Starting phenix.real_space_refine on Fri Feb 16 03:25:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zdh_11174/02_2024/6zdh_11174_trim.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zdh_11174/02_2024/6zdh_11174.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zdh_11174/02_2024/6zdh_11174.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zdh_11174/02_2024/6zdh_11174.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zdh_11174/02_2024/6zdh_11174_trim.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zdh_11174/02_2024/6zdh_11174_trim.pdb" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.038 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 144 5.16 5 C 21614 2.51 5 N 5602 2.21 5 O 6698 1.98 5 H 32513 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped 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 TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 43": "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 86": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" 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 PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 408": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A PHE 429": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 451": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 707": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 759": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 782": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 789": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 797": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 802": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 823": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 855": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 873": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 888": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 917": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 1047": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 1052": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 1075": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 1095": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" 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 37": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 408": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" 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 TYR 505": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 663": "OD1" <-> "OD2" Residue "B TYR 707": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 759": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 782": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 797": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 802": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 817": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 823": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 855": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 873": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 888": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 898": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 917": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 1047": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 1052": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 1095": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 1109": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 408": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C TYR 423": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 451": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 505": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 612": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 707": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 759": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 782": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 789": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 797": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 802": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 823": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 855": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" 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 TYR 917": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 970": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 1047": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 1052": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 1062": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 1075": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 1095": "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 "H PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H TYR 153": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 154": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H TYR 184": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L ARG 109": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L PHE 119": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 154": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 184": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ARG 109": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F PHE 119": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G PHE 154": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G TYR 184": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I ARG 109": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I PHE 119": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I TYR 193": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 66571 Number of models: 1 Model: "" Number of chains: 25 Chain: "A" Number of atoms: 15447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1002, 15447 Classifications: {'peptide': 1002} Link IDs: {'PTRANS': 49, 'TRANS': 952} Chain breaks: 7 Chain: "B" Number of atoms: 15447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1002, 15447 Classifications: {'peptide': 1002} Link IDs: {'PTRANS': 49, 'TRANS': 952} Chain breaks: 7 Chain: "C" Number of atoms: 15448 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1002, 15448 Classifications: {'peptide': 1002} Link IDs: {'PTRANS': 49, 'TRANS': 952} Chain breaks: 7 Chain: "H" Number of atoms: 3282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 3282 Classifications: {'peptide': 219} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 207} Chain breaks: 1 Chain: "L" Number of atoms: 3232 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 3232 Classifications: {'peptide': 215} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 204} Chain: "D" Number of atoms: 3282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 3282 Classifications: {'peptide': 219} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 207} Chain breaks: 1 Chain: "F" Number of atoms: 3233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 3233 Classifications: {'peptide': 215} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 204} Chain: "G" Number of atoms: 3281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 3281 Classifications: {'peptide': 219} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 207} Chain breaks: 1 Chain: "I" Number of atoms: 3233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 3233 Classifications: {'peptide': 215} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 204} Chain: "E" 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: "K" 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: "M" 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: "N" 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: "O" 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: "P" 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: "Q" 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: "R" 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: "S" 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: "T" 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: "U" 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: "V" 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: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "B" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "C" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Time building chain proxies: 21.36, per 1000 atoms: 0.32 Number of scatterers: 66571 At special positions: 0 Unit cell: (144.42, 159.36, 214.14, 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 144 16.00 O 6698 8.00 N 5602 7.00 C 21614 6.00 H 32513 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=54, symmetry=0 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=2.04 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=2.03 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 738 " - pdb=" SG CYS A 760 " 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=2.03 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 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 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 738 " - pdb=" SG CYS B 760 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 148 " - pdb=" SG CYS H 204 " distance=2.03 Simple disulfide: pdb=" SG CYS H 224 " - pdb=" SG CYS L 215 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS L 135 " - pdb=" SG CYS L 195 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 148 " - pdb=" SG CYS D 204 " distance=2.03 Simple disulfide: pdb=" SG CYS D 224 " - pdb=" SG CYS F 215 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.03 Simple disulfide: pdb=" SG CYS F 135 " - pdb=" SG CYS F 195 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS G 148 " - pdb=" SG CYS G 204 " distance=2.03 Simple disulfide: pdb=" SG CYS G 224 " - pdb=" SG CYS I 215 " distance=2.03 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.03 Simple disulfide: pdb=" SG CYS I 135 " - pdb=" SG CYS I 195 " 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 E 1 " - " NAG E 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 234 " " NAG A1303 " - " ASN A 282 " " NAG A1304 " - " ASN A 331 " " NAG A1305 " - " ASN A 616 " " NAG A1306 " - " ASN A 657 " " NAG A1307 " - " ASN A 709 " " NAG A1312 " - " ASN A1074 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 234 " " NAG B1303 " - " ASN B 282 " " NAG B1304 " - " ASN B 331 " " NAG B1305 " - " ASN B 616 " " NAG B1306 " - " ASN B 657 " " NAG B1307 " - " ASN B 709 " " NAG B1312 " - " ASN B1074 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 234 " " NAG C1303 " - " ASN C 282 " " NAG C1306 " - " ASN C 616 " " NAG C1307 " - " ASN C 657 " " NAG C1308 " - " ASN C 709 " " NAG C1313 " - " ASN C1074 " " NAG E 1 " - " ASN A 717 " " NAG J 1 " - " ASN A 801 " " NAG K 1 " - " ASN A1098 " " NAG M 1 " - " ASN A1134 " " NAG N 1 " - " ASN B 717 " " NAG O 1 " - " ASN B 801 " " NAG P 1 " - " ASN B1098 " " NAG Q 1 " - " ASN B1134 " " NAG R 1 " - " ASN C 331 " " NAG S 1 " - " ASN C 717 " " NAG T 1 " - " ASN C 801 " " NAG U 1 " - " ASN C1098 " " NAG V 1 " - " ASN C1134 " Time building additional restraints: 42.90 Conformation dependent library (CDL) restraints added in 4.9 seconds 8484 Ramachandran restraints generated. 4242 Oldfield, 0 Emsley, 4242 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8046 Finding SS restraints... Secondary structure from input PDB file: 86 helices and 74 sheets defined 20.5% alpha, 32.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.42 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 365 through 371 Processing helix chain 'A' and resid 383 through 388 removed outlier: 4.459A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 408 removed outlier: 4.438A pdb=" N ARG A 408 " --> pdb=" O GLY A 404 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 404 through 408' Processing helix chain 'A' and resid 416 through 422 removed outlier: 3.684A pdb=" N ASN A 422 " --> pdb=" O ILE A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 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: 3.920A pdb=" N LEU A 763 " --> pdb=" O PHE A 759 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ASN A 764 " --> pdb=" O CYS A 760 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.516A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 913 through 919 removed outlier: 3.541A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 966 removed outlier: 3.790A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU A 966 " --> pdb=" O LEU A 962 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.165A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL A1033 " --> pdb=" O MET A1029 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 4.198A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 365 through 371 removed outlier: 3.606A pdb=" N TYR B 369 " --> pdb=" O TYR B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 388 removed outlier: 4.021A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.265A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 759 removed outlier: 6.788A pdb=" N SER B 758 " --> pdb=" O GLN B 755 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N PHE B 759 " --> pdb=" O TYR B 756 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 755 through 759' Processing helix chain 'B' and resid 760 through 783 removed outlier: 3.931A pdb=" N ASN B 764 " --> pdb=" O CYS B 760 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 824 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.595A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 913 through 919 removed outlier: 3.604A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 966 removed outlier: 3.964A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU B 966 " --> pdb=" O LEU B 962 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1032 removed outlier: 4.310A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1147 removed outlier: 4.124A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 removed outlier: 3.880A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 371 removed outlier: 3.562A pdb=" N TYR C 369 " --> pdb=" O TYR C 365 " (cutoff:3.500A) Processing helix chain 'C' and resid 385 through 389 removed outlier: 3.957A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 408 removed outlier: 4.287A pdb=" N ARG C 408 " --> pdb=" O GLY C 404 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 404 through 408' Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 755 removed outlier: 3.687A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 756 through 759 Processing helix chain 'C' and resid 760 through 783 removed outlier: 3.776A pdb=" N ASN C 764 " --> pdb=" O CYS C 760 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 824 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.515A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 913 through 919 removed outlier: 3.514A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.924A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.507A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.238A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL C1033 " --> pdb=" O MET C1029 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1147 removed outlier: 4.230A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.904A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'H' and resid 164 through 166 No H-bonds generated for 'chain 'H' and resid 164 through 166' Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.716A pdb=" N PHE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'L' and resid 93 through 97 removed outlier: 3.772A pdb=" N LEU L 97 " --> pdb=" O THR L 94 " (cutoff:3.500A) Processing helix chain 'L' and resid 122 through 129 Processing helix chain 'L' and resid 184 through 189 Processing helix chain 'D' and resid 28 through 32 removed outlier: 3.522A pdb=" N TYR D 32 " --> pdb=" O PHE D 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 91 Processing helix chain 'D' and resid 164 through 166 No H-bonds generated for 'chain 'D' and resid 164 through 166' Processing helix chain 'F' and resid 79 through 83 removed outlier: 3.781A pdb=" N PHE F 83 " --> pdb=" O PRO F 80 " (cutoff:3.500A) Processing helix chain 'F' and resid 93 through 97 removed outlier: 3.914A pdb=" N LEU F 97 " --> pdb=" O THR F 94 " (cutoff:3.500A) Processing helix chain 'F' and resid 122 through 129 Processing helix chain 'F' and resid 184 through 189 Processing helix chain 'G' and resid 28 through 32 removed outlier: 3.659A pdb=" N TYR G 32 " --> pdb=" O PHE G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 87 through 91 Processing helix chain 'G' and resid 164 through 166 No H-bonds generated for 'chain 'G' and resid 164 through 166' Processing helix chain 'I' and resid 79 through 83 removed outlier: 3.682A pdb=" N PHE I 83 " --> pdb=" O PRO I 80 " (cutoff:3.500A) Processing helix chain 'I' and resid 93 through 97 removed outlier: 4.009A pdb=" N LEU I 97 " --> pdb=" O THR I 94 " (cutoff:3.500A) Processing helix chain 'I' and resid 122 through 129 Processing helix chain 'I' and resid 184 through 189 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.231A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 4.025A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N GLU C 324 " --> pdb=" O CYS C 538 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.825A 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: 6.406A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.895A pdb=" N ARG A 237 " --> pdb=" O PHE A 106 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N PHE A 106 " --> pdb=" O ARG A 237 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N GLN A 239 " --> pdb=" O TRP A 104 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N TRP A 104 " --> pdb=" O GLN A 239 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N LEU A 241 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 6.754A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.503A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (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 361 through 362 removed outlier: 4.062A pdb=" N CYS A 525 " --> pdb=" O CYS A 361 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 376 through 380 Processing sheet with id=AB2, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB3, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB4, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.504A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 712 through 715 Processing sheet with id=AB6, first strand: chain 'A' and resid 718 through 728 removed outlier: 5.889A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.592A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.300A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AC1, first strand: chain 'B' and resid 28 through 30 removed outlier: 8.292A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.886A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.487A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 9.474A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.960A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 84 through 85 removed outlier: 6.493A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 84 through 85 removed outlier: 6.974A pdb=" N ARG B 237 " --> pdb=" O PHE B 106 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N PHE B 106 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N GLN B 239 " --> pdb=" O TRP B 104 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N TRP B 104 " --> pdb=" O GLN B 239 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N LEU B 241 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 311 through 319 removed outlier: 6.634A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 324 through 328 removed outlier: 6.721A pdb=" N GLU B 324 " --> pdb=" O ASN B 540 " (cutoff:3.500A) removed outlier: 8.147A pdb=" N ASN B 542 " --> pdb=" O GLU B 324 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ILE B 326 " --> pdb=" O ASN B 542 " (cutoff:3.500A) removed outlier: 5.424A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AC8, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC9, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.430A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 711 through 715 Processing sheet with id=AD2, first strand: chain 'B' and resid 718 through 728 removed outlier: 6.955A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD4, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.120A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 28 through 31 removed outlier: 4.141A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 8.138A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.885A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 84 through 85 removed outlier: 6.700A pdb=" N LEU C 141 " --> pdb=" O LEU C 244 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 84 through 85 removed outlier: 6.974A pdb=" N ARG C 237 " --> pdb=" O PHE C 106 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N PHE C 106 " --> pdb=" O ARG C 237 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N GLN C 239 " --> pdb=" O TRP C 104 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N TRP C 104 " --> pdb=" O GLN C 239 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N LEU C 241 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 311 through 319 removed outlier: 7.013A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 354 through 358 Processing sheet with id=AE2, first strand: chain 'C' and resid 391 through 392 Processing sheet with id=AE3, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE4, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.501A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.580A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 711 through 715 Processing sheet with id=AE7, first strand: chain 'C' and resid 718 through 728 removed outlier: 6.946A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.585A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.487A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AF2, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.746A pdb=" N MET H 34 " --> pdb=" O VAL H 50 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N VAL H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'H' and resid 128 through 132 removed outlier: 6.018A pdb=" N TYR H 184 " --> pdb=" O ASP H 152 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'H' and resid 128 through 132 removed outlier: 6.018A pdb=" N TYR H 184 " --> pdb=" O ASP H 152 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'H' and resid 159 through 162 removed outlier: 4.495A pdb=" N TYR H 202 " --> pdb=" O VAL H 219 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'L' and resid 4 through 7 removed outlier: 12.227A pdb=" N CYS L 23 " --> pdb=" O THR L 74 " (cutoff:3.500A) removed outlier: 11.197A pdb=" N THR L 74 " --> pdb=" O CYS L 23 " (cutoff:3.500A) removed outlier: 12.172A pdb=" N ALA L 25 " --> pdb=" O THR L 72 " (cutoff:3.500A) removed outlier: 11.989A pdb=" N THR L 72 " --> pdb=" O ALA L 25 " (cutoff:3.500A) removed outlier: 11.122A pdb=" N GLN L 27 " --> pdb=" O ASP L 70 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ASP L 70 " --> pdb=" O GLN L 27 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.661A pdb=" N LEU L 11 " --> pdb=" O GLU L 106 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N TYR L 86 " --> pdb=" O THR L 103 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'L' and resid 115 through 119 removed outlier: 5.217A pdb=" N SER L 132 " --> pdb=" O LEU L 182 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N LEU L 182 " --> pdb=" O SER L 132 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N VAL L 134 " --> pdb=" O LEU L 180 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N LEU L 180 " --> pdb=" O VAL L 134 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N LEU L 136 " --> pdb=" O SER L 178 " (cutoff:3.500A) removed outlier: 7.356A pdb=" N SER L 178 " --> pdb=" O LEU L 136 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N ASN L 138 " --> pdb=" O LEU L 176 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N LEU L 176 " --> pdb=" O ASN L 138 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'L' and resid 154 through 156 removed outlier: 4.360A pdb=" N TRP L 149 " --> pdb=" O GLN L 156 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'D' and resid 3 through 7 Processing sheet with id=AG2, first strand: chain 'D' and resid 11 through 12 removed outlier: 5.953A pdb=" N ARG D 38 " --> pdb=" O TRP D 47 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N TRP D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'D' and resid 128 through 132 removed outlier: 6.006A pdb=" N TYR D 184 " --> pdb=" O ASP D 152 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'D' and resid 128 through 132 removed outlier: 6.006A pdb=" N TYR D 184 " --> pdb=" O ASP D 152 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'D' and resid 159 through 162 removed outlier: 4.413A pdb=" N TYR D 202 " --> pdb=" O VAL D 219 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'F' and resid 4 through 7 removed outlier: 12.258A pdb=" N CYS F 23 " --> pdb=" O THR F 74 " (cutoff:3.500A) removed outlier: 11.225A pdb=" N THR F 74 " --> pdb=" O CYS F 23 " (cutoff:3.500A) removed outlier: 12.084A pdb=" N ALA F 25 " --> pdb=" O THR F 72 " (cutoff:3.500A) removed outlier: 11.899A pdb=" N THR F 72 " --> pdb=" O ALA F 25 " (cutoff:3.500A) removed outlier: 11.101A pdb=" N GLN F 27 " --> pdb=" O ASP F 70 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N ASP F 70 " --> pdb=" O GLN F 27 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLY F 68 " --> pdb=" O ILE F 29 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'F' and resid 10 through 13 removed outlier: 6.759A pdb=" N LEU F 11 " --> pdb=" O GLU F 106 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N TYR F 86 " --> pdb=" O THR F 103 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N LEU F 33 " --> pdb=" O TYR F 49 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N TYR F 49 " --> pdb=" O LEU F 33 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N TRP F 35 " --> pdb=" O LEU F 47 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'F' and resid 10 through 13 removed outlier: 6.759A pdb=" N LEU F 11 " --> pdb=" O GLU F 106 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N TYR F 86 " --> pdb=" O THR F 103 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N THR F 98 " --> pdb=" O GLN F 90 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'F' and resid 115 through 119 removed outlier: 5.223A pdb=" N SER F 132 " --> pdb=" O LEU F 182 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N LEU F 182 " --> pdb=" O SER F 132 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N VAL F 134 " --> pdb=" O LEU F 180 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N LEU F 180 " --> pdb=" O VAL F 134 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N LEU F 136 " --> pdb=" O SER F 178 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N SER F 178 " --> pdb=" O LEU F 136 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N ASN F 138 " --> pdb=" O LEU F 176 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N LEU F 176 " --> pdb=" O ASN F 138 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'F' and resid 154 through 156 removed outlier: 4.316A pdb=" N TRP F 149 " --> pdb=" O GLN F 156 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'G' and resid 3 through 7 Processing sheet with id=AH3, first strand: chain 'G' and resid 11 through 12 removed outlier: 6.057A pdb=" N ARG G 38 " --> pdb=" O TRP G 47 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N TRP G 47 " --> pdb=" O ARG G 38 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'G' and resid 128 through 132 removed outlier: 6.156A pdb=" N TYR G 184 " --> pdb=" O ASP G 152 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'G' and resid 128 through 132 removed outlier: 6.156A pdb=" N TYR G 184 " --> pdb=" O ASP G 152 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'G' and resid 159 through 162 removed outlier: 3.963A pdb=" N TYR G 202 " --> pdb=" O VAL G 219 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'I' and resid 4 through 7 removed outlier: 12.293A pdb=" N CYS I 23 " --> pdb=" O THR I 74 " (cutoff:3.500A) removed outlier: 11.257A pdb=" N THR I 74 " --> pdb=" O CYS I 23 " (cutoff:3.500A) removed outlier: 12.141A pdb=" N ALA I 25 " --> pdb=" O THR I 72 " (cutoff:3.500A) removed outlier: 11.982A pdb=" N THR I 72 " --> pdb=" O ALA I 25 " (cutoff:3.500A) removed outlier: 11.170A pdb=" N GLN I 27 " --> pdb=" O ASP I 70 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ASP I 70 " --> pdb=" O GLN I 27 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'I' and resid 10 through 13 removed outlier: 6.723A pdb=" N LEU I 11 " --> pdb=" O GLU I 106 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N TYR I 86 " --> pdb=" O THR I 103 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N LEU I 33 " --> pdb=" O TYR I 49 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N TYR I 49 " --> pdb=" O LEU I 33 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N TRP I 35 " --> pdb=" O LEU I 47 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'I' and resid 10 through 13 removed outlier: 6.723A pdb=" N LEU I 11 " --> pdb=" O GLU I 106 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N TYR I 86 " --> pdb=" O THR I 103 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N THR I 98 " --> pdb=" O GLN I 90 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'I' and resid 115 through 119 removed outlier: 5.229A pdb=" N SER I 132 " --> pdb=" O LEU I 182 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N LEU I 182 " --> pdb=" O SER I 132 " (cutoff:3.500A) removed outlier: 5.670A pdb=" N VAL I 134 " --> pdb=" O LEU I 180 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N LEU I 180 " --> pdb=" O VAL I 134 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N LEU I 136 " --> pdb=" O SER I 178 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N SER I 178 " --> pdb=" O LEU I 136 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N ASN I 138 " --> pdb=" O LEU I 176 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N LEU I 176 " --> pdb=" O ASN I 138 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'I' and resid 154 through 156 removed outlier: 4.258A pdb=" N TRP I 149 " --> pdb=" O GLN I 156 " (cutoff:3.500A) 1409 hydrogen bonds defined for protein. 3741 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: 29.82 Time building geometry restraints manager: 44.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 32508 1.03 - 1.23: 267 1.23 - 1.43: 14551 1.43 - 1.62: 19821 1.62 - 1.82: 177 Bond restraints: 67324 Sorted by residual: bond pdb=" C VAL C 860 " pdb=" N LEU C 861 " ideal model delta sigma weight residual 1.330 1.286 0.044 1.47e-02 4.63e+03 8.81e+00 bond pdb=" C1 NAG B1304 " pdb=" O5 NAG B1304 " ideal model delta sigma weight residual 1.406 1.443 -0.037 2.00e-02 2.50e+03 3.38e+00 bond pdb=" C1 NAG A1304 " pdb=" O5 NAG A1304 " ideal model delta sigma weight residual 1.406 1.443 -0.037 2.00e-02 2.50e+03 3.37e+00 bond pdb=" C1 NAG B1312 " pdb=" O5 NAG B1312 " ideal model delta sigma weight residual 1.406 1.441 -0.035 2.00e-02 2.50e+03 3.07e+00 bond pdb=" C1 NAG A1312 " pdb=" O5 NAG A1312 " ideal model delta sigma weight residual 1.406 1.441 -0.035 2.00e-02 2.50e+03 3.05e+00 ... (remaining 67319 not shown) Histogram of bond angle deviations from ideal: 100.07 - 106.86: 1103 106.86 - 113.64: 79015 113.64 - 120.42: 21806 120.42 - 127.21: 18735 127.21 - 133.99: 336 Bond angle restraints: 120995 Sorted by residual: angle pdb=" N THR B 333 " pdb=" CA THR B 333 " pdb=" C THR B 333 " ideal model delta sigma weight residual 113.55 109.41 4.14 1.26e+00 6.30e-01 1.08e+01 angle pdb=" N CYS B1032 " pdb=" CA CYS B1032 " pdb=" C CYS B1032 " ideal model delta sigma weight residual 113.18 108.96 4.22 1.33e+00 5.65e-01 1.01e+01 angle pdb=" CA SER C 31 " pdb=" C SER C 31 " pdb=" O SER C 31 " ideal model delta sigma weight residual 122.37 118.75 3.62 1.15e+00 7.56e-01 9.90e+00 angle pdb=" N CYS C1032 " pdb=" CA CYS C1032 " pdb=" C CYS C1032 " ideal model delta sigma weight residual 113.18 109.08 4.10 1.33e+00 5.65e-01 9.49e+00 angle pdb=" CA SER A 31 " pdb=" C SER A 31 " pdb=" O SER A 31 " ideal model delta sigma weight residual 122.37 118.87 3.50 1.15e+00 7.56e-01 9.24e+00 ... (remaining 120990 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.45: 31199 17.45 - 34.90: 1266 34.90 - 52.34: 442 52.34 - 69.79: 131 69.79 - 87.24: 14 Dihedral angle restraints: 33052 sinusoidal: 18112 harmonic: 14940 Sorted by residual: dihedral pdb=" CB CYS C1032 " pdb=" SG CYS C1032 " pdb=" SG CYS C1043 " pdb=" CB CYS C1043 " ideal model delta sinusoidal sigma weight residual -86.00 -157.86 71.86 1 1.00e+01 1.00e-02 6.61e+01 dihedral pdb=" CB CYS B1032 " pdb=" SG CYS B1032 " pdb=" SG CYS B1043 " pdb=" CB CYS B1043 " ideal model delta sinusoidal sigma weight residual -86.00 -156.21 70.21 1 1.00e+01 1.00e-02 6.35e+01 dihedral pdb=" CB CYS A1032 " pdb=" SG CYS A1032 " pdb=" SG CYS A1043 " pdb=" CB CYS A1043 " ideal model delta sinusoidal sigma weight residual -86.00 -155.75 69.75 1 1.00e+01 1.00e-02 6.28e+01 ... (remaining 33049 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 3255 0.029 - 0.059: 1515 0.059 - 0.088: 271 0.088 - 0.117: 396 0.117 - 0.147: 88 Chirality restraints: 5525 Sorted by residual: chirality pdb=" CA ILE A 119 " pdb=" N ILE A 119 " pdb=" C ILE A 119 " pdb=" CB ILE A 119 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.37e-01 chirality pdb=" CA VAL I 58 " pdb=" N VAL I 58 " pdb=" C VAL I 58 " pdb=" CB VAL I 58 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.95e-01 chirality pdb=" CA ILE A 434 " pdb=" N ILE A 434 " pdb=" C ILE A 434 " pdb=" CB ILE A 434 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.94e-01 ... (remaining 5522 not shown) Planarity restraints: 10137 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN B 122 " 0.014 2.00e-02 2.50e+03 2.74e-02 7.51e+00 pdb=" C ASN B 122 " -0.047 2.00e-02 2.50e+03 pdb=" O ASN B 122 " 0.018 2.00e-02 2.50e+03 pdb=" N ALA B 123 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN C 122 " 0.010 2.00e-02 2.50e+03 2.04e-02 4.14e+00 pdb=" C ASN C 122 " -0.035 2.00e-02 2.50e+03 pdb=" O ASN C 122 " 0.013 2.00e-02 2.50e+03 pdb=" N ALA C 123 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU B 84 " -0.033 5.00e-02 4.00e+02 4.94e-02 3.91e+00 pdb=" N PRO B 85 " 0.085 5.00e-02 4.00e+02 pdb=" CA PRO B 85 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 85 " -0.027 5.00e-02 4.00e+02 ... (remaining 10134 not shown) Histogram of nonbonded interaction distances: 1.56 - 2.16: 2272 2.16 - 2.77: 129871 2.77 - 3.38: 177422 3.38 - 3.99: 239855 3.99 - 4.60: 368794 Nonbonded interactions: 918214 Sorted by model distance: nonbonded pdb=" O ASN B 122 " pdb=" H THR B 124 " model vdw 1.555 1.850 nonbonded pdb=" O ASN C 122 " pdb=" H THR C 124 " model vdw 1.556 1.850 nonbonded pdb=" O ASN A 122 " pdb=" H THR A 124 " model vdw 1.564 1.850 nonbonded pdb=" HG1 THR C 393 " pdb=" O GLU C 516 " model vdw 1.569 1.850 nonbonded pdb=" H LYS C 462 " pdb=" OE1 GLU C 465 " model vdw 1.575 1.850 ... (remaining 918209 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 27 through 330 or (resid 331 and (name N or name CA or nam \ e C or name O or name CB or name CG or name OD1 or name ND2 or name H or name HA \ or name HB2 or name HB3)) or resid 332 through 476 or (resid 477 and (name N or \ name CA or name C or name O or name CB or name OG or name HA or name HB2 or nam \ e HB3)) or resid 478 through 716 or (resid 717 and (name N or name CA or name C \ or name O or name CB or name CG or name OD1 or name ND2 or name H or name HA or \ name HB2 or name HB3)) or resid 718 through 1147 or resid 1301 through 1307)) selection = (chain 'B' and (resid 27 through 330 or (resid 331 and (name N or name CA or nam \ e C or name O or name CB or name CG or name OD1 or name ND2 or name H or name HA \ or name HB2 or name HB3)) or resid 332 through 615 or (resid 616 and (name N or \ name CA or name C or name O or name CB or name CG or name OD1 or name ND2 or na \ me H or name HA or name HB2 or name HB3)) or resid 617 through 800 or (resid 801 \ and (name N or name CA or name C or name O or name CB or name CG or name OD1 or \ name ND2 or name H or name HA or name HB2 or name HB3)) or resid 802 through 10 \ 73 or (resid 1074 and (name N or name CA or name C or name O or name CB or name \ CG or name OD1 or name ND2 or name H or name HA or name HB2 or name HB3)) or res \ id 1075 through 1147 or resid 1301 through 1307)) selection = (chain 'C' and (resid 27 through 476 or (resid 477 and (name N or name CA or nam \ e C or name O or name CB or name OG or name HA or name HB2 or name HB3)) or resi \ d 478 through 656 or (resid 657 and (name N or name CA or name C or name O or na \ me CB or name CG or name OD1 or name ND2 or name H or name HA or name HB2 or nam \ e HB3)) or resid 658 through 708 or (resid 709 and (name N or name CA or name C \ or name O or name CB or name CG or name OD1 or name ND2 or name H or name HA or \ name HB2 or name HB3)) or resid 710 through 1073 or (resid 1074 and (name N or n \ ame CA or name C or name O or name CB or name CG or name OD1 or name ND2 or name \ H or name HA or name HB2 or name HB3)) or resid 1075 through 1147 or resid 1301 \ through 1313)) } ncs_group { reference = (chain 'D' and (resid 1 through 198 or (resid 199 and (name N or name CA or name \ C or name O or name CB or name OG1 or name CG2 or name H or name HA or name HB \ or name HG21 or name HG22 or name HG23)) or resid 200 through 224)) selection = chain 'G' selection = (chain 'H' and (resid 1 through 198 or (resid 199 and (name N or name CA or name \ C or name O or name CB or name OG1 or name CG2 or name H or name HA or name HB \ or name HG21 or name HG22 or name HG23)) or resid 200 through 224)) } ncs_group { reference = chain 'E' selection = chain 'J' selection = chain 'K' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' } ncs_group { reference = (chain 'F' and (resid 1 through 214 or (resid 215 and (name N or name CA or name \ C or name O or name CB or name SG or name H or name HA or name HB2 or name HB3) \ ))) selection = (chain 'I' and (resid 1 through 214 or (resid 215 and (name N or name CA or name \ C or name O or name CB or name SG or name H or name HA or name HB2 or name HB3) \ ))) selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.580 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: 0.750 Extract box with map and model: 30.830 Check model and map are aligned: 0.730 Set scattering table: 0.470 Process input model: 165.300 Find NCS groups from input model: 3.250 Set up NCS constraints: 0.540 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:2.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 212.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 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 : 0.004 0.044 34811 Z= 0.253 Angle : 0.573 6.641 47353 Z= 0.329 Chirality : 0.043 0.147 5525 Planarity : 0.003 0.049 6037 Dihedral : 9.664 87.238 13197 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.08 % Favored : 95.90 % Rotamer: Outliers : 0.83 % Allowed : 3.20 % Favored : 95.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.13), residues: 4242 helix: 1.24 (0.21), residues: 678 sheet: 0.30 (0.14), residues: 1329 loop : -0.42 (0.13), residues: 2235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 47 HIS 0.006 0.001 HIS H 35 PHE 0.014 0.001 PHE C 238 TYR 0.012 0.001 TYR A1067 ARG 0.003 0.000 ARG H 72 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8484 Ramachandran restraints generated. 4242 Oldfield, 0 Emsley, 4242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8484 Ramachandran restraints generated. 4242 Oldfield, 0 Emsley, 4242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 477 is missing expected H atoms. Skipping. Residue THR 199 is missing expected H atoms. Skipping. Evaluate side-chains 671 residues out of total 3747 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 640 time to evaluate : 4.103 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 54 LEU cc_start: 0.8664 (mt) cc_final: 0.8286 (mp) REVERT: A 307 THR cc_start: 0.8457 (m) cc_final: 0.8158 (p) REVERT: A 421 TYR cc_start: 0.8079 (m-10) cc_final: 0.7401 (m-10) REVERT: A 867 ASP cc_start: 0.8028 (m-30) cc_final: 0.7727 (m-30) REVERT: A 1135 ASN cc_start: 0.8083 (t0) cc_final: 0.7774 (t0) REVERT: B 427 ASP cc_start: 0.7711 (m-30) cc_final: 0.7037 (t70) REVERT: B 466 ARG cc_start: 0.7817 (ttt180) cc_final: 0.7530 (ttm-80) REVERT: C 308 VAL cc_start: 0.8701 (t) cc_final: 0.8431 (t) REVERT: C 396 TYR cc_start: 0.6264 (m-10) cc_final: 0.5779 (m-80) REVERT: C 571 ASP cc_start: 0.6608 (t70) cc_final: 0.6377 (t70) REVERT: C 710 ASN cc_start: 0.8672 (p0) cc_final: 0.8470 (p0) REVERT: C 867 ASP cc_start: 0.8195 (m-30) cc_final: 0.7933 (m-30) REVERT: D 154 PHE cc_start: 0.8731 (t80) cc_final: 0.8451 (t80) REVERT: F 59 PRO cc_start: 0.7581 (Cg_exo) cc_final: 0.7366 (Cg_endo) REVERT: F 139 ASN cc_start: 0.8743 (m-40) cc_final: 0.8467 (m110) REVERT: G 99 ASP cc_start: 0.7112 (t70) cc_final: 0.6313 (p0) outliers start: 31 outliers final: 14 residues processed: 665 average time/residue: 0.9689 time to fit residues: 1010.8242 Evaluate side-chains 362 residues out of total 3747 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 348 time to evaluate : 3.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 773 GLU Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 657 ASN Chi-restraints excluded: chain H residue 50 VAL Chi-restraints excluded: chain H residue 105 VAL Chi-restraints excluded: chain H residue 217 LYS Chi-restraints excluded: chain G residue 105 VAL Chi-restraints excluded: chain G residue 217 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 359 optimal weight: 0.9990 chunk 322 optimal weight: 7.9990 chunk 179 optimal weight: 4.9990 chunk 110 optimal weight: 0.0070 chunk 217 optimal weight: 2.9990 chunk 172 optimal weight: 0.7980 chunk 333 optimal weight: 7.9990 chunk 129 optimal weight: 3.9990 chunk 203 optimal weight: 0.5980 chunk 248 optimal weight: 2.9990 chunk 386 optimal weight: 9.9990 overall best weight: 1.0802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 ASN A 317 ASN ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN ** B 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 655 HIS C 196 ASN C 207 HIS C 955 ASN C1010 GLN ** L 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 39 GLN ** D 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.1690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 34811 Z= 0.240 Angle : 0.521 13.751 47353 Z= 0.276 Chirality : 0.043 0.248 5525 Planarity : 0.004 0.062 6037 Dihedral : 6.203 58.181 5666 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.01 % Favored : 95.97 % Rotamer: Outliers : 1.23 % Allowed : 8.11 % Favored : 90.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.13), residues: 4242 helix: 1.46 (0.20), residues: 717 sheet: 0.17 (0.14), residues: 1314 loop : -0.42 (0.14), residues: 2211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 47 HIS 0.003 0.001 HIS H 35 PHE 0.016 0.001 PHE I 71 TYR 0.020 0.001 TYR F 49 ARG 0.005 0.000 ARG B 815 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8484 Ramachandran restraints generated. 4242 Oldfield, 0 Emsley, 4242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8484 Ramachandran restraints generated. 4242 Oldfield, 0 Emsley, 4242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 477 is missing expected H atoms. Skipping. Residue THR 199 is missing expected H atoms. Skipping. Evaluate side-chains 415 residues out of total 3747 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 369 time to evaluate : 4.411 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: symmetry clash revert: 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 169 GLU cc_start: 0.8123 (tt0) cc_final: 0.7648 (tm-30) REVERT: A 302 THR cc_start: 0.8878 (m) cc_final: 0.8635 (p) REVERT: A 307 THR cc_start: 0.8464 (m) cc_final: 0.8132 (p) REVERT: A 421 TYR cc_start: 0.8158 (m-10) cc_final: 0.7718 (m-80) REVERT: A 867 ASP cc_start: 0.7944 (m-30) cc_final: 0.7689 (m-30) REVERT: A 1135 ASN cc_start: 0.7974 (t0) cc_final: 0.7686 (t0) REVERT: B 52 GLN cc_start: 0.8236 (tm-30) cc_final: 0.8008 (tm-30) REVERT: B 427 ASP cc_start: 0.7746 (m-30) cc_final: 0.7075 (t70) REVERT: B 466 ARG cc_start: 0.7850 (ttt180) cc_final: 0.7548 (ttm-80) REVERT: C 396 TYR cc_start: 0.6243 (m-10) cc_final: 0.5801 (m-80) REVERT: C 571 ASP cc_start: 0.6608 (t70) cc_final: 0.6366 (t70) REVERT: C 710 ASN cc_start: 0.8645 (p0) cc_final: 0.8431 (p0) REVERT: C 855 PHE cc_start: 0.7750 (m-10) cc_final: 0.7499 (m-10) REVERT: C 867 ASP cc_start: 0.8155 (m-30) cc_final: 0.7882 (m-30) REVERT: C 1037 SER cc_start: 0.8798 (t) cc_final: 0.8241 (p) REVERT: L 18 ARG cc_start: 0.8215 (tmm-80) cc_final: 0.8015 (tmm-80) REVERT: D 99 ASP cc_start: 0.8587 (t70) cc_final: 0.8097 (t70) REVERT: D 154 PHE cc_start: 0.8711 (t80) cc_final: 0.8450 (t80) REVERT: F 73 LEU cc_start: 0.8339 (tp) cc_final: 0.8020 (tp) REVERT: F 139 ASN cc_start: 0.8707 (m-40) cc_final: 0.8402 (m110) REVERT: G 99 ASP cc_start: 0.7180 (t70) cc_final: 0.6279 (p0) REVERT: G 109 ASP cc_start: 0.7606 (t70) cc_final: 0.7397 (t70) REVERT: I 47 LEU cc_start: 0.8788 (mt) cc_final: 0.8522 (mm) REVERT: I 138 ASN cc_start: 0.8886 (m-40) cc_final: 0.8603 (m-40) outliers start: 46 outliers final: 28 residues processed: 402 average time/residue: 0.9604 time to fit residues: 610.5469 Evaluate side-chains 350 residues out of total 3747 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 322 time to evaluate : 3.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ASN Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 196 ASN Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 657 ASN Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain H residue 33 ASP Chi-restraints excluded: chain H residue 50 VAL Chi-restraints excluded: chain H residue 105 VAL Chi-restraints excluded: chain H residue 217 LYS Chi-restraints excluded: chain G residue 27 PHE Chi-restraints excluded: chain G residue 105 VAL Chi-restraints excluded: chain G residue 178 LEU Chi-restraints excluded: chain G residue 217 LYS Chi-restraints excluded: chain I residue 4 MET Chi-restraints excluded: chain I residue 117 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 214 optimal weight: 0.0370 chunk 120 optimal weight: 0.8980 chunk 321 optimal weight: 5.9990 chunk 263 optimal weight: 4.9990 chunk 106 optimal weight: 1.9990 chunk 387 optimal weight: 9.9990 chunk 418 optimal weight: 40.0000 chunk 345 optimal weight: 10.0000 chunk 384 optimal weight: 9.9990 chunk 132 optimal weight: 4.9990 chunk 310 optimal weight: 0.9980 overall best weight: 1.7862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 ASN ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 69 HIS B 196 ASN ** B 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 134 GLN C 207 HIS C 965 GLN ** L 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.2101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.110 34811 Z= 0.355 Angle : 0.553 15.038 47353 Z= 0.295 Chirality : 0.044 0.301 5525 Planarity : 0.004 0.051 6037 Dihedral : 6.034 57.992 5661 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.90 % Favored : 95.07 % Rotamer: Outliers : 1.55 % Allowed : 8.81 % Favored : 89.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.13), residues: 4242 helix: 1.40 (0.19), residues: 717 sheet: -0.01 (0.14), residues: 1308 loop : -0.51 (0.13), residues: 2217 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP H 47 HIS 0.004 0.001 HIS A1064 PHE 0.029 0.002 PHE F 62 TYR 0.019 0.001 TYR F 49 ARG 0.005 0.000 ARG C 983 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8484 Ramachandran restraints generated. 4242 Oldfield, 0 Emsley, 4242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8484 Ramachandran restraints generated. 4242 Oldfield, 0 Emsley, 4242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 477 is missing expected H atoms. Skipping. Residue THR 199 is missing expected H atoms. Skipping. Evaluate side-chains 394 residues out of total 3747 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 336 time to evaluate : 3.854 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: symmetry clash revert: symmetry clash revert: 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 54 LEU cc_start: 0.8545 (mt) cc_final: 0.8345 (mp) REVERT: A 302 THR cc_start: 0.8902 (m) cc_final: 0.8677 (p) REVERT: A 307 THR cc_start: 0.8409 (m) cc_final: 0.8127 (p) REVERT: A 421 TYR cc_start: 0.8163 (m-10) cc_final: 0.7730 (m-80) REVERT: A 614 ASP cc_start: 0.6870 (t0) cc_final: 0.6621 (t0) REVERT: B 427 ASP cc_start: 0.7716 (m-30) cc_final: 0.7048 (t70) REVERT: B 466 ARG cc_start: 0.7859 (ttt180) cc_final: 0.7526 (ttm-80) REVERT: C 396 TYR cc_start: 0.6459 (m-10) cc_final: 0.5942 (m-80) REVERT: C 571 ASP cc_start: 0.6503 (t70) cc_final: 0.6230 (t70) REVERT: C 710 ASN cc_start: 0.8709 (p0) cc_final: 0.8478 (p0) REVERT: C 867 ASP cc_start: 0.8213 (m-30) cc_final: 0.7952 (m-30) REVERT: L 18 ARG cc_start: 0.8212 (tmm-80) cc_final: 0.7936 (tmm-80) REVERT: D 99 ASP cc_start: 0.8430 (t70) cc_final: 0.8027 (t70) REVERT: D 154 PHE cc_start: 0.8705 (t80) cc_final: 0.8443 (t80) REVERT: F 139 ASN cc_start: 0.8648 (m-40) cc_final: 0.8319 (m110) REVERT: G 34 MET cc_start: 0.7304 (tpt) cc_final: 0.7092 (tpt) REVERT: G 109 ASP cc_start: 0.7695 (t70) cc_final: 0.7425 (t70) REVERT: I 138 ASN cc_start: 0.8949 (m-40) cc_final: 0.8054 (m-40) REVERT: I 139 ASN cc_start: 0.8976 (m-40) cc_final: 0.8139 (p0) outliers start: 58 outliers final: 44 residues processed: 384 average time/residue: 0.9776 time to fit residues: 597.4505 Evaluate side-chains 352 residues out of total 3747 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 308 time to evaluate : 3.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 125 ASN Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 388 ASN Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 564 GLN Chi-restraints excluded: chain A residue 748 GLU Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain A residue 1126 CYS Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 578 ASP Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 703 ASN Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 657 ASN Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain H residue 33 ASP Chi-restraints excluded: chain H residue 50 VAL Chi-restraints excluded: chain H residue 105 VAL Chi-restraints excluded: chain H residue 217 LYS Chi-restraints excluded: chain D residue 105 VAL Chi-restraints excluded: chain G residue 27 PHE Chi-restraints excluded: chain G residue 105 VAL Chi-restraints excluded: chain G residue 217 LYS Chi-restraints excluded: chain I residue 75 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 382 optimal weight: 7.9990 chunk 291 optimal weight: 0.9990 chunk 201 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 184 optimal weight: 3.9990 chunk 260 optimal weight: 0.5980 chunk 388 optimal weight: 8.9990 chunk 411 optimal weight: 30.0000 chunk 203 optimal weight: 0.9980 chunk 368 optimal weight: 4.9990 chunk 110 optimal weight: 0.5980 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 965 GLN C 87 ASN C 207 HIS C 955 ASN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.2298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.089 34811 Z= 0.206 Angle : 0.500 15.191 47353 Z= 0.263 Chirality : 0.043 0.322 5525 Planarity : 0.003 0.052 6037 Dihedral : 5.743 59.311 5661 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.70 % Favored : 96.28 % Rotamer: Outliers : 1.33 % Allowed : 9.53 % Favored : 89.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.13), residues: 4242 helix: 1.62 (0.20), residues: 720 sheet: 0.03 (0.14), residues: 1299 loop : -0.45 (0.13), residues: 2223 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 47 HIS 0.003 0.001 HIS H 35 PHE 0.013 0.001 PHE F 62 TYR 0.017 0.001 TYR F 49 ARG 0.004 0.000 ARG A 815 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8484 Ramachandran restraints generated. 4242 Oldfield, 0 Emsley, 4242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8484 Ramachandran restraints generated. 4242 Oldfield, 0 Emsley, 4242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 477 is missing expected H atoms. Skipping. Residue THR 199 is missing expected H atoms. Skipping. Evaluate side-chains 384 residues out of total 3747 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 334 time to evaluate : 3.874 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: 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 302 THR cc_start: 0.8870 (m) cc_final: 0.8663 (p) REVERT: A 307 THR cc_start: 0.8463 (m) cc_final: 0.8175 (p) REVERT: A 421 TYR cc_start: 0.8144 (m-10) cc_final: 0.7710 (m-80) REVERT: A 614 ASP cc_start: 0.6811 (t0) cc_final: 0.6547 (t0) REVERT: A 759 PHE cc_start: 0.7391 (OUTLIER) cc_final: 0.6939 (t80) REVERT: A 1135 ASN cc_start: 0.7924 (t0) cc_final: 0.7636 (t0) REVERT: B 427 ASP cc_start: 0.7708 (m-30) cc_final: 0.7056 (t70) REVERT: B 466 ARG cc_start: 0.7866 (ttt180) cc_final: 0.7563 (ttm-80) REVERT: C 396 TYR cc_start: 0.6491 (m-10) cc_final: 0.6002 (m-80) REVERT: C 571 ASP cc_start: 0.6580 (t70) cc_final: 0.6312 (t70) REVERT: C 710 ASN cc_start: 0.8660 (p0) cc_final: 0.8439 (p0) REVERT: C 867 ASP cc_start: 0.8118 (m-30) cc_final: 0.7849 (m-30) REVERT: C 957 GLN cc_start: 0.8198 (tp40) cc_final: 0.7913 (tm-30) REVERT: C 1037 SER cc_start: 0.8804 (t) cc_final: 0.8227 (p) REVERT: L 18 ARG cc_start: 0.8192 (tmm-80) cc_final: 0.7749 (tmm-80) REVERT: L 140 PHE cc_start: 0.7559 (p90) cc_final: 0.6829 (p90) REVERT: D 99 ASP cc_start: 0.8421 (t70) cc_final: 0.8045 (t70) REVERT: D 154 PHE cc_start: 0.8674 (t80) cc_final: 0.8404 (t80) REVERT: F 139 ASN cc_start: 0.8640 (m-40) cc_final: 0.8293 (m-40) REVERT: G 34 MET cc_start: 0.7328 (tpt) cc_final: 0.7071 (tpt) REVERT: G 109 ASP cc_start: 0.7641 (t70) cc_final: 0.7296 (p0) REVERT: I 138 ASN cc_start: 0.8924 (m-40) cc_final: 0.7962 (m-40) REVERT: I 139 ASN cc_start: 0.8979 (m-40) cc_final: 0.8109 (p0) outliers start: 50 outliers final: 39 residues processed: 376 average time/residue: 0.9396 time to fit residues: 557.7783 Evaluate side-chains 345 residues out of total 3747 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 305 time to evaluate : 3.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 564 GLN Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain A residue 1126 CYS Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 703 ASN Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 657 ASN Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain H residue 33 ASP Chi-restraints excluded: chain H residue 50 VAL Chi-restraints excluded: chain H residue 105 VAL Chi-restraints excluded: chain H residue 179 GLN Chi-restraints excluded: chain H residue 217 LYS Chi-restraints excluded: chain D residue 96 CYS Chi-restraints excluded: chain D residue 105 VAL Chi-restraints excluded: chain G residue 27 PHE Chi-restraints excluded: chain G residue 105 VAL Chi-restraints excluded: chain G residue 217 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 342 optimal weight: 10.0000 chunk 233 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 306 optimal weight: 0.0000 chunk 169 optimal weight: 0.9990 chunk 351 optimal weight: 3.9990 chunk 284 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 210 optimal weight: 4.9990 chunk 369 optimal weight: 20.0000 chunk 103 optimal weight: 0.9990 overall best weight: 1.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 159 ASN ** D 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.2493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 34811 Z= 0.251 Angle : 0.502 13.814 47353 Z= 0.265 Chirality : 0.043 0.249 5525 Planarity : 0.003 0.051 6037 Dihedral : 5.573 58.770 5660 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.86 % Favored : 95.10 % Rotamer: Outliers : 1.60 % Allowed : 9.79 % Favored : 88.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.13), residues: 4242 helix: 1.57 (0.20), residues: 723 sheet: -0.04 (0.14), residues: 1305 loop : -0.47 (0.14), residues: 2214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP H 47 HIS 0.004 0.001 HIS A 655 PHE 0.018 0.001 PHE C 541 TYR 0.020 0.001 TYR F 49 ARG 0.005 0.000 ARG H 218 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8484 Ramachandran restraints generated. 4242 Oldfield, 0 Emsley, 4242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8484 Ramachandran restraints generated. 4242 Oldfield, 0 Emsley, 4242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 477 is missing expected H atoms. Skipping. Residue THR 199 is missing expected H atoms. Skipping. Evaluate side-chains 378 residues out of total 3747 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 318 time to evaluate : 3.951 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 226 LEU cc_start: 0.7952 (OUTLIER) cc_final: 0.7739 (tt) REVERT: A 302 THR cc_start: 0.8871 (m) cc_final: 0.8659 (p) REVERT: A 307 THR cc_start: 0.8450 (m) cc_final: 0.8168 (p) REVERT: A 421 TYR cc_start: 0.8161 (m-10) cc_final: 0.7717 (m-80) REVERT: A 614 ASP cc_start: 0.6922 (t0) cc_final: 0.6666 (t0) REVERT: A 759 PHE cc_start: 0.7372 (OUTLIER) cc_final: 0.6929 (t80) REVERT: A 1135 ASN cc_start: 0.7989 (t0) cc_final: 0.7698 (t0) REVERT: B 427 ASP cc_start: 0.7712 (m-30) cc_final: 0.7096 (t70) REVERT: B 466 ARG cc_start: 0.7902 (ttt180) cc_final: 0.7596 (ttm-80) REVERT: C 133 PHE cc_start: 0.5888 (OUTLIER) cc_final: 0.4748 (m-80) REVERT: C 318 PHE cc_start: 0.9002 (OUTLIER) cc_final: 0.8737 (p90) REVERT: C 396 TYR cc_start: 0.6569 (m-10) cc_final: 0.6019 (m-80) REVERT: C 421 TYR cc_start: 0.7373 (m-10) cc_final: 0.7131 (m-10) REVERT: C 571 ASP cc_start: 0.6575 (t70) cc_final: 0.6312 (t70) REVERT: C 710 ASN cc_start: 0.8699 (p0) cc_final: 0.8459 (p0) REVERT: C 867 ASP cc_start: 0.8142 (m-30) cc_final: 0.7877 (m-30) REVERT: C 957 GLN cc_start: 0.8149 (tp40) cc_final: 0.7820 (tm-30) REVERT: C 1037 SER cc_start: 0.8822 (t) cc_final: 0.8268 (p) REVERT: L 18 ARG cc_start: 0.8197 (tmm-80) cc_final: 0.7709 (tmm-80) REVERT: L 140 PHE cc_start: 0.7578 (p90) cc_final: 0.6845 (p90) REVERT: D 99 ASP cc_start: 0.8401 (t70) cc_final: 0.8093 (t70) REVERT: D 154 PHE cc_start: 0.8715 (t80) cc_final: 0.8438 (t80) REVERT: F 73 LEU cc_start: 0.7945 (tp) cc_final: 0.7686 (mp) REVERT: F 139 ASN cc_start: 0.8630 (m-40) cc_final: 0.8282 (m-40) REVERT: G 34 MET cc_start: 0.7446 (tpt) cc_final: 0.7191 (tpt) REVERT: G 109 ASP cc_start: 0.7697 (t70) cc_final: 0.7351 (p0) REVERT: I 138 ASN cc_start: 0.8876 (m-40) cc_final: 0.7904 (m-40) REVERT: I 139 ASN cc_start: 0.8966 (m-40) cc_final: 0.8083 (p0) outliers start: 60 outliers final: 45 residues processed: 368 average time/residue: 0.9608 time to fit residues: 560.8379 Evaluate side-chains 348 residues out of total 3747 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 299 time to evaluate : 3.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 564 GLN Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain A residue 1126 CYS Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 703 ASN Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 133 PHE Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 657 ASN Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 967 SER Chi-restraints excluded: chain H residue 33 ASP Chi-restraints excluded: chain H residue 50 VAL Chi-restraints excluded: chain H residue 79 LEU Chi-restraints excluded: chain H residue 105 VAL Chi-restraints excluded: chain H residue 179 GLN Chi-restraints excluded: chain H residue 217 LYS Chi-restraints excluded: chain D residue 105 VAL Chi-restraints excluded: chain G residue 27 PHE Chi-restraints excluded: chain G residue 105 VAL Chi-restraints excluded: chain G residue 217 LYS Chi-restraints excluded: chain I residue 4 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 138 optimal weight: 9.9990 chunk 370 optimal weight: 10.0000 chunk 81 optimal weight: 1.9990 chunk 241 optimal weight: 3.9990 chunk 101 optimal weight: 0.9990 chunk 412 optimal weight: 5.9990 chunk 342 optimal weight: 8.9990 chunk 190 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 136 optimal weight: 4.9990 chunk 216 optimal weight: 0.0040 overall best weight: 1.1998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 907 ASN C 207 HIS ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.2647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 34811 Z= 0.248 Angle : 0.501 13.432 47353 Z= 0.264 Chirality : 0.043 0.357 5525 Planarity : 0.003 0.051 6037 Dihedral : 5.457 59.075 5658 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.29 % Favored : 95.66 % Rotamer: Outliers : 1.76 % Allowed : 10.01 % Favored : 88.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.13), residues: 4242 helix: 1.64 (0.20), residues: 720 sheet: -0.05 (0.14), residues: 1311 loop : -0.44 (0.14), residues: 2211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 47 HIS 0.004 0.001 HIS A1064 PHE 0.017 0.001 PHE C 541 TYR 0.020 0.001 TYR F 49 ARG 0.004 0.000 ARG L 24 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8484 Ramachandran restraints generated. 4242 Oldfield, 0 Emsley, 4242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8484 Ramachandran restraints generated. 4242 Oldfield, 0 Emsley, 4242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 477 is missing expected H atoms. Skipping. Residue THR 199 is missing expected H atoms. Skipping. Evaluate side-chains 374 residues out of total 3747 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 308 time to evaluate : 3.898 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: symmetry clash REVERT: A 302 THR cc_start: 0.8874 (m) cc_final: 0.8659 (p) REVERT: A 307 THR cc_start: 0.8454 (m) cc_final: 0.8179 (p) REVERT: A 614 ASP cc_start: 0.7001 (t0) cc_final: 0.6750 (t0) REVERT: A 759 PHE cc_start: 0.7291 (OUTLIER) cc_final: 0.6877 (t80) REVERT: A 1135 ASN cc_start: 0.7986 (t0) cc_final: 0.7694 (t0) REVERT: B 427 ASP cc_start: 0.7704 (m-30) cc_final: 0.7114 (t70) REVERT: B 466 ARG cc_start: 0.7857 (ttt180) cc_final: 0.7596 (ttm-80) REVERT: C 133 PHE cc_start: 0.5948 (OUTLIER) cc_final: 0.4788 (m-80) REVERT: C 318 PHE cc_start: 0.9015 (OUTLIER) cc_final: 0.8811 (p90) REVERT: C 396 TYR cc_start: 0.6636 (m-10) cc_final: 0.6091 (m-80) REVERT: C 421 TYR cc_start: 0.7378 (m-10) cc_final: 0.7155 (m-10) REVERT: C 571 ASP cc_start: 0.6581 (t70) cc_final: 0.6319 (t70) REVERT: C 710 ASN cc_start: 0.8715 (p0) cc_final: 0.8457 (p0) REVERT: C 867 ASP cc_start: 0.8142 (m-30) cc_final: 0.7875 (m-30) REVERT: C 957 GLN cc_start: 0.8102 (tp40) cc_final: 0.7810 (tm-30) REVERT: C 1037 SER cc_start: 0.8828 (t) cc_final: 0.8275 (p) REVERT: H 34 MET cc_start: 0.8545 (mmm) cc_final: 0.8265 (mmm) REVERT: L 18 ARG cc_start: 0.8192 (tmm-80) cc_final: 0.7736 (tmm-80) REVERT: L 140 PHE cc_start: 0.7583 (p90) cc_final: 0.6854 (p90) REVERT: D 99 ASP cc_start: 0.8443 (t70) cc_final: 0.8165 (t70) REVERT: D 154 PHE cc_start: 0.8707 (t80) cc_final: 0.8426 (t80) REVERT: F 73 LEU cc_start: 0.8004 (tp) cc_final: 0.7783 (mp) REVERT: F 139 ASN cc_start: 0.8657 (m-40) cc_final: 0.8309 (m-40) REVERT: G 34 MET cc_start: 0.7464 (tpt) cc_final: 0.7189 (tpt) REVERT: G 109 ASP cc_start: 0.7767 (t70) cc_final: 0.7409 (p0) REVERT: I 138 ASN cc_start: 0.8871 (m-40) cc_final: 0.7925 (m-40) REVERT: I 139 ASN cc_start: 0.8911 (m-40) cc_final: 0.8028 (p0) outliers start: 66 outliers final: 52 residues processed: 363 average time/residue: 0.9435 time to fit residues: 541.4936 Evaluate side-chains 352 residues out of total 3747 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 297 time to evaluate : 3.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 564 GLN Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain A residue 1126 CYS Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 578 ASP Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 703 ASN Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 133 PHE Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 657 ASN Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 967 SER Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain H residue 33 ASP Chi-restraints excluded: chain H residue 50 VAL Chi-restraints excluded: chain H residue 76 LYS Chi-restraints excluded: chain H residue 105 VAL Chi-restraints excluded: chain H residue 179 GLN Chi-restraints excluded: chain H residue 217 LYS Chi-restraints excluded: chain D residue 96 CYS Chi-restraints excluded: chain D residue 105 VAL Chi-restraints excluded: chain G residue 27 PHE Chi-restraints excluded: chain G residue 105 VAL Chi-restraints excluded: chain G residue 217 LYS Chi-restraints excluded: chain I residue 4 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 397 optimal weight: 30.0000 chunk 46 optimal weight: 0.9990 chunk 234 optimal weight: 2.9990 chunk 300 optimal weight: 10.0000 chunk 233 optimal weight: 0.9980 chunk 346 optimal weight: 0.0370 chunk 230 optimal weight: 4.9990 chunk 410 optimal weight: 9.9990 chunk 256 optimal weight: 2.9990 chunk 250 optimal weight: 2.9990 chunk 189 optimal weight: 1.9990 overall best weight: 1.4064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS C 360 ASN C1119 ASN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.2875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 34811 Z= 0.283 Angle : 0.513 12.884 47353 Z= 0.272 Chirality : 0.043 0.269 5525 Planarity : 0.003 0.050 6037 Dihedral : 5.414 59.907 5658 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.21 % Favored : 94.74 % Rotamer: Outliers : 1.97 % Allowed : 10.14 % Favored : 87.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.13), residues: 4242 helix: 1.59 (0.19), residues: 720 sheet: -0.12 (0.14), residues: 1311 loop : -0.49 (0.14), residues: 2211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP H 47 HIS 0.004 0.001 HIS A1064 PHE 0.021 0.002 PHE F 62 TYR 0.022 0.001 TYR F 49 ARG 0.007 0.000 ARG L 24 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8484 Ramachandran restraints generated. 4242 Oldfield, 0 Emsley, 4242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8484 Ramachandran restraints generated. 4242 Oldfield, 0 Emsley, 4242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 477 is missing expected H atoms. Skipping. Residue THR 199 is missing expected H atoms. Skipping. Evaluate side-chains 382 residues out of total 3747 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 308 time to evaluate : 4.076 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: symmetry clash revert: symmetry clash REVERT: A 302 THR cc_start: 0.8872 (m) cc_final: 0.8645 (p) REVERT: A 307 THR cc_start: 0.8460 (m) cc_final: 0.8199 (p) REVERT: A 614 ASP cc_start: 0.7021 (t0) cc_final: 0.6804 (t0) REVERT: A 759 PHE cc_start: 0.7276 (OUTLIER) cc_final: 0.6935 (t80) REVERT: B 52 GLN cc_start: 0.8325 (tm-30) cc_final: 0.7858 (tm-30) REVERT: B 427 ASP cc_start: 0.7743 (m-30) cc_final: 0.7182 (t70) REVERT: C 133 PHE cc_start: 0.5993 (OUTLIER) cc_final: 0.4791 (m-80) REVERT: C 571 ASP cc_start: 0.6625 (t70) cc_final: 0.6367 (t70) REVERT: C 710 ASN cc_start: 0.8736 (p0) cc_final: 0.8477 (p0) REVERT: C 867 ASP cc_start: 0.8191 (m-30) cc_final: 0.7936 (m-30) REVERT: C 957 GLN cc_start: 0.8095 (tp40) cc_final: 0.7666 (tm-30) REVERT: C 1037 SER cc_start: 0.8850 (t) cc_final: 0.8292 (p) REVERT: L 140 PHE cc_start: 0.7639 (p90) cc_final: 0.6893 (p90) REVERT: D 99 ASP cc_start: 0.8453 (t70) cc_final: 0.8193 (t70) REVERT: D 154 PHE cc_start: 0.8717 (t80) cc_final: 0.8435 (t80) REVERT: F 73 LEU cc_start: 0.8109 (tp) cc_final: 0.7903 (mp) REVERT: F 139 ASN cc_start: 0.8695 (m-40) cc_final: 0.8350 (m-40) REVERT: G 34 MET cc_start: 0.7480 (tpt) cc_final: 0.7231 (tpt) REVERT: G 83 MET cc_start: 0.7804 (mmm) cc_final: 0.7480 (mmt) REVERT: G 109 ASP cc_start: 0.7742 (t70) cc_final: 0.7369 (p0) REVERT: I 138 ASN cc_start: 0.8891 (m-40) cc_final: 0.7939 (m-40) REVERT: I 139 ASN cc_start: 0.8924 (m-40) cc_final: 0.8039 (p0) outliers start: 74 outliers final: 61 residues processed: 368 average time/residue: 0.9460 time to fit residues: 556.0919 Evaluate side-chains 360 residues out of total 3747 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 297 time to evaluate : 3.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 125 ASN Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 564 GLN Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain A residue 1126 CYS Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 578 ASP Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 703 ASN Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 133 PHE Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 657 ASN Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain C residue 967 SER Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain H residue 33 ASP Chi-restraints excluded: chain H residue 50 VAL Chi-restraints excluded: chain H residue 60 TYR Chi-restraints excluded: chain H residue 76 LYS Chi-restraints excluded: chain H residue 105 VAL Chi-restraints excluded: chain H residue 179 GLN Chi-restraints excluded: chain H residue 217 LYS Chi-restraints excluded: chain D residue 96 CYS Chi-restraints excluded: chain D residue 105 VAL Chi-restraints excluded: chain G residue 27 PHE Chi-restraints excluded: chain G residue 105 VAL Chi-restraints excluded: chain G residue 217 LYS Chi-restraints excluded: chain I residue 4 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 254 optimal weight: 0.9980 chunk 163 optimal weight: 4.9990 chunk 245 optimal weight: 0.7980 chunk 123 optimal weight: 0.9980 chunk 80 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 261 optimal weight: 1.9990 chunk 279 optimal weight: 4.9990 chunk 203 optimal weight: 0.8980 chunk 38 optimal weight: 0.0040 chunk 322 optimal weight: 4.9990 overall best weight: 0.7392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 3 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.2972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 34811 Z= 0.182 Angle : 0.482 12.781 47353 Z= 0.253 Chirality : 0.043 0.223 5525 Planarity : 0.003 0.050 6037 Dihedral : 5.166 58.810 5656 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.91 % Favored : 96.04 % Rotamer: Outliers : 1.63 % Allowed : 10.46 % Favored : 87.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.13), residues: 4242 helix: 1.78 (0.20), residues: 720 sheet: -0.04 (0.14), residues: 1305 loop : -0.40 (0.14), residues: 2217 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 47 HIS 0.003 0.001 HIS H 35 PHE 0.020 0.001 PHE B 643 TYR 0.021 0.001 TYR F 49 ARG 0.006 0.000 ARG L 24 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8484 Ramachandran restraints generated. 4242 Oldfield, 0 Emsley, 4242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8484 Ramachandran restraints generated. 4242 Oldfield, 0 Emsley, 4242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 477 is missing expected H atoms. Skipping. Residue THR 199 is missing expected H atoms. Skipping. Evaluate side-chains 374 residues out of total 3747 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 313 time to evaluate : 3.951 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: symmetry clash revert: symmetry clash REVERT: A 302 THR cc_start: 0.8838 (m) cc_final: 0.8600 (p) REVERT: A 307 THR cc_start: 0.8468 (m) cc_final: 0.8203 (p) REVERT: A 759 PHE cc_start: 0.7173 (OUTLIER) cc_final: 0.6811 (t80) REVERT: A 1135 ASN cc_start: 0.7938 (t0) cc_final: 0.7657 (t0) REVERT: B 52 GLN cc_start: 0.8130 (tm-30) cc_final: 0.7856 (tm-30) REVERT: B 427 ASP cc_start: 0.7763 (m-30) cc_final: 0.7210 (t70) REVERT: B 465 GLU cc_start: 0.7666 (tt0) cc_final: 0.7107 (tt0) REVERT: C 133 PHE cc_start: 0.5939 (OUTLIER) cc_final: 0.4739 (m-80) REVERT: C 396 TYR cc_start: 0.7112 (m-80) cc_final: 0.6735 (m-80) REVERT: C 571 ASP cc_start: 0.6620 (t70) cc_final: 0.6374 (t70) REVERT: C 710 ASN cc_start: 0.8684 (p0) cc_final: 0.8432 (p0) REVERT: C 867 ASP cc_start: 0.8111 (m-30) cc_final: 0.7829 (m-30) REVERT: C 957 GLN cc_start: 0.8031 (tp40) cc_final: 0.7624 (tm-30) REVERT: C 1037 SER cc_start: 0.8841 (t) cc_final: 0.8260 (p) REVERT: L 140 PHE cc_start: 0.7606 (p90) cc_final: 0.6847 (p90) REVERT: D 154 PHE cc_start: 0.8686 (t80) cc_final: 0.8401 (t80) REVERT: D 203 ILE cc_start: 0.9076 (mm) cc_final: 0.8849 (tp) REVERT: F 73 LEU cc_start: 0.8116 (tp) cc_final: 0.7854 (mp) REVERT: F 86 TYR cc_start: 0.7817 (m-80) cc_final: 0.7452 (m-80) REVERT: F 139 ASN cc_start: 0.8694 (m-40) cc_final: 0.8437 (m-40) REVERT: G 34 MET cc_start: 0.7504 (tpt) cc_final: 0.7245 (tpt) REVERT: G 83 MET cc_start: 0.7813 (mmm) cc_final: 0.7543 (mmt) REVERT: G 109 ASP cc_start: 0.7729 (t70) cc_final: 0.7368 (p0) REVERT: I 138 ASN cc_start: 0.8893 (m-40) cc_final: 0.7942 (m-40) REVERT: I 139 ASN cc_start: 0.8908 (m-40) cc_final: 0.8014 (p0) outliers start: 61 outliers final: 53 residues processed: 364 average time/residue: 0.9467 time to fit residues: 546.8271 Evaluate side-chains 356 residues out of total 3747 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 301 time to evaluate : 3.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 564 GLN Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain A residue 1126 CYS Chi-restraints excluded: chain B residue 40 ASP Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 703 ASN Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 133 PHE Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 657 ASN Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 967 SER Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain H residue 33 ASP Chi-restraints excluded: chain H residue 50 VAL Chi-restraints excluded: chain H residue 60 TYR Chi-restraints excluded: chain H residue 76 LYS Chi-restraints excluded: chain H residue 105 VAL Chi-restraints excluded: chain H residue 179 GLN Chi-restraints excluded: chain H residue 217 LYS Chi-restraints excluded: chain D residue 96 CYS Chi-restraints excluded: chain D residue 105 VAL Chi-restraints excluded: chain G residue 27 PHE Chi-restraints excluded: chain G residue 105 VAL Chi-restraints excluded: chain G residue 217 LYS Chi-restraints excluded: chain I residue 4 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 373 optimal weight: 20.0000 chunk 393 optimal weight: 9.9990 chunk 358 optimal weight: 30.0000 chunk 382 optimal weight: 8.9990 chunk 230 optimal weight: 2.9990 chunk 166 optimal weight: 1.9990 chunk 300 optimal weight: 10.0000 chunk 117 optimal weight: 2.9990 chunk 345 optimal weight: 9.9990 chunk 361 optimal weight: 10.0000 chunk 381 optimal weight: 20.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 914 ASN ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1135 ASN ** B 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1036 GLN C 207 HIS C 580 GLN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.3678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.015 0.147 34811 Z= 0.993 Angle : 0.884 12.423 47353 Z= 0.485 Chirality : 0.057 0.376 5525 Planarity : 0.006 0.071 6037 Dihedral : 6.584 56.795 5656 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 15.97 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.98 % Favored : 90.90 % Rotamer: Outliers : 2.32 % Allowed : 10.49 % Favored : 87.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.45 (0.12), residues: 4242 helix: -0.15 (0.18), residues: 735 sheet: -0.67 (0.15), residues: 1191 loop : -1.38 (0.13), residues: 2316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.003 TRP B 64 HIS 0.009 0.002 HIS C1088 PHE 0.055 0.004 PHE A 429 TYR 0.038 0.003 TYR A1067 ARG 0.008 0.001 ARG A 577 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8484 Ramachandran restraints generated. 4242 Oldfield, 0 Emsley, 4242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8484 Ramachandran restraints generated. 4242 Oldfield, 0 Emsley, 4242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 477 is missing expected H atoms. Skipping. Residue THR 199 is missing expected H atoms. Skipping. Evaluate side-chains 393 residues out of total 3747 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 306 time to evaluate : 3.927 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: A 302 THR cc_start: 0.8974 (m) cc_final: 0.8734 (p) REVERT: A 759 PHE cc_start: 0.7487 (OUTLIER) cc_final: 0.7167 (t80) REVERT: A 979 ASP cc_start: 0.9113 (t0) cc_final: 0.8879 (t0) REVERT: B 427 ASP cc_start: 0.7762 (m-30) cc_final: 0.7327 (t70) REVERT: B 465 GLU cc_start: 0.7649 (tt0) cc_final: 0.7111 (tt0) REVERT: B 521 PRO cc_start: 0.8822 (Cg_exo) cc_final: 0.8505 (Cg_endo) REVERT: C 133 PHE cc_start: 0.6387 (OUTLIER) cc_final: 0.5065 (m-80) REVERT: C 571 ASP cc_start: 0.6959 (t70) cc_final: 0.6484 (t70) REVERT: C 1130 ILE cc_start: 0.8468 (mt) cc_final: 0.8121 (tp) REVERT: L 18 ARG cc_start: 0.8413 (tmm-80) cc_final: 0.7982 (tmm-80) REVERT: L 140 PHE cc_start: 0.7820 (p90) cc_final: 0.7118 (p90) REVERT: D 34 MET cc_start: 0.8624 (mmm) cc_final: 0.8144 (mmm) REVERT: D 154 PHE cc_start: 0.8821 (t80) cc_final: 0.8528 (t80) REVERT: F 73 LEU cc_start: 0.8184 (tp) cc_final: 0.7943 (mp) REVERT: F 139 ASN cc_start: 0.8957 (m-40) cc_final: 0.8632 (m110) REVERT: G 83 MET cc_start: 0.7796 (mmm) cc_final: 0.7593 (mmt) REVERT: G 109 ASP cc_start: 0.7772 (t70) cc_final: 0.7363 (p0) REVERT: I 138 ASN cc_start: 0.8978 (m-40) cc_final: 0.8039 (m-40) REVERT: I 139 ASN cc_start: 0.8972 (m-40) cc_final: 0.8120 (p0) outliers start: 87 outliers final: 68 residues processed: 375 average time/residue: 1.0363 time to fit residues: 611.8661 Evaluate side-chains 357 residues out of total 3747 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 287 time to evaluate : 3.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 125 ASN Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 564 GLN Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 1111 GLU Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain A residue 1126 CYS Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 578 ASP Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 695 TYR Chi-restraints excluded: chain B residue 703 ASN Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 133 PHE Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 657 ASN Chi-restraints excluded: chain C residue 742 ILE Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain C residue 967 SER Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain H residue 33 ASP Chi-restraints excluded: chain H residue 50 VAL Chi-restraints excluded: chain H residue 60 TYR Chi-restraints excluded: chain H residue 76 LYS Chi-restraints excluded: chain H residue 105 VAL Chi-restraints excluded: chain H residue 179 GLN Chi-restraints excluded: chain H residue 217 LYS Chi-restraints excluded: chain D residue 54 ASP Chi-restraints excluded: chain D residue 96 CYS Chi-restraints excluded: chain D residue 105 VAL Chi-restraints excluded: chain G residue 27 PHE Chi-restraints excluded: chain G residue 217 LYS Chi-restraints excluded: chain I residue 4 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 251 optimal weight: 0.5980 chunk 404 optimal weight: 9.9990 chunk 246 optimal weight: 0.0050 chunk 191 optimal weight: 0.5980 chunk 281 optimal weight: 0.5980 chunk 424 optimal weight: 10.0000 chunk 390 optimal weight: 10.0000 chunk 337 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 261 optimal weight: 0.5980 chunk 207 optimal weight: 0.8980 overall best weight: 0.4794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 ASN C 360 ASN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.3556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 34811 Z= 0.184 Angle : 0.541 13.465 47353 Z= 0.288 Chirality : 0.045 0.222 5525 Planarity : 0.004 0.056 6037 Dihedral : 5.828 59.638 5653 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.43 % Favored : 95.52 % Rotamer: Outliers : 1.36 % Allowed : 11.69 % Favored : 86.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.13), residues: 4242 helix: 0.99 (0.19), residues: 717 sheet: -0.47 (0.14), residues: 1284 loop : -0.90 (0.13), residues: 2241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP H 47 HIS 0.005 0.001 HIS A 655 PHE 0.021 0.002 PHE A 823 TYR 0.033 0.001 TYR A1067 ARG 0.009 0.001 ARG I 61 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8484 Ramachandran restraints generated. 4242 Oldfield, 0 Emsley, 4242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8484 Ramachandran restraints generated. 4242 Oldfield, 0 Emsley, 4242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 477 is missing expected H atoms. Skipping. Residue THR 199 is missing expected H atoms. Skipping. Evaluate side-chains 356 residues out of total 3747 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 305 time to evaluate : 3.986 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: A 302 THR cc_start: 0.8823 (m) cc_final: 0.8590 (p) REVERT: A 759 PHE cc_start: 0.7218 (OUTLIER) cc_final: 0.6939 (t80) REVERT: A 979 ASP cc_start: 0.9093 (t0) cc_final: 0.8868 (t0) REVERT: A 1135 ASN cc_start: 0.7857 (t0) cc_final: 0.7608 (t0) REVERT: B 427 ASP cc_start: 0.7681 (m-30) cc_final: 0.7471 (p0) REVERT: B 465 GLU cc_start: 0.7689 (tt0) cc_final: 0.7139 (tt0) REVERT: C 133 PHE cc_start: 0.6053 (OUTLIER) cc_final: 0.4806 (m-80) REVERT: C 571 ASP cc_start: 0.6790 (t70) cc_final: 0.6445 (t70) REVERT: C 957 GLN cc_start: 0.8085 (tp40) cc_final: 0.7674 (tm-30) REVERT: C 1037 SER cc_start: 0.8716 (t) cc_final: 0.8118 (p) REVERT: L 18 ARG cc_start: 0.8350 (tmm-80) cc_final: 0.7883 (tmm-80) REVERT: L 140 PHE cc_start: 0.7468 (p90) cc_final: 0.6710 (p90) REVERT: D 36 TRP cc_start: 0.5923 (m100) cc_final: 0.5512 (m100) REVERT: D 154 PHE cc_start: 0.8719 (t80) cc_final: 0.8424 (t80) REVERT: F 73 LEU cc_start: 0.8155 (tp) cc_final: 0.7930 (mp) REVERT: F 86 TYR cc_start: 0.7880 (m-80) cc_final: 0.7634 (m-80) REVERT: F 139 ASN cc_start: 0.8899 (m-40) cc_final: 0.8573 (m-40) REVERT: G 83 MET cc_start: 0.7759 (mmm) cc_final: 0.7544 (mmt) REVERT: G 109 ASP cc_start: 0.7687 (t70) cc_final: 0.7408 (p0) REVERT: I 138 ASN cc_start: 0.8892 (m-40) cc_final: 0.7937 (m-40) REVERT: I 139 ASN cc_start: 0.8911 (m-40) cc_final: 0.8073 (p0) outliers start: 51 outliers final: 46 residues processed: 346 average time/residue: 0.9798 time to fit residues: 529.8708 Evaluate side-chains 337 residues out of total 3747 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 289 time to evaluate : 3.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 564 GLN Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain A residue 1126 CYS Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 703 ASN Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 133 PHE Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 657 ASN Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 967 SER Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain H residue 33 ASP Chi-restraints excluded: chain H residue 60 TYR Chi-restraints excluded: chain H residue 76 LYS Chi-restraints excluded: chain H residue 105 VAL Chi-restraints excluded: chain H residue 179 GLN Chi-restraints excluded: chain H residue 217 LYS Chi-restraints excluded: chain D residue 105 VAL Chi-restraints excluded: chain G residue 27 PHE Chi-restraints excluded: chain G residue 217 LYS Chi-restraints excluded: chain I residue 4 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 268 optimal weight: 0.9980 chunk 360 optimal weight: 20.0000 chunk 103 optimal weight: 1.9990 chunk 311 optimal weight: 7.9990 chunk 49 optimal weight: 0.9980 chunk 93 optimal weight: 0.0970 chunk 338 optimal weight: 20.0000 chunk 141 optimal weight: 7.9990 chunk 347 optimal weight: 0.5980 chunk 42 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.154437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.097827 restraints weight = 176237.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.102517 restraints weight = 91264.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.103239 restraints weight = 62118.038| |-----------------------------------------------------------------------------| r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.3639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.091 34811 Z= 0.233 Angle : 0.530 12.789 47353 Z= 0.280 Chirality : 0.044 0.278 5525 Planarity : 0.004 0.052 6037 Dihedral : 5.588 58.164 5652 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.35 % Favored : 94.60 % Rotamer: Outliers : 1.39 % Allowed : 11.98 % Favored : 86.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.13), residues: 4242 helix: 1.34 (0.19), residues: 714 sheet: -0.42 (0.14), residues: 1296 loop : -0.82 (0.13), residues: 2232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP F 35 HIS 0.007 0.001 HIS A 655 PHE 0.021 0.001 PHE C 970 TYR 0.028 0.001 TYR A1067 ARG 0.008 0.000 ARG I 61 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11650.36 seconds wall clock time: 203 minutes 55.97 seconds (12235.97 seconds total)