Starting phenix.real_space_refine on Sun Feb 25 14:27:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r4i_14313/02_2024/7r4i_14313_trim.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r4i_14313/02_2024/7r4i_14313.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/7r4i_14313/02_2024/7r4i_14313.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r4i_14313/02_2024/7r4i_14313.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r4i_14313/02_2024/7r4i_14313_trim.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r4i_14313/02_2024/7r4i_14313_trim.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= 0.001 sd= 0.021 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: 5 Type Number sf(0) Gaussians S 124 5.16 5 C 17369 2.51 5 N 4513 2.21 5 O 5319 1.98 5 H 24148 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 40": "OD1" <-> "OD2" Residue "A PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 96": "OE1" <-> "OE2" Residue "A PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 138": "OD1" <-> "OD2" Residue "A TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 191": "OE1" <-> "OE2" Residue "A PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 204": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 215": "OD1" <-> "OD2" Residue "A PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 228": "OD1" <-> "OD2" Residue "A PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 253": "OD1" <-> "OD2" Residue "A TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 287": "OD1" <-> "OD2" Residue "A ASP 294": "OD1" <-> "OD2" Residue "A GLU 309": "OE1" <-> "OE2" Residue "A ARG 319": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 340": "OE1" <-> "OE2" Residue "A PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 346": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 364": "OD1" <-> "OD2" Residue "A TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 398": "OD1" <-> "OD2" Residue "A PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 405": "OD1" <-> "OD2" Residue "A TYR 451": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 466": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ASP 467": "OD1" <-> "OD2" Residue "A TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 554": "OE1" <-> "OE2" Residue "A ASP 571": "OD1" <-> "OD2" Residue "A ASP 574": "OD1" <-> "OD2" Residue "A PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 654": "OE1" <-> "OE2" Residue "A GLU 748": "OE1" <-> "OE2" Residue "A PHE 759": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 796": "OD1" <-> "OD2" Residue "A PHE 802": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 808": "OD1" <-> "OD2" Residue "A ARG 815": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A PHE 855": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 918": "OE1" <-> "OE2" Residue "A PHE 927": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 950": "OD1" <-> "OD2" Residue "A ASP 979": "OD1" <-> "OD2" Residue "A TYR 1007": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 1031": "OE1" <-> "OE2" Residue "A ASP 1041": "OD1" <-> "OD2" Residue "A PHE 1109": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 88": "OD1" <-> "OD2" Residue "B GLU 132": "OE1" <-> "OE2" Residue "B PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 138": "OD1" <-> "OD2" Residue "B PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 178": "OD1" <-> "OD2" Residue "B PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 215": "OD1" <-> "OD2" Residue "B ASP 228": "OD1" <-> "OD2" Residue "B ASP 253": "OD1" <-> "OD2" Residue "B TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 318": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 319": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 324": "OE1" <-> "OE2" Residue "B GLU 340": "OE1" <-> "OE2" Residue "B ARG 346": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B TYR 369": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 389": "OD1" <-> "OD2" Residue "B PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 398": "OD1" <-> "OD2" Residue "B PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 427": "OD1" <-> "OD2" Residue "B ASP 428": "OD1" <-> "OD2" Residue "B TYR 451": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 465": "OE1" <-> "OE2" Residue "B ARG 466": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 471": "OE1" <-> "OE2" Residue "B TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 554": "OE1" <-> "OE2" Residue "B PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 568": "OD1" <-> "OD2" Residue "B ASP 571": "OD1" <-> "OD2" Residue "B TYR 612": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 619": "OE1" <-> "OE2" Residue "B TYR 674": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 725": "OE1" <-> "OE2" Residue "B TYR 741": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 748": "OE1" <-> "OE2" Residue "B TYR 789": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 796": "OD1" <-> "OD2" Residue "B ASP 808": "OD1" <-> "OD2" Residue "B ARG 815": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B PHE 817": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 820": "OD1" <-> "OD2" Residue "B TYR 873": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 898": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 927": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 936": "OD1" <-> "OD2" Residue "B ASP 950": "OD1" <-> "OD2" Residue "B PHE 970": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 1031": "OE1" <-> "OE2" Residue "B PHE 1075": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 1084": "OD1" <-> "OD2" Residue "B PHE 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 1110": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 1138": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 96": "OE1" <-> "OE2" Residue "C GLU 132": "OE1" <-> "OE2" Residue "C PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 138": "OD1" <-> "OD2" Residue "C PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 180": "OE1" <-> "OE2" Residue "C GLU 191": "OE1" <-> "OE2" Residue "C PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 204": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 228": "OD1" <-> "OD2" Residue "C PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 253": "OD1" <-> "OD2" Residue "C ASP 287": "OD1" <-> "OD2" Residue "C GLU 309": "OE1" <-> "OE2" Residue "C ARG 319": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C GLU 324": "OE1" <-> "OE2" Residue "C PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 340": "OE1" <-> "OE2" Residue "C ARG 346": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C TYR 369": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 405": "OD1" <-> "OD2" Residue "C TYR 421": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 427": "OD1" <-> "OD2" Residue "C ASP 428": "OD1" <-> "OD2" Residue "C ASP 442": "OD1" <-> "OD2" Residue "C TYR 451": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 465": "OE1" <-> "OE2" Residue "C ARG 466": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C TYR 489": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 516": "OE1" <-> "OE2" Residue "C GLU 554": "OE1" <-> "OE2" Residue "C ASP 571": "OD1" <-> "OD2" Residue "C TYR 612": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 654": "OE1" <-> "OE2" Residue "C TYR 707": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 737": "OD1" <-> "OD2" Residue "C TYR 741": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 748": "OE1" <-> "OE2" Residue "C TYR 756": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 759": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 815": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ASP 820": "OD1" <-> "OD2" Residue "C TYR 873": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 888": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 970": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 979": "OD1" <-> "OD2" Residue "C TYR 1007": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 1031": "OE1" <-> "OE2" Residue "C ASP 1041": "OD1" <-> "OD2" Residue "C TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 1109": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 1144": "OE1" <-> "OE2" Residue "D PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 105": "OD1" <-> "OD2" Residue "D TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 47": "OE1" <-> "OE2" Residue "E PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 54": "OD1" <-> "OD2" Residue "E ASP 56": "OD1" <-> "OD2" Residue "E TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 105": "OD1" <-> "OD2" Residue "E ASP 113": "OD1" <-> "OD2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 51473 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 16320 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1057, 16308 Classifications: {'peptide': 1057} Link IDs: {'PTRANS': 52, 'TRANS': 1004} Chain breaks: 7 Conformer: "B" Number of residues, atoms: 1057, 16308 Classifications: {'peptide': 1057} Link IDs: {'PTRANS': 52, 'TRANS': 1004} Chain breaks: 7 bond proxies already assigned to first conformer: 16485 Chain: "B" Number of atoms: 16302 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1056, 16282 Classifications: {'peptide': 1056} Link IDs: {'PTRANS': 52, 'TRANS': 1003} Chain breaks: 6 Conformer: "B" Number of residues, atoms: 1056, 16282 Classifications: {'peptide': 1056} Link IDs: {'PTRANS': 52, 'TRANS': 1003} Chain breaks: 6 bond proxies already assigned to first conformer: 16451 Chain: "C" Number of atoms: 16361 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1060, 16360 Classifications: {'peptide': 1060} Link IDs: {'PTRANS': 53, 'TRANS': 1006} Chain breaks: 7 Conformer: "B" Number of residues, atoms: 1060, 16360 Classifications: {'peptide': 1060} Link IDs: {'PTRANS': 53, 'TRANS': 1006} Chain breaks: 7 bond proxies already assigned to first conformer: 16549 Chain: "D" Number of atoms: 944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 944 Classifications: {'peptide': 125} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 121} Chain: "E" Number of atoms: 944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 944 Classifications: {'peptide': 125} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 121} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 196 Unusual residues: {'NAG': 14} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 14 Chain: "B" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "C" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Residues with excluded nonbonded symmetry interactions: 10 residue: pdb=" N ASER A 459 " occ=0.60 ... (20 atoms not shown) pdb=" HG BSER A 459 " occ=0.40 residue: pdb=" N ASER B 459 " occ=0.60 ... (20 atoms not shown) pdb=" HG BSER B 459 " occ=0.40 residue: pdb=" N SER D 11 " occ=0.47 ... (4 atoms not shown) pdb=" OG SER D 11 " occ=0.47 residue: pdb=" N VAL D 12 " occ=0.47 ... (5 atoms not shown) pdb=" CG2 VAL D 12 " occ=0.47 residue: pdb=" N SER D 21 " occ=0.44 ... (4 atoms not shown) pdb=" OG SER D 21 " occ=0.44 residue: pdb=" N SER D 124 " occ=0.61 ... (4 atoms not shown) pdb=" OG SER D 124 " occ=0.61 residue: pdb=" N SER E 11 " occ=0.47 ... (4 atoms not shown) pdb=" OG SER E 11 " occ=0.47 residue: pdb=" N VAL E 12 " occ=0.47 ... (5 atoms not shown) pdb=" CG2 VAL E 12 " occ=0.47 residue: pdb=" N SER E 21 " occ=0.44 ... (4 atoms not shown) pdb=" OG SER E 21 " occ=0.44 residue: pdb=" N SER E 124 " occ=0.61 ... (4 atoms not shown) pdb=" OG SER E 124 " occ=0.61 Time building chain proxies: 38.83, per 1000 atoms: 0.75 Number of scatterers: 51473 At special positions: 0 Unit cell: (158.175, 151.335, 212.04, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 124 16.00 O 5319 8.00 N 4513 7.00 C 17369 6.00 H 24148 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.04 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.04 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.04 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.04 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.02 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.04 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.04 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.04 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.04 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.04 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.04 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 97 " distance=2.03 Simple disulfide: pdb=" SG CYS D 34 " - pdb=" SG CYS D 104 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 97 " distance=2.03 Simple disulfide: pdb=" SG CYS E 34 " - pdb=" SG CYS E 104 " distance=2.03 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 Links applied BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " NAG-ASN " NAG A1304 " - " ASN A 331 " " NAG A1306 " - " ASN A 603 " " NAG A1307 " - " ASN A 61 " " NAG A1308 " - " ASN A 616 " " NAG A1309 " - " ASN A 657 " " NAG A1310 " - " ASN A 709 " " NAG A1311 " - " ASN A 717 " " NAG A1313 " - " ASN A1098 " " NAG A1314 " - " ASN A1134 " " NAG B1301 " - " ASN B 122 " " NAG B1304 " - " ASN B 282 " " NAG B1307 " - " ASN B 61 " " NAG B1308 " - " ASN B 616 " " NAG B1309 " - " ASN B 709 " " NAG B1311 " - " ASN B1074 " " NAG B1312 " - " ASN B1098 " " NAG B1313 " - " ASN B1134 " " NAG C1301 " - " ASN C 282 " " NAG C1302 " - " ASN C 603 " " NAG C1303 " - " ASN C 61 " " NAG C1305 " - " ASN C 657 " " NAG C1306 " - " ASN C 709 " " NAG H 1 " - " ASN C 122 " " NAG I 1 " - " ASN C 17 " " NAG J 1 " - " ASN C 234 " Time building additional restraints: 39.60 Conformation dependent library (CDL) restraints added in 9.4 seconds 6752 Ramachandran restraints generated. 3376 Oldfield, 0 Emsley, 3376 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6376 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 59 sheets defined 22.0% alpha, 23.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.66 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 removed outlier: 3.712A pdb=" N LYS A 300 " --> pdb=" O LEU A 296 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N CYS A 301 " --> pdb=" O SER A 297 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N THR A 302 " --> pdb=" O GLU A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 364 through 370 removed outlier: 4.072A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 409 removed outlier: 3.898A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 568 through 572 removed outlier: 3.721A pdb=" N THR A 572 " --> pdb=" O ILE A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 744 removed outlier: 3.562A pdb=" N TYR A 741 " --> pdb=" O ASP A 737 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ILE A 742 " --> pdb=" O CYS A 738 " (cutoff:3.500A) Processing helix chain 'A' and resid 747 through 754 removed outlier: 3.580A pdb=" N ASN A 751 " --> pdb=" O THR A 747 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 4.889A pdb=" N ASN A 764 " --> pdb=" O CYS A 760 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ARG A 765 " --> pdb=" O THR A 761 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N ILE A 770 " --> pdb=" O ALA A 766 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLU A 773 " --> pdb=" O GLY A 769 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLN A 779 " --> pdb=" O ASP A 775 " (cutoff:3.500A) Processing helix chain 'A' and resid 801 through 805 removed outlier: 4.291A pdb=" N GLN A 804 " --> pdb=" O ASN A 801 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 825 removed outlier: 4.102A pdb=" N LEU A 822 " --> pdb=" O ILE A 818 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 880 removed outlier: 3.569A pdb=" N TYR A 873 " --> pdb=" O MET A 869 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N THR A 874 " --> pdb=" O ILE A 870 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLY A 880 " --> pdb=" O ALA A 876 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 890 removed outlier: 3.895A pdb=" N GLY A 889 " --> pdb=" O TRP A 886 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ALA A 890 " --> pdb=" O THR A 887 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 886 through 890' Processing helix chain 'A' and resid 898 through 910 removed outlier: 4.034A pdb=" N ASN A 907 " --> pdb=" O ALA A 903 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 918 Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.576A pdb=" N GLN A 926 " --> pdb=" O LEU A 922 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ILE A 931 " --> pdb=" O PHE A 927 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N GLY A 932 " --> pdb=" O ASN A 928 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LYS A 933 " --> pdb=" O SER A 929 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ILE A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N SER A 937 " --> pdb=" O LYS A 933 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.780A pdb=" N GLN A 949 " --> pdb=" O LEU A 945 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLN A 954 " --> pdb=" O ASP A 950 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU A 959 " --> pdb=" O ASN A 955 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 982 removed outlier: 3.660A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1030 removed outlier: 3.731A pdb=" N ILE A 993 " --> pdb=" O ALA A 989 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N THR A 998 " --> pdb=" O ASP A 994 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N GLN A1002 " --> pdb=" O THR A 998 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ILE A1013 " --> pdb=" O THR A1009 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ARG A1014 " --> pdb=" O GLN A1010 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ILE A1018 " --> pdb=" O ARG A1014 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ARG A1019 " --> pdb=" O ALA A1015 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1146 Processing helix chain 'B' and resid 294 through 303 removed outlier: 4.119A pdb=" N THR B 302 " --> pdb=" O GLU B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 365 through 371 Processing helix chain 'B' and resid 383 through 387 removed outlier: 3.804A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 408 removed outlier: 4.373A pdb=" N ARG B 408 " --> pdb=" O GLY B 404 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 404 through 408' Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 616 through 620 removed outlier: 3.579A pdb=" N VAL B 620 " --> pdb=" O CYS B 617 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 742 Processing helix chain 'B' and resid 746 through 754 removed outlier: 3.811A pdb=" N SER B 750 " --> pdb=" O SER B 746 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ASN B 751 " --> pdb=" O THR B 747 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 772 removed outlier: 3.762A pdb=" N ASN B 764 " --> pdb=" O CYS B 760 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LEU B 767 " --> pdb=" O LEU B 763 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ILE B 770 " --> pdb=" O ALA B 766 " (cutoff:3.500A) Processing helix chain 'B' and resid 772 through 781 removed outlier: 4.017A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLN B 779 " --> pdb=" O ASP B 775 " (cutoff:3.500A) Processing helix chain 'B' and resid 801 through 805 removed outlier: 4.536A pdb=" N GLN B 804 " --> pdb=" O ASN B 801 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 825 removed outlier: 3.895A pdb=" N LEU B 822 " --> pdb=" O ILE B 818 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN B 824 " --> pdb=" O ASP B 820 " (cutoff:3.500A) Processing helix chain 'B' and resid 868 through 885 removed outlier: 3.749A pdb=" N SER B 875 " --> pdb=" O ALA B 871 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 910 removed outlier: 3.942A pdb=" N ALA B 903 " --> pdb=" O ALA B 899 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ASN B 907 " --> pdb=" O ALA B 903 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLY B 908 " --> pdb=" O TYR B 904 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 919 removed outlier: 3.567A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 940 removed outlier: 3.736A pdb=" N SER B 929 " --> pdb=" O ASN B 925 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLY B 932 " --> pdb=" O ASN B 928 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LYS B 933 " --> pdb=" O SER B 929 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N SER B 937 " --> pdb=" O LYS B 933 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 964 removed outlier: 3.505A pdb=" N GLN B 949 " --> pdb=" O LEU B 945 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLN B 954 " --> pdb=" O ASP B 950 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ALA B 958 " --> pdb=" O GLN B 954 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N LEU B 959 " --> pdb=" O ASN B 955 " (cutoff:3.500A) Processing helix chain 'B' and resid 965 through 968 removed outlier: 3.749A pdb=" N SER B 968 " --> pdb=" O GLN B 965 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 965 through 968' Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.620A pdb=" N LEU B 984 " --> pdb=" O ILE B 980 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1013 removed outlier: 4.794A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILE B 993 " --> pdb=" O ALA B 989 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLY B 999 " --> pdb=" O ARG B 995 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N SER B1003 " --> pdb=" O GLY B 999 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N THR B1009 " --> pdb=" O GLN B1005 " (cutoff:3.500A) Processing helix chain 'B' and resid 1013 through 1023 removed outlier: 3.768A pdb=" N ILE B1018 " --> pdb=" O ARG B1014 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N ARG B1019 " --> pdb=" O ALA B1015 " (cutoff:3.500A) Processing helix chain 'B' and resid 1024 through 1032 removed outlier: 3.760A pdb=" N MET B1029 " --> pdb=" O ALA B1025 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N SER B1030 " --> pdb=" O ALA B1026 " (cutoff:3.500A) Processing helix chain 'B' and resid 1142 through 1146 Processing helix chain 'C' and resid 294 through 303 removed outlier: 3.597A pdb=" N GLU C 298 " --> pdb=" O ASP C 294 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 405 through 407 No H-bonds generated for 'chain 'C' and resid 405 through 407' Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 737 through 743 removed outlier: 3.513A pdb=" N TYR C 741 " --> pdb=" O ASP C 737 " (cutoff:3.500A) Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.592A pdb=" N ASN C 764 " --> pdb=" O CYS C 760 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N THR C 768 " --> pdb=" O ASN C 764 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL C 781 " --> pdb=" O ASN C 777 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N PHE C 782 " --> pdb=" O THR C 778 " (cutoff:3.500A) Processing helix chain 'C' and resid 801 through 805 removed outlier: 4.061A pdb=" N GLN C 804 " --> pdb=" O ASN C 801 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 825 removed outlier: 3.628A pdb=" N LEU C 821 " --> pdb=" O PHE C 817 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LYS C 825 " --> pdb=" O LEU C 821 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 removed outlier: 3.607A pdb=" N ALA C 871 " --> pdb=" O ASP C 867 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N THR C 881 " --> pdb=" O LEU C 877 " (cutoff:3.500A) Processing helix chain 'C' and resid 899 through 908 removed outlier: 3.840A pdb=" N GLY C 908 " --> pdb=" O TYR C 904 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.692A pdb=" N ASN C 928 " --> pdb=" O ALA C 924 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N GLY C 932 " --> pdb=" O ASN C 928 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LYS C 933 " --> pdb=" O SER C 929 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N SER C 937 " --> pdb=" O LYS C 933 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 958 removed outlier: 3.581A pdb=" N GLN C 949 " --> pdb=" O LEU C 945 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 958 through 966 removed outlier: 3.977A pdb=" N LYS C 964 " --> pdb=" O ASN C 960 " (cutoff:3.500A) Processing helix chain 'C' and resid 977 through 982 Processing helix chain 'C' and resid 985 through 1003 removed outlier: 3.916A pdb=" N ASP C 994 " --> pdb=" O GLU C 990 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N THR C 998 " --> pdb=" O ASP C 994 " (cutoff:3.500A) Processing helix chain 'C' and resid 1003 through 1018 removed outlier: 3.839A pdb=" N ARG C1014 " --> pdb=" O GLN C1010 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ALA C1015 " --> pdb=" O GLN C1011 " (cutoff:3.500A) Processing helix chain 'C' and resid 1018 through 1032 removed outlier: 4.348A pdb=" N LEU C1024 " --> pdb=" O ALA C1020 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ALA C1025 " --> pdb=" O SER C1021 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N MET C1029 " --> pdb=" O ALA C1025 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 110 removed outlier: 3.645A pdb=" N TYR D 108 " --> pdb=" O CYS D 104 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ARG D 109 " --> pdb=" O ASP D 105 " (cutoff:3.500A) Processing helix chain 'E' and resid 64 through 69 removed outlier: 3.912A pdb=" N ARG E 68 " --> pdb=" O SER E 64 " (cutoff:3.500A) Processing helix chain 'E' and resid 105 through 109 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 4.100A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N TRP A 64 " --> pdb=" O ALA A 27 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N THR A 29 " --> pdb=" O VAL A 62 " (cutoff:3.500A) removed outlier: 8.652A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N PHE A 92 " --> pdb=" O PHE A 192 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N PHE A 192 " --> pdb=" O PHE A 92 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.675A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.648A pdb=" N LEU A 141 " --> pdb=" O LEU A 242 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LEU A 244 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 7.898A pdb=" N PHE A 140 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 5.724A pdb=" N PHE A 157 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N GLY A 142 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N MET A 153 " --> pdb=" O TYR A 144 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 5.809A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LEU A 118 " --> pdb=" O LYS A 129 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LYS A 129 " --> pdb=" O LEU A 118 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 4.897A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 5.144A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLN A 613 " --> pdb=" O GLY A 594 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N SER A 596 " --> pdb=" O LEU A 611 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ALA A 609 " --> pdb=" O ILE A 598 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 323 through 327 removed outlier: 5.154A pdb=" N ASN A 540 " --> pdb=" O GLU A 324 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU A 546 " --> pdb=" O PHE A 543 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA9, first strand: chain 'A' and resid 354 through 358 removed outlier: 6.346A pdb=" N PHE A 392 " --> pdb=" O THR A 523 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB2, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB3, first strand: chain 'A' and resid 655 through 660 removed outlier: 6.882A pdb=" N ALA A 694 " --> pdb=" O VAL A 656 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N ASN A 658 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N THR A 696 " --> pdb=" O ASN A 658 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N SER A 673 " --> pdb=" O ILE A 693 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 713 Processing sheet with id=AB5, first strand: chain 'A' and resid 720 through 722 removed outlier: 3.852A pdb=" N SER A 721 " --> pdb=" O THR A1066 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLU A 725 " --> pdb=" O PHE A1062 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 720 through 722 removed outlier: 3.852A pdb=" N SER A 721 " --> pdb=" O THR A1066 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 734 through 736 removed outlier: 4.003A pdb=" N SER A 735 " --> pdb=" O THR A 859 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1081 through 1083 removed outlier: 3.595A pdb=" N HIS A1088 " --> pdb=" O ILE A1081 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 1094 through 1096 Processing sheet with id=AC1, first strand: chain 'B' and resid 27 through 30 removed outlier: 4.038A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.526A pdb=" N PHE B 275 " --> pdb=" O THR B 51 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 66 through 67 removed outlier: 3.625A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N THR B 95 " --> pdb=" O ALA B 264 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N TYR B 266 " --> pdb=" O ALA B 93 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ALA B 93 " --> pdb=" O TYR B 266 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N VAL B 90 " --> pdb=" O PHE B 194 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N PHE B 194 " --> pdb=" O VAL B 90 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLU B 96 " --> pdb=" O ASN B 188 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N ASN B 188 " --> pdb=" O GLU B 96 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 83 through 85 removed outlier: 6.831A pdb=" N ARG B 237 " --> pdb=" O PHE B 106 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N PHE B 106 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N GLN B 239 " --> pdb=" O TRP B 104 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N TRP B 104 " --> pdb=" O GLN B 239 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N LEU B 241 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ASN B 121 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N TRP B 104 " --> pdb=" O ILE B 119 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N ILE B 119 " --> pdb=" O TRP B 104 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N PHE B 106 " --> pdb=" O LEU B 117 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ILE B 128 " --> pdb=" O TYR B 170 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 151 through 158 removed outlier: 6.244A pdb=" N TRP B 152 " --> pdb=" O HIS B 146 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N HIS B 146 " --> pdb=" O TRP B 152 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N GLU B 154 " --> pdb=" O TYR B 144 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N TYR B 144 " --> pdb=" O GLU B 154 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N GLY B 142 " --> pdb=" O GLU B 156 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 311 through 317 removed outlier: 4.102A pdb=" N GLY B 311 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N THR B 599 " --> pdb=" O GLY B 311 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N SER B 596 " --> pdb=" O LEU B 611 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 324 through 328 removed outlier: 6.734A pdb=" N GLU B 324 " --> pdb=" O ASN B 540 " (cutoff:3.500A) removed outlier: 8.811A pdb=" N ASN B 542 " --> pdb=" O GLU B 324 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N ILE B 326 " --> pdb=" O ASN B 542 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 355 through 356 removed outlier: 3.538A pdb=" N TYR B 396 " --> pdb=" O SER B 514 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N CYS B 432 " --> pdb=" O LEU B 513 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 391 through 392 Processing sheet with id=AD1, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD2, first strand: chain 'B' and resid 551 through 554 Processing sheet with id=AD3, first strand: chain 'B' and resid 567 through 568 Processing sheet with id=AD4, first strand: chain 'B' and resid 655 through 660 removed outlier: 5.665A pdb=" N THR B 696 " --> pdb=" O VAL B 656 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N ASN B 658 " --> pdb=" O THR B 696 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 702 through 703 Processing sheet with id=AD6, first strand: chain 'B' and resid 711 through 714 Processing sheet with id=AD7, first strand: chain 'B' and resid 717 through 728 removed outlier: 3.687A pdb=" N ALA B1070 " --> pdb=" O ASN B 717 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N SER B 721 " --> pdb=" O THR B1066 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N THR B1066 " --> pdb=" O SER B 721 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N TYR B1047 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD9, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 6.731A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N HIS B1083 " --> pdb=" O LYS B1086 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 27 through 29 removed outlier: 4.072A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N PHE C 65 " --> pdb=" O TYR C 265 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N TYR C 265 " --> pdb=" O PHE C 65 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N TYR C 266 " --> pdb=" O ALA C 93 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N PHE C 92 " --> pdb=" O PHE C 192 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLU C 96 " --> pdb=" O ASN C 188 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ASN C 188 " --> pdb=" O GLU C 96 " (cutoff:3.500A) removed outlier: 7.518A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 48 through 49 removed outlier: 3.787A pdb=" N HIS C 49 " --> pdb=" O LEU C 277 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 53 through 55 removed outlier: 4.053A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 84 through 85 removed outlier: 5.376A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 141 through 146 removed outlier: 6.411A pdb=" N GLY C 142 " --> pdb=" O SER C 155 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N SER C 151 " --> pdb=" O HIS C 146 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 311 through 319 removed outlier: 4.914A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 323 through 327 removed outlier: 5.086A pdb=" N ASN C 540 " --> pdb=" O GLU C 324 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 354 through 358 Processing sheet with id=AE9, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AF1, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AF2, first strand: chain 'C' and resid 655 through 660 removed outlier: 5.941A pdb=" N ALA C 694 " --> pdb=" O VAL C 656 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N ASN C 658 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N THR C 696 " --> pdb=" O ASN C 658 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N TYR C 660 " --> pdb=" O THR C 696 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 712 through 713 removed outlier: 3.700A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 722 through 728 removed outlier: 3.669A pdb=" N HIS C1064 " --> pdb=" O THR C 723 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N PHE C1062 " --> pdb=" O GLU C 725 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AF6, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 5.116A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE C1081 " --> pdb=" O HIS C1088 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N CYS C1082 " --> pdb=" O VAL C1133 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'D' and resid 5 through 7 Processing sheet with id=AF8, first strand: chain 'D' and resid 12 through 13 removed outlier: 6.577A pdb=" N VAL D 12 " --> pdb=" O SER D 124 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF8 Processing sheet with id=AF9, first strand: chain 'D' and resid 34 through 38 removed outlier: 4.071A pdb=" N TRP D 37 " --> pdb=" O ALA D 50 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N ALA D 50 " --> pdb=" O TRP D 37 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'D' and resid 93 through 95 Processing sheet with id=AG2, first strand: chain 'D' and resid 98 through 99 Processing sheet with id=AG3, first strand: chain 'E' and resid 5 through 7 Processing sheet with id=AG4, first strand: chain 'E' and resid 10 through 12 removed outlier: 3.517A pdb=" N GLY E 36 " --> pdb=" O THR E 98 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N TRP E 37 " --> pdb=" O ALA E 50 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ALA E 50 " --> pdb=" O TRP E 37 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ARG E 39 " --> pdb=" O GLY E 48 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N GLY E 48 " --> pdb=" O ARG E 39 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'E' and resid 10 through 12 849 hydrogen bonds defined for protein. 2262 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: 22.50 Time building geometry restraints manager: 41.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.26: 28598 1.26 - 1.68: 23318 1.68 - 2.11: 163 2.11 - 2.53: 7 2.53 - 2.95: 1 Bond restraints: 52087 Sorted by residual: bond pdb=" C ASN B 481 " pdb=" N GLY B 482 " ideal model delta sigma weight residual 1.331 2.954 -1.624 1.46e-02 4.69e+03 1.24e+04 bond pdb=" CA SER B 494 " pdb=" CB SER B 494 " ideal model delta sigma weight residual 1.530 1.977 -0.446 1.50e-02 4.44e+03 8.85e+02 bond pdb=" CA SER A 494 " pdb=" CB SER A 494 " ideal model delta sigma weight residual 1.531 1.981 -0.450 1.52e-02 4.33e+03 8.77e+02 bond pdb=" CD1 PHE E 55 " pdb=" CE1 PHE E 55 " ideal model delta sigma weight residual 1.382 2.245 -0.863 3.00e-02 1.11e+03 8.28e+02 bond pdb=" CD2 PHE D 55 " pdb=" CE2 PHE D 55 " ideal model delta sigma weight residual 1.382 2.208 -0.826 3.00e-02 1.11e+03 7.59e+02 ... (remaining 52082 not shown) Histogram of bond angle deviations from ideal: 60.10 - 75.23: 1 75.23 - 90.36: 10 90.36 - 105.50: 594 105.50 - 120.63: 77642 120.63 - 135.76: 14422 Bond angle restraints: 92669 Sorted by residual: angle pdb=" O ASN B 481 " pdb=" C ASN B 481 " pdb=" N GLY B 482 " ideal model delta sigma weight residual 122.59 60.10 62.49 1.33e+00 5.65e-01 2.21e+03 angle pdb=" C ASN B 481 " pdb=" N GLY B 482 " pdb=" CA GLY B 482 " ideal model delta sigma weight residual 121.41 86.02 35.39 1.96e+00 2.60e-01 3.26e+02 angle pdb=" CA SER B 494 " pdb=" CB SER B 494 " pdb=" OG SER B 494 " ideal model delta sigma weight residual 111.10 131.74 -20.64 2.00e+00 2.50e-01 1.06e+02 angle pdb=" OG SER A 494 " pdb=" CB SER A 494 " pdb=" HB3 SER A 494 " ideal model delta sigma weight residual 109.00 80.76 28.24 3.00e+00 1.11e-01 8.86e+01 angle pdb=" CA SER A 494 " pdb=" CB SER A 494 " pdb=" OG SER A 494 " ideal model delta sigma weight residual 111.10 129.68 -18.58 2.00e+00 2.50e-01 8.63e+01 ... (remaining 92664 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.07: 24123 25.07 - 50.14: 1377 50.14 - 75.22: 259 75.22 - 100.29: 21 100.29 - 125.36: 3 Dihedral angle restraints: 25783 sinusoidal: 13987 harmonic: 11796 Sorted by residual: dihedral pdb=" CA ASN B 481 " pdb=" C ASN B 481 " pdb=" N GLY B 482 " pdb=" CA GLY B 482 " ideal model delta harmonic sigma weight residual 180.00 141.10 38.90 0 5.00e+00 4.00e-02 6.05e+01 dihedral pdb=" CB CYS A 538 " pdb=" SG CYS A 538 " pdb=" SG CYS A 590 " pdb=" CB CYS A 590 " ideal model delta sinusoidal sigma weight residual -86.00 -23.70 -62.30 1 1.00e+01 1.00e-02 5.14e+01 dihedral pdb=" CB CYS B 617 " pdb=" SG CYS B 617 " pdb=" SG CYS B 649 " pdb=" CB CYS B 649 " ideal model delta sinusoidal sigma weight residual 93.00 35.81 57.19 1 1.00e+01 1.00e-02 4.40e+01 ... (remaining 25780 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.284: 4386 0.284 - 0.568: 1 0.568 - 0.852: 0 0.852 - 1.136: 0 1.136 - 1.420: 1 Chirality restraints: 4388 Sorted by residual: chirality pdb=" CB THR C 478 " pdb=" CA THR C 478 " pdb=" OG1 THR C 478 " pdb=" CG2 THR C 478 " both_signs ideal model delta sigma weight residual False 2.55 1.13 1.42 2.00e-01 2.50e+01 5.04e+01 chirality pdb=" C1 NAG C1301 " pdb=" ND2 ASN C 282 " pdb=" C2 NAG C1301 " pdb=" O5 NAG C1301 " both_signs ideal model delta sigma weight residual False -2.40 -1.91 -0.49 2.00e-01 2.50e+01 5.92e+00 chirality pdb=" CA SER A 494 " pdb=" N SER A 494 " pdb=" C SER A 494 " pdb=" CB SER A 494 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.30e+00 ... (remaining 4385 not shown) Planarity restraints: 7892 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN B 481 " 0.178 2.00e-02 2.50e+03 2.68e-01 7.20e+02 pdb=" C ASN B 481 " -0.427 2.00e-02 2.50e+03 pdb=" O ASN B 481 " 0.271 2.00e-02 2.50e+03 pdb=" N GLY B 482 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN B 481 " -0.030 2.00e-02 2.50e+03 2.06e-01 4.23e+02 pdb=" N GLY B 482 " 0.335 2.00e-02 2.50e+03 pdb=" CA GLY B 482 " -0.082 2.00e-02 2.50e+03 pdb=" H GLY B 482 " -0.223 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR C 941 " -0.107 5.00e-02 4.00e+02 1.51e-01 3.64e+01 pdb=" N PRO C 942 " 0.260 5.00e-02 4.00e+02 pdb=" CA PRO C 942 " -0.081 5.00e-02 4.00e+02 pdb=" CD PRO C 942 " -0.072 5.00e-02 4.00e+02 ... (remaining 7889 not shown) Histogram of nonbonded interaction distances: 1.31 - 1.97: 884 1.97 - 2.63: 68542 2.63 - 3.28: 149901 3.28 - 3.94: 192919 3.94 - 4.60: 299122 Nonbonded interactions: 711368 Sorted by model distance: nonbonded pdb=" HE ARG B 21 " pdb=" O PHE B 79 " model vdw 1.310 1.850 nonbonded pdb=" OD1 ASN B 280 " pdb=" H THR B 284 " model vdw 1.428 1.850 nonbonded pdb=" HH TYR B 37 " pdb=" O LEU B 54 " model vdw 1.438 1.850 nonbonded pdb=" OE2 GLU C 96 " pdb=" H ILE C 101 " model vdw 1.441 1.850 nonbonded pdb=" O ASP A 253 " pdb=" H GLY A 257 " model vdw 1.441 1.850 ... (remaining 711363 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 14 through 458 or resid 461 through 476 or resid 478 throu \ gh 577 or (resid 584 and (name N or name CA or name C or name O or name CB or na \ me CG1 or name CG2 or name CD1 or name HA or name HB or name HG12 or name HG13 o \ r name HG21 or name HG22 or name HG23 or name HD11 or name HD12 or name HD13)) o \ r resid 585 through 1063 or (resid 1064 and (name N or name CA or name C or name \ O or name CB or name CG or name ND1 or name CD2 or name CE1 or name NE2 or name \ H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or name HE2)) or r \ esid 1065 through 1146 or resid 1301 through 1306)) selection = (chain 'B' and (resid 14 through 458 or resid 461 through 476 or resid 478 throu \ gh 516 or resid 522 through 1146 or resid 1301 through 1306)) selection = (chain 'C' and (resid 14 through 458 or resid 461 through 476 or resid 478 throu \ gh 516 or resid 522 through 577 or (resid 584 and (name N or name CA or name C o \ r name O or name CB or name CG1 or name CG2 or name CD1 or name HA or name HB or \ name HG12 or name HG13 or name HG21 or name HG22 or name HG23 or name HD11 or n \ ame HD12 or name HD13)) or resid 585 through 1063 or (resid 1064 and (name N or \ name CA or name C or name O or name CB or name CG or name ND1 or name CD2 or nam \ e CE1 or name NE2 or name H or name HA or name HB2 or name HB3 or name HD2 or na \ me HE1 or name HE2)) or resid 1065 through 1146 or resid 1301 through 1306)) } ncs_group { reference = chain 'D' selection = chain 'E' } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.33 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: 7.860 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: 0.760 Extract box with map and model: 26.820 Check model and map are aligned: 0.740 Set scattering table: 0.440 Process input model: 176.330 Find NCS groups from input model: 2.960 Set up NCS constraints: 0.360 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 218.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6371 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 : 0.019 1.624 27939 Z= 1.205 Angle : 0.997 62.490 37997 Z= 0.613 Chirality : 0.051 1.420 4388 Planarity : 0.008 0.268 4870 Dihedral : 14.614 125.359 10650 Min Nonbonded Distance : 1.819 Molprobity Statistics. All-atom Clashscore : 36.30 Ramachandran Plot: Outliers : 0.06 % Allowed : 13.05 % Favored : 86.89 % Rotamer: Outliers : 0.17 % Allowed : 2.83 % Favored : 97.01 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.62 % 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: -5.90 (0.10), residues: 3376 helix: -4.99 (0.07), residues: 614 sheet: -2.96 (0.18), residues: 630 loop : -4.13 (0.10), residues: 2132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 886 HIS 0.008 0.002 HIS C1048 PHE 0.041 0.002 PHE D 55 TYR 0.019 0.002 TYR C 269 ARG 0.011 0.001 ARG C 346 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6752 Ramachandran restraints generated. 3376 Oldfield, 0 Emsley, 3376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6752 Ramachandran restraints generated. 3376 Oldfield, 0 Emsley, 3376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 743 residues out of total 2964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 738 time to evaluate : 4.164 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 SER cc_start: 0.8057 (t) cc_final: 0.7731 (m) REVERT: A 177 MET cc_start: -0.0592 (tpt) cc_final: -0.2093 (tpt) REVERT: A 308 VAL cc_start: 0.8371 (t) cc_final: 0.7996 (p) REVERT: A 309 GLU cc_start: 0.7455 (mm-30) cc_final: 0.7136 (mm-30) REVERT: A 537 LYS cc_start: 0.7536 (mttp) cc_final: 0.7180 (tttm) REVERT: A 578 ASP cc_start: 0.8074 (p0) cc_final: 0.7562 (t70) REVERT: A 597 VAL cc_start: 0.8288 (t) cc_final: 0.7873 (p) REVERT: A 610 VAL cc_start: 0.8237 (t) cc_final: 0.7979 (p) REVERT: A 666 ILE cc_start: 0.7989 (mt) cc_final: 0.7702 (mm) REVERT: A 725 GLU cc_start: 0.7396 (tt0) cc_final: 0.7171 (tt0) REVERT: A 821 LEU cc_start: 0.6850 (mt) cc_final: 0.6438 (mt) REVERT: A 870 ILE cc_start: 0.8192 (mt) cc_final: 0.7923 (tp) REVERT: A 884 SER cc_start: 0.8433 (m) cc_final: 0.7807 (p) REVERT: A 900 MET cc_start: 0.6558 (mtp) cc_final: 0.6260 (mtp) REVERT: A 925 ASN cc_start: 0.7998 (m-40) cc_final: 0.7388 (t0) REVERT: A 931 ILE cc_start: 0.7713 (mm) cc_final: 0.7228 (mt) REVERT: A 1018 ILE cc_start: 0.8181 (mm) cc_final: 0.7976 (mt) REVERT: A 1041 ASP cc_start: 0.6907 (m-30) cc_final: 0.6464 (m-30) REVERT: A 1101 HIS cc_start: 0.7437 (m90) cc_final: 0.7145 (m90) REVERT: A 1133 VAL cc_start: 0.8218 (t) cc_final: 0.7966 (m) REVERT: B 382 VAL cc_start: 0.8408 (m) cc_final: 0.7483 (p) REVERT: B 531 THR cc_start: 0.8275 (m) cc_final: 0.7940 (p) REVERT: B 540 ASN cc_start: 0.7432 (m110) cc_final: 0.7124 (m-40) REVERT: B 557 LYS cc_start: 0.6932 (ptpt) cc_final: 0.6720 (ptpp) REVERT: B 725 GLU cc_start: 0.7183 (tt0) cc_final: 0.6975 (tt0) REVERT: B 732 THR cc_start: 0.7722 (m) cc_final: 0.7470 (p) REVERT: B 790 LYS cc_start: 0.7502 (mtpp) cc_final: 0.7242 (mtpp) REVERT: B 800 PHE cc_start: 0.7008 (m-10) cc_final: 0.5389 (m-10) REVERT: B 859 THR cc_start: 0.8351 (m) cc_final: 0.7992 (p) REVERT: B 868 GLU cc_start: 0.6763 (mp0) cc_final: 0.6438 (mp0) REVERT: B 931 ILE cc_start: 0.7709 (mm) cc_final: 0.7229 (mt) REVERT: B 979 ASP cc_start: 0.7346 (t70) cc_final: 0.6890 (t0) REVERT: B 1009 THR cc_start: 0.7783 (m) cc_final: 0.7019 (t) REVERT: B 1030 SER cc_start: 0.8333 (m) cc_final: 0.8041 (p) REVERT: B 1037 SER cc_start: 0.7933 (t) cc_final: 0.7470 (p) REVERT: B 1045 LYS cc_start: 0.7799 (mptt) cc_final: 0.7460 (tptt) REVERT: B 1054 GLN cc_start: 0.7561 (mm-40) cc_final: 0.7281 (mm-40) REVERT: B 1136 THR cc_start: 0.6169 (t) cc_final: 0.5771 (m) REVERT: C 91 TYR cc_start: 0.5982 (t80) cc_final: 0.5549 (t80) REVERT: C 140 PHE cc_start: 0.7748 (p90) cc_final: 0.7288 (p90) REVERT: C 192 PHE cc_start: 0.5701 (m-80) cc_final: 0.5481 (m-10) REVERT: C 224 GLU cc_start: 0.6847 (pt0) cc_final: 0.6193 (pm20) REVERT: C 537 LYS cc_start: 0.8110 (mttp) cc_final: 0.7795 (mttp) REVERT: C 619 GLU cc_start: 0.7062 (mp0) cc_final: 0.6802 (mp0) REVERT: C 663 ASP cc_start: 0.6248 (t70) cc_final: 0.6015 (t70) REVERT: C 666 ILE cc_start: 0.8630 (mt) cc_final: 0.8395 (mm) REVERT: C 671 CYS cc_start: 0.5512 (m) cc_final: 0.5044 (m) REVERT: C 721 SER cc_start: 0.8389 (t) cc_final: 0.8115 (p) REVERT: C 725 GLU cc_start: 0.6338 (tt0) cc_final: 0.6012 (tt0) REVERT: C 727 LEU cc_start: 0.8228 (mt) cc_final: 0.7936 (mt) REVERT: C 736 VAL cc_start: 0.7171 (t) cc_final: 0.6340 (p) REVERT: C 931 ILE cc_start: 0.7304 (mm) cc_final: 0.6864 (mt) REVERT: C 935 GLN cc_start: 0.7121 (tm-30) cc_final: 0.6820 (tm-30) REVERT: C 950 ASP cc_start: 0.7023 (t0) cc_final: 0.6744 (t0) REVERT: C 1084 ASP cc_start: 0.7151 (t0) cc_final: 0.6809 (t0) REVERT: C 1091 ARG cc_start: 0.7253 (mtt-85) cc_final: 0.6970 (mtt-85) REVERT: C 1116 THR cc_start: 0.7910 (m) cc_final: 0.7491 (p) outliers start: 5 outliers final: 4 residues processed: 742 average time/residue: 0.8403 time to fit residues: 970.7471 Evaluate side-chains 597 residues out of total 2964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 593 time to evaluate : 3.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain C residue 61 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 287 optimal weight: 0.8980 chunk 257 optimal weight: 8.9990 chunk 142 optimal weight: 4.9990 chunk 88 optimal weight: 1.9990 chunk 173 optimal weight: 1.9990 chunk 137 optimal weight: 0.7980 chunk 266 optimal weight: 0.7980 chunk 103 optimal weight: 0.9980 chunk 162 optimal weight: 0.8980 chunk 198 optimal weight: 0.4980 chunk 308 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 GLN A 52 GLN A 69 HIS ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 137 ASN A 343 ASN A 448 ASN A 450 ASN A 487 ASN ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 784 GLN ** A1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1142 GLN ** B 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 173 GLN B 245 HIS B 314 GLN B 331 ASN ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 498 GLN ** B 717 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 872 GLN B 926 GLN ** B1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 99 ASN C 185 ASN ** C 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 388 ASN ** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 493 GLN C 777 ASN C 784 GLN C 901 GLN C 965 GLN ** D 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 106 ASN ** E 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6552 moved from start: 0.2680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.015 0.880 27939 Z= 1.027 Angle : 0.801 20.921 37997 Z= 0.428 Chirality : 0.054 1.414 4388 Planarity : 0.006 0.065 4870 Dihedral : 9.082 118.524 4586 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 25.59 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.98 % Favored : 90.93 % Rotamer: Outliers : 1.35 % Allowed : 10.86 % Favored : 87.79 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.62 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.72 (0.11), residues: 3378 helix: -3.62 (0.13), residues: 658 sheet: -2.39 (0.18), residues: 721 loop : -3.38 (0.11), residues: 1999 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 64 HIS 0.009 0.002 HIS B 207 PHE 0.037 0.002 PHE D 55 TYR 0.025 0.002 TYR C 917 ARG 0.008 0.001 ARG B 357 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6756 Ramachandran restraints generated. 3378 Oldfield, 0 Emsley, 3378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6756 Ramachandran restraints generated. 3378 Oldfield, 0 Emsley, 3378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 690 residues out of total 2964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 650 time to evaluate : 3.994 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 VAL cc_start: 0.8363 (t) cc_final: 0.8010 (m) REVERT: A 177 MET cc_start: -0.0695 (tpt) cc_final: -0.2254 (tpt) REVERT: A 278 LYS cc_start: 0.6987 (tttt) cc_final: 0.6688 (ttmm) REVERT: A 290 ASP cc_start: 0.6891 (t0) cc_final: 0.6681 (t0) REVERT: A 308 VAL cc_start: 0.8413 (t) cc_final: 0.8095 (p) REVERT: A 537 LYS cc_start: 0.7786 (mttp) cc_final: 0.7270 (ttpt) REVERT: A 610 VAL cc_start: 0.8318 (t) cc_final: 0.8040 (p) REVERT: A 619 GLU cc_start: 0.6907 (mp0) cc_final: 0.6582 (mp0) REVERT: A 651 ILE cc_start: 0.8132 (mt) cc_final: 0.7842 (mm) REVERT: A 663 ASP cc_start: 0.7137 (t70) cc_final: 0.6845 (t70) REVERT: A 666 ILE cc_start: 0.8290 (mt) cc_final: 0.8053 (mm) REVERT: A 756 TYR cc_start: 0.7630 (t80) cc_final: 0.7386 (m-80) REVERT: A 779 GLN cc_start: 0.7702 (mm110) cc_final: 0.7487 (mp10) REVERT: A 819 GLU cc_start: 0.7088 (mt-10) cc_final: 0.6474 (mt-10) REVERT: A 866 THR cc_start: 0.8216 (OUTLIER) cc_final: 0.7843 (p) REVERT: A 868 GLU cc_start: 0.7135 (mp0) cc_final: 0.6756 (mp0) REVERT: A 883 THR cc_start: 0.8258 (m) cc_final: 0.7994 (p) REVERT: A 884 SER cc_start: 0.8459 (m) cc_final: 0.7961 (p) REVERT: A 913 GLN cc_start: 0.7975 (mt0) cc_final: 0.7749 (mp10) REVERT: A 931 ILE cc_start: 0.7752 (mm) cc_final: 0.7329 (mt) REVERT: A 933 LYS cc_start: 0.7981 (mtpp) cc_final: 0.7694 (mtpp) REVERT: A 957 GLN cc_start: 0.7828 (tp40) cc_final: 0.7222 (tt0) REVERT: A 1034 LEU cc_start: 0.8758 (mt) cc_final: 0.8558 (mm) REVERT: A 1041 ASP cc_start: 0.7015 (m-30) cc_final: 0.6356 (m-30) REVERT: A 1071 GLN cc_start: 0.7755 (mp10) cc_final: 0.7496 (mp10) REVERT: A 1113 GLN cc_start: 0.7055 (mp10) cc_final: 0.6758 (mp10) REVERT: A 1133 VAL cc_start: 0.8199 (t) cc_final: 0.7986 (m) REVERT: B 43 PHE cc_start: 0.8024 (t80) cc_final: 0.7745 (t80) REVERT: B 192 PHE cc_start: 0.6692 (m-80) cc_final: 0.6407 (m-80) REVERT: B 298 GLU cc_start: 0.7887 (tt0) cc_final: 0.7095 (mt-10) REVERT: B 382 VAL cc_start: 0.8479 (m) cc_final: 0.8274 (p) REVERT: B 543 PHE cc_start: 0.7065 (m-10) cc_final: 0.6708 (m-10) REVERT: B 619 GLU cc_start: 0.7103 (mt-10) cc_final: 0.6702 (mt-10) REVERT: B 655 HIS cc_start: 0.7693 (t70) cc_final: 0.7478 (t70) REVERT: B 703 ASN cc_start: 0.8112 (OUTLIER) cc_final: 0.7821 (p0) REVERT: B 762 GLN cc_start: 0.7697 (mt0) cc_final: 0.7445 (mt0) REVERT: B 790 LYS cc_start: 0.7862 (mtpp) cc_final: 0.7568 (mtpp) REVERT: B 858 LEU cc_start: 0.8583 (tp) cc_final: 0.8287 (tt) REVERT: B 859 THR cc_start: 0.8429 (m) cc_final: 0.8211 (p) REVERT: B 926 GLN cc_start: 0.7734 (OUTLIER) cc_final: 0.7206 (mt0) REVERT: B 955 ASN cc_start: 0.8303 (m-40) cc_final: 0.7680 (t0) REVERT: B 964 LYS cc_start: 0.8138 (mmtm) cc_final: 0.7813 (mtpp) REVERT: B 979 ASP cc_start: 0.6909 (t70) cc_final: 0.6458 (t0) REVERT: B 1030 SER cc_start: 0.8345 (m) cc_final: 0.7961 (p) REVERT: B 1037 SER cc_start: 0.8024 (t) cc_final: 0.7593 (p) REVERT: B 1045 LYS cc_start: 0.8011 (mptt) cc_final: 0.7580 (tptt) REVERT: B 1123 SER cc_start: 0.7819 (t) cc_final: 0.7547 (t) REVERT: B 1139 ASP cc_start: 0.7453 (t0) cc_final: 0.6995 (t70) REVERT: B 1144 GLU cc_start: 0.8035 (mm-30) cc_final: 0.7829 (mm-30) REVERT: C 55 PHE cc_start: 0.6643 (m-80) cc_final: 0.6355 (m-80) REVERT: C 140 PHE cc_start: 0.7774 (p90) cc_final: 0.7292 (p90) REVERT: C 192 PHE cc_start: 0.6471 (m-80) cc_final: 0.6238 (m-10) REVERT: C 227 VAL cc_start: 0.7463 (p) cc_final: 0.7117 (m) REVERT: C 324 GLU cc_start: 0.7036 (mp0) cc_final: 0.6776 (mp0) REVERT: C 537 LYS cc_start: 0.8139 (mttp) cc_final: 0.7543 (mttp) REVERT: C 663 ASP cc_start: 0.6866 (t70) cc_final: 0.6627 (t70) REVERT: C 664 ILE cc_start: 0.8149 (mt) cc_final: 0.7863 (mt) REVERT: C 666 ILE cc_start: 0.8755 (mt) cc_final: 0.8543 (mm) REVERT: C 671 CYS cc_start: 0.5417 (m) cc_final: 0.3989 (m) REVERT: C 673 SER cc_start: 0.7689 (t) cc_final: 0.6986 (m) REVERT: C 721 SER cc_start: 0.8283 (t) cc_final: 0.7798 (p) REVERT: C 736 VAL cc_start: 0.7719 (t) cc_final: 0.6615 (p) REVERT: C 776 LYS cc_start: 0.7819 (ttpt) cc_final: 0.7544 (ttpt) REVERT: C 819 GLU cc_start: 0.7665 (mt-10) cc_final: 0.7230 (mt-10) REVERT: C 931 ILE cc_start: 0.7878 (mm) cc_final: 0.7179 (mt) REVERT: C 954 GLN cc_start: 0.7713 (mm-40) cc_final: 0.7267 (mt0) REVERT: C 1054 GLN cc_start: 0.7507 (mt0) cc_final: 0.6414 (mm-40) REVERT: C 1084 ASP cc_start: 0.6838 (t0) cc_final: 0.6565 (t0) REVERT: C 1091 ARG cc_start: 0.7393 (mtt-85) cc_final: 0.7064 (mtt-85) REVERT: C 1097 SER cc_start: 0.8032 (p) cc_final: 0.7828 (p) REVERT: C 1116 THR cc_start: 0.7884 (m) cc_final: 0.7299 (p) outliers start: 40 outliers final: 24 residues processed: 666 average time/residue: 0.8381 time to fit residues: 884.9818 Evaluate side-chains 629 residues out of total 2964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 602 time to evaluate : 3.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain A residue 774 GLN Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 1037 SER Chi-restraints excluded: chain A residue 1127 ASP Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 160 TYR Chi-restraints excluded: chain B residue 173 GLN Chi-restraints excluded: chain B residue 440 ASN Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain B residue 673 SER Chi-restraints excluded: chain B residue 703 ASN Chi-restraints excluded: chain B residue 870 ILE Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 926 GLN Chi-restraints excluded: chain B residue 1068 VAL Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 746 SER Chi-restraints excluded: chain C residue 765 ARG Chi-restraints excluded: chain E residue 122 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 171 optimal weight: 0.9990 chunk 95 optimal weight: 2.9990 chunk 256 optimal weight: 9.9990 chunk 210 optimal weight: 6.9990 chunk 85 optimal weight: 1.9990 chunk 309 optimal weight: 0.9980 chunk 334 optimal weight: 0.0070 chunk 275 optimal weight: 0.5980 chunk 306 optimal weight: 1.9990 chunk 105 optimal weight: 5.9990 chunk 248 optimal weight: 10.0000 overall best weight: 0.9202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 907 ASN A 965 GLN ** A1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 115 GLN ** B 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 519 HIS B 717 ASN ** B 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 777 ASN ** B1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6664 moved from start: 0.3499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.015 0.826 27939 Z= 1.026 Angle : 0.722 20.846 37997 Z= 0.387 Chirality : 0.051 1.409 4388 Planarity : 0.005 0.062 4870 Dihedral : 8.185 117.048 4582 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 23.53 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.42 % Favored : 91.55 % Rotamer: Outliers : 1.61 % Allowed : 12.95 % Favored : 85.44 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.12 (0.12), residues: 3378 helix: -2.72 (0.16), residues: 677 sheet: -2.40 (0.18), residues: 682 loop : -2.98 (0.11), residues: 2019 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 64 HIS 0.007 0.001 HIS B1083 PHE 0.040 0.002 PHE D 55 TYR 0.018 0.002 TYR A1067 ARG 0.007 0.001 ARG E 46 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6756 Ramachandran restraints generated. 3378 Oldfield, 0 Emsley, 3378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6756 Ramachandran restraints generated. 3378 Oldfield, 0 Emsley, 3378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 675 residues out of total 2964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 627 time to evaluate : 3.739 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 VAL cc_start: 0.8451 (t) cc_final: 0.8089 (m) REVERT: A 102 ARG cc_start: 0.5702 (mmt90) cc_final: 0.5496 (mmt90) REVERT: A 177 MET cc_start: -0.0730 (tpt) cc_final: -0.2056 (tpt) REVERT: A 278 LYS cc_start: 0.7126 (tttt) cc_final: 0.6745 (ttmm) REVERT: A 300 LYS cc_start: 0.7220 (mttt) cc_final: 0.6794 (mttt) REVERT: A 537 LYS cc_start: 0.7878 (mttp) cc_final: 0.7378 (ttpt) REVERT: A 610 VAL cc_start: 0.8341 (t) cc_final: 0.8021 (p) REVERT: A 619 GLU cc_start: 0.7029 (mp0) cc_final: 0.6731 (mp0) REVERT: A 651 ILE cc_start: 0.8232 (mt) cc_final: 0.8031 (mp) REVERT: A 663 ASP cc_start: 0.7140 (t70) cc_final: 0.6891 (t70) REVERT: A 756 TYR cc_start: 0.7618 (t80) cc_final: 0.7394 (m-80) REVERT: A 800 PHE cc_start: 0.7281 (OUTLIER) cc_final: 0.6960 (m-80) REVERT: A 819 GLU cc_start: 0.7334 (mt-10) cc_final: 0.6859 (mt-10) REVERT: A 866 THR cc_start: 0.8246 (OUTLIER) cc_final: 0.7930 (p) REVERT: A 883 THR cc_start: 0.8365 (m) cc_final: 0.8002 (p) REVERT: A 884 SER cc_start: 0.8550 (m) cc_final: 0.7972 (p) REVERT: A 931 ILE cc_start: 0.7829 (mm) cc_final: 0.7400 (mt) REVERT: A 933 LYS cc_start: 0.7856 (mtpp) cc_final: 0.7594 (mtpp) REVERT: A 950 ASP cc_start: 0.6791 (m-30) cc_final: 0.6372 (m-30) REVERT: A 970 PHE cc_start: 0.8302 (m-80) cc_final: 0.7911 (m-80) REVERT: A 1041 ASP cc_start: 0.6746 (m-30) cc_final: 0.6301 (m-30) REVERT: A 1071 GLN cc_start: 0.7840 (mp10) cc_final: 0.7569 (mp10) REVERT: A 1073 LYS cc_start: 0.7586 (ttpt) cc_final: 0.7252 (tttm) REVERT: A 1113 GLN cc_start: 0.7092 (mp10) cc_final: 0.6777 (mp10) REVERT: B 192 PHE cc_start: 0.6750 (m-80) cc_final: 0.6454 (m-80) REVERT: B 298 GLU cc_start: 0.7854 (tt0) cc_final: 0.7543 (tt0) REVERT: B 386 LYS cc_start: 0.8487 (mttp) cc_final: 0.8046 (mttp) REVERT: B 525 CYS cc_start: 0.5719 (m) cc_final: 0.5311 (m) REVERT: B 543 PHE cc_start: 0.7113 (m-10) cc_final: 0.6904 (m-10) REVERT: B 568 ASP cc_start: 0.5979 (t0) cc_final: 0.5744 (t0) REVERT: B 619 GLU cc_start: 0.7174 (mt-10) cc_final: 0.6727 (mt-10) REVERT: B 703 ASN cc_start: 0.8055 (OUTLIER) cc_final: 0.7708 (p0) REVERT: B 718 PHE cc_start: 0.8427 (p90) cc_final: 0.8188 (p90) REVERT: B 725 GLU cc_start: 0.7203 (tt0) cc_final: 0.6944 (tt0) REVERT: B 790 LYS cc_start: 0.8073 (mtpp) cc_final: 0.7781 (mtpp) REVERT: B 814 LYS cc_start: 0.7720 (mmtt) cc_final: 0.7495 (mptt) REVERT: B 858 LEU cc_start: 0.8605 (tp) cc_final: 0.8242 (tt) REVERT: B 884 SER cc_start: 0.7984 (p) cc_final: 0.7256 (t) REVERT: B 894 LEU cc_start: 0.7956 (mt) cc_final: 0.7330 (mt) REVERT: B 955 ASN cc_start: 0.8293 (OUTLIER) cc_final: 0.7828 (t0) REVERT: B 964 LYS cc_start: 0.8284 (mmtm) cc_final: 0.7923 (mtpp) REVERT: B 979 ASP cc_start: 0.6918 (t70) cc_final: 0.6513 (t0) REVERT: B 1030 SER cc_start: 0.8463 (m) cc_final: 0.8134 (p) REVERT: B 1037 SER cc_start: 0.8131 (t) cc_final: 0.7710 (p) REVERT: B 1045 LYS cc_start: 0.8067 (mptt) cc_final: 0.7653 (tptt) REVERT: B 1123 SER cc_start: 0.8108 (t) cc_final: 0.7877 (t) REVERT: B 1139 ASP cc_start: 0.7722 (t0) cc_final: 0.7074 (m-30) REVERT: B 1141 LEU cc_start: 0.7940 (tt) cc_final: 0.7661 (tt) REVERT: B 1144 GLU cc_start: 0.8056 (mm-30) cc_final: 0.7827 (mm-30) REVERT: C 55 PHE cc_start: 0.6807 (m-80) cc_final: 0.6518 (m-80) REVERT: C 99 ASN cc_start: 0.7759 (t0) cc_final: 0.7402 (t0) REVERT: C 227 VAL cc_start: 0.7726 (p) cc_final: 0.7428 (m) REVERT: C 562 PHE cc_start: 0.6628 (p90) cc_final: 0.6225 (p90) REVERT: C 663 ASP cc_start: 0.7079 (t70) cc_final: 0.6777 (t70) REVERT: C 664 ILE cc_start: 0.8177 (mt) cc_final: 0.7876 (mt) REVERT: C 673 SER cc_start: 0.7685 (t) cc_final: 0.7010 (m) REVERT: C 721 SER cc_start: 0.8292 (t) cc_final: 0.7737 (p) REVERT: C 736 VAL cc_start: 0.7881 (t) cc_final: 0.6901 (p) REVERT: C 776 LYS cc_start: 0.7895 (ttpt) cc_final: 0.7436 (ttpt) REVERT: C 780 GLU cc_start: 0.7403 (mm-30) cc_final: 0.6864 (mm-30) REVERT: C 805 ILE cc_start: 0.8140 (pt) cc_final: 0.7929 (pt) REVERT: C 819 GLU cc_start: 0.7774 (mt-10) cc_final: 0.7471 (mt-10) REVERT: C 931 ILE cc_start: 0.7901 (mm) cc_final: 0.7414 (mt) REVERT: C 935 GLN cc_start: 0.7592 (tm-30) cc_final: 0.7330 (tm-30) REVERT: C 954 GLN cc_start: 0.7778 (mm-40) cc_final: 0.7372 (mt0) REVERT: C 955 ASN cc_start: 0.8301 (t0) cc_final: 0.8028 (t0) REVERT: C 1002 GLN cc_start: 0.7836 (tt0) cc_final: 0.7610 (tt0) REVERT: C 1054 GLN cc_start: 0.7621 (mt0) cc_final: 0.6957 (mm-40) REVERT: C 1084 ASP cc_start: 0.6924 (t0) cc_final: 0.6642 (t0) REVERT: C 1091 ARG cc_start: 0.7528 (mtt-85) cc_final: 0.7282 (mtt-85) REVERT: C 1097 SER cc_start: 0.8116 (p) cc_final: 0.7898 (p) REVERT: C 1116 THR cc_start: 0.7603 (m) cc_final: 0.7103 (p) REVERT: E 46 ARG cc_start: 0.7253 (OUTLIER) cc_final: 0.6886 (ptp-110) REVERT: E 115 TRP cc_start: 0.5083 (m100) cc_final: 0.4517 (m100) outliers start: 48 outliers final: 25 residues processed: 647 average time/residue: 0.8237 time to fit residues: 842.9481 Evaluate side-chains 630 residues out of total 2964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 600 time to evaluate : 3.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 712 ILE Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain A residue 800 PHE Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 965 GLN Chi-restraints excluded: chain A residue 1037 SER Chi-restraints excluded: chain A residue 1127 ASP Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 614 ASP Chi-restraints excluded: chain B residue 703 ASN Chi-restraints excluded: chain B residue 717 ASN Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 825 LYS Chi-restraints excluded: chain B residue 955 ASN Chi-restraints excluded: chain B residue 961 THR Chi-restraints excluded: chain B residue 1068 VAL Chi-restraints excluded: chain C residue 618 THR Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 746 SER Chi-restraints excluded: chain C residue 765 ARG Chi-restraints excluded: chain C residue 867 ASP Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain E residue 46 ARG Chi-restraints excluded: chain E residue 60 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 305 optimal weight: 0.5980 chunk 232 optimal weight: 2.9990 chunk 160 optimal weight: 0.9990 chunk 34 optimal weight: 4.9990 chunk 147 optimal weight: 0.9980 chunk 207 optimal weight: 1.9990 chunk 310 optimal weight: 0.9980 chunk 328 optimal weight: 5.9990 chunk 162 optimal weight: 0.4980 chunk 294 optimal weight: 1.9990 chunk 88 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 774 GLN ** A1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 164 ASN B 165 ASN ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 717 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 774 GLN B 777 ASN B 949 GLN ** B1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1142 GLN ** C 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1106 GLN ** C1142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6699 moved from start: 0.4015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.015 0.833 27939 Z= 1.015 Angle : 0.681 20.374 37997 Z= 0.362 Chirality : 0.050 1.402 4388 Planarity : 0.005 0.050 4870 Dihedral : 7.658 116.087 4580 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 22.19 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.83 % Favored : 92.14 % Rotamer: Outliers : 1.68 % Allowed : 14.46 % Favored : 83.85 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.67 (0.12), residues: 3378 helix: -2.15 (0.17), residues: 680 sheet: -2.21 (0.18), residues: 677 loop : -2.72 (0.12), residues: 2021 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 64 HIS 0.007 0.001 HIS A 655 PHE 0.035 0.002 PHE D 55 TYR 0.018 0.001 TYR A 904 ARG 0.005 0.000 ARG B 158 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6756 Ramachandran restraints generated. 3378 Oldfield, 0 Emsley, 3378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6756 Ramachandran restraints generated. 3378 Oldfield, 0 Emsley, 3378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 682 residues out of total 2964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 632 time to evaluate : 3.740 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 VAL cc_start: 0.8532 (t) cc_final: 0.8160 (m) REVERT: A 102 ARG cc_start: 0.5634 (mmt90) cc_final: 0.5387 (mmt90) REVERT: A 177 MET cc_start: -0.0741 (tpt) cc_final: -0.2158 (tpt) REVERT: A 266 TYR cc_start: 0.6967 (m-80) cc_final: 0.6695 (m-80) REVERT: A 276 LEU cc_start: 0.7716 (tp) cc_final: 0.7422 (tp) REVERT: A 278 LYS cc_start: 0.7161 (tttt) cc_final: 0.6823 (ttmm) REVERT: A 289 VAL cc_start: 0.7903 (t) cc_final: 0.7450 (m) REVERT: A 300 LYS cc_start: 0.7436 (mttt) cc_final: 0.6981 (mttt) REVERT: A 309 GLU cc_start: 0.7360 (mm-30) cc_final: 0.7006 (mm-30) REVERT: A 537 LYS cc_start: 0.7855 (mttp) cc_final: 0.7191 (ttpt) REVERT: A 551 VAL cc_start: 0.6683 (p) cc_final: 0.6050 (t) REVERT: A 610 VAL cc_start: 0.8374 (t) cc_final: 0.8075 (p) REVERT: A 619 GLU cc_start: 0.7083 (mp0) cc_final: 0.6787 (mp0) REVERT: A 663 ASP cc_start: 0.7123 (t70) cc_final: 0.6854 (t70) REVERT: A 800 PHE cc_start: 0.7435 (OUTLIER) cc_final: 0.7081 (m-80) REVERT: A 819 GLU cc_start: 0.7301 (mt-10) cc_final: 0.6484 (mt-10) REVERT: A 866 THR cc_start: 0.8315 (OUTLIER) cc_final: 0.7935 (p) REVERT: A 883 THR cc_start: 0.8298 (m) cc_final: 0.7994 (p) REVERT: A 884 SER cc_start: 0.8539 (m) cc_final: 0.8010 (p) REVERT: A 900 MET cc_start: 0.7045 (mtp) cc_final: 0.6673 (mtt) REVERT: A 904 TYR cc_start: 0.7277 (m-80) cc_final: 0.7061 (m-80) REVERT: A 931 ILE cc_start: 0.7861 (mm) cc_final: 0.7331 (mt) REVERT: A 933 LYS cc_start: 0.7821 (mtpp) cc_final: 0.7537 (mtpp) REVERT: A 950 ASP cc_start: 0.6826 (m-30) cc_final: 0.6312 (m-30) REVERT: A 957 GLN cc_start: 0.7907 (tp40) cc_final: 0.7441 (tt0) REVERT: A 970 PHE cc_start: 0.8233 (m-80) cc_final: 0.7851 (m-80) REVERT: A 1054 GLN cc_start: 0.7200 (mm-40) cc_final: 0.6676 (mm-40) REVERT: A 1091 ARG cc_start: 0.6617 (mtt-85) cc_final: 0.6373 (mtt90) REVERT: A 1113 GLN cc_start: 0.7203 (mp10) cc_final: 0.6903 (mp10) REVERT: A 1141 LEU cc_start: 0.8161 (tt) cc_final: 0.7936 (tp) REVERT: B 51 THR cc_start: 0.7835 (t) cc_final: 0.7527 (p) REVERT: B 129 LYS cc_start: 0.7063 (tttt) cc_final: 0.6513 (tttt) REVERT: B 274 THR cc_start: 0.7525 (t) cc_final: 0.7234 (p) REVERT: B 386 LYS cc_start: 0.8530 (mttp) cc_final: 0.8067 (mttp) REVERT: B 619 GLU cc_start: 0.7126 (mt-10) cc_final: 0.6702 (mt-10) REVERT: B 703 ASN cc_start: 0.7991 (OUTLIER) cc_final: 0.7631 (p0) REVERT: B 725 GLU cc_start: 0.7240 (tt0) cc_final: 0.6975 (tt0) REVERT: B 737 ASP cc_start: 0.6980 (m-30) cc_final: 0.6730 (m-30) REVERT: B 790 LYS cc_start: 0.8093 (mtpp) cc_final: 0.7802 (mtpp) REVERT: B 884 SER cc_start: 0.8103 (p) cc_final: 0.7288 (t) REVERT: B 894 LEU cc_start: 0.8063 (mt) cc_final: 0.7389 (mt) REVERT: B 955 ASN cc_start: 0.8321 (m-40) cc_final: 0.7959 (t0) REVERT: B 964 LYS cc_start: 0.8275 (mmtm) cc_final: 0.7944 (mtpp) REVERT: B 979 ASP cc_start: 0.6861 (t70) cc_final: 0.6549 (t0) REVERT: B 1030 SER cc_start: 0.8440 (m) cc_final: 0.8161 (p) REVERT: B 1037 SER cc_start: 0.8178 (t) cc_final: 0.7770 (p) REVERT: B 1045 LYS cc_start: 0.8100 (mptt) cc_final: 0.7691 (tptt) REVERT: B 1123 SER cc_start: 0.8178 (t) cc_final: 0.7952 (t) REVERT: B 1139 ASP cc_start: 0.7778 (t0) cc_final: 0.7184 (m-30) REVERT: B 1141 LEU cc_start: 0.7933 (tt) cc_final: 0.7552 (tt) REVERT: B 1144 GLU cc_start: 0.8048 (mm-30) cc_final: 0.7816 (mm-30) REVERT: C 55 PHE cc_start: 0.6852 (m-80) cc_final: 0.6504 (m-80) REVERT: C 99 ASN cc_start: 0.7781 (t0) cc_final: 0.7449 (t0) REVERT: C 227 VAL cc_start: 0.7838 (p) cc_final: 0.7558 (m) REVERT: C 562 PHE cc_start: 0.6580 (p90) cc_final: 0.6193 (p90) REVERT: C 583 GLU cc_start: 0.7598 (mm-30) cc_final: 0.7269 (mm-30) REVERT: C 663 ASP cc_start: 0.7333 (t70) cc_final: 0.6766 (t0) REVERT: C 673 SER cc_start: 0.7663 (t) cc_final: 0.6978 (m) REVERT: C 720 ILE cc_start: 0.8552 (mm) cc_final: 0.7957 (mt) REVERT: C 721 SER cc_start: 0.8218 (t) cc_final: 0.7653 (p) REVERT: C 727 LEU cc_start: 0.8155 (mt) cc_final: 0.7884 (mp) REVERT: C 736 VAL cc_start: 0.7982 (t) cc_final: 0.7064 (p) REVERT: C 740 MET cc_start: 0.8254 (ttm) cc_final: 0.7985 (ttt) REVERT: C 776 LYS cc_start: 0.7929 (ttpt) cc_final: 0.7455 (ttpt) REVERT: C 780 GLU cc_start: 0.7442 (mm-30) cc_final: 0.6919 (mm-30) REVERT: C 790 LYS cc_start: 0.8033 (ttmm) cc_final: 0.7788 (ttpp) REVERT: C 805 ILE cc_start: 0.8168 (pt) cc_final: 0.7937 (pt) REVERT: C 819 GLU cc_start: 0.7818 (mt-10) cc_final: 0.7334 (mt-10) REVERT: C 884 SER cc_start: 0.8224 (p) cc_final: 0.7447 (t) REVERT: C 931 ILE cc_start: 0.7924 (mm) cc_final: 0.7457 (mt) REVERT: C 954 GLN cc_start: 0.7822 (mm-40) cc_final: 0.7520 (mt0) REVERT: C 955 ASN cc_start: 0.8364 (t0) cc_final: 0.8086 (t0) REVERT: C 1002 GLN cc_start: 0.7816 (tt0) cc_final: 0.7555 (tt0) REVERT: C 1051 SER cc_start: 0.8112 (t) cc_final: 0.7566 (p) REVERT: C 1054 GLN cc_start: 0.7629 (mt0) cc_final: 0.6847 (mm-40) REVERT: C 1097 SER cc_start: 0.8152 (p) cc_final: 0.7890 (p) REVERT: C 1116 THR cc_start: 0.7555 (m) cc_final: 0.7106 (p) outliers start: 50 outliers final: 33 residues processed: 653 average time/residue: 0.8527 time to fit residues: 876.0012 Evaluate side-chains 643 residues out of total 2964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 607 time to evaluate : 3.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 614 ASP Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain A residue 800 PHE Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 1037 SER Chi-restraints excluded: chain A residue 1127 ASP Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 160 TYR Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 614 ASP Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 703 ASN Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 767 LEU Chi-restraints excluded: chain B residue 825 LYS Chi-restraints excluded: chain B residue 949 GLN Chi-restraints excluded: chain B residue 1024 LEU Chi-restraints excluded: chain B residue 1068 VAL Chi-restraints excluded: chain B residue 1142 GLN Chi-restraints excluded: chain C residue 596 SER Chi-restraints excluded: chain C residue 618 THR Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 746 SER Chi-restraints excluded: chain C residue 969 ASN Chi-restraints excluded: chain E residue 46 ARG Chi-restraints excluded: chain E residue 60 TYR Chi-restraints excluded: chain E residue 119 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 273 optimal weight: 1.9990 chunk 186 optimal weight: 1.9990 chunk 4 optimal weight: 0.6980 chunk 244 optimal weight: 5.9990 chunk 135 optimal weight: 0.9990 chunk 280 optimal weight: 0.9990 chunk 227 optimal weight: 0.6980 chunk 0 optimal weight: 5.9990 chunk 167 optimal weight: 1.9990 chunk 294 optimal weight: 0.9980 chunk 82 optimal weight: 0.8980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN ** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 907 ASN A 913 GLN ** A1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 173 GLN ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 717 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN B 777 ASN ** B1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 GLN C1106 GLN ** E 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 85 ASN ** E 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6737 moved from start: 0.4394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.015 0.830 27939 Z= 1.019 Angle : 0.677 20.094 37997 Z= 0.360 Chirality : 0.050 1.403 4388 Planarity : 0.005 0.054 4870 Dihedral : 7.368 115.104 4580 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 21.84 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.98 % Favored : 92.00 % Rotamer: Outliers : 2.12 % Allowed : 15.20 % Favored : 82.68 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.35 (0.13), residues: 3378 helix: -1.71 (0.18), residues: 683 sheet: -2.02 (0.18), residues: 679 loop : -2.57 (0.12), residues: 2016 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 64 HIS 0.005 0.001 HIS B1083 PHE 0.032 0.002 PHE D 55 TYR 0.018 0.001 TYR C 313 ARG 0.010 0.000 ARG B1091 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6756 Ramachandran restraints generated. 3378 Oldfield, 0 Emsley, 3378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6756 Ramachandran restraints generated. 3378 Oldfield, 0 Emsley, 3378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 690 residues out of total 2964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 628 time to evaluate : 3.966 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 VAL cc_start: 0.8554 (t) cc_final: 0.8228 (m) REVERT: A 102 ARG cc_start: 0.5681 (mmt90) cc_final: 0.5404 (mmt90) REVERT: A 177 MET cc_start: -0.0801 (tpt) cc_final: -0.2296 (tpt) REVERT: A 266 TYR cc_start: 0.6943 (m-80) cc_final: 0.6553 (m-80) REVERT: A 276 LEU cc_start: 0.7722 (tp) cc_final: 0.7458 (tp) REVERT: A 278 LYS cc_start: 0.7172 (tttt) cc_final: 0.6794 (ttmm) REVERT: A 289 VAL cc_start: 0.7993 (t) cc_final: 0.7571 (m) REVERT: A 300 LYS cc_start: 0.7536 (mttt) cc_final: 0.7066 (mttt) REVERT: A 309 GLU cc_start: 0.7339 (mm-30) cc_final: 0.6966 (mm-30) REVERT: A 537 LYS cc_start: 0.7891 (mttp) cc_final: 0.7208 (ttpt) REVERT: A 551 VAL cc_start: 0.6774 (p) cc_final: 0.6181 (t) REVERT: A 610 VAL cc_start: 0.8410 (t) cc_final: 0.8083 (p) REVERT: A 619 GLU cc_start: 0.7097 (mp0) cc_final: 0.6815 (mp0) REVERT: A 644 GLN cc_start: 0.7237 (tp40) cc_final: 0.6998 (tp40) REVERT: A 663 ASP cc_start: 0.7074 (t70) cc_final: 0.6817 (t70) REVERT: A 692 ILE cc_start: 0.8359 (tt) cc_final: 0.8078 (mt) REVERT: A 779 GLN cc_start: 0.7837 (mm-40) cc_final: 0.7585 (mt0) REVERT: A 800 PHE cc_start: 0.7565 (OUTLIER) cc_final: 0.7299 (m-80) REVERT: A 819 GLU cc_start: 0.7360 (mt-10) cc_final: 0.6569 (mt-10) REVERT: A 866 THR cc_start: 0.8314 (OUTLIER) cc_final: 0.7933 (p) REVERT: A 884 SER cc_start: 0.8561 (m) cc_final: 0.7885 (p) REVERT: A 900 MET cc_start: 0.7059 (mtp) cc_final: 0.6734 (mtt) REVERT: A 931 ILE cc_start: 0.7863 (mm) cc_final: 0.7383 (mt) REVERT: A 933 LYS cc_start: 0.7863 (mtpp) cc_final: 0.7582 (mtpp) REVERT: A 950 ASP cc_start: 0.6915 (m-30) cc_final: 0.6330 (m-30) REVERT: A 957 GLN cc_start: 0.7963 (tp40) cc_final: 0.7453 (tt0) REVERT: A 1041 ASP cc_start: 0.7034 (m-30) cc_final: 0.6799 (m-30) REVERT: A 1054 GLN cc_start: 0.7257 (mm-40) cc_final: 0.6506 (mm-40) REVERT: A 1073 LYS cc_start: 0.7662 (ttpt) cc_final: 0.7291 (tttm) REVERT: A 1091 ARG cc_start: 0.6726 (mtt-85) cc_final: 0.6465 (mtt90) REVERT: B 51 THR cc_start: 0.7808 (t) cc_final: 0.7478 (p) REVERT: B 129 LYS cc_start: 0.7062 (tttt) cc_final: 0.6416 (tttt) REVERT: B 274 THR cc_start: 0.7550 (t) cc_final: 0.7261 (p) REVERT: B 386 LYS cc_start: 0.8575 (mttp) cc_final: 0.8293 (mttp) REVERT: B 528 LYS cc_start: 0.8482 (tttm) cc_final: 0.8057 (ttmm) REVERT: B 619 GLU cc_start: 0.7171 (mt-10) cc_final: 0.6713 (mt-10) REVERT: B 703 ASN cc_start: 0.8037 (OUTLIER) cc_final: 0.7662 (p0) REVERT: B 737 ASP cc_start: 0.7106 (m-30) cc_final: 0.6871 (m-30) REVERT: B 780 GLU cc_start: 0.7540 (OUTLIER) cc_final: 0.7217 (mm-30) REVERT: B 790 LYS cc_start: 0.8122 (mtpp) cc_final: 0.7797 (mtpp) REVERT: B 882 ILE cc_start: 0.8094 (pt) cc_final: 0.7861 (mt) REVERT: B 884 SER cc_start: 0.8134 (p) cc_final: 0.7929 (p) REVERT: B 894 LEU cc_start: 0.8085 (mt) cc_final: 0.7861 (mt) REVERT: B 955 ASN cc_start: 0.8309 (OUTLIER) cc_final: 0.7982 (t0) REVERT: B 964 LYS cc_start: 0.8239 (mmtm) cc_final: 0.7929 (mtpp) REVERT: B 979 ASP cc_start: 0.6778 (t70) cc_final: 0.6466 (t0) REVERT: B 1030 SER cc_start: 0.8433 (m) cc_final: 0.8059 (p) REVERT: B 1037 SER cc_start: 0.8218 (t) cc_final: 0.7826 (p) REVERT: B 1045 LYS cc_start: 0.8114 (mptt) cc_final: 0.7698 (tptt) REVERT: B 1068 VAL cc_start: 0.7923 (OUTLIER) cc_final: 0.7646 (m) REVERT: B 1123 SER cc_start: 0.8237 (t) cc_final: 0.8037 (t) REVERT: B 1139 ASP cc_start: 0.7908 (t0) cc_final: 0.7287 (m-30) REVERT: B 1141 LEU cc_start: 0.7968 (tt) cc_final: 0.7653 (tt) REVERT: B 1144 GLU cc_start: 0.8111 (mm-30) cc_final: 0.7890 (mm-30) REVERT: B 1146 ASP cc_start: 0.7317 (m-30) cc_final: 0.6863 (t0) REVERT: C 55 PHE cc_start: 0.6957 (m-80) cc_final: 0.6559 (m-80) REVERT: C 99 ASN cc_start: 0.7846 (t0) cc_final: 0.7493 (t0) REVERT: C 227 VAL cc_start: 0.7939 (p) cc_final: 0.7649 (m) REVERT: C 314 GLN cc_start: 0.8170 (tt0) cc_final: 0.7941 (mt0) REVERT: C 556 ASN cc_start: 0.6264 (p0) cc_final: 0.5885 (p0) REVERT: C 562 PHE cc_start: 0.6592 (p90) cc_final: 0.6287 (p90) REVERT: C 583 GLU cc_start: 0.7625 (mm-30) cc_final: 0.7289 (mm-30) REVERT: C 663 ASP cc_start: 0.7393 (t70) cc_final: 0.6841 (t0) REVERT: C 673 SER cc_start: 0.7646 (t) cc_final: 0.6962 (m) REVERT: C 720 ILE cc_start: 0.8571 (mm) cc_final: 0.7990 (mt) REVERT: C 721 SER cc_start: 0.8163 (t) cc_final: 0.7595 (p) REVERT: C 727 LEU cc_start: 0.8169 (mt) cc_final: 0.7900 (mp) REVERT: C 736 VAL cc_start: 0.8086 (t) cc_final: 0.7193 (p) REVERT: C 776 LYS cc_start: 0.7947 (ttpt) cc_final: 0.7681 (ttpt) REVERT: C 790 LYS cc_start: 0.8009 (ttmm) cc_final: 0.7771 (ttpp) REVERT: C 805 ILE cc_start: 0.8205 (pt) cc_final: 0.7986 (pt) REVERT: C 819 GLU cc_start: 0.7843 (mt-10) cc_final: 0.7308 (mt-10) REVERT: C 884 SER cc_start: 0.8260 (p) cc_final: 0.7480 (t) REVERT: C 931 ILE cc_start: 0.7965 (mm) cc_final: 0.7508 (mt) REVERT: C 954 GLN cc_start: 0.7803 (mm-40) cc_final: 0.7543 (mt0) REVERT: C 955 ASN cc_start: 0.8380 (t0) cc_final: 0.8085 (t0) REVERT: C 1002 GLN cc_start: 0.7839 (tt0) cc_final: 0.7621 (tt0) REVERT: C 1051 SER cc_start: 0.8174 (t) cc_final: 0.7612 (p) REVERT: C 1054 GLN cc_start: 0.7600 (mt0) cc_final: 0.6912 (mm-40) REVERT: C 1097 SER cc_start: 0.8179 (p) cc_final: 0.7928 (p) REVERT: C 1116 THR cc_start: 0.7589 (m) cc_final: 0.7130 (p) REVERT: E 115 TRP cc_start: 0.5284 (m100) cc_final: 0.5058 (m100) outliers start: 62 outliers final: 45 residues processed: 655 average time/residue: 0.8663 time to fit residues: 899.6501 Evaluate side-chains 668 residues out of total 2964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 617 time to evaluate : 3.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 614 ASP Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 751 ASN Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 774 GLN Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain A residue 800 PHE Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 913 GLN Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 1037 SER Chi-restraints excluded: chain A residue 1127 ASP Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 173 GLN Chi-restraints excluded: chain B residue 440 ASN Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 614 ASP Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 703 ASN Chi-restraints excluded: chain B residue 767 LEU Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 825 LYS Chi-restraints excluded: chain B residue 955 ASN Chi-restraints excluded: chain B residue 967 SER Chi-restraints excluded: chain B residue 993 ILE Chi-restraints excluded: chain B residue 1068 VAL Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 596 SER Chi-restraints excluded: chain C residue 618 THR Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 746 SER Chi-restraints excluded: chain C residue 765 ARG Chi-restraints excluded: chain C residue 969 ASN Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain E residue 46 ARG Chi-restraints excluded: chain E residue 60 TYR Chi-restraints excluded: chain E residue 119 THR Chi-restraints excluded: chain E residue 122 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 110 optimal weight: 0.8980 chunk 295 optimal weight: 3.9990 chunk 64 optimal weight: 0.4980 chunk 192 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 328 optimal weight: 0.0020 chunk 273 optimal weight: 1.9990 chunk 152 optimal weight: 3.9990 chunk 27 optimal weight: 0.9990 chunk 108 optimal weight: 0.9980 chunk 172 optimal weight: 0.5980 overall best weight: 0.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 717 ASN ** B 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN B 777 ASN ** B 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 GLN C1106 GLN ** E 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6737 moved from start: 0.4610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.015 0.829 27939 Z= 1.007 Angle : 0.649 19.909 37997 Z= 0.345 Chirality : 0.049 1.402 4388 Planarity : 0.005 0.054 4870 Dihedral : 7.124 114.156 4580 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 20.44 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.38 % Favored : 92.59 % Rotamer: Outliers : 1.98 % Allowed : 16.21 % Favored : 81.80 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.11 (0.13), residues: 3378 helix: -1.43 (0.19), residues: 678 sheet: -1.88 (0.19), residues: 666 loop : -2.45 (0.12), residues: 2034 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 64 HIS 0.005 0.001 HIS A1064 PHE 0.031 0.001 PHE D 55 TYR 0.034 0.001 TYR A 904 ARG 0.009 0.000 ARG B 815 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6756 Ramachandran restraints generated. 3378 Oldfield, 0 Emsley, 3378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6756 Ramachandran restraints generated. 3378 Oldfield, 0 Emsley, 3378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 693 residues out of total 2964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 635 time to evaluate : 3.477 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 VAL cc_start: 0.8588 (t) cc_final: 0.8214 (m) REVERT: A 43 PHE cc_start: 0.7931 (t80) cc_final: 0.7463 (t80) REVERT: A 177 MET cc_start: -0.0804 (tpt) cc_final: -0.2543 (tpt) REVERT: A 266 TYR cc_start: 0.6990 (m-80) cc_final: 0.6602 (m-80) REVERT: A 276 LEU cc_start: 0.7834 (tp) cc_final: 0.7536 (tp) REVERT: A 278 LYS cc_start: 0.7162 (tttt) cc_final: 0.6759 (ttmm) REVERT: A 280 ASN cc_start: 0.6386 (t0) cc_final: 0.5924 (t0) REVERT: A 289 VAL cc_start: 0.7982 (t) cc_final: 0.7568 (m) REVERT: A 300 LYS cc_start: 0.7557 (mttt) cc_final: 0.7082 (mttt) REVERT: A 309 GLU cc_start: 0.7314 (mm-30) cc_final: 0.6929 (mm-30) REVERT: A 537 LYS cc_start: 0.7847 (mttp) cc_final: 0.7177 (ttpt) REVERT: A 551 VAL cc_start: 0.6791 (p) cc_final: 0.6209 (t) REVERT: A 610 VAL cc_start: 0.8418 (t) cc_final: 0.8099 (p) REVERT: A 619 GLU cc_start: 0.7116 (mp0) cc_final: 0.6855 (mp0) REVERT: A 646 ARG cc_start: 0.7202 (tpt-90) cc_final: 0.6838 (tpt-90) REVERT: A 663 ASP cc_start: 0.7078 (t70) cc_final: 0.6810 (t70) REVERT: A 692 ILE cc_start: 0.8395 (tt) cc_final: 0.8175 (mt) REVERT: A 779 GLN cc_start: 0.7796 (mm-40) cc_final: 0.7450 (mm-40) REVERT: A 800 PHE cc_start: 0.7560 (OUTLIER) cc_final: 0.7312 (m-80) REVERT: A 866 THR cc_start: 0.8308 (OUTLIER) cc_final: 0.7915 (p) REVERT: A 884 SER cc_start: 0.8553 (m) cc_final: 0.7858 (p) REVERT: A 900 MET cc_start: 0.6949 (mtp) cc_final: 0.6540 (mtt) REVERT: A 931 ILE cc_start: 0.7845 (mm) cc_final: 0.7393 (mt) REVERT: A 933 LYS cc_start: 0.7828 (mtpp) cc_final: 0.7542 (mtpp) REVERT: A 950 ASP cc_start: 0.6811 (m-30) cc_final: 0.6216 (m-30) REVERT: A 957 GLN cc_start: 0.7952 (tp40) cc_final: 0.7454 (tt0) REVERT: A 970 PHE cc_start: 0.8214 (m-80) cc_final: 0.7925 (m-80) REVERT: A 1041 ASP cc_start: 0.7101 (m-30) cc_final: 0.6885 (m-30) REVERT: A 1054 GLN cc_start: 0.7259 (mm-40) cc_final: 0.6918 (mm-40) REVERT: A 1073 LYS cc_start: 0.7644 (ttpt) cc_final: 0.7295 (tttm) REVERT: B 129 LYS cc_start: 0.7000 (tttt) cc_final: 0.6406 (tttt) REVERT: B 173 GLN cc_start: 0.6005 (OUTLIER) cc_final: 0.5524 (pp30) REVERT: B 274 THR cc_start: 0.7554 (t) cc_final: 0.7240 (p) REVERT: B 528 LYS cc_start: 0.8488 (tttm) cc_final: 0.8056 (ttmm) REVERT: B 619 GLU cc_start: 0.7155 (mt-10) cc_final: 0.6688 (mt-10) REVERT: B 703 ASN cc_start: 0.8025 (OUTLIER) cc_final: 0.7583 (p0) REVERT: B 725 GLU cc_start: 0.7327 (tt0) cc_final: 0.7096 (tt0) REVERT: B 737 ASP cc_start: 0.7172 (m-30) cc_final: 0.6928 (m-30) REVERT: B 780 GLU cc_start: 0.7557 (OUTLIER) cc_final: 0.7221 (mm-30) REVERT: B 790 LYS cc_start: 0.8124 (mtpp) cc_final: 0.7842 (mtpp) REVERT: B 882 ILE cc_start: 0.8085 (pt) cc_final: 0.7842 (mt) REVERT: B 884 SER cc_start: 0.8128 (p) cc_final: 0.7903 (p) REVERT: B 894 LEU cc_start: 0.8041 (mt) cc_final: 0.7822 (mt) REVERT: B 955 ASN cc_start: 0.8284 (OUTLIER) cc_final: 0.7994 (t0) REVERT: B 964 LYS cc_start: 0.8211 (mmtm) cc_final: 0.7963 (mtpp) REVERT: B 979 ASP cc_start: 0.6761 (t70) cc_final: 0.6442 (t0) REVERT: B 1014 ARG cc_start: 0.8134 (ttm110) cc_final: 0.7926 (ttm110) REVERT: B 1030 SER cc_start: 0.8385 (m) cc_final: 0.8059 (p) REVERT: B 1037 SER cc_start: 0.8236 (t) cc_final: 0.7844 (p) REVERT: B 1045 LYS cc_start: 0.8123 (mptt) cc_final: 0.7715 (tptt) REVERT: B 1068 VAL cc_start: 0.7961 (OUTLIER) cc_final: 0.7697 (m) REVERT: B 1123 SER cc_start: 0.8245 (t) cc_final: 0.8026 (t) REVERT: B 1139 ASP cc_start: 0.7871 (t0) cc_final: 0.7282 (m-30) REVERT: C 52 GLN cc_start: 0.7353 (tm-30) cc_final: 0.6937 (tm-30) REVERT: C 55 PHE cc_start: 0.6952 (m-80) cc_final: 0.6525 (m-80) REVERT: C 99 ASN cc_start: 0.7792 (t0) cc_final: 0.7398 (t0) REVERT: C 227 VAL cc_start: 0.7938 (p) cc_final: 0.7649 (m) REVERT: C 314 GLN cc_start: 0.8163 (tt0) cc_final: 0.7946 (mt0) REVERT: C 556 ASN cc_start: 0.6425 (p0) cc_final: 0.6059 (p0) REVERT: C 562 PHE cc_start: 0.6604 (p90) cc_final: 0.6317 (p90) REVERT: C 583 GLU cc_start: 0.7624 (mm-30) cc_final: 0.7295 (mm-30) REVERT: C 663 ASP cc_start: 0.7411 (t70) cc_final: 0.6866 (t0) REVERT: C 673 SER cc_start: 0.7630 (t) cc_final: 0.6950 (m) REVERT: C 720 ILE cc_start: 0.8580 (mm) cc_final: 0.7989 (mt) REVERT: C 721 SER cc_start: 0.8196 (t) cc_final: 0.7618 (p) REVERT: C 736 VAL cc_start: 0.8091 (t) cc_final: 0.7194 (p) REVERT: C 776 LYS cc_start: 0.8007 (ttpt) cc_final: 0.7698 (ttpt) REVERT: C 790 LYS cc_start: 0.7974 (ttmm) cc_final: 0.7738 (ttpp) REVERT: C 805 ILE cc_start: 0.8208 (pt) cc_final: 0.7994 (pt) REVERT: C 819 GLU cc_start: 0.7826 (mt-10) cc_final: 0.7340 (mt-10) REVERT: C 820 ASP cc_start: 0.8115 (m-30) cc_final: 0.7695 (m-30) REVERT: C 884 SER cc_start: 0.8283 (p) cc_final: 0.7453 (t) REVERT: C 921 LYS cc_start: 0.8063 (mtpp) cc_final: 0.7831 (mmmm) REVERT: C 931 ILE cc_start: 0.7966 (mm) cc_final: 0.7521 (mt) REVERT: C 954 GLN cc_start: 0.7754 (mm-40) cc_final: 0.7509 (mt0) REVERT: C 955 ASN cc_start: 0.8372 (t0) cc_final: 0.8078 (t0) REVERT: C 1002 GLN cc_start: 0.7822 (tt0) cc_final: 0.7616 (tt0) REVERT: C 1051 SER cc_start: 0.8169 (t) cc_final: 0.7630 (p) REVERT: C 1054 GLN cc_start: 0.7579 (mt0) cc_final: 0.7012 (mm-40) REVERT: C 1097 SER cc_start: 0.8177 (p) cc_final: 0.7925 (p) REVERT: C 1116 THR cc_start: 0.7563 (m) cc_final: 0.7115 (p) REVERT: E 46 ARG cc_start: 0.7047 (OUTLIER) cc_final: 0.6303 (ttp-170) REVERT: E 115 TRP cc_start: 0.5344 (m100) cc_final: 0.3767 (m100) outliers start: 58 outliers final: 39 residues processed: 658 average time/residue: 0.8120 time to fit residues: 839.2043 Evaluate side-chains 666 residues out of total 2964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 619 time to evaluate : 3.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 614 ASP Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 774 GLN Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain A residue 800 PHE Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 1037 SER Chi-restraints excluded: chain A residue 1071 GLN Chi-restraints excluded: chain A residue 1127 ASP Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 160 TYR Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 173 GLN Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 614 ASP Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 703 ASN Chi-restraints excluded: chain B residue 717 ASN Chi-restraints excluded: chain B residue 767 LEU Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 955 ASN Chi-restraints excluded: chain B residue 967 SER Chi-restraints excluded: chain B residue 993 ILE Chi-restraints excluded: chain B residue 1068 VAL Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 596 SER Chi-restraints excluded: chain C residue 618 THR Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 765 ARG Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain E residue 46 ARG Chi-restraints excluded: chain E residue 60 TYR Chi-restraints excluded: chain E residue 119 THR Chi-restraints excluded: chain E residue 122 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 317 optimal weight: 0.8980 chunk 37 optimal weight: 3.9990 chunk 187 optimal weight: 0.9980 chunk 240 optimal weight: 1.9990 chunk 186 optimal weight: 0.5980 chunk 276 optimal weight: 0.8980 chunk 183 optimal weight: 1.9990 chunk 327 optimal weight: 10.0000 chunk 205 optimal weight: 0.8980 chunk 199 optimal weight: 0.6980 chunk 151 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 GLN ** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 907 ASN A 969 ASN ** A1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 173 GLN ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 717 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 751 ASN B 777 ASN ** B 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 GLN ** C 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1106 GLN ** E 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 117 GLN ** E 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6771 moved from start: 0.4937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.015 0.829 27939 Z= 1.016 Angle : 0.660 19.674 37997 Z= 0.349 Chirality : 0.049 1.403 4388 Planarity : 0.005 0.064 4870 Dihedral : 6.960 112.951 4580 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 20.80 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.95 % Favored : 92.02 % Rotamer: Outliers : 1.92 % Allowed : 16.48 % Favored : 81.60 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.94 (0.13), residues: 3378 helix: -1.20 (0.19), residues: 688 sheet: -1.82 (0.18), residues: 711 loop : -2.34 (0.12), residues: 1979 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 64 HIS 0.006 0.001 HIS A 655 PHE 0.044 0.002 PHE B 718 TYR 0.061 0.001 TYR A 904 ARG 0.009 0.000 ARG C 815 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6756 Ramachandran restraints generated. 3378 Oldfield, 0 Emsley, 3378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6756 Ramachandran restraints generated. 3378 Oldfield, 0 Emsley, 3378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 701 residues out of total 2964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 645 time to evaluate : 3.653 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 VAL cc_start: 0.8613 (t) cc_final: 0.8092 (p) REVERT: A 43 PHE cc_start: 0.7941 (t80) cc_final: 0.7452 (t80) REVERT: A 140 PHE cc_start: 0.7115 (p90) cc_final: 0.6409 (p90) REVERT: A 177 MET cc_start: -0.0791 (tpt) cc_final: -0.2564 (tpt) REVERT: A 266 TYR cc_start: 0.7014 (m-80) cc_final: 0.6638 (m-80) REVERT: A 276 LEU cc_start: 0.7854 (tp) cc_final: 0.7608 (tp) REVERT: A 278 LYS cc_start: 0.7147 (tttt) cc_final: 0.6736 (ttmm) REVERT: A 289 VAL cc_start: 0.8040 (t) cc_final: 0.7623 (m) REVERT: A 300 LYS cc_start: 0.7658 (mttt) cc_final: 0.7184 (mttt) REVERT: A 309 GLU cc_start: 0.7287 (mm-30) cc_final: 0.6914 (mm-30) REVERT: A 537 LYS cc_start: 0.7900 (mttp) cc_final: 0.7252 (ttpt) REVERT: A 551 VAL cc_start: 0.6877 (p) cc_final: 0.6303 (t) REVERT: A 587 ILE cc_start: 0.8108 (mt) cc_final: 0.7681 (mt) REVERT: A 610 VAL cc_start: 0.8445 (t) cc_final: 0.8108 (p) REVERT: A 619 GLU cc_start: 0.7129 (mp0) cc_final: 0.6870 (mp0) REVERT: A 646 ARG cc_start: 0.7284 (tpt-90) cc_final: 0.6919 (tpt-90) REVERT: A 663 ASP cc_start: 0.7060 (t70) cc_final: 0.6807 (t70) REVERT: A 779 GLN cc_start: 0.7781 (mm-40) cc_final: 0.7436 (mm-40) REVERT: A 866 THR cc_start: 0.8328 (OUTLIER) cc_final: 0.7917 (p) REVERT: A 884 SER cc_start: 0.8578 (m) cc_final: 0.7890 (p) REVERT: A 900 MET cc_start: 0.7131 (mtp) cc_final: 0.6788 (mtt) REVERT: A 904 TYR cc_start: 0.7285 (m-80) cc_final: 0.7067 (m-80) REVERT: A 931 ILE cc_start: 0.7861 (mm) cc_final: 0.7411 (mt) REVERT: A 933 LYS cc_start: 0.7811 (mtpp) cc_final: 0.7510 (mtpp) REVERT: A 950 ASP cc_start: 0.6807 (m-30) cc_final: 0.6179 (m-30) REVERT: A 957 GLN cc_start: 0.7989 (tp40) cc_final: 0.7500 (tt0) REVERT: A 1054 GLN cc_start: 0.7309 (mm-40) cc_final: 0.7053 (mm-40) REVERT: A 1073 LYS cc_start: 0.7684 (ttpt) cc_final: 0.7322 (tttm) REVERT: A 1117 THR cc_start: 0.8331 (p) cc_final: 0.7952 (t) REVERT: B 129 LYS cc_start: 0.7009 (tttt) cc_final: 0.6421 (tttt) REVERT: B 274 THR cc_start: 0.7641 (t) cc_final: 0.7352 (p) REVERT: B 528 LYS cc_start: 0.8518 (tttm) cc_final: 0.8062 (ttmm) REVERT: B 619 GLU cc_start: 0.7207 (mt-10) cc_final: 0.6839 (mt-10) REVERT: B 703 ASN cc_start: 0.8096 (OUTLIER) cc_final: 0.7673 (p0) REVERT: B 737 ASP cc_start: 0.7274 (m-30) cc_final: 0.7024 (m-30) REVERT: B 780 GLU cc_start: 0.7555 (OUTLIER) cc_final: 0.7222 (mm-30) REVERT: B 781 VAL cc_start: 0.8197 (t) cc_final: 0.7911 (p) REVERT: B 790 LYS cc_start: 0.8133 (mtpp) cc_final: 0.7886 (mtpp) REVERT: B 882 ILE cc_start: 0.8068 (pt) cc_final: 0.7839 (mt) REVERT: B 884 SER cc_start: 0.8178 (p) cc_final: 0.7939 (p) REVERT: B 894 LEU cc_start: 0.8077 (mt) cc_final: 0.7869 (mt) REVERT: B 955 ASN cc_start: 0.8270 (OUTLIER) cc_final: 0.8015 (t0) REVERT: B 979 ASP cc_start: 0.6782 (t70) cc_final: 0.6430 (t0) REVERT: B 1019 ARG cc_start: 0.7562 (ttp-110) cc_final: 0.7234 (ttp-110) REVERT: B 1030 SER cc_start: 0.8419 (m) cc_final: 0.8093 (p) REVERT: B 1037 SER cc_start: 0.8260 (t) cc_final: 0.7896 (p) REVERT: B 1045 LYS cc_start: 0.8150 (mptt) cc_final: 0.7728 (tptt) REVERT: B 1052 PHE cc_start: 0.8023 (m-80) cc_final: 0.7704 (m-80) REVERT: B 1068 VAL cc_start: 0.8049 (t) cc_final: 0.7795 (m) REVERT: B 1107 ARG cc_start: 0.7520 (mtt90) cc_final: 0.7236 (mtm-85) REVERT: B 1139 ASP cc_start: 0.7958 (t0) cc_final: 0.7362 (m-30) REVERT: B 1146 ASP cc_start: 0.7331 (m-30) cc_final: 0.7071 (t0) REVERT: C 43 PHE cc_start: 0.7962 (t80) cc_final: 0.7729 (t80) REVERT: C 52 GLN cc_start: 0.7385 (tm-30) cc_final: 0.6941 (tm-30) REVERT: C 99 ASN cc_start: 0.7843 (t0) cc_final: 0.7451 (t0) REVERT: C 227 VAL cc_start: 0.7962 (p) cc_final: 0.7677 (m) REVERT: C 274 THR cc_start: 0.7705 (m) cc_final: 0.7116 (p) REVERT: C 314 GLN cc_start: 0.8179 (tt0) cc_final: 0.7958 (mt0) REVERT: C 556 ASN cc_start: 0.6669 (p0) cc_final: 0.6298 (p0) REVERT: C 562 PHE cc_start: 0.6623 (p90) cc_final: 0.6344 (p90) REVERT: C 583 GLU cc_start: 0.7696 (mm-30) cc_final: 0.7377 (mm-30) REVERT: C 663 ASP cc_start: 0.7521 (t70) cc_final: 0.6942 (t0) REVERT: C 673 SER cc_start: 0.7633 (t) cc_final: 0.6983 (m) REVERT: C 720 ILE cc_start: 0.8595 (mm) cc_final: 0.7992 (mt) REVERT: C 721 SER cc_start: 0.8167 (t) cc_final: 0.7579 (p) REVERT: C 736 VAL cc_start: 0.8166 (t) cc_final: 0.7305 (p) REVERT: C 776 LYS cc_start: 0.8044 (ttpt) cc_final: 0.7722 (ttpt) REVERT: C 790 LYS cc_start: 0.7976 (ttmm) cc_final: 0.7736 (ttpp) REVERT: C 819 GLU cc_start: 0.7781 (mt-10) cc_final: 0.7308 (mt-10) REVERT: C 820 ASP cc_start: 0.8153 (m-30) cc_final: 0.7849 (m-30) REVERT: C 884 SER cc_start: 0.8249 (p) cc_final: 0.7348 (t) REVERT: C 921 LYS cc_start: 0.8078 (mtpp) cc_final: 0.7856 (mmmm) REVERT: C 931 ILE cc_start: 0.8009 (mm) cc_final: 0.7576 (mt) REVERT: C 955 ASN cc_start: 0.8372 (t0) cc_final: 0.8131 (t0) REVERT: C 960 ASN cc_start: 0.8055 (m-40) cc_final: 0.7748 (t0) REVERT: C 1051 SER cc_start: 0.8196 (t) cc_final: 0.7643 (p) REVERT: C 1054 GLN cc_start: 0.7565 (mt0) cc_final: 0.7072 (mm-40) REVERT: C 1097 SER cc_start: 0.8224 (p) cc_final: 0.7958 (p) REVERT: C 1111 GLU cc_start: 0.8037 (tt0) cc_final: 0.7141 (pt0) REVERT: C 1116 THR cc_start: 0.7521 (m) cc_final: 0.7114 (p) REVERT: E 115 TRP cc_start: 0.5390 (m100) cc_final: 0.5107 (m100) REVERT: E 117 GLN cc_start: 0.6888 (OUTLIER) cc_final: 0.6640 (pm20) outliers start: 56 outliers final: 43 residues processed: 670 average time/residue: 0.8692 time to fit residues: 920.6395 Evaluate side-chains 676 residues out of total 2964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 628 time to evaluate : 3.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 614 ASP Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 774 GLN Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 969 ASN Chi-restraints excluded: chain A residue 1037 SER Chi-restraints excluded: chain A residue 1071 GLN Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 173 GLN Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 440 ASN Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 614 ASP Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 703 ASN Chi-restraints excluded: chain B residue 767 LEU Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 955 ASN Chi-restraints excluded: chain B residue 967 SER Chi-restraints excluded: chain B residue 993 ILE Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 596 SER Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 765 ARG Chi-restraints excluded: chain C residue 967 SER Chi-restraints excluded: chain C residue 1106 GLN Chi-restraints excluded: chain D residue 84 MET Chi-restraints excluded: chain E residue 46 ARG Chi-restraints excluded: chain E residue 60 TYR Chi-restraints excluded: chain E residue 117 GLN Chi-restraints excluded: chain E residue 119 THR Chi-restraints excluded: chain E residue 122 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 202 optimal weight: 0.5980 chunk 130 optimal weight: 0.5980 chunk 195 optimal weight: 0.9990 chunk 98 optimal weight: 0.7980 chunk 64 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 208 optimal weight: 0.9990 chunk 223 optimal weight: 6.9990 chunk 162 optimal weight: 0.9990 chunk 30 optimal weight: 0.9980 chunk 257 optimal weight: 9.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 969 ASN ** A1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 717 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 777 ASN ** B 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 GLN ** C 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1106 GLN ** E 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6770 moved from start: 0.5007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.015 0.830 27939 Z= 1.026 Angle : 0.831 59.200 37997 Z= 0.473 Chirality : 0.050 1.395 4388 Planarity : 0.006 0.178 4870 Dihedral : 6.959 112.936 4580 Min Nonbonded Distance : 1.673 Molprobity Statistics. All-atom Clashscore : 23.17 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.00 % Favored : 91.97 % Rotamer: Outliers : 1.82 % Allowed : 17.29 % Favored : 80.89 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.91 (0.13), residues: 3378 helix: -1.18 (0.19), residues: 688 sheet: -1.81 (0.18), residues: 703 loop : -2.33 (0.12), residues: 1987 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 64 HIS 0.007 0.001 HIS A 655 PHE 0.033 0.002 PHE D 55 TYR 0.045 0.001 TYR A 904 ARG 0.016 0.000 ARG C1107 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6756 Ramachandran restraints generated. 3378 Oldfield, 0 Emsley, 3378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6756 Ramachandran restraints generated. 3378 Oldfield, 0 Emsley, 3378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 683 residues out of total 2964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 630 time to evaluate : 3.626 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 VAL cc_start: 0.8568 (t) cc_final: 0.8083 (p) REVERT: A 43 PHE cc_start: 0.7938 (t80) cc_final: 0.7480 (t80) REVERT: A 140 PHE cc_start: 0.7115 (p90) cc_final: 0.6406 (p90) REVERT: A 177 MET cc_start: -0.0787 (tpt) cc_final: -0.2561 (tpt) REVERT: A 266 TYR cc_start: 0.7012 (m-80) cc_final: 0.6638 (m-80) REVERT: A 276 LEU cc_start: 0.7863 (tp) cc_final: 0.7619 (tp) REVERT: A 278 LYS cc_start: 0.7149 (tttt) cc_final: 0.6734 (ttmm) REVERT: A 289 VAL cc_start: 0.8041 (t) cc_final: 0.7626 (m) REVERT: A 300 LYS cc_start: 0.7677 (mttt) cc_final: 0.7206 (mttt) REVERT: A 309 GLU cc_start: 0.7283 (mm-30) cc_final: 0.6911 (mm-30) REVERT: A 537 LYS cc_start: 0.7898 (mttp) cc_final: 0.7250 (ttpt) REVERT: A 551 VAL cc_start: 0.6883 (p) cc_final: 0.6302 (t) REVERT: A 587 ILE cc_start: 0.7924 (mt) cc_final: 0.7660 (mt) REVERT: A 610 VAL cc_start: 0.8442 (t) cc_final: 0.8106 (p) REVERT: A 619 GLU cc_start: 0.7134 (mp0) cc_final: 0.6863 (mp0) REVERT: A 646 ARG cc_start: 0.7282 (tpt-90) cc_final: 0.6926 (tpt-90) REVERT: A 663 ASP cc_start: 0.7063 (t70) cc_final: 0.6813 (t70) REVERT: A 779 GLN cc_start: 0.7780 (mm-40) cc_final: 0.7438 (mm-40) REVERT: A 815 ARG cc_start: 0.8776 (mtm-85) cc_final: 0.8533 (mtm180) REVERT: A 866 THR cc_start: 0.8327 (OUTLIER) cc_final: 0.7913 (p) REVERT: A 884 SER cc_start: 0.8583 (m) cc_final: 0.7890 (p) REVERT: A 900 MET cc_start: 0.7120 (mtp) cc_final: 0.6796 (mtt) REVERT: A 931 ILE cc_start: 0.7864 (mm) cc_final: 0.7411 (mt) REVERT: A 933 LYS cc_start: 0.7812 (mtpp) cc_final: 0.7508 (mtpp) REVERT: A 950 ASP cc_start: 0.6801 (m-30) cc_final: 0.6164 (m-30) REVERT: A 957 GLN cc_start: 0.7991 (tp40) cc_final: 0.7503 (tt0) REVERT: A 1054 GLN cc_start: 0.7302 (mm-40) cc_final: 0.7054 (mm-40) REVERT: A 1073 LYS cc_start: 0.7681 (ttpt) cc_final: 0.7322 (tttm) REVERT: A 1117 THR cc_start: 0.8285 (p) cc_final: 0.7947 (t) REVERT: B 129 LYS cc_start: 0.7011 (tttt) cc_final: 0.6459 (tttt) REVERT: B 274 THR cc_start: 0.7641 (t) cc_final: 0.7349 (p) REVERT: B 528 LYS cc_start: 0.8527 (tttm) cc_final: 0.8068 (ttmm) REVERT: B 619 GLU cc_start: 0.7210 (mt-10) cc_final: 0.6841 (mt-10) REVERT: B 703 ASN cc_start: 0.8095 (OUTLIER) cc_final: 0.7673 (p0) REVERT: B 737 ASP cc_start: 0.7234 (m-30) cc_final: 0.7023 (m-30) REVERT: B 780 GLU cc_start: 0.7556 (OUTLIER) cc_final: 0.7221 (mm-30) REVERT: B 790 LYS cc_start: 0.8134 (mtpp) cc_final: 0.7885 (mtpp) REVERT: B 882 ILE cc_start: 0.8071 (pt) cc_final: 0.7839 (mt) REVERT: B 884 SER cc_start: 0.8181 (p) cc_final: 0.7936 (p) REVERT: B 894 LEU cc_start: 0.8081 (mt) cc_final: 0.7869 (mt) REVERT: B 955 ASN cc_start: 0.8266 (OUTLIER) cc_final: 0.8013 (t0) REVERT: B 979 ASP cc_start: 0.6761 (t70) cc_final: 0.6434 (t0) REVERT: B 1019 ARG cc_start: 0.7560 (ttp-110) cc_final: 0.7247 (ttp-110) REVERT: B 1030 SER cc_start: 0.8329 (m) cc_final: 0.8002 (p) REVERT: B 1037 SER cc_start: 0.8263 (t) cc_final: 0.7891 (p) REVERT: B 1045 LYS cc_start: 0.8151 (mptt) cc_final: 0.7728 (tptt) REVERT: B 1052 PHE cc_start: 0.8023 (m-80) cc_final: 0.7702 (m-80) REVERT: B 1068 VAL cc_start: 0.8072 (t) cc_final: 0.7818 (m) REVERT: B 1107 ARG cc_start: 0.7357 (mtt90) cc_final: 0.6964 (mtt90) REVERT: B 1139 ASP cc_start: 0.7956 (t0) cc_final: 0.7360 (m-30) REVERT: B 1146 ASP cc_start: 0.7392 (m-30) cc_final: 0.7134 (t0) REVERT: C 43 PHE cc_start: 0.7954 (t80) cc_final: 0.7710 (t80) REVERT: C 52 GLN cc_start: 0.7382 (tm-30) cc_final: 0.6942 (tm-30) REVERT: C 99 ASN cc_start: 0.7851 (t0) cc_final: 0.7451 (t0) REVERT: C 224 GLU cc_start: 0.6282 (pp20) cc_final: 0.5977 (pp20) REVERT: C 227 VAL cc_start: 0.7967 (p) cc_final: 0.7680 (m) REVERT: C 274 THR cc_start: 0.7709 (m) cc_final: 0.7124 (p) REVERT: C 314 GLN cc_start: 0.8182 (tt0) cc_final: 0.7958 (mt0) REVERT: C 556 ASN cc_start: 0.6678 (p0) cc_final: 0.6313 (p0) REVERT: C 562 PHE cc_start: 0.6608 (p90) cc_final: 0.6346 (p90) REVERT: C 583 GLU cc_start: 0.7698 (mm-30) cc_final: 0.7385 (mm-30) REVERT: C 643 PHE cc_start: 0.7235 (t80) cc_final: 0.6995 (t80) REVERT: C 663 ASP cc_start: 0.7523 (t70) cc_final: 0.6957 (t0) REVERT: C 673 SER cc_start: 0.7633 (t) cc_final: 0.6985 (m) REVERT: C 720 ILE cc_start: 0.8594 (mm) cc_final: 0.7993 (mt) REVERT: C 721 SER cc_start: 0.8166 (t) cc_final: 0.7577 (p) REVERT: C 736 VAL cc_start: 0.8168 (t) cc_final: 0.7304 (p) REVERT: C 776 LYS cc_start: 0.8046 (ttpt) cc_final: 0.7722 (ttpt) REVERT: C 790 LYS cc_start: 0.7972 (ttmm) cc_final: 0.7719 (ttpp) REVERT: C 819 GLU cc_start: 0.7779 (mt-10) cc_final: 0.7312 (mt-10) REVERT: C 820 ASP cc_start: 0.8155 (m-30) cc_final: 0.7852 (m-30) REVERT: C 884 SER cc_start: 0.8219 (p) cc_final: 0.7348 (t) REVERT: C 921 LYS cc_start: 0.8079 (mtpp) cc_final: 0.7858 (mmmm) REVERT: C 931 ILE cc_start: 0.8012 (mm) cc_final: 0.7578 (mt) REVERT: C 955 ASN cc_start: 0.8350 (t0) cc_final: 0.8131 (t0) REVERT: C 960 ASN cc_start: 0.8049 (m-40) cc_final: 0.7748 (t0) REVERT: C 1051 SER cc_start: 0.8192 (t) cc_final: 0.7645 (p) REVERT: C 1054 GLN cc_start: 0.7566 (mt0) cc_final: 0.7076 (mm-40) REVERT: C 1097 SER cc_start: 0.8223 (p) cc_final: 0.7953 (p) REVERT: C 1111 GLU cc_start: 0.7993 (tt0) cc_final: 0.7429 (pt0) REVERT: C 1116 THR cc_start: 0.7525 (m) cc_final: 0.7108 (p) REVERT: E 115 TRP cc_start: 0.5404 (m100) cc_final: 0.5116 (m100) outliers start: 53 outliers final: 47 residues processed: 652 average time/residue: 0.8220 time to fit residues: 835.0831 Evaluate side-chains 680 residues out of total 2964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 629 time to evaluate : 3.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 614 ASP Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 774 GLN Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 969 ASN Chi-restraints excluded: chain A residue 1037 SER Chi-restraints excluded: chain A residue 1071 GLN Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 440 ASN Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 614 ASP Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 703 ASN Chi-restraints excluded: chain B residue 767 LEU Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 955 ASN Chi-restraints excluded: chain B residue 967 SER Chi-restraints excluded: chain B residue 993 ILE Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 596 SER Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 765 ARG Chi-restraints excluded: chain C residue 896 ILE Chi-restraints excluded: chain C residue 967 SER Chi-restraints excluded: chain C residue 1107 ARG Chi-restraints excluded: chain D residue 84 MET Chi-restraints excluded: chain E residue 46 ARG Chi-restraints excluded: chain E residue 60 TYR Chi-restraints excluded: chain E residue 117 GLN Chi-restraints excluded: chain E residue 119 THR Chi-restraints excluded: chain E residue 122 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 298 optimal weight: 0.8980 chunk 313 optimal weight: 1.9990 chunk 286 optimal weight: 1.9990 chunk 305 optimal weight: 0.4980 chunk 183 optimal weight: 0.9990 chunk 133 optimal weight: 1.9990 chunk 239 optimal weight: 0.9980 chunk 93 optimal weight: 1.9990 chunk 275 optimal weight: 0.0980 chunk 288 optimal weight: 0.9990 chunk 304 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 969 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 717 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 774 GLN B 777 ASN ** B 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 GLN ** C 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6770 moved from start: 0.5020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.015 0.830 27939 Z= 1.026 Angle : 0.806 47.793 37997 Z= 0.458 Chirality : 0.050 1.395 4388 Planarity : 0.006 0.178 4870 Dihedral : 6.959 112.936 4580 Min Nonbonded Distance : 1.503 Molprobity Statistics. All-atom Clashscore : 23.97 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.00 % Favored : 91.97 % Rotamer: Outliers : 1.75 % Allowed : 17.42 % Favored : 80.83 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.91 (0.13), residues: 3378 helix: -1.18 (0.19), residues: 688 sheet: -1.81 (0.18), residues: 703 loop : -2.33 (0.12), residues: 1987 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 64 HIS 0.007 0.001 HIS A 655 PHE 0.033 0.002 PHE D 55 TYR 0.045 0.001 TYR A 904 ARG 0.016 0.000 ARG C1107 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6756 Ramachandran restraints generated. 3378 Oldfield, 0 Emsley, 3378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6756 Ramachandran restraints generated. 3378 Oldfield, 0 Emsley, 3378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 680 residues out of total 2964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 629 time to evaluate : 3.049 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 VAL cc_start: 0.8565 (t) cc_final: 0.8081 (p) REVERT: A 43 PHE cc_start: 0.7938 (t80) cc_final: 0.7480 (t80) REVERT: A 140 PHE cc_start: 0.7115 (p90) cc_final: 0.6406 (p90) REVERT: A 177 MET cc_start: -0.0786 (tpt) cc_final: -0.2561 (tpt) REVERT: A 266 TYR cc_start: 0.7012 (m-80) cc_final: 0.6638 (m-80) REVERT: A 276 LEU cc_start: 0.7864 (tp) cc_final: 0.7619 (tp) REVERT: A 278 LYS cc_start: 0.7147 (tttt) cc_final: 0.6734 (ttmm) REVERT: A 289 VAL cc_start: 0.8043 (t) cc_final: 0.7626 (m) REVERT: A 300 LYS cc_start: 0.7678 (mttt) cc_final: 0.7206 (mttt) REVERT: A 309 GLU cc_start: 0.7284 (mm-30) cc_final: 0.6911 (mm-30) REVERT: A 537 LYS cc_start: 0.7897 (mttp) cc_final: 0.7251 (ttpt) REVERT: A 551 VAL cc_start: 0.6880 (p) cc_final: 0.6297 (t) REVERT: A 610 VAL cc_start: 0.8443 (t) cc_final: 0.8105 (p) REVERT: A 619 GLU cc_start: 0.7135 (mp0) cc_final: 0.6863 (mp0) REVERT: A 646 ARG cc_start: 0.7288 (tpt-90) cc_final: 0.6926 (tpt-90) REVERT: A 663 ASP cc_start: 0.7063 (t70) cc_final: 0.6813 (t70) REVERT: A 779 GLN cc_start: 0.7782 (mm-40) cc_final: 0.7438 (mm-40) REVERT: A 815 ARG cc_start: 0.8777 (mtm-85) cc_final: 0.8533 (mtm180) REVERT: A 866 THR cc_start: 0.8326 (OUTLIER) cc_final: 0.7913 (p) REVERT: A 884 SER cc_start: 0.8587 (m) cc_final: 0.7890 (p) REVERT: A 931 ILE cc_start: 0.7864 (mm) cc_final: 0.7410 (mt) REVERT: A 933 LYS cc_start: 0.7812 (mtpp) cc_final: 0.7508 (mtpp) REVERT: A 950 ASP cc_start: 0.6802 (m-30) cc_final: 0.6164 (m-30) REVERT: A 957 GLN cc_start: 0.7992 (tp40) cc_final: 0.7503 (tt0) REVERT: A 1054 GLN cc_start: 0.7302 (mm-40) cc_final: 0.7054 (mm-40) REVERT: A 1073 LYS cc_start: 0.7681 (ttpt) cc_final: 0.7290 (tttm) REVERT: B 129 LYS cc_start: 0.7046 (tttt) cc_final: 0.6459 (tttt) REVERT: B 274 THR cc_start: 0.7642 (t) cc_final: 0.7349 (p) REVERT: B 528 LYS cc_start: 0.8526 (tttm) cc_final: 0.8068 (ttmm) REVERT: B 619 GLU cc_start: 0.7210 (mt-10) cc_final: 0.6841 (mt-10) REVERT: B 703 ASN cc_start: 0.8094 (OUTLIER) cc_final: 0.7673 (p0) REVERT: B 737 ASP cc_start: 0.7237 (m-30) cc_final: 0.7023 (m-30) REVERT: B 780 GLU cc_start: 0.7555 (OUTLIER) cc_final: 0.7221 (mm-30) REVERT: B 790 LYS cc_start: 0.8134 (mtpp) cc_final: 0.7885 (mtpp) REVERT: B 882 ILE cc_start: 0.8071 (pt) cc_final: 0.7839 (mt) REVERT: B 884 SER cc_start: 0.8180 (p) cc_final: 0.7935 (p) REVERT: B 894 LEU cc_start: 0.8081 (mt) cc_final: 0.7871 (mt) REVERT: B 955 ASN cc_start: 0.8264 (OUTLIER) cc_final: 0.8013 (t0) REVERT: B 979 ASP cc_start: 0.6761 (t70) cc_final: 0.6434 (t0) REVERT: B 1019 ARG cc_start: 0.7559 (ttp-110) cc_final: 0.7247 (ttp-110) REVERT: B 1030 SER cc_start: 0.8258 (m) cc_final: 0.8002 (p) REVERT: B 1037 SER cc_start: 0.8262 (t) cc_final: 0.7891 (p) REVERT: B 1045 LYS cc_start: 0.8152 (mptt) cc_final: 0.7728 (tptt) REVERT: B 1052 PHE cc_start: 0.8022 (m-80) cc_final: 0.7702 (m-80) REVERT: B 1068 VAL cc_start: 0.8073 (t) cc_final: 0.7819 (m) REVERT: B 1107 ARG cc_start: 0.7354 (mtt90) cc_final: 0.6964 (mtt90) REVERT: B 1139 ASP cc_start: 0.7955 (t0) cc_final: 0.7358 (m-30) REVERT: B 1146 ASP cc_start: 0.7391 (m-30) cc_final: 0.7134 (t0) REVERT: C 43 PHE cc_start: 0.7964 (t80) cc_final: 0.7710 (t80) REVERT: C 99 ASN cc_start: 0.7850 (t0) cc_final: 0.7450 (t0) REVERT: C 224 GLU cc_start: 0.6282 (pp20) cc_final: 0.5976 (pp20) REVERT: C 227 VAL cc_start: 0.7967 (p) cc_final: 0.7680 (m) REVERT: C 274 THR cc_start: 0.7710 (m) cc_final: 0.7136 (p) REVERT: C 314 GLN cc_start: 0.8183 (tt0) cc_final: 0.7958 (mt0) REVERT: C 556 ASN cc_start: 0.6677 (p0) cc_final: 0.6313 (p0) REVERT: C 562 PHE cc_start: 0.6608 (p90) cc_final: 0.6346 (p90) REVERT: C 583 GLU cc_start: 0.7697 (mm-30) cc_final: 0.7385 (mm-30) REVERT: C 643 PHE cc_start: 0.7235 (t80) cc_final: 0.6995 (t80) REVERT: C 663 ASP cc_start: 0.7524 (t70) cc_final: 0.6957 (t0) REVERT: C 673 SER cc_start: 0.7633 (t) cc_final: 0.6986 (m) REVERT: C 720 ILE cc_start: 0.8593 (mm) cc_final: 0.7992 (mt) REVERT: C 721 SER cc_start: 0.8165 (t) cc_final: 0.7577 (p) REVERT: C 736 VAL cc_start: 0.8168 (t) cc_final: 0.7304 (p) REVERT: C 776 LYS cc_start: 0.8046 (ttpt) cc_final: 0.7722 (ttpt) REVERT: C 790 LYS cc_start: 0.7972 (ttmm) cc_final: 0.7719 (ttpp) REVERT: C 819 GLU cc_start: 0.7779 (mt-10) cc_final: 0.7312 (mt-10) REVERT: C 820 ASP cc_start: 0.8157 (m-30) cc_final: 0.7852 (m-30) REVERT: C 884 SER cc_start: 0.8219 (p) cc_final: 0.7348 (t) REVERT: C 921 LYS cc_start: 0.8079 (mtpp) cc_final: 0.7858 (mmmm) REVERT: C 931 ILE cc_start: 0.8011 (mm) cc_final: 0.7578 (mt) REVERT: C 955 ASN cc_start: 0.8350 (t0) cc_final: 0.8131 (t0) REVERT: C 960 ASN cc_start: 0.8049 (m-40) cc_final: 0.7748 (t0) REVERT: C 1051 SER cc_start: 0.8191 (t) cc_final: 0.7644 (p) REVERT: C 1054 GLN cc_start: 0.7565 (mt0) cc_final: 0.7076 (mm-40) REVERT: C 1097 SER cc_start: 0.8218 (p) cc_final: 0.7953 (p) REVERT: C 1111 GLU cc_start: 0.7969 (tt0) cc_final: 0.7429 (pt0) REVERT: C 1116 THR cc_start: 0.7523 (m) cc_final: 0.7109 (p) REVERT: E 115 TRP cc_start: 0.5404 (m100) cc_final: 0.5116 (m100) outliers start: 51 outliers final: 47 residues processed: 650 average time/residue: 0.8136 time to fit residues: 828.4151 Evaluate side-chains 678 residues out of total 2964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 627 time to evaluate : 3.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 614 ASP Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 774 GLN Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 969 ASN Chi-restraints excluded: chain A residue 1037 SER Chi-restraints excluded: chain A residue 1071 GLN Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 440 ASN Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 614 ASP Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 703 ASN Chi-restraints excluded: chain B residue 767 LEU Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 955 ASN Chi-restraints excluded: chain B residue 967 SER Chi-restraints excluded: chain B residue 993 ILE Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 596 SER Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 765 ARG Chi-restraints excluded: chain C residue 896 ILE Chi-restraints excluded: chain C residue 967 SER Chi-restraints excluded: chain C residue 1107 ARG Chi-restraints excluded: chain D residue 84 MET Chi-restraints excluded: chain E residue 46 ARG Chi-restraints excluded: chain E residue 60 TYR Chi-restraints excluded: chain E residue 117 GLN Chi-restraints excluded: chain E residue 119 THR Chi-restraints excluded: chain E residue 122 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 200 optimal weight: 1.9990 chunk 322 optimal weight: 6.9990 chunk 197 optimal weight: 0.9990 chunk 153 optimal weight: 2.9990 chunk 224 optimal weight: 0.5980 chunk 338 optimal weight: 0.9980 chunk 311 optimal weight: 0.6980 chunk 269 optimal weight: 0.7980 chunk 28 optimal weight: 0.7980 chunk 208 optimal weight: 0.9990 chunk 165 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 717 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 774 GLN B 777 ASN ** B 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 GLN ** B1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 GLN ** E 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6777 moved from start: 0.5209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.015 0.831 27939 Z= 1.011 Angle : 0.651 19.548 37997 Z= 0.345 Chirality : 0.049 1.403 4388 Planarity : 0.005 0.077 4870 Dihedral : 6.832 112.009 4580 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 20.89 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.41 % Favored : 92.56 % Rotamer: Outliers : 1.65 % Allowed : 17.66 % Favored : 80.69 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.71 (0.13), residues: 3378 helix: -0.94 (0.19), residues: 689 sheet: -1.67 (0.18), residues: 685 loop : -2.24 (0.12), residues: 2004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 64 HIS 0.005 0.001 HIS A 655 PHE 0.046 0.002 PHE A 970 TYR 0.062 0.001 TYR A 904 ARG 0.008 0.000 ARG B 815 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6756 Ramachandran restraints generated. 3378 Oldfield, 0 Emsley, 3378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6756 Ramachandran restraints generated. 3378 Oldfield, 0 Emsley, 3378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 676 residues out of total 2964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 628 time to evaluate : 2.911 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 VAL cc_start: 0.8572 (t) cc_final: 0.8133 (p) REVERT: A 43 PHE cc_start: 0.7956 (t80) cc_final: 0.7490 (t80) REVERT: A 140 PHE cc_start: 0.7155 (p90) cc_final: 0.6462 (p90) REVERT: A 177 MET cc_start: -0.0835 (tpt) cc_final: -0.2613 (tpt) REVERT: A 266 TYR cc_start: 0.7043 (m-80) cc_final: 0.6703 (m-80) REVERT: A 276 LEU cc_start: 0.7879 (tp) cc_final: 0.7651 (tp) REVERT: A 278 LYS cc_start: 0.7162 (tttt) cc_final: 0.6759 (ttmm) REVERT: A 289 VAL cc_start: 0.8036 (t) cc_final: 0.7638 (m) REVERT: A 300 LYS cc_start: 0.7732 (mttt) cc_final: 0.7260 (mttt) REVERT: A 309 GLU cc_start: 0.7266 (mm-30) cc_final: 0.6823 (mm-30) REVERT: A 537 LYS cc_start: 0.7852 (mttp) cc_final: 0.7183 (ttpt) REVERT: A 551 VAL cc_start: 0.6890 (p) cc_final: 0.6327 (t) REVERT: A 610 VAL cc_start: 0.8446 (t) cc_final: 0.8109 (p) REVERT: A 646 ARG cc_start: 0.7275 (tpt-90) cc_final: 0.6910 (tpt-90) REVERT: A 779 GLN cc_start: 0.7783 (mm-40) cc_final: 0.7448 (mm-40) REVERT: A 803 SER cc_start: 0.8428 (p) cc_final: 0.8213 (t) REVERT: A 815 ARG cc_start: 0.8750 (mtm-85) cc_final: 0.8510 (mtm180) REVERT: A 866 THR cc_start: 0.8291 (OUTLIER) cc_final: 0.7885 (p) REVERT: A 884 SER cc_start: 0.8587 (m) cc_final: 0.7877 (p) REVERT: A 931 ILE cc_start: 0.7868 (mm) cc_final: 0.7416 (mt) REVERT: A 933 LYS cc_start: 0.7794 (mtpp) cc_final: 0.7491 (mtpp) REVERT: A 957 GLN cc_start: 0.8002 (tp40) cc_final: 0.7544 (tt0) REVERT: A 1073 LYS cc_start: 0.7660 (ttpt) cc_final: 0.7295 (tttm) REVERT: A 1113 GLN cc_start: 0.7304 (mp10) cc_final: 0.6523 (mp10) REVERT: A 1117 THR cc_start: 0.8252 (p) cc_final: 0.7958 (t) REVERT: B 129 LYS cc_start: 0.7007 (tttt) cc_final: 0.6395 (tttt) REVERT: B 274 THR cc_start: 0.7618 (t) cc_final: 0.7348 (p) REVERT: B 386 LYS cc_start: 0.8590 (mttp) cc_final: 0.8261 (mtmm) REVERT: B 528 LYS cc_start: 0.8491 (tttm) cc_final: 0.7994 (ttmm) REVERT: B 619 GLU cc_start: 0.7225 (mt-10) cc_final: 0.6847 (mt-10) REVERT: B 703 ASN cc_start: 0.8112 (OUTLIER) cc_final: 0.7359 (p0) REVERT: B 737 ASP cc_start: 0.7254 (m-30) cc_final: 0.7019 (m-30) REVERT: B 790 LYS cc_start: 0.8141 (mtpp) cc_final: 0.7884 (mtpp) REVERT: B 817 PHE cc_start: 0.6887 (t80) cc_final: 0.6583 (t80) REVERT: B 884 SER cc_start: 0.8183 (p) cc_final: 0.7925 (p) REVERT: B 894 LEU cc_start: 0.8073 (mt) cc_final: 0.7861 (mt) REVERT: B 907 ASN cc_start: 0.8181 (m-40) cc_final: 0.7971 (t0) REVERT: B 955 ASN cc_start: 0.8255 (OUTLIER) cc_final: 0.8044 (t0) REVERT: B 979 ASP cc_start: 0.6730 (t70) cc_final: 0.6409 (t0) REVERT: B 1019 ARG cc_start: 0.7588 (ttp-110) cc_final: 0.7278 (ttp-110) REVERT: B 1030 SER cc_start: 0.8343 (m) cc_final: 0.8122 (p) REVERT: B 1037 SER cc_start: 0.8274 (t) cc_final: 0.7918 (p) REVERT: B 1045 LYS cc_start: 0.8161 (mptt) cc_final: 0.7750 (tptt) REVERT: B 1052 PHE cc_start: 0.8091 (m-80) cc_final: 0.7771 (m-80) REVERT: B 1068 VAL cc_start: 0.8093 (t) cc_final: 0.7783 (m) REVERT: B 1107 ARG cc_start: 0.7387 (mtt90) cc_final: 0.7132 (mtm-85) REVERT: B 1139 ASP cc_start: 0.7949 (t0) cc_final: 0.7243 (m-30) REVERT: B 1146 ASP cc_start: 0.7389 (m-30) cc_final: 0.7151 (t0) REVERT: C 43 PHE cc_start: 0.8017 (t80) cc_final: 0.7715 (t80) REVERT: C 99 ASN cc_start: 0.7845 (t0) cc_final: 0.7486 (t0) REVERT: C 169 GLU cc_start: 0.7913 (pt0) cc_final: 0.7432 (tm-30) REVERT: C 227 VAL cc_start: 0.8013 (p) cc_final: 0.7807 (t) REVERT: C 274 THR cc_start: 0.7758 (m) cc_final: 0.7159 (p) REVERT: C 314 GLN cc_start: 0.8180 (tt0) cc_final: 0.7962 (mt0) REVERT: C 556 ASN cc_start: 0.6825 (p0) cc_final: 0.6460 (p0) REVERT: C 562 PHE cc_start: 0.6594 (p90) cc_final: 0.6356 (p90) REVERT: C 583 GLU cc_start: 0.7649 (mm-30) cc_final: 0.7346 (mm-30) REVERT: C 643 PHE cc_start: 0.7274 (t80) cc_final: 0.7047 (t80) REVERT: C 663 ASP cc_start: 0.7521 (t70) cc_final: 0.7056 (t0) REVERT: C 673 SER cc_start: 0.7650 (t) cc_final: 0.6967 (m) REVERT: C 720 ILE cc_start: 0.8632 (mm) cc_final: 0.8017 (mt) REVERT: C 721 SER cc_start: 0.8176 (t) cc_final: 0.7583 (p) REVERT: C 736 VAL cc_start: 0.8212 (t) cc_final: 0.7391 (p) REVERT: C 776 LYS cc_start: 0.8061 (ttpt) cc_final: 0.7728 (ttpt) REVERT: C 790 LYS cc_start: 0.7996 (ttmm) cc_final: 0.7747 (ttpp) REVERT: C 819 GLU cc_start: 0.7758 (mt-10) cc_final: 0.7172 (mt-10) REVERT: C 820 ASP cc_start: 0.8198 (m-30) cc_final: 0.7917 (m-30) REVERT: C 866 THR cc_start: 0.7947 (t) cc_final: 0.7724 (p) REVERT: C 884 SER cc_start: 0.8292 (p) cc_final: 0.7415 (t) REVERT: C 921 LYS cc_start: 0.8061 (mtpp) cc_final: 0.7845 (mmmm) REVERT: C 931 ILE cc_start: 0.8023 (mm) cc_final: 0.7587 (mt) REVERT: C 955 ASN cc_start: 0.8353 (t0) cc_final: 0.8147 (t0) REVERT: C 960 ASN cc_start: 0.8011 (m-40) cc_final: 0.7710 (t0) REVERT: C 1051 SER cc_start: 0.8208 (t) cc_final: 0.7687 (p) REVERT: C 1054 GLN cc_start: 0.7534 (mt0) cc_final: 0.6985 (mm-40) REVERT: C 1097 SER cc_start: 0.8218 (p) cc_final: 0.7957 (p) REVERT: C 1111 GLU cc_start: 0.7991 (tt0) cc_final: 0.7456 (pt0) REVERT: C 1116 THR cc_start: 0.7511 (m) cc_final: 0.7160 (p) outliers start: 48 outliers final: 35 residues processed: 650 average time/residue: 0.7783 time to fit residues: 791.7674 Evaluate side-chains 652 residues out of total 2964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 614 time to evaluate : 2.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 614 ASP Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 774 GLN Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 1037 SER Chi-restraints excluded: chain A residue 1071 GLN Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain B residue 703 ASN Chi-restraints excluded: chain B residue 767 LEU Chi-restraints excluded: chain B residue 955 ASN Chi-restraints excluded: chain B residue 964 LYS Chi-restraints excluded: chain B residue 967 SER Chi-restraints excluded: chain B residue 993 ILE Chi-restraints excluded: chain C residue 596 SER Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 756 TYR Chi-restraints excluded: chain C residue 765 ARG Chi-restraints excluded: chain C residue 896 ILE Chi-restraints excluded: chain C residue 967 SER Chi-restraints excluded: chain D residue 84 MET Chi-restraints excluded: chain E residue 46 ARG Chi-restraints excluded: chain E residue 122 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 214 optimal weight: 0.9980 chunk 287 optimal weight: 0.6980 chunk 82 optimal weight: 0.0370 chunk 248 optimal weight: 7.9990 chunk 39 optimal weight: 20.0000 chunk 74 optimal weight: 0.4980 chunk 270 optimal weight: 1.9990 chunk 113 optimal weight: 4.9990 chunk 277 optimal weight: 0.6980 chunk 34 optimal weight: 0.8980 chunk 49 optimal weight: 9.9990 overall best weight: 0.5658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS ** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 717 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 774 GLN B 777 ASN ** B 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 GLN ** E 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4480 r_free = 0.4480 target = 0.194991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.153493 restraints weight = 168165.581| |-----------------------------------------------------------------------------| r_work (start): 0.3950 rms_B_bonded: 4.16 r_work: 0.3807 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3807 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3813 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3813 r_free = 0.3813 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3810 r_free = 0.3810 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3810 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7201 moved from start: 0.5387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.015 0.829 27939 Z= 1.005 Angle : 0.639 19.496 37997 Z= 0.337 Chirality : 0.049 1.403 4388 Planarity : 0.004 0.054 4870 Dihedral : 6.668 110.899 4580 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 20.65 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.17 % Favored : 92.80 % Rotamer: Outliers : 1.35 % Allowed : 18.33 % Favored : 80.32 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.55 (0.13), residues: 3378 helix: -0.66 (0.20), residues: 686 sheet: -1.67 (0.18), residues: 714 loop : -2.14 (0.13), residues: 1978 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP E 115 HIS 0.005 0.001 HIS A1064 PHE 0.030 0.002 PHE D 55 TYR 0.057 0.001 TYR A 904 ARG 0.007 0.000 ARG B 815 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15679.92 seconds wall clock time: 276 minutes 1.24 seconds (16561.24 seconds total)