints excluded: chain J residue 384 CYS Chi-restraints excluded: chain J residue 395 ASN Chi-restraints excluded: chain J residue 413 SER Chi-restraints excluded: chain J residue 416 ILE Chi-restraints excluded: chain K residue 18 GLU Chi-restraints excluded: chain K residue 43 LEU Chi-restraints excluded: chain K residue 71 THR Chi-restraints excluded: chain K residue 125 LEU Chi-restraints excluded: chain K residue 137 LEU Chi-restraints excluded: chain K residue 174 LEU Chi-restraints excluded: chain K residue 241 ARG Chi-restraints excluded: chain K residue 246 HIS Chi-restraints excluded: chain K residue 265 ARG Chi-restraints excluded: chain K residue 271 THR Chi-restraints excluded: chain K residue 302 THR Chi-restraints excluded: chain K residue 315 ASN Chi-restraints excluded: chain K residue 320 THR Chi-restraints excluded: chain K residue 326 ASP Chi-restraints excluded: chain K residue 329 THR Chi-restraints excluded: chain K residue 330 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 180 optimal weight: 1.9990 chunk 100 optimal weight: 7.9990 chunk 269 optimal weight: 4.9990 chunk 220 optimal weight: 5.9990 chunk 89 optimal weight: 7.9990 chunk 324 optimal weight: 4.9990 chunk 350 optimal weight: 7.9990 chunk 289 optimal weight: 7.9990 chunk 322 optimal weight: 0.0030 chunk 110 optimal weight: 0.9990 chunk 260 optimal weight: 0.7980 overall best weight: 1.7596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 762 HIS ** A 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1142 GLN ** A1173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1095 ASN C 37 ASN D 125 ASN D 324 ASN E 335 ASN E 414 GLN E 423 HIS F 165 HIS ** H 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 187 ASN ** J 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 215 ASN ** K 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.1950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 30093 Z= 0.265 Angle : 0.584 10.071 40750 Z= 0.305 Chirality : 0.043 0.186 4434 Planarity : 0.004 0.069 5267 Dihedral : 8.199 63.462 4125 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 5.44 % Allowed : 22.66 % Favored : 71.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.14), residues: 3583 helix: 0.98 (0.13), residues: 1660 sheet: -0.37 (0.23), residues: 530 loop : -2.11 (0.15), residues: 1393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B1120 HIS 0.004 0.001 HIS F 140 PHE 0.032 0.002 PHE B 415 TYR 0.023 0.002 TYR F 142 ARG 0.007 0.000 ARG J 241 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7166 Ramachandran restraints generated. 3583 Oldfield, 0 Emsley, 3583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7166 Ramachandran restraints generated. 3583 Oldfield, 0 Emsley, 3583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 3269 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 176 poor density : 249 time to evaluate : 3.648 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 823 TYR cc_start: 0.7989 (m-80) cc_final: 0.7717 (m-80) REVERT: A 854 MET cc_start: 0.7856 (mtm) cc_final: 0.7611 (mtt) REVERT: A 1089 ASN cc_start: 0.7937 (p0) cc_final: 0.7684 (p0) REVERT: A 1182 ARG cc_start: 0.6869 (ttm110) cc_final: 0.6159 (ptp90) REVERT: A 1210 MET cc_start: 0.4554 (pmm) cc_final: 0.4337 (pmm) REVERT: B 465 PHE cc_start: 0.7206 (OUTLIER) cc_final: 0.6886 (t80) REVERT: B 688 ARG cc_start: 0.7854 (ttp-110) cc_final: 0.7576 (mtm-85) REVERT: B 742 LYS cc_start: 0.7149 (OUTLIER) cc_final: 0.5855 (mmtt) REVERT: B 940 LEU cc_start: 0.8058 (OUTLIER) cc_final: 0.7606 (tt) REVERT: B 1017 MET cc_start: 0.7613 (mtt) cc_final: 0.7383 (mmm) REVERT: B 1039 MET cc_start: 0.7261 (ptt) cc_final: 0.7021 (ptt) REVERT: C 44 LEU cc_start: 0.9121 (OUTLIER) cc_final: 0.8479 (tt) REVERT: E 355 LEU cc_start: 0.8185 (pp) cc_final: 0.7968 (tt) REVERT: E 373 LYS cc_start: 0.8659 (OUTLIER) cc_final: 0.7471 (mttm) REVERT: F 8 ILE cc_start: 0.7324 (mm) cc_final: 0.7102 (mm) REVERT: F 66 ILE cc_start: 0.8108 (OUTLIER) cc_final: 0.7821 (mm) REVERT: F 168 PHE cc_start: 0.8658 (OUTLIER) cc_final: 0.8089 (p90) REVERT: G 1 MET cc_start: 0.7338 (ptt) cc_final: 0.6819 (ptt) REVERT: G 94 TYR cc_start: 0.7682 (t80) cc_final: 0.7427 (t80) REVERT: I 267 LEU cc_start: 0.8156 (mt) cc_final: 0.7862 (mp) REVERT: J 42 ASP cc_start: 0.5511 (OUTLIER) cc_final: 0.5279 (m-30) REVERT: J 51 TRP cc_start: 0.7145 (OUTLIER) cc_final: 0.6669 (m100) REVERT: J 58 TRP cc_start: 0.7107 (m100) cc_final: 0.6906 (m100) REVERT: J 98 LEU cc_start: 0.3722 (OUTLIER) cc_final: 0.3333 (tt) REVERT: J 338 GLU cc_start: 0.5492 (OUTLIER) cc_final: 0.4918 (pt0) REVERT: J 377 MET cc_start: 0.6697 (ttt) cc_final: 0.6117 (ptm) REVERT: J 384 CYS cc_start: 0.8029 (OUTLIER) cc_final: 0.7546 (p) REVERT: K 18 GLU cc_start: 0.3874 (OUTLIER) cc_final: 0.3316 (mp0) REVERT: K 30 TYR cc_start: 0.2256 (OUTLIER) cc_final: 0.2020 (t80) REVERT: K 148 VAL cc_start: 0.0010 (OUTLIER) cc_final: -0.0242 (t) REVERT: K 171 GLU cc_start: 0.2807 (mm-30) cc_final: 0.2589 (tp30) REVERT: K 215 ASN cc_start: 0.2613 (m110) cc_final: 0.1202 (t0) REVERT: K 241 ARG cc_start: 0.2299 (OUTLIER) cc_final: 0.0168 (ptm160) REVERT: K 246 HIS cc_start: 0.1638 (OUTLIER) cc_final: 0.1129 (t-90) REVERT: K 265 ARG cc_start: 0.3213 (OUTLIER) cc_final: 0.2654 (mmm160) REVERT: K 315 ASN cc_start: 0.1420 (OUTLIER) cc_final: 0.0556 (m-40) REVERT: K 326 ASP cc_start: 0.1686 (OUTLIER) cc_final: 0.0674 (p0) REVERT: K 330 LYS cc_start: 0.0719 (OUTLIER) cc_final: -0.1385 (ttpp) REVERT: K 388 MET cc_start: 0.2191 (ptt) cc_final: 0.1248 (mtp) outliers start: 176 outliers final: 110 residues processed: 411 average time/residue: 0.4237 time to fit residues: 280.5199 Evaluate side-chains 362 residues out of total 3269 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 231 time to evaluate : 3.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain A residue 684 LEU Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 706 SER Chi-restraints excluded: chain A residue 731 ASN Chi-restraints excluded: chain A residue 735 THR Chi-restraints excluded: chain A residue 747 ASP Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 973 THR Chi-restraints excluded: chain A residue 1033 MET Chi-restraints excluded: chain A residue 1055 HIS Chi-restraints excluded: chain A residue 1079 GLU Chi-restraints excluded: chain A residue 1102 HIS Chi-restraints excluded: chain A residue 1113 VAL Chi-restraints excluded: chain A residue 1158 GLU Chi-restraints excluded: chain A residue 1193 THR Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain B residue 440 GLU Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 462 THR Chi-restraints excluded: chain B residue 465 PHE Chi-restraints excluded: chain B residue 473 ASP Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 491 GLU Chi-restraints excluded: chain B residue 538 LYS Chi-restraints excluded: chain B residue 582 THR Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain B residue 713 VAL Chi-restraints excluded: chain B residue 742 LYS Chi-restraints excluded: chain B residue 940 LEU Chi-restraints excluded: chain B residue 944 LEU Chi-restraints excluded: chain B residue 960 THR Chi-restraints excluded: chain B residue 961 THR Chi-restraints excluded: chain B residue 1119 ASN Chi-restraints excluded: chain B residue 1120 TRP Chi-restraints excluded: chain B residue 1137 THR Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 123 SER Chi-restraints excluded: chain C residue 152 ASP Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 231 ASP Chi-restraints excluded: chain C residue 261 ASP Chi-restraints excluded: chain C residue 347 MET Chi-restraints excluded: chain D residue 42 TYR Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 178 ASP Chi-restraints excluded: chain D residue 180 VAL Chi-restraints excluded: chain D residue 188 ASP Chi-restraints excluded: chain D residue 192 THR Chi-restraints excluded: chain D residue 231 ASP Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 329 ASP Chi-restraints excluded: chain E residue 366 LEU Chi-restraints excluded: chain E residue 373 LYS Chi-restraints excluded: chain E residue 415 LEU Chi-restraints excluded: chain E residue 422 VAL Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 59 ILE Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain F residue 119 ILE Chi-restraints excluded: chain F residue 154 LEU Chi-restraints excluded: chain F residue 168 PHE Chi-restraints excluded: chain F residue 225 ASN Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain G residue 42 ILE Chi-restraints excluded: chain G residue 248 THR Chi-restraints excluded: chain G residue 251 ASP Chi-restraints excluded: chain H residue 37 ASP Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 42 ASP Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 97 ILE Chi-restraints excluded: chain H residue 101 ILE Chi-restraints excluded: chain H residue 115 ILE Chi-restraints excluded: chain H residue 119 LEU Chi-restraints excluded: chain I residue 178 ASP Chi-restraints excluded: chain I residue 198 VAL Chi-restraints excluded: chain I residue 204 THR Chi-restraints excluded: chain I residue 258 LEU Chi-restraints excluded: chain I residue 332 THR Chi-restraints excluded: chain J residue 42 ASP Chi-restraints excluded: chain J residue 51 TRP Chi-restraints excluded: chain J residue 64 ILE Chi-restraints excluded: chain J residue 71 THR Chi-restraints excluded: chain J residue 98 LEU Chi-restraints excluded: chain J residue 142 ASP Chi-restraints excluded: chain J residue 170 SER Chi-restraints excluded: chain J residue 174 LEU Chi-restraints excluded: chain J residue 181 THR Chi-restraints excluded: chain J residue 263 ASP Chi-restraints excluded: chain J residue 287 VAL Chi-restraints excluded: chain J residue 302 THR Chi-restraints excluded: chain J residue 305 THR Chi-restraints excluded: chain J residue 306 ILE Chi-restraints excluded: chain J residue 316 GLN Chi-restraints excluded: chain J residue 320 THR Chi-restraints excluded: chain J residue 338 GLU Chi-restraints excluded: chain J residue 358 ILE Chi-restraints excluded: chain J residue 361 ASP Chi-restraints excluded: chain J residue 382 THR Chi-restraints excluded: chain J residue 383 SER Chi-restraints excluded: chain J residue 384 CYS Chi-restraints excluded: chain J residue 395 ASN Chi-restraints excluded: chain J residue 413 SER Chi-restraints excluded: chain J residue 416 ILE Chi-restraints excluded: chain K residue 18 GLU Chi-restraints excluded: chain K residue 30 TYR Chi-restraints excluded: chain K residue 43 LEU Chi-restraints excluded: chain K residue 77 LEU Chi-restraints excluded: chain K residue 137 LEU Chi-restraints excluded: chain K residue 143 SER Chi-restraints excluded: chain K residue 148 VAL Chi-restraints excluded: chain K residue 174 LEU Chi-restraints excluded: chain K residue 241 ARG Chi-restraints excluded: chain K residue 246 HIS Chi-restraints excluded: chain K residue 263 ASP Chi-restraints excluded: chain K residue 265 ARG Chi-restraints excluded: chain K residue 271 THR Chi-restraints excluded: chain K residue 302 THR Chi-restraints excluded: chain K residue 315 ASN Chi-restraints excluded: chain K residue 320 THR Chi-restraints excluded: chain K residue 326 ASP Chi-restraints excluded: chain K residue 329 THR Chi-restraints excluded: chain K residue 330 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 320 optimal weight: 8.9990 chunk 244 optimal weight: 9.9990 chunk 168 optimal weight: 0.9990 chunk 35 optimal weight: 0.6980 chunk 154 optimal weight: 0.7980 chunk 218 optimal weight: 3.9990 chunk 325 optimal weight: 50.0000 chunk 345 optimal weight: 9.9990 chunk 170 optimal weight: 0.9990 chunk 308 optimal weight: 0.0070 chunk 92 optimal weight: 9.9990 overall best weight: 0.7002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 37 ASN E 335 ASN E 414 GLN E 423 HIS H 95 ASN ** J 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 319 HIS ** K 262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.2376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 30093 Z= 0.153 Angle : 0.524 9.251 40750 Z= 0.273 Chirality : 0.041 0.206 4434 Planarity : 0.004 0.058 5267 Dihedral : 7.365 59.224 4102 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 4.79 % Allowed : 23.65 % Favored : 71.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.14), residues: 3583 helix: 1.44 (0.13), residues: 1645 sheet: -0.11 (0.23), residues: 514 loop : -1.82 (0.15), residues: 1424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP J 309 HIS 0.004 0.001 HIS F 140 PHE 0.033 0.001 PHE B 415 TYR 0.017 0.001 TYR F 142 ARG 0.006 0.000 ARG J 241 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7166 Ramachandran restraints generated. 3583 Oldfield, 0 Emsley, 3583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7166 Ramachandran restraints generated. 3583 Oldfield, 0 Emsley, 3583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 3269 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 155 poor density : 260 time to evaluate : 3.255 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 823 TYR cc_start: 0.7999 (m-80) cc_final: 0.7757 (m-80) REVERT: A 854 MET cc_start: 0.7791 (mtm) cc_final: 0.7573 (mtt) REVERT: A 1089 ASN cc_start: 0.7917 (p0) cc_final: 0.7672 (p0) REVERT: A 1182 ARG cc_start: 0.6837 (ttm110) cc_final: 0.6126 (ptp90) REVERT: B 440 GLU cc_start: 0.7904 (OUTLIER) cc_final: 0.7057 (tp30) REVERT: B 688 ARG cc_start: 0.7812 (ttp-110) cc_final: 0.7527 (mtm-85) REVERT: B 940 LEU cc_start: 0.8038 (OUTLIER) cc_final: 0.7692 (tt) REVERT: C 44 LEU cc_start: 0.9066 (OUTLIER) cc_final: 0.8455 (tt) REVERT: E 355 LEU cc_start: 0.8100 (pp) cc_final: 0.7878 (tt) REVERT: F 8 ILE cc_start: 0.7272 (mm) cc_final: 0.7052 (mm) REVERT: F 66 ILE cc_start: 0.8061 (OUTLIER) cc_final: 0.7790 (mm) REVERT: F 168 PHE cc_start: 0.8591 (OUTLIER) cc_final: 0.7986 (p90) REVERT: G 1 MET cc_start: 0.7264 (ptt) cc_final: 0.6860 (ptt) REVERT: I 267 LEU cc_start: 0.8101 (mt) cc_final: 0.7853 (mp) REVERT: J 51 TRP cc_start: 0.6974 (OUTLIER) cc_final: 0.6525 (m100) REVERT: J 54 MET cc_start: 0.6172 (ttm) cc_final: 0.5743 (ttm) REVERT: J 58 TRP cc_start: 0.7047 (m100) cc_final: 0.6841 (m100) REVERT: J 98 LEU cc_start: 0.3473 (OUTLIER) cc_final: 0.2994 (tt) REVERT: J 174 LEU cc_start: 0.6356 (OUTLIER) cc_final: 0.5985 (mp) REVERT: J 266 ARG cc_start: 0.5910 (OUTLIER) cc_final: 0.5612 (mtp-110) REVERT: J 296 ILE cc_start: 0.6836 (OUTLIER) cc_final: 0.6447 (mm) REVERT: J 306 ILE cc_start: 0.7609 (OUTLIER) cc_final: 0.7038 (mt) REVERT: J 377 MET cc_start: 0.6772 (ttt) cc_final: 0.6414 (ptm) REVERT: J 388 MET cc_start: 0.6937 (OUTLIER) cc_final: 0.6523 (tmm) REVERT: K 18 GLU cc_start: 0.4055 (OUTLIER) cc_final: 0.2903 (tp30) REVERT: K 148 VAL cc_start: 0.0470 (OUTLIER) cc_final: 0.0263 (t) REVERT: K 215 ASN cc_start: 0.2746 (m110) cc_final: 0.1199 (t0) REVERT: K 236 GLN cc_start: 0.3127 (mp10) cc_final: 0.2078 (mt0) REVERT: K 241 ARG cc_start: 0.1689 (OUTLIER) cc_final: 0.0258 (ptm160) REVERT: K 246 HIS cc_start: 0.1724 (OUTLIER) cc_final: 0.1227 (t-90) REVERT: K 315 ASN cc_start: 0.1558 (OUTLIER) cc_final: 0.0710 (m-40) REVERT: K 329 THR cc_start: -0.0631 (OUTLIER) cc_final: -0.1006 (p) REVERT: K 330 LYS cc_start: 0.0850 (OUTLIER) cc_final: 0.0540 (ttpp) REVERT: K 388 MET cc_start: 0.2144 (ptt) cc_final: 0.0643 (mtm) outliers start: 155 outliers final: 95 residues processed: 397 average time/residue: 0.4225 time to fit residues: 269.7596 Evaluate side-chains 346 residues out of total 3269 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 232 time to evaluate : 3.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 684 LEU Chi-restraints excluded: chain A residue 731 ASN Chi-restraints excluded: chain A residue 735 THR Chi-restraints excluded: chain A residue 747 ASP Chi-restraints excluded: chain A residue 778 VAL Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 978 VAL Chi-restraints excluded: chain A residue 1033 MET Chi-restraints excluded: chain A residue 1055 HIS Chi-restraints excluded: chain A residue 1079 GLU Chi-restraints excluded: chain A residue 1113 VAL Chi-restraints excluded: chain A residue 1117 ILE Chi-restraints excluded: chain A residue 1120 LEU Chi-restraints excluded: chain A residue 1125 THR Chi-restraints excluded: chain A residue 1167 LEU Chi-restraints excluded: chain A residue 1193 THR Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain B residue 416 THR Chi-restraints excluded: chain B residue 440 GLU Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 473 ASP Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 491 GLU Chi-restraints excluded: chain B residue 495 CYS Chi-restraints excluded: chain B residue 575 LEU Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain B residue 713 VAL Chi-restraints excluded: chain B residue 904 LEU Chi-restraints excluded: chain B residue 937 GLU Chi-restraints excluded: chain B residue 940 LEU Chi-restraints excluded: chain B residue 944 LEU Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1119 ASN Chi-restraints excluded: chain B residue 1137 THR Chi-restraints excluded: chain C residue 37 ASN Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 123 SER Chi-restraints excluded: chain C residue 152 ASP Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 231 ASP Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 261 ASP Chi-restraints excluded: chain C residue 319 GLU Chi-restraints excluded: chain C residue 347 MET Chi-restraints excluded: chain D residue 42 TYR Chi-restraints excluded: chain D residue 57 THR Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 178 ASP Chi-restraints excluded: chain D residue 192 THR Chi-restraints excluded: chain D residue 329 ASP Chi-restraints excluded: chain E residue 366 LEU Chi-restraints excluded: chain E residue 398 ARG Chi-restraints excluded: chain E residue 415 LEU Chi-restraints excluded: chain E residue 422 VAL Chi-restraints excluded: chain F residue 23 ASP Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 59 ILE Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain F residue 119 ILE Chi-restraints excluded: chain F residue 154 LEU Chi-restraints excluded: chain F residue 156 ASP Chi-restraints excluded: chain F residue 168 PHE Chi-restraints excluded: chain F residue 225 ASN Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain G residue 248 THR Chi-restraints excluded: chain G residue 262 GLU Chi-restraints excluded: chain H residue 37 ASP Chi-restraints excluded: chain H residue 42 ASP Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 97 ILE Chi-restraints excluded: chain H residue 101 ILE Chi-restraints excluded: chain H residue 115 ILE Chi-restraints excluded: chain H residue 125 ASP Chi-restraints excluded: chain H residue 129 LEU Chi-restraints excluded: chain I residue 178 ASP Chi-restraints excluded: chain I residue 198 VAL Chi-restraints excluded: chain I residue 204 THR Chi-restraints excluded: chain I residue 251 ASP Chi-restraints excluded: chain I residue 332 THR Chi-restraints excluded: chain J residue 51 TRP Chi-restraints excluded: chain J residue 98 LEU Chi-restraints excluded: chain J residue 142 ASP Chi-restraints excluded: chain J residue 170 SER Chi-restraints excluded: chain J residue 174 LEU Chi-restraints excluded: chain J residue 181 THR Chi-restraints excluded: chain J residue 266 ARG Chi-restraints excluded: chain J residue 296 ILE Chi-restraints excluded: chain J residue 302 THR Chi-restraints excluded: chain J residue 305 THR Chi-restraints excluded: chain J residue 306 ILE Chi-restraints excluded: chain J residue 316 GLN Chi-restraints excluded: chain J residue 320 THR Chi-restraints excluded: chain J residue 361 ASP Chi-restraints excluded: chain J residue 382 THR Chi-restraints excluded: chain J residue 388 MET Chi-restraints excluded: chain J residue 395 ASN Chi-restraints excluded: chain J residue 416 ILE Chi-restraints excluded: chain K residue 18 GLU Chi-restraints excluded: chain K residue 43 LEU Chi-restraints excluded: chain K residue 77 LEU Chi-restraints excluded: chain K residue 143 SER Chi-restraints excluded: chain K residue 148 VAL Chi-restraints excluded: chain K residue 241 ARG Chi-restraints excluded: chain K residue 246 HIS Chi-restraints excluded: chain K residue 263 ASP Chi-restraints excluded: chain K residue 271 THR Chi-restraints excluded: chain K residue 302 THR Chi-restraints excluded: chain K residue 315 ASN Chi-restraints excluded: chain K residue 320 THR Chi-restraints excluded: chain K residue 329 THR Chi-restraints excluded: chain K residue 330 LYS Chi-restraints excluded: chain K residue 361 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 287 optimal weight: 9.9990 chunk 195 optimal weight: 3.9990 chunk 5 optimal weight: 0.9990 chunk 256 optimal weight: 0.9980 chunk 142 optimal weight: 3.9990 chunk 294 optimal weight: 10.0000 chunk 238 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 176 optimal weight: 2.9990 chunk 309 optimal weight: 3.9990 chunk 87 optimal weight: 6.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 414 GLN E 423 HIS ** J 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 319 HIS K 27 ASN ** K 262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 280 HIS K 319 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.2347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 30093 Z= 0.355 Angle : 0.601 9.673 40750 Z= 0.312 Chirality : 0.044 0.188 4434 Planarity : 0.005 0.068 5267 Dihedral : 7.226 59.471 4075 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 6.09 % Allowed : 23.37 % Favored : 70.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.14), residues: 3583 helix: 1.26 (0.13), residues: 1663 sheet: -0.29 (0.23), residues: 530 loop : -1.87 (0.16), residues: 1390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B1120 HIS 0.006 0.001 HIS C 244 PHE 0.024 0.002 PHE C 3 TYR 0.028 0.002 TYR G 83 ARG 0.008 0.000 ARG J 317 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7166 Ramachandran restraints generated. 3583 Oldfield, 0 Emsley, 3583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7166 Ramachandran restraints generated. 3583 Oldfield, 0 Emsley, 3583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 443 residues out of total 3269 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 197 poor density : 246 time to evaluate : 3.908 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 823 TYR cc_start: 0.8016 (m-80) cc_final: 0.7799 (m-80) REVERT: A 854 MET cc_start: 0.7785 (mtm) cc_final: 0.7561 (mtt) REVERT: A 1182 ARG cc_start: 0.6872 (OUTLIER) cc_final: 0.6126 (ptp90) REVERT: B 465 PHE cc_start: 0.7259 (OUTLIER) cc_final: 0.6949 (t80) REVERT: B 742 LYS cc_start: 0.7208 (OUTLIER) cc_final: 0.5950 (mmtt) REVERT: B 834 LEU cc_start: 0.2636 (OUTLIER) cc_final: 0.2354 (mp) REVERT: B 836 GLU cc_start: 0.0490 (OUTLIER) cc_final: -0.0737 (tm-30) REVERT: B 940 LEU cc_start: 0.8149 (OUTLIER) cc_final: 0.7755 (tt) REVERT: C 44 LEU cc_start: 0.9154 (OUTLIER) cc_final: 0.8509 (tt) REVERT: E 355 LEU cc_start: 0.8125 (pp) cc_final: 0.7900 (tt) REVERT: E 373 LYS cc_start: 0.8683 (OUTLIER) cc_final: 0.7436 (mttm) REVERT: F 8 ILE cc_start: 0.7440 (mm) cc_final: 0.7214 (mm) REVERT: F 66 ILE cc_start: 0.8107 (mm) cc_final: 0.7759 (mm) REVERT: F 168 PHE cc_start: 0.8704 (OUTLIER) cc_final: 0.8211 (p90) REVERT: G 1 MET cc_start: 0.7361 (ptt) cc_final: 0.6877 (ptt) REVERT: I 267 LEU cc_start: 0.8125 (mt) cc_final: 0.7853 (mp) REVERT: I 298 ARG cc_start: 0.8809 (OUTLIER) cc_final: 0.8032 (mtt90) REVERT: J 50 GLU cc_start: 0.7620 (OUTLIER) cc_final: 0.7401 (mp0) REVERT: J 51 TRP cc_start: 0.7043 (OUTLIER) cc_final: 0.6538 (m100) REVERT: J 54 MET cc_start: 0.6425 (ttm) cc_final: 0.6042 (ttm) REVERT: J 58 TRP cc_start: 0.7089 (m100) cc_final: 0.6887 (m100) REVERT: J 98 LEU cc_start: 0.3436 (OUTLIER) cc_final: 0.3205 (tt) REVERT: J 130 GLU cc_start: 0.5236 (OUTLIER) cc_final: 0.4882 (tt0) REVERT: J 174 LEU cc_start: 0.6510 (OUTLIER) cc_final: 0.6096 (mp) REVERT: J 266 ARG cc_start: 0.5863 (OUTLIER) cc_final: 0.5558 (mtp-110) REVERT: J 296 ILE cc_start: 0.6934 (OUTLIER) cc_final: 0.6535 (mm) REVERT: J 377 MET cc_start: 0.6905 (ttt) cc_final: 0.6641 (ptm) REVERT: J 384 CYS cc_start: 0.8256 (OUTLIER) cc_final: 0.7846 (p) REVERT: K 18 GLU cc_start: 0.4004 (OUTLIER) cc_final: 0.2872 (tp30) REVERT: K 39 PHE cc_start: 0.4116 (t80) cc_final: 0.3473 (m-10) REVERT: K 171 GLU cc_start: 0.2623 (mm-30) cc_final: 0.2154 (tp30) REVERT: K 215 ASN cc_start: 0.2929 (m110) cc_final: 0.1139 (t0) REVERT: K 236 GLN cc_start: 0.3259 (mp10) cc_final: 0.2054 (mt0) REVERT: K 241 ARG cc_start: 0.1718 (OUTLIER) cc_final: 0.0304 (ptm160) REVERT: K 246 HIS cc_start: 0.2045 (OUTLIER) cc_final: 0.1328 (t-170) REVERT: K 315 ASN cc_start: 0.1442 (OUTLIER) cc_final: 0.0604 (m-40) REVERT: K 326 ASP cc_start: 0.1437 (OUTLIER) cc_final: 0.0859 (p0) REVERT: K 329 THR cc_start: -0.0689 (OUTLIER) cc_final: -0.1070 (p) REVERT: K 330 LYS cc_start: 0.0901 (OUTLIER) cc_final: 0.0548 (ttpp) REVERT: K 388 MET cc_start: 0.2468 (ptt) cc_final: 0.0867 (mtm) outliers start: 197 outliers final: 133 residues processed: 421 average time/residue: 0.4157 time to fit residues: 283.4875 Evaluate side-chains 397 residues out of total 3269 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 158 poor density : 239 time to evaluate : 3.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 522 ARG Chi-restraints excluded: chain A residue 589 ASP Chi-restraints excluded: chain A residue 684 LEU Chi-restraints excluded: chain A residue 706 SER Chi-restraints excluded: chain A residue 731 ASN Chi-restraints excluded: chain A residue 735 THR Chi-restraints excluded: chain A residue 747 ASP Chi-restraints excluded: chain A residue 778 VAL Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 830 THR Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 1033 MET Chi-restraints excluded: chain A residue 1053 VAL Chi-restraints excluded: chain A residue 1055 HIS Chi-restraints excluded: chain A residue 1079 GLU Chi-restraints excluded: chain A residue 1102 HIS Chi-restraints excluded: chain A residue 1113 VAL Chi-restraints excluded: chain A residue 1117 ILE Chi-restraints excluded: chain A residue 1120 LEU Chi-restraints excluded: chain A residue 1125 THR Chi-restraints excluded: chain A residue 1167 LEU Chi-restraints excluded: chain A residue 1182 ARG Chi-restraints excluded: chain A residue 1193 THR Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 416 THR Chi-restraints excluded: chain B residue 440 GLU Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 462 THR Chi-restraints excluded: chain B residue 465 PHE Chi-restraints excluded: chain B residue 473 ASP Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 491 GLU Chi-restraints excluded: chain B residue 566 ASN Chi-restraints excluded: chain B residue 582 THR Chi-restraints excluded: chain B residue 612 GLU Chi-restraints excluded: chain B residue 619 ASP Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain B residue 713 VAL Chi-restraints excluded: chain B residue 742 LYS Chi-restraints excluded: chain B residue 761 LEU Chi-restraints excluded: chain B residue 834 LEU Chi-restraints excluded: chain B residue 836 GLU Chi-restraints excluded: chain B residue 904 LEU Chi-restraints excluded: chain B residue 940 LEU Chi-restraints excluded: chain B residue 944 LEU Chi-restraints excluded: chain B residue 960 THR Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1119 ASN Chi-restraints excluded: chain B residue 1137 THR Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 123 SER Chi-restraints excluded: chain C residue 152 ASP Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 231 ASP Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 261 ASP Chi-restraints excluded: chain C residue 347 MET Chi-restraints excluded: chain D residue 15 ASP Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 42 TYR Chi-restraints excluded: chain D residue 57 THR Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 127 GLU Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 178 ASP Chi-restraints excluded: chain D residue 188 ASP Chi-restraints excluded: chain D residue 192 THR Chi-restraints excluded: chain D residue 231 ASP Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 329 ASP Chi-restraints excluded: chain E residue 366 LEU Chi-restraints excluded: chain E residue 373 LYS Chi-restraints excluded: chain E residue 415 LEU Chi-restraints excluded: chain E residue 422 VAL Chi-restraints excluded: chain E residue 424 ASP Chi-restraints excluded: chain E residue 468 ILE Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 59 ILE Chi-restraints excluded: chain F residue 119 ILE Chi-restraints excluded: chain F residue 154 LEU Chi-restraints excluded: chain F residue 168 PHE Chi-restraints excluded: chain F residue 225 ASN Chi-restraints excluded: chain G residue 42 ILE Chi-restraints excluded: chain G residue 100 THR Chi-restraints excluded: chain G residue 248 THR Chi-restraints excluded: chain G residue 251 ASP Chi-restraints excluded: chain G residue 254 SER Chi-restraints excluded: chain G residue 262 GLU Chi-restraints excluded: chain H residue 37 ASP Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 42 ASP Chi-restraints excluded: chain H residue 67 GLU Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 97 ILE Chi-restraints excluded: chain H residue 101 ILE Chi-restraints excluded: chain H residue 115 ILE Chi-restraints excluded: chain H residue 119 LEU Chi-restraints excluded: chain H residue 125 ASP Chi-restraints excluded: chain I residue 178 ASP Chi-restraints excluded: chain I residue 198 VAL Chi-restraints excluded: chain I residue 204 THR Chi-restraints excluded: chain I residue 226 ILE Chi-restraints excluded: chain I residue 258 LEU Chi-restraints excluded: chain I residue 298 ARG Chi-restraints excluded: chain I residue 305 ASP Chi-restraints excluded: chain I residue 332 THR Chi-restraints excluded: chain J residue 50 GLU Chi-restraints excluded: chain J residue 51 TRP Chi-restraints excluded: chain J residue 71 THR Chi-restraints excluded: chain J residue 88 LEU Chi-restraints excluded: chain J residue 98 LEU Chi-restraints excluded: chain J residue 130 GLU Chi-restraints excluded: chain J residue 142 ASP Chi-restraints excluded: chain J residue 170 SER Chi-restraints excluded: chain J residue 174 LEU Chi-restraints excluded: chain J residue 181 THR Chi-restraints excluded: chain J residue 249 LEU Chi-restraints excluded: chain J residue 264 ILE Chi-restraints excluded: chain J residue 266 ARG Chi-restraints excluded: chain J residue 296 ILE Chi-restraints excluded: chain J residue 302 THR Chi-restraints excluded: chain J residue 305 THR Chi-restraints excluded: chain J residue 306 ILE Chi-restraints excluded: chain J residue 316 GLN Chi-restraints excluded: chain J residue 320 THR Chi-restraints excluded: chain J residue 329 THR Chi-restraints excluded: chain J residue 361 ASP Chi-restraints excluded: chain J residue 383 SER Chi-restraints excluded: chain J residue 384 CYS Chi-restraints excluded: chain J residue 395 ASN Chi-restraints excluded: chain J residue 413 SER Chi-restraints excluded: chain J residue 416 ILE Chi-restraints excluded: chain K residue 18 GLU Chi-restraints excluded: chain K residue 43 LEU Chi-restraints excluded: chain K residue 46 THR Chi-restraints excluded: chain K residue 77 LEU Chi-restraints excluded: chain K residue 124 ASN Chi-restraints excluded: chain K residue 137 LEU Chi-restraints excluded: chain K residue 241 ARG Chi-restraints excluded: chain K residue 246 HIS Chi-restraints excluded: chain K residue 263 ASP Chi-restraints excluded: chain K residue 271 THR Chi-restraints excluded: chain K residue 295 PHE Chi-restraints excluded: chain K residue 302 THR Chi-restraints excluded: chain K residue 315 ASN Chi-restraints excluded: chain K residue 320 THR Chi-restraints excluded: chain K residue 326 ASP Chi-restraints excluded: chain K residue 329 THR Chi-restraints excluded: chain K residue 330 LYS Chi-restraints excluded: chain K residue 361 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 116 optimal weight: 3.9990 chunk 310 optimal weight: 9.9990 chunk 68 optimal weight: 0.0040 chunk 202 optimal weight: 0.9990 chunk 85 optimal weight: 0.6980 chunk 345 optimal weight: 50.0000 chunk 286 optimal weight: 4.9990 chunk 159 optimal weight: 2.9990 chunk 28 optimal weight: 10.0000 chunk 114 optimal weight: 2.9990 chunk 181 optimal weight: 2.9990 overall best weight: 1.5398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1142 GLN ** A1173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 377 ASN E 414 GLN E 423 HIS ** J 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 319 HIS ** K 262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.2548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 30093 Z= 0.230 Angle : 0.555 13.366 40750 Z= 0.288 Chirality : 0.042 0.169 4434 Planarity : 0.004 0.064 5267 Dihedral : 6.965 58.628 4075 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 5.53 % Allowed : 23.68 % Favored : 70.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.14), residues: 3583 helix: 1.41 (0.13), residues: 1658 sheet: -0.30 (0.23), residues: 519 loop : -1.74 (0.16), residues: 1406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP K 353 HIS 0.006 0.001 HIS K 233 PHE 0.019 0.001 PHE I 264 TYR 0.028 0.001 TYR G 83 ARG 0.005 0.000 ARG J 317 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7166 Ramachandran restraints generated. 3583 Oldfield, 0 Emsley, 3583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7166 Ramachandran restraints generated. 3583 Oldfield, 0 Emsley, 3583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 433 residues out of total 3269 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 179 poor density : 254 time to evaluate : 3.982 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 510 LYS cc_start: 0.5788 (OUTLIER) cc_final: 0.4796 (tppt) REVERT: A 823 TYR cc_start: 0.8012 (m-80) cc_final: 0.7779 (m-80) REVERT: A 854 MET cc_start: 0.7781 (mtm) cc_final: 0.7571 (mtt) REVERT: A 1089 ASN cc_start: 0.7984 (p0) cc_final: 0.7775 (p0) REVERT: A 1182 ARG cc_start: 0.6858 (OUTLIER) cc_final: 0.6267 (ptp90) REVERT: B 440 GLU cc_start: 0.7875 (OUTLIER) cc_final: 0.7093 (tp30) REVERT: B 465 PHE cc_start: 0.7257 (OUTLIER) cc_final: 0.6932 (t80) REVERT: B 742 LYS cc_start: 0.7022 (OUTLIER) cc_final: 0.5850 (mmtt) REVERT: B 836 GLU cc_start: 0.0465 (OUTLIER) cc_final: -0.0591 (tm-30) REVERT: B 940 LEU cc_start: 0.8098 (OUTLIER) cc_final: 0.7758 (tt) REVERT: C 44 LEU cc_start: 0.9140 (OUTLIER) cc_final: 0.8495 (tt) REVERT: C 257 GLN cc_start: 0.8688 (OUTLIER) cc_final: 0.7835 (tm-30) REVERT: D 227 ASP cc_start: 0.7898 (OUTLIER) cc_final: 0.7549 (m-30) REVERT: E 355 LEU cc_start: 0.8094 (pp) cc_final: 0.7858 (tt) REVERT: F 8 ILE cc_start: 0.7401 (mm) cc_final: 0.7183 (mm) REVERT: F 13 GLN cc_start: 0.8236 (tt0) cc_final: 0.7822 (tt0) REVERT: F 66 ILE cc_start: 0.8069 (mm) cc_final: 0.7744 (mm) REVERT: F 168 PHE cc_start: 0.8670 (OUTLIER) cc_final: 0.8190 (p90) REVERT: G 1 MET cc_start: 0.7379 (ptt) cc_final: 0.6915 (ptt) REVERT: G 94 TYR cc_start: 0.7424 (t80) cc_final: 0.7142 (t80) REVERT: G 234 ARG cc_start: 0.6875 (ptt90) cc_final: 0.6662 (ttm110) REVERT: J 51 TRP cc_start: 0.7064 (OUTLIER) cc_final: 0.6567 (m100) REVERT: J 54 MET cc_start: 0.6262 (ttm) cc_final: 0.5953 (ttm) REVERT: J 58 TRP cc_start: 0.7058 (m100) cc_final: 0.6764 (m100) REVERT: J 130 GLU cc_start: 0.5099 (OUTLIER) cc_final: 0.4436 (tt0) REVERT: J 174 LEU cc_start: 0.6531 (OUTLIER) cc_final: 0.6168 (mp) REVERT: J 266 ARG cc_start: 0.5823 (OUTLIER) cc_final: 0.5529 (mtp-110) REVERT: J 296 ILE cc_start: 0.6857 (OUTLIER) cc_final: 0.6459 (mm) REVERT: J 377 MET cc_start: 0.7021 (ttt) cc_final: 0.6754 (ptm) REVERT: J 384 CYS cc_start: 0.8225 (OUTLIER) cc_final: 0.7967 (p) REVERT: K 18 GLU cc_start: 0.4134 (OUTLIER) cc_final: 0.2857 (tp30) REVERT: K 39 PHE cc_start: 0.4011 (t80) cc_final: 0.3303 (m-10) REVERT: K 171 GLU cc_start: 0.2244 (mm-30) cc_final: 0.1804 (tp30) REVERT: K 215 ASN cc_start: 0.2737 (m110) cc_final: 0.0960 (t0) REVERT: K 236 GLN cc_start: 0.3609 (mp10) cc_final: 0.2375 (mt0) REVERT: K 241 ARG cc_start: 0.1670 (OUTLIER) cc_final: 0.0318 (ptm160) REVERT: K 246 HIS cc_start: 0.1814 (OUTLIER) cc_final: 0.1529 (m-70) REVERT: K 315 ASN cc_start: 0.1191 (OUTLIER) cc_final: 0.0444 (m-40) REVERT: K 326 ASP cc_start: 0.1125 (OUTLIER) cc_final: 0.0700 (p0) REVERT: K 329 THR cc_start: -0.0338 (OUTLIER) cc_final: -0.0651 (p) REVERT: K 388 MET cc_start: 0.2618 (ptt) cc_final: 0.0983 (mtm) outliers start: 179 outliers final: 124 residues processed: 410 average time/residue: 0.4001 time to fit residues: 271.0822 Evaluate side-chains 383 residues out of total 3269 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 236 time to evaluate : 3.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 510 LYS Chi-restraints excluded: chain A residue 684 LEU Chi-restraints excluded: chain A residue 731 ASN Chi-restraints excluded: chain A residue 735 THR Chi-restraints excluded: chain A residue 747 ASP Chi-restraints excluded: chain A residue 778 VAL Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 1033 MET Chi-restraints excluded: chain A residue 1055 HIS Chi-restraints excluded: chain A residue 1079 GLU Chi-restraints excluded: chain A residue 1113 VAL Chi-restraints excluded: chain A residue 1117 ILE Chi-restraints excluded: chain A residue 1120 LEU Chi-restraints excluded: chain A residue 1167 LEU Chi-restraints excluded: chain A residue 1176 THR Chi-restraints excluded: chain A residue 1182 ARG Chi-restraints excluded: chain A residue 1193 THR Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 416 THR Chi-restraints excluded: chain B residue 440 GLU Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain B residue 462 THR Chi-restraints excluded: chain B residue 465 PHE Chi-restraints excluded: chain B residue 473 ASP Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 491 GLU Chi-restraints excluded: chain B residue 538 LYS Chi-restraints excluded: chain B residue 566 ASN Chi-restraints excluded: chain B residue 582 THR Chi-restraints excluded: chain B residue 612 GLU Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain B residue 713 VAL Chi-restraints excluded: chain B residue 742 LYS Chi-restraints excluded: chain B residue 834 LEU Chi-restraints excluded: chain B residue 836 GLU Chi-restraints excluded: chain B residue 904 LEU Chi-restraints excluded: chain B residue 937 GLU Chi-restraints excluded: chain B residue 940 LEU Chi-restraints excluded: chain B residue 944 LEU Chi-restraints excluded: chain B residue 960 THR Chi-restraints excluded: chain B residue 1119 ASN Chi-restraints excluded: chain B residue 1136 ASN Chi-restraints excluded: chain B residue 1137 THR Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 123 SER Chi-restraints excluded: chain C residue 152 ASP Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 201 TYR Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 231 ASP Chi-restraints excluded: chain C residue 233 SER Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 257 GLN Chi-restraints excluded: chain C residue 261 ASP Chi-restraints excluded: chain C residue 337 ASP Chi-restraints excluded: chain C residue 347 MET Chi-restraints excluded: chain D residue 15 ASP Chi-restraints excluded: chain D residue 42 TYR Chi-restraints excluded: chain D residue 57 THR Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 127 GLU Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 178 ASP Chi-restraints excluded: chain D residue 188 ASP Chi-restraints excluded: chain D residue 192 THR Chi-restraints excluded: chain D residue 227 ASP Chi-restraints excluded: chain D residue 231 ASP Chi-restraints excluded: chain D residue 329 ASP Chi-restraints excluded: chain E residue 366 LEU Chi-restraints excluded: chain E residue 398 ARG Chi-restraints excluded: chain E residue 415 LEU Chi-restraints excluded: chain E residue 422 VAL Chi-restraints excluded: chain E residue 424 ASP Chi-restraints excluded: chain F residue 32 LEU Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 59 ILE Chi-restraints excluded: chain F residue 119 ILE Chi-restraints excluded: chain F residue 154 LEU Chi-restraints excluded: chain F residue 156 ASP Chi-restraints excluded: chain F residue 168 PHE Chi-restraints excluded: chain F residue 225 ASN Chi-restraints excluded: chain G residue 42 ILE Chi-restraints excluded: chain G residue 240 VAL Chi-restraints excluded: chain G residue 248 THR Chi-restraints excluded: chain G residue 254 SER Chi-restraints excluded: chain G residue 262 GLU Chi-restraints excluded: chain H residue 37 ASP Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 42 ASP Chi-restraints excluded: chain H residue 67 GLU Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 97 ILE Chi-restraints excluded: chain H residue 101 ILE Chi-restraints excluded: chain H residue 115 ILE Chi-restraints excluded: chain H residue 119 LEU Chi-restraints excluded: chain H residue 129 LEU Chi-restraints excluded: chain I residue 178 ASP Chi-restraints excluded: chain I residue 198 VAL Chi-restraints excluded: chain I residue 204 THR Chi-restraints excluded: chain I residue 226 ILE Chi-restraints excluded: chain I residue 256 THR Chi-restraints excluded: chain I residue 258 LEU Chi-restraints excluded: chain I residue 305 ASP Chi-restraints excluded: chain I residue 332 THR Chi-restraints excluded: chain J residue 51 TRP Chi-restraints excluded: chain J residue 71 THR Chi-restraints excluded: chain J residue 88 LEU Chi-restraints excluded: chain J residue 130 GLU Chi-restraints excluded: chain J residue 142 ASP Chi-restraints excluded: chain J residue 174 LEU Chi-restraints excluded: chain J residue 181 THR Chi-restraints excluded: chain J residue 266 ARG Chi-restraints excluded: chain J residue 296 ILE Chi-restraints excluded: chain J residue 302 THR Chi-restraints excluded: chain J residue 305 THR Chi-restraints excluded: chain J residue 306 ILE Chi-restraints excluded: chain J residue 316 GLN Chi-restraints excluded: chain J residue 320 THR Chi-restraints excluded: chain J residue 329 THR Chi-restraints excluded: chain J residue 361 ASP Chi-restraints excluded: chain J residue 382 THR Chi-restraints excluded: chain J residue 384 CYS Chi-restraints excluded: chain J residue 395 ASN Chi-restraints excluded: chain J residue 413 SER Chi-restraints excluded: chain J residue 416 ILE Chi-restraints excluded: chain K residue 18 GLU Chi-restraints excluded: chain K residue 43 LEU Chi-restraints excluded: chain K residue 77 LEU Chi-restraints excluded: chain K residue 124 ASN Chi-restraints excluded: chain K residue 137 LEU Chi-restraints excluded: chain K residue 241 ARG Chi-restraints excluded: chain K residue 246 HIS Chi-restraints excluded: chain K residue 263 ASP Chi-restraints excluded: chain K residue 271 THR Chi-restraints excluded: chain K residue 295 PHE Chi-restraints excluded: chain K residue 302 THR Chi-restraints excluded: chain K residue 315 ASN Chi-restraints excluded: chain K residue 320 THR Chi-restraints excluded: chain K residue 326 ASP Chi-restraints excluded: chain K residue 329 THR Chi-restraints excluded: chain K residue 341 LEU Chi-restraints excluded: chain K residue 361 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 333 optimal weight: 0.9980 chunk 38 optimal weight: 3.9990 chunk 196 optimal weight: 2.9990 chunk 252 optimal weight: 0.7980 chunk 195 optimal weight: 3.9990 chunk 290 optimal weight: 0.0050 chunk 192 optimal weight: 0.1980 chunk 344 optimal weight: 50.0000 chunk 215 optimal weight: 4.9990 chunk 209 optimal weight: 5.9990 chunk 158 optimal weight: 0.9990 overall best weight: 0.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1142 GLN ** A1173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 414 GLN E 423 HIS J 22 GLN ** J 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 193 ASN ** J 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 319 HIS ** K 262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.2829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 30093 Z= 0.144 Angle : 0.522 11.405 40750 Z= 0.271 Chirality : 0.040 0.152 4434 Planarity : 0.004 0.054 5267 Dihedral : 6.518 60.524 4072 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 4.54 % Allowed : 25.01 % Favored : 70.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.14), residues: 3583 helix: 1.70 (0.13), residues: 1642 sheet: -0.26 (0.22), residues: 528 loop : -1.56 (0.16), residues: 1413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP J 417 HIS 0.006 0.000 HIS K 243 PHE 0.048 0.001 PHE A 836 TYR 0.035 0.001 TYR G 83 ARG 0.006 0.000 ARG J 317 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7166 Ramachandran restraints generated. 3583 Oldfield, 0 Emsley, 3583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7166 Ramachandran restraints generated. 3583 Oldfield, 0 Emsley, 3583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 3269 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 252 time to evaluate : 3.416 Fit side-chains revert: symmetry clash REVERT: A 823 TYR cc_start: 0.7914 (m-80) cc_final: 0.7701 (m-80) REVERT: A 1182 ARG cc_start: 0.6759 (OUTLIER) cc_final: 0.6168 (ptp90) REVERT: B 440 GLU cc_start: 0.7876 (OUTLIER) cc_final: 0.7167 (tp30) REVERT: B 742 LYS cc_start: 0.6885 (OUTLIER) cc_final: 0.5681 (mmtt) REVERT: B 836 GLU cc_start: 0.0375 (OUTLIER) cc_final: -0.0649 (tm-30) REVERT: C 44 LEU cc_start: 0.9066 (OUTLIER) cc_final: 0.8461 (tt) REVERT: C 257 GLN cc_start: 0.8657 (OUTLIER) cc_final: 0.7974 (tm-30) REVERT: F 8 ILE cc_start: 0.7443 (mm) cc_final: 0.7187 (mm) REVERT: F 13 GLN cc_start: 0.8272 (tt0) cc_final: 0.7839 (tt0) REVERT: F 66 ILE cc_start: 0.8022 (mm) cc_final: 0.7707 (mm) REVERT: F 168 PHE cc_start: 0.8635 (OUTLIER) cc_final: 0.8169 (p90) REVERT: G 1 MET cc_start: 0.7261 (ptt) cc_final: 0.6815 (ptt) REVERT: H 41 ARG cc_start: 0.7631 (ptm160) cc_final: 0.7337 (ttm170) REVERT: J 51 TRP cc_start: 0.6939 (OUTLIER) cc_final: 0.6457 (m100) REVERT: J 54 MET cc_start: 0.5962 (ttm) cc_final: 0.5645 (ttm) REVERT: J 58 TRP cc_start: 0.7243 (m100) cc_final: 0.6786 (m100) REVERT: J 130 GLU cc_start: 0.4985 (OUTLIER) cc_final: 0.4321 (tt0) REVERT: J 174 LEU cc_start: 0.6583 (OUTLIER) cc_final: 0.6282 (mp) REVERT: J 266 ARG cc_start: 0.5831 (OUTLIER) cc_final: 0.5596 (mtp-110) REVERT: J 296 ILE cc_start: 0.6814 (OUTLIER) cc_final: 0.6452 (mm) REVERT: J 305 THR cc_start: 0.7741 (OUTLIER) cc_final: 0.7502 (p) REVERT: J 377 MET cc_start: 0.7000 (ttt) cc_final: 0.6760 (ptm) REVERT: J 398 MET cc_start: 0.7206 (tpp) cc_final: 0.7000 (mmm) REVERT: K 18 GLU cc_start: 0.4163 (OUTLIER) cc_final: 0.2908 (tp30) REVERT: K 39 PHE cc_start: 0.3875 (t80) cc_final: 0.3244 (m-10) REVERT: K 171 GLU cc_start: 0.2240 (mm-30) cc_final: 0.1774 (tp30) REVERT: K 236 GLN cc_start: 0.4037 (mp10) cc_final: 0.2719 (mt0) REVERT: K 241 ARG cc_start: 0.1312 (OUTLIER) cc_final: 0.0344 (ptm160) REVERT: K 246 HIS cc_start: 0.2674 (OUTLIER) cc_final: 0.2206 (m-70) REVERT: K 315 ASN cc_start: 0.1462 (OUTLIER) cc_final: 0.0641 (m-40) REVERT: K 326 ASP cc_start: 0.1093 (OUTLIER) cc_final: 0.0793 (p0) REVERT: K 388 MET cc_start: 0.2421 (ptt) cc_final: 0.1047 (mtm) outliers start: 147 outliers final: 102 residues processed: 382 average time/residue: 0.4249 time to fit residues: 264.3163 Evaluate side-chains 357 residues out of total 3269 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 237 time to evaluate : 3.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 589 ASP Chi-restraints excluded: chain A residue 684 LEU Chi-restraints excluded: chain A residue 706 SER Chi-restraints excluded: chain A residue 731 ASN Chi-restraints excluded: chain A residue 747 ASP Chi-restraints excluded: chain A residue 778 VAL Chi-restraints excluded: chain A residue 1033 MET Chi-restraints excluded: chain A residue 1055 HIS Chi-restraints excluded: chain A residue 1102 HIS Chi-restraints excluded: chain A residue 1113 VAL Chi-restraints excluded: chain A residue 1117 ILE Chi-restraints excluded: chain A residue 1120 LEU Chi-restraints excluded: chain A residue 1125 THR Chi-restraints excluded: chain A residue 1167 LEU Chi-restraints excluded: chain A residue 1182 ARG Chi-restraints excluded: chain A residue 1193 THR Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 416 THR Chi-restraints excluded: chain B residue 440 GLU Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 462 THR Chi-restraints excluded: chain B residue 473 ASP Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 491 GLU Chi-restraints excluded: chain B residue 538 LYS Chi-restraints excluded: chain B residue 566 ASN Chi-restraints excluded: chain B residue 612 GLU Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain B residue 713 VAL Chi-restraints excluded: chain B residue 742 LYS Chi-restraints excluded: chain B residue 836 GLU Chi-restraints excluded: chain B residue 904 LEU Chi-restraints excluded: chain B residue 944 LEU Chi-restraints excluded: chain B residue 960 THR Chi-restraints excluded: chain B residue 1119 ASN Chi-restraints excluded: chain B residue 1136 ASN Chi-restraints excluded: chain B residue 1137 THR Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 123 SER Chi-restraints excluded: chain C residue 152 ASP Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 231 ASP Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 257 GLN Chi-restraints excluded: chain C residue 261 ASP Chi-restraints excluded: chain C residue 319 GLU Chi-restraints excluded: chain C residue 347 MET Chi-restraints excluded: chain D residue 42 TYR Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 57 THR Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 127 GLU Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 178 ASP Chi-restraints excluded: chain D residue 192 THR Chi-restraints excluded: chain D residue 231 ASP Chi-restraints excluded: chain D residue 292 MET Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 329 ASP Chi-restraints excluded: chain E residue 366 LEU Chi-restraints excluded: chain E residue 398 ARG Chi-restraints excluded: chain E residue 415 LEU Chi-restraints excluded: chain E residue 422 VAL Chi-restraints excluded: chain F residue 23 ASP Chi-restraints excluded: chain F residue 32 LEU Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 59 ILE Chi-restraints excluded: chain F residue 119 ILE Chi-restraints excluded: chain F residue 154 LEU Chi-restraints excluded: chain F residue 168 PHE Chi-restraints excluded: chain F residue 225 ASN Chi-restraints excluded: chain G residue 251 ASP Chi-restraints excluded: chain G residue 262 GLU Chi-restraints excluded: chain H residue 37 ASP Chi-restraints excluded: chain H residue 42 ASP Chi-restraints excluded: chain H residue 67 GLU Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 97 ILE Chi-restraints excluded: chain H residue 101 ILE Chi-restraints excluded: chain H residue 129 LEU Chi-restraints excluded: chain I residue 178 ASP Chi-restraints excluded: chain I residue 198 VAL Chi-restraints excluded: chain I residue 204 THR Chi-restraints excluded: chain I residue 226 ILE Chi-restraints excluded: chain I residue 305 ASP Chi-restraints excluded: chain I residue 332 THR Chi-restraints excluded: chain J residue 51 TRP Chi-restraints excluded: chain J residue 71 THR Chi-restraints excluded: chain J residue 88 LEU Chi-restraints excluded: chain J residue 130 GLU Chi-restraints excluded: chain J residue 142 ASP Chi-restraints excluded: chain J residue 174 LEU Chi-restraints excluded: chain J residue 181 THR Chi-restraints excluded: chain J residue 266 ARG Chi-restraints excluded: chain J residue 287 VAL Chi-restraints excluded: chain J residue 296 ILE Chi-restraints excluded: chain J residue 302 THR Chi-restraints excluded: chain J residue 305 THR Chi-restraints excluded: chain J residue 316 GLN Chi-restraints excluded: chain J residue 361 ASP Chi-restraints excluded: chain J residue 382 THR Chi-restraints excluded: chain J residue 395 ASN Chi-restraints excluded: chain J residue 413 SER Chi-restraints excluded: chain J residue 416 ILE Chi-restraints excluded: chain K residue 18 GLU Chi-restraints excluded: chain K residue 43 LEU Chi-restraints excluded: chain K residue 77 LEU Chi-restraints excluded: chain K residue 137 LEU Chi-restraints excluded: chain K residue 241 ARG Chi-restraints excluded: chain K residue 246 HIS Chi-restraints excluded: chain K residue 263 ASP Chi-restraints excluded: chain K residue 271 THR Chi-restraints excluded: chain K residue 295 PHE Chi-restraints excluded: chain K residue 302 THR Chi-restraints excluded: chain K residue 315 ASN Chi-restraints excluded: chain K residue 326 ASP Chi-restraints excluded: chain K residue 341 LEU Chi-restraints excluded: chain K residue 361 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 212 optimal weight: 0.0570 chunk 137 optimal weight: 4.9990 chunk 205 optimal weight: 0.9990 chunk 103 optimal weight: 9.9990 chunk 67 optimal weight: 2.9990 chunk 66 optimal weight: 4.9990 chunk 218 optimal weight: 0.2980 chunk 234 optimal weight: 3.9990 chunk 170 optimal weight: 1.9990 chunk 32 optimal weight: 0.0000 chunk 270 optimal weight: 0.8980 overall best weight: 0.4504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 803 GLN ** A 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1142 GLN ** A1173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 722 ASN E 414 GLN E 423 HIS J 124 ASN ** J 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 319 HIS ** K 262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.3063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 30093 Z= 0.133 Angle : 0.506 10.985 40750 Z= 0.263 Chirality : 0.040 0.144 4434 Planarity : 0.004 0.049 5267 Dihedral : 6.010 61.612 4062 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 3.77 % Allowed : 25.50 % Favored : 70.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.14), residues: 3583 helix: 1.90 (0.13), residues: 1639 sheet: -0.05 (0.23), residues: 533 loop : -1.46 (0.16), residues: 1411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP J 33 HIS 0.005 0.000 HIS F 140 PHE 0.052 0.001 PHE A 836 TYR 0.036 0.001 TYR G 83 ARG 0.014 0.000 ARG A1140 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7166 Ramachandran restraints generated. 3583 Oldfield, 0 Emsley, 3583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7166 Ramachandran restraints generated. 3583 Oldfield, 0 Emsley, 3583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 3269 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 255 time to evaluate : 3.764 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 683 MET cc_start: 0.7370 (ttm) cc_final: 0.7129 (ttm) REVERT: A 1182 ARG cc_start: 0.6694 (OUTLIER) cc_final: 0.6072 (ptp90) REVERT: B 440 GLU cc_start: 0.7763 (OUTLIER) cc_final: 0.7040 (tp30) REVERT: B 465 PHE cc_start: 0.7243 (OUTLIER) cc_final: 0.6926 (t80) REVERT: B 742 LYS cc_start: 0.6873 (OUTLIER) cc_final: 0.5694 (mmtt) REVERT: B 836 GLU cc_start: 0.0289 (OUTLIER) cc_final: -0.0700 (tm-30) REVERT: C 44 LEU cc_start: 0.8996 (OUTLIER) cc_final: 0.8405 (tt) REVERT: E 335 ASN cc_start: 0.6280 (m110) cc_final: 0.6007 (m110) REVERT: F 8 ILE cc_start: 0.7450 (mm) cc_final: 0.7191 (mm) REVERT: F 13 GLN cc_start: 0.8359 (tt0) cc_final: 0.7944 (tt0) REVERT: F 66 ILE cc_start: 0.8017 (mm) cc_final: 0.7687 (mm) REVERT: F 168 PHE cc_start: 0.8597 (OUTLIER) cc_final: 0.8045 (p90) REVERT: G 1 MET cc_start: 0.7275 (ptt) cc_final: 0.6815 (ptt) REVERT: J 51 TRP cc_start: 0.6735 (OUTLIER) cc_final: 0.6326 (m100) REVERT: J 54 MET cc_start: 0.5840 (ttm) cc_final: 0.5569 (ttm) REVERT: J 58 TRP cc_start: 0.7140 (m100) cc_final: 0.6620 (m100) REVERT: J 174 LEU cc_start: 0.6620 (OUTLIER) cc_final: 0.6296 (mp) REVERT: J 266 ARG cc_start: 0.5669 (OUTLIER) cc_final: 0.5447 (mtp-110) REVERT: J 296 ILE cc_start: 0.6775 (OUTLIER) cc_final: 0.6418 (mm) REVERT: J 353 TRP cc_start: 0.6874 (m100) cc_final: 0.6514 (m100) REVERT: J 377 MET cc_start: 0.7034 (ttt) cc_final: 0.6761 (ptm) REVERT: K 18 GLU cc_start: 0.4149 (mt-10) cc_final: 0.2781 (tp30) REVERT: K 39 PHE cc_start: 0.3900 (t80) cc_final: 0.3267 (m-10) REVERT: K 171 GLU cc_start: 0.2180 (mm-30) cc_final: 0.1904 (tp30) REVERT: K 236 GLN cc_start: 0.4132 (mp10) cc_final: 0.3877 (mm110) REVERT: K 241 ARG cc_start: 0.1617 (OUTLIER) cc_final: 0.0585 (ttt90) REVERT: K 246 HIS cc_start: 0.2199 (OUTLIER) cc_final: 0.1846 (m-70) REVERT: K 388 MET cc_start: 0.2330 (ptt) cc_final: 0.1099 (mtm) REVERT: K 414 ARG cc_start: 0.3472 (mtt180) cc_final: 0.3023 (mtt-85) outliers start: 122 outliers final: 91 residues processed: 365 average time/residue: 0.4261 time to fit residues: 254.1804 Evaluate side-chains 346 residues out of total 3269 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 242 time to evaluate : 3.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 589 ASP Chi-restraints excluded: chain A residue 684 LEU Chi-restraints excluded: chain A residue 706 SER Chi-restraints excluded: chain A residue 747 ASP Chi-restraints excluded: chain A residue 778 VAL Chi-restraints excluded: chain A residue 1033 MET Chi-restraints excluded: chain A residue 1055 HIS Chi-restraints excluded: chain A residue 1113 VAL Chi-restraints excluded: chain A residue 1125 THR Chi-restraints excluded: chain A residue 1167 LEU Chi-restraints excluded: chain A residue 1182 ARG Chi-restraints excluded: chain A residue 1193 THR Chi-restraints excluded: chain B residue 416 THR Chi-restraints excluded: chain B residue 440 GLU Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain B residue 462 THR Chi-restraints excluded: chain B residue 465 PHE Chi-restraints excluded: chain B residue 473 ASP Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 491 GLU Chi-restraints excluded: chain B residue 538 LYS Chi-restraints excluded: chain B residue 566 ASN Chi-restraints excluded: chain B residue 612 GLU Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain B residue 713 VAL Chi-restraints excluded: chain B residue 742 LYS Chi-restraints excluded: chain B residue 761 LEU Chi-restraints excluded: chain B residue 836 GLU Chi-restraints excluded: chain B residue 904 LEU Chi-restraints excluded: chain B residue 944 LEU Chi-restraints excluded: chain B residue 960 THR Chi-restraints excluded: chain B residue 1119 ASN Chi-restraints excluded: chain B residue 1136 ASN Chi-restraints excluded: chain B residue 1137 THR Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 123 SER Chi-restraints excluded: chain C residue 152 ASP Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 231 ASP Chi-restraints excluded: chain C residue 233 SER Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 261 ASP Chi-restraints excluded: chain C residue 319 GLU Chi-restraints excluded: chain D residue 42 TYR Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 57 THR Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 188 ASP Chi-restraints excluded: chain D residue 231 ASP Chi-restraints excluded: chain D residue 329 ASP Chi-restraints excluded: chain E residue 398 ARG Chi-restraints excluded: chain E residue 422 VAL Chi-restraints excluded: chain F residue 23 ASP Chi-restraints excluded: chain F residue 32 LEU Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 59 ILE Chi-restraints excluded: chain F residue 119 ILE Chi-restraints excluded: chain F residue 154 LEU Chi-restraints excluded: chain F residue 168 PHE Chi-restraints excluded: chain F residue 225 ASN Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain G residue 248 THR Chi-restraints excluded: chain G residue 251 ASP Chi-restraints excluded: chain G residue 262 GLU Chi-restraints excluded: chain H residue 37 ASP Chi-restraints excluded: chain H residue 42 ASP Chi-restraints excluded: chain H residue 67 GLU Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 97 ILE Chi-restraints excluded: chain H residue 101 ILE Chi-restraints excluded: chain H residue 119 LEU Chi-restraints excluded: chain H residue 129 LEU Chi-restraints excluded: chain I residue 178 ASP Chi-restraints excluded: chain I residue 226 ILE Chi-restraints excluded: chain I residue 258 LEU Chi-restraints excluded: chain I residue 305 ASP Chi-restraints excluded: chain I residue 332 THR Chi-restraints excluded: chain J residue 37 SER Chi-restraints excluded: chain J residue 51 TRP Chi-restraints excluded: chain J residue 71 THR Chi-restraints excluded: chain J residue 88 LEU Chi-restraints excluded: chain J residue 142 ASP Chi-restraints excluded: chain J residue 174 LEU Chi-restraints excluded: chain J residue 249 LEU Chi-restraints excluded: chain J residue 266 ARG Chi-restraints excluded: chain J residue 287 VAL Chi-restraints excluded: chain J residue 296 ILE Chi-restraints excluded: chain J residue 302 THR Chi-restraints excluded: chain J residue 329 THR Chi-restraints excluded: chain J residue 361 ASP Chi-restraints excluded: chain J residue 382 THR Chi-restraints excluded: chain J residue 395 ASN Chi-restraints excluded: chain J residue 413 SER Chi-restraints excluded: chain K residue 43 LEU Chi-restraints excluded: chain K residue 77 LEU Chi-restraints excluded: chain K residue 137 LEU Chi-restraints excluded: chain K residue 241 ARG Chi-restraints excluded: chain K residue 246 HIS Chi-restraints excluded: chain K residue 263 ASP Chi-restraints excluded: chain K residue 271 THR Chi-restraints excluded: chain K residue 302 THR Chi-restraints excluded: chain K residue 330 LYS Chi-restraints excluded: chain K residue 341 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 313 optimal weight: 0.7980 chunk 329 optimal weight: 0.8980 chunk 300 optimal weight: 3.9990 chunk 320 optimal weight: 5.9990 chunk 192 optimal weight: 0.8980 chunk 139 optimal weight: 0.8980 chunk 251 optimal weight: 0.9990 chunk 98 optimal weight: 0.6980 chunk 289 optimal weight: 2.9990 chunk 303 optimal weight: 5.9990 chunk 319 optimal weight: 9.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 731 ASN ** A 775 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1142 GLN ** A1173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 335 ASN E 423 HIS ** J 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 319 HIS ** K 262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 316 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.3100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 30093 Z= 0.158 Angle : 0.519 12.309 40750 Z= 0.269 Chirality : 0.040 0.143 4434 Planarity : 0.004 0.049 5267 Dihedral : 5.749 62.281 4041 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 3.96 % Allowed : 25.26 % Favored : 70.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.14), residues: 3583 helix: 1.92 (0.13), residues: 1636 sheet: -0.07 (0.22), residues: 543 loop : -1.41 (0.16), residues: 1404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP J 33 HIS 0.005 0.001 HIS F 140 PHE 0.050 0.001 PHE A 836 TYR 0.041 0.001 TYR G 83 ARG 0.007 0.000 ARG A1140 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7166 Ramachandran restraints generated. 3583 Oldfield, 0 Emsley, 3583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7166 Ramachandran restraints generated. 3583 Oldfield, 0 Emsley, 3583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 3269 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 251 time to evaluate : 3.551 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 508 GLN cc_start: 0.5552 (OUTLIER) cc_final: 0.5129 (pp30) REVERT: A 1182 ARG cc_start: 0.6667 (OUTLIER) cc_final: 0.6060 (ptp90) REVERT: B 440 GLU cc_start: 0.7757 (OUTLIER) cc_final: 0.6878 (tp30) REVERT: B 465 PHE cc_start: 0.7230 (OUTLIER) cc_final: 0.6923 (t80) REVERT: B 742 LYS cc_start: 0.6862 (OUTLIER) cc_final: 0.5732 (mmtt) REVERT: B 836 GLU cc_start: 0.0292 (OUTLIER) cc_final: -0.0703 (tm-30) REVERT: C 44 LEU cc_start: 0.9032 (OUTLIER) cc_final: 0.8401 (tt) REVERT: C 257 GLN cc_start: 0.8666 (OUTLIER) cc_final: 0.7989 (tm-30) REVERT: E 335 ASN cc_start: 0.6615 (m-40) cc_final: 0.6340 (m110) REVERT: E 355 LEU cc_start: 0.7863 (pp) cc_final: 0.7531 (tt) REVERT: F 8 ILE cc_start: 0.7437 (mm) cc_final: 0.7177 (mm) REVERT: F 13 GLN cc_start: 0.8418 (tt0) cc_final: 0.8007 (tt0) REVERT: F 66 ILE cc_start: 0.8039 (mm) cc_final: 0.7709 (mm) REVERT: F 168 PHE cc_start: 0.8614 (OUTLIER) cc_final: 0.8157 (p90) REVERT: G 1 MET cc_start: 0.7280 (ptt) cc_final: 0.6831 (ptt) REVERT: I 298 ARG cc_start: 0.8802 (OUTLIER) cc_final: 0.8228 (mtt90) REVERT: J 51 TRP cc_start: 0.6762 (OUTLIER) cc_final: 0.6320 (m100) REVERT: J 58 TRP cc_start: 0.7145 (m100) cc_final: 0.6637 (m100) REVERT: J 174 LEU cc_start: 0.6645 (OUTLIER) cc_final: 0.6301 (mp) REVERT: J 266 ARG cc_start: 0.5674 (OUTLIER) cc_final: 0.5454 (mtp-110) REVERT: J 296 ILE cc_start: 0.6807 (OUTLIER) cc_final: 0.6451 (mm) REVERT: J 353 TRP cc_start: 0.6890 (m100) cc_final: 0.6541 (m100) REVERT: J 377 MET cc_start: 0.6974 (ttt) cc_final: 0.6710 (ptm) REVERT: J 398 MET cc_start: 0.7024 (tpp) cc_final: 0.6605 (mmm) REVERT: K 171 GLU cc_start: 0.2151 (mm-30) cc_final: 0.1613 (tp30) REVERT: K 236 GLN cc_start: 0.4188 (mp10) cc_final: 0.3940 (mm110) REVERT: K 241 ARG cc_start: 0.1259 (OUTLIER) cc_final: 0.0784 (ttt90) REVERT: K 246 HIS cc_start: 0.2408 (OUTLIER) cc_final: 0.1947 (m-70) REVERT: K 316 GLN cc_start: 0.1669 (OUTLIER) cc_final: -0.0229 (tp40) REVERT: K 330 LYS cc_start: 0.0673 (OUTLIER) cc_final: -0.1510 (ttpp) REVERT: K 361 ASP cc_start: 0.0035 (OUTLIER) cc_final: -0.0222 (m-30) REVERT: K 388 MET cc_start: 0.2357 (ptt) cc_final: 0.0821 (mtm) REVERT: K 414 ARG cc_start: 0.3461 (mtt180) cc_final: 0.3020 (mtt-85) outliers start: 128 outliers final: 97 residues processed: 364 average time/residue: 0.4198 time to fit residues: 250.3423 Evaluate side-chains 353 residues out of total 3269 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 237 time to evaluate : 3.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 508 GLN Chi-restraints excluded: chain A residue 589 ASP Chi-restraints excluded: chain A residue 684 LEU Chi-restraints excluded: chain A residue 706 SER Chi-restraints excluded: chain A residue 731 ASN Chi-restraints excluded: chain A residue 747 ASP Chi-restraints excluded: chain A residue 778 VAL Chi-restraints excluded: chain A residue 1033 MET Chi-restraints excluded: chain A residue 1055 HIS Chi-restraints excluded: chain A residue 1110 GLU Chi-restraints excluded: chain A residue 1113 VAL Chi-restraints excluded: chain A residue 1125 THR Chi-restraints excluded: chain A residue 1167 LEU Chi-restraints excluded: chain A residue 1182 ARG Chi-restraints excluded: chain A residue 1193 THR Chi-restraints excluded: chain B residue 416 THR Chi-restraints excluded: chain B residue 440 GLU Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain B residue 462 THR Chi-restraints excluded: chain B residue 465 PHE Chi-restraints excluded: chain B residue 473 ASP Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 491 GLU Chi-restraints excluded: chain B residue 538 LYS Chi-restraints excluded: chain B residue 566 ASN Chi-restraints excluded: chain B residue 575 LEU Chi-restraints excluded: chain B residue 582 THR Chi-restraints excluded: chain B residue 612 GLU Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain B residue 713 VAL Chi-restraints excluded: chain B residue 742 LYS Chi-restraints excluded: chain B residue 836 GLU Chi-restraints excluded: chain B residue 904 LEU Chi-restraints excluded: chain B residue 937 GLU Chi-restraints excluded: chain B residue 944 LEU Chi-restraints excluded: chain B residue 960 THR Chi-restraints excluded: chain B residue 1119 ASN Chi-restraints excluded: chain B residue 1136 ASN Chi-restraints excluded: chain B residue 1137 THR Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 85 GLN Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 123 SER Chi-restraints excluded: chain C residue 152 ASP Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 231 ASP Chi-restraints excluded: chain C residue 233 SER Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 257 GLN Chi-restraints excluded: chain C residue 261 ASP Chi-restraints excluded: chain D residue 42 TYR Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 57 THR Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 178 ASP Chi-restraints excluded: chain D residue 188 ASP Chi-restraints excluded: chain D residue 231 ASP Chi-restraints excluded: chain D residue 292 MET Chi-restraints excluded: chain D residue 329 ASP Chi-restraints excluded: chain E residue 398 ARG Chi-restraints excluded: chain E residue 422 VAL Chi-restraints excluded: chain F residue 32 LEU Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 59 ILE Chi-restraints excluded: chain F residue 119 ILE Chi-restraints excluded: chain F residue 154 LEU Chi-restraints excluded: chain F residue 168 PHE Chi-restraints excluded: chain F residue 225 ASN Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain G residue 248 THR Chi-restraints excluded: chain G residue 251 ASP Chi-restraints excluded: chain G residue 262 GLU Chi-restraints excluded: chain H residue 37 ASP Chi-restraints excluded: chain H residue 42 ASP Chi-restraints excluded: chain H residue 67 GLU Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 97 ILE Chi-restraints excluded: chain H residue 101 ILE Chi-restraints excluded: chain H residue 119 LEU Chi-restraints excluded: chain H residue 129 LEU Chi-restraints excluded: chain I residue 178 ASP Chi-restraints excluded: chain I residue 226 ILE Chi-restraints excluded: chain I residue 258 LEU Chi-restraints excluded: chain I residue 298 ARG Chi-restraints excluded: chain I residue 305 ASP Chi-restraints excluded: chain I residue 332 THR Chi-restraints excluded: chain J residue 37 SER Chi-restraints excluded: chain J residue 51 TRP Chi-restraints excluded: chain J residue 71 THR Chi-restraints excluded: chain J residue 88 LEU Chi-restraints excluded: chain J residue 142 ASP Chi-restraints excluded: chain J residue 157 VAL Chi-restraints excluded: chain J residue 174 LEU Chi-restraints excluded: chain J residue 249 LEU Chi-restraints excluded: chain J residue 266 ARG Chi-restraints excluded: chain J residue 287 VAL Chi-restraints excluded: chain J residue 296 ILE Chi-restraints excluded: chain J residue 302 THR Chi-restraints excluded: chain J residue 319 HIS Chi-restraints excluded: chain J residue 329 THR Chi-restraints excluded: chain J residue 361 ASP Chi-restraints excluded: chain J residue 395 ASN Chi-restraints excluded: chain J residue 413 SER Chi-restraints excluded: chain J residue 414 ARG Chi-restraints excluded: chain K residue 43 LEU Chi-restraints excluded: chain K residue 46 THR Chi-restraints excluded: chain K residue 77 LEU Chi-restraints excluded: chain K residue 137 LEU Chi-restraints excluded: chain K residue 241 ARG Chi-restraints excluded: chain K residue 246 HIS Chi-restraints excluded: chain K residue 263 ASP Chi-restraints excluded: chain K residue 302 THR Chi-restraints excluded: chain K residue 316 GLN Chi-restraints excluded: chain K residue 330 LYS Chi-restraints excluded: chain K residue 361 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 210 optimal weight: 1.9990 chunk 339 optimal weight: 8.9990 chunk 206 optimal weight: 2.9990 chunk 160 optimal weight: 3.9990 chunk 235 optimal weight: 1.9990 chunk 355 optimal weight: 8.9990 chunk 327 optimal weight: 9.9990 chunk 283 optimal weight: 0.9980 chunk 29 optimal weight: 0.0670 chunk 218 optimal weight: 3.9990 chunk 173 optimal weight: 3.9990 overall best weight: 1.6124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 646 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 775 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 722 ASN ** J 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 319 HIS ** K 262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.3056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 30093 Z= 0.237 Angle : 0.550 11.428 40750 Z= 0.285 Chirality : 0.042 0.150 4434 Planarity : 0.004 0.055 5267 Dihedral : 5.844 62.350 4041 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 3.68 % Allowed : 25.38 % Favored : 70.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.14), residues: 3583 helix: 1.82 (0.13), residues: 1637 sheet: -0.13 (0.22), residues: 543 loop : -1.45 (0.16), residues: 1403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP J 417 HIS 0.011 0.001 HIS J 319 PHE 0.050 0.002 PHE A 836 TYR 0.044 0.001 TYR G 83 ARG 0.014 0.000 ARG K 317 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7166 Ramachandran restraints generated. 3583 Oldfield, 0 Emsley, 3583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7166 Ramachandran restraints generated. 3583 Oldfield, 0 Emsley, 3583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 3269 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 242 time to evaluate : 3.951 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1182 ARG cc_start: 0.6681 (OUTLIER) cc_final: 0.6074 (ptp90) REVERT: B 440 GLU cc_start: 0.7763 (OUTLIER) cc_final: 0.6945 (tp30) REVERT: B 465 PHE cc_start: 0.7173 (OUTLIER) cc_final: 0.6848 (t80) REVERT: B 742 LYS cc_start: 0.6920 (OUTLIER) cc_final: 0.5736 (mmtt) REVERT: B 836 GLU cc_start: 0.0296 (OUTLIER) cc_final: -0.0698 (tm-30) REVERT: C 44 LEU cc_start: 0.9080 (OUTLIER) cc_final: 0.8477 (tt) REVERT: C 257 GLN cc_start: 0.8682 (OUTLIER) cc_final: 0.7915 (tm-30) REVERT: E 335 ASN cc_start: 0.6706 (m-40) cc_final: 0.6435 (m110) REVERT: E 355 LEU cc_start: 0.7944 (pp) cc_final: 0.7550 (tt) REVERT: F 8 ILE cc_start: 0.7516 (mm) cc_final: 0.7256 (mm) REVERT: F 13 GLN cc_start: 0.8428 (tt0) cc_final: 0.8012 (tt0) REVERT: F 66 ILE cc_start: 0.8055 (mm) cc_final: 0.7725 (mm) REVERT: F 168 PHE cc_start: 0.8658 (OUTLIER) cc_final: 0.8188 (p90) REVERT: G 1 MET cc_start: 0.7330 (ptt) cc_final: 0.6882 (ptt) REVERT: H 41 ARG cc_start: 0.7509 (ptm160) cc_final: 0.7139 (ttm170) REVERT: I 298 ARG cc_start: 0.8819 (OUTLIER) cc_final: 0.8195 (mtt90) REVERT: J 51 TRP cc_start: 0.6858 (OUTLIER) cc_final: 0.6370 (m100) REVERT: J 58 TRP cc_start: 0.7179 (m100) cc_final: 0.6660 (m100) REVERT: J 266 ARG cc_start: 0.5689 (OUTLIER) cc_final: 0.5461 (mtp-110) REVERT: J 296 ILE cc_start: 0.6744 (OUTLIER) cc_final: 0.6376 (mm) REVERT: J 353 TRP cc_start: 0.6929 (m100) cc_final: 0.6584 (m100) REVERT: J 377 MET cc_start: 0.7020 (ttt) cc_final: 0.6759 (ptm) REVERT: K 18 GLU cc_start: 0.3988 (mt-10) cc_final: 0.2766 (tm-30) REVERT: K 171 GLU cc_start: 0.2219 (mm-30) cc_final: 0.1573 (tp30) REVERT: K 236 GLN cc_start: 0.4261 (mp10) cc_final: 0.4003 (mm110) REVERT: K 241 ARG cc_start: 0.1322 (OUTLIER) cc_final: 0.0781 (ttt90) REVERT: K 246 HIS cc_start: 0.2433 (OUTLIER) cc_final: 0.1980 (m-70) REVERT: K 361 ASP cc_start: -0.0095 (OUTLIER) cc_final: -0.0316 (m-30) REVERT: K 388 MET cc_start: 0.2379 (ptt) cc_final: 0.1136 (mtm) REVERT: K 414 ARG cc_start: 0.3325 (mtt180) cc_final: 0.3015 (mtt-85) outliers start: 119 outliers final: 100 residues processed: 349 average time/residue: 0.4218 time to fit residues: 239.9948 Evaluate side-chains 351 residues out of total 3269 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 236 time to evaluate : 3.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 589 ASP Chi-restraints excluded: chain A residue 684 LEU Chi-restraints excluded: chain A residue 706 SER Chi-restraints excluded: chain A residue 747 ASP Chi-restraints excluded: chain A residue 778 VAL Chi-restraints excluded: chain A residue 1033 MET Chi-restraints excluded: chain A residue 1055 HIS Chi-restraints excluded: chain A residue 1079 GLU Chi-restraints excluded: chain A residue 1110 GLU Chi-restraints excluded: chain A residue 1113 VAL Chi-restraints excluded: chain A residue 1125 THR Chi-restraints excluded: chain A residue 1167 LEU Chi-restraints excluded: chain A residue 1182 ARG Chi-restraints excluded: chain A residue 1193 THR Chi-restraints excluded: chain B residue 416 THR Chi-restraints excluded: chain B residue 440 GLU Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain B residue 465 PHE Chi-restraints excluded: chain B residue 473 ASP Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 491 GLU Chi-restraints excluded: chain B residue 538 LYS Chi-restraints excluded: chain B residue 566 ASN Chi-restraints excluded: chain B residue 575 LEU Chi-restraints excluded: chain B residue 582 THR Chi-restraints excluded: chain B residue 612 GLU Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain B residue 713 VAL Chi-restraints excluded: chain B residue 742 LYS Chi-restraints excluded: chain B residue 836 GLU Chi-restraints excluded: chain B residue 904 LEU Chi-restraints excluded: chain B residue 937 GLU Chi-restraints excluded: chain B residue 944 LEU Chi-restraints excluded: chain B residue 960 THR Chi-restraints excluded: chain B residue 1119 ASN Chi-restraints excluded: chain B residue 1136 ASN Chi-restraints excluded: chain B residue 1137 THR Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 85 GLN Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 123 SER Chi-restraints excluded: chain C residue 152 ASP Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 231 ASP Chi-restraints excluded: chain C residue 233 SER Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 257 GLN Chi-restraints excluded: chain C residue 261 ASP Chi-restraints excluded: chain D residue 42 TYR Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 57 THR Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 127 GLU Chi-restraints excluded: chain D residue 178 ASP Chi-restraints excluded: chain D residue 188 ASP Chi-restraints excluded: chain D residue 231 ASP Chi-restraints excluded: chain D residue 292 MET Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 329 ASP Chi-restraints excluded: chain E residue 398 ARG Chi-restraints excluded: chain E residue 422 VAL Chi-restraints excluded: chain F residue 32 LEU Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 59 ILE Chi-restraints excluded: chain F residue 84 GLU Chi-restraints excluded: chain F residue 119 ILE Chi-restraints excluded: chain F residue 154 LEU Chi-restraints excluded: chain F residue 156 ASP Chi-restraints excluded: chain F residue 168 PHE Chi-restraints excluded: chain F residue 225 ASN Chi-restraints excluded: chain G residue 248 THR Chi-restraints excluded: chain G residue 251 ASP Chi-restraints excluded: chain G residue 254 SER Chi-restraints excluded: chain G residue 262 GLU Chi-restraints excluded: chain H residue 37 ASP Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 42 ASP Chi-restraints excluded: chain H residue 67 GLU Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 97 ILE Chi-restraints excluded: chain H residue 101 ILE Chi-restraints excluded: chain H residue 119 LEU Chi-restraints excluded: chain H residue 129 LEU Chi-restraints excluded: chain I residue 178 ASP Chi-restraints excluded: chain I residue 226 ILE Chi-restraints excluded: chain I residue 258 LEU Chi-restraints excluded: chain I residue 298 ARG Chi-restraints excluded: chain I residue 305 ASP Chi-restraints excluded: chain I residue 332 THR Chi-restraints excluded: chain J residue 37 SER Chi-restraints excluded: chain J residue 51 TRP Chi-restraints excluded: chain J residue 71 THR Chi-restraints excluded: chain J residue 88 LEU Chi-restraints excluded: chain J residue 142 ASP Chi-restraints excluded: chain J residue 174 LEU Chi-restraints excluded: chain J residue 249 LEU Chi-restraints excluded: chain J residue 266 ARG Chi-restraints excluded: chain J residue 287 VAL Chi-restraints excluded: chain J residue 296 ILE Chi-restraints excluded: chain J residue 302 THR Chi-restraints excluded: chain J residue 329 THR Chi-restraints excluded: chain J residue 361 ASP Chi-restraints excluded: chain J residue 395 ASN Chi-restraints excluded: chain J residue 413 SER Chi-restraints excluded: chain K residue 43 LEU Chi-restraints excluded: chain K residue 46 THR Chi-restraints excluded: chain K residue 77 LEU Chi-restraints excluded: chain K residue 137 LEU Chi-restraints excluded: chain K residue 241 ARG Chi-restraints excluded: chain K residue 246 HIS Chi-restraints excluded: chain K residue 263 ASP Chi-restraints excluded: chain K residue 302 THR Chi-restraints excluded: chain K residue 330 LYS Chi-restraints excluded: chain K residue 361 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 224 optimal weight: 0.9980 chunk 301 optimal weight: 20.0000 chunk 86 optimal weight: 0.9980 chunk 261 optimal weight: 0.6980 chunk 41 optimal weight: 2.9990 chunk 78 optimal weight: 4.9990 chunk 283 optimal weight: 0.0970 chunk 118 optimal weight: 10.0000 chunk 291 optimal weight: 10.0000 chunk 35 optimal weight: 9.9990 chunk 52 optimal weight: 0.0030 overall best weight: 0.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 731 ASN ** A 775 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 722 ASN ** B1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 335 ASN E 423 HIS ** J 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 319 HIS ** K 262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 316 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.163324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 93)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.106872 restraints weight = 49059.528| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 2.08 r_work: 0.3223 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3092 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.3243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 30093 Z= 0.139 Angle : 0.520 11.191 40750 Z= 0.269 Chirality : 0.040 0.187 4434 Planarity : 0.004 0.048 5267 Dihedral : 5.688 64.466 4041 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 3.46 % Allowed : 25.78 % Favored : 70.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.14), residues: 3583 helix: 1.93 (0.13), residues: 1643 sheet: 0.01 (0.22), residues: 543 loop : -1.33 (0.16), residues: 1397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP J 33 HIS 0.004 0.000 HIS F 140 PHE 0.049 0.001 PHE A 836 TYR 0.039 0.001 TYR G 83 ARG 0.004 0.000 ARG J 317 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7626.95 seconds wall clock time: 139 minutes 49.96 seconds (8389.96 seconds total)