Starting phenix.real_space_refine (version: 1.21rc1) on Thu Apr 27 16:45:38 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l06_23095/04_2023/7l06_23095_neut_trim.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l06_23095/04_2023/7l06_23095.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l06_23095/04_2023/7l06_23095.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l06_23095/04_2023/7l06_23095.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l06_23095/04_2023/7l06_23095_neut_trim.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l06_23095/04_2023/7l06_23095_neut_trim.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= -0.002 sd= 0.047 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 147 5.16 5 C 23369 2.51 5 N 6047 2.21 5 O 7309 1.98 5 H 35068 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 55": "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 135": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 194": "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 TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 377": "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 TYR 421": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 428": "OD1" <-> "OD2" 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 464": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 465": "OE1" <-> "OE2" Residue "A TYR 489": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 497": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 505": "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 612": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 661": "OE1" <-> "OE2" Residue "A ASP 663": "OD1" <-> "OD2" Residue "A TYR 707": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 741": "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 817": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 855": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 868": "OE1" <-> "OE2" 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 PHE 898": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 917": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 970": "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 PHE 1062": "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 GLU 1092": "OE1" <-> "OE2" 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 "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 TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 55": "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 135": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 377": "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 PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 421": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 428": "OD1" <-> "OD2" 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 PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 465": "OE1" <-> "OE2" Residue "B TYR 489": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 497": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 505": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 543": "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 TYR 612": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 661": "OE1" <-> "OE2" Residue "B ASP 663": "OD1" <-> "OD2" Residue "B TYR 707": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 741": "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 TYR 789": "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 855": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 868": "OE1" <-> "OE2" 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 PHE 970": "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 PHE 1062": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 1075": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 1092": "OE1" <-> "OE2" 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 "C PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 186": "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 265": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 421": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 428": "OD1" <-> "OD2" 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 PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 465": "OE1" <-> "OE2" Residue "C TYR 489": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 497": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 505": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 543": "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 ASP 663": "OD1" <-> "OD2" 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 817": "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 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 6": "OE1" <-> "OE2" Residue "D ARG 28": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D GLU 46": "OE1" <-> "OE2" Residue "D ASP 58": "OD1" <-> "OD2" Residue "D PHE 148": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 174": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 226": "OE1" <-> "OE2" Residue "E GLU 30": "OE1" <-> "OE2" Residue "E TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 105": "OE1" <-> "OE2" Residue "E ARG 108": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ASP 167": "OD1" <-> "OD2" Residue "E GLU 187": "OE1" <-> "OE2" Residue "E ARG 211": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F GLU 105": "OE1" <-> "OE2" Residue "F GLU 195": "OE1" <-> "OE2" Residue "F ARG 211": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G GLU 6": "OE1" <-> "OE2" Residue "G ASP 61": "OD1" <-> "OD2" Residue "G ASP 73": "OD1" <-> "OD2" Residue "G ARG 99": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ASP 100": "OD1" <-> "OD2" Residue "G TYR 147": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G GLU 226": "OE1" <-> "OE2" Residue "H GLU 6": "OE1" <-> "OE2" Residue "H ARG 28": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H GLU 46": "OE1" <-> "OE2" Residue "H ASP 58": "OD1" <-> "OD2" Residue "H PHE 148": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 174": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H GLU 226": "OE1" <-> "OE2" Residue "K GLU 30": "OE1" <-> "OE2" Residue "K TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K GLU 105": "OE1" <-> "OE2" Residue "K ARG 108": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K ASP 167": "OD1" <-> "OD2" Residue "K GLU 187": "OE1" <-> "OE2" Residue "K ARG 211": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L GLU 105": "OE1" <-> "OE2" Residue "L GLU 195": "OE1" <-> "OE2" Residue "L ARG 211": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M GLU 6": "OE1" <-> "OE2" Residue "M ASP 61": "OD1" <-> "OD2" Residue "M ASP 73": "OD1" <-> "OD2" Residue "M ARG 99": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M ASP 100": "OD1" <-> "OD2" Residue "M TYR 147": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M GLU 226": "OE1" <-> "OE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 71940 Number of models: 1 Model: "" Number of chains: 28 Chain: "A" Number of atoms: 15038 Number of conformers: 1 Conformer: "" Number of residues, atoms: 972, 15038 Classifications: {'peptide': 972} Link IDs: {'PTRANS': 48, 'TRANS': 923} Chain breaks: 11 Chain: "B" Number of atoms: 15038 Number of conformers: 1 Conformer: "" Number of residues, atoms: 972, 15038 Classifications: {'peptide': 972} Link IDs: {'PTRANS': 48, 'TRANS': 923} Chain breaks: 11 Chain: "C" Number of atoms: 15018 Number of conformers: 1 Conformer: "" Number of residues, atoms: 972, 15018 Classifications: {'peptide': 972} Link IDs: {'PTRANS': 48, 'TRANS': 923} Chain breaks: 11 Chain: "D" Number of atoms: 3247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 3247 Classifications: {'peptide': 218} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 204} Chain breaks: 1 Chain: "E" Number of atoms: 3228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 3228 Classifications: {'peptide': 213} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 203} Chain: "F" Number of atoms: 3198 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 3198 Classifications: {'peptide': 211} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 201} Chain: "G" Number of atoms: 3247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 3247 Classifications: {'peptide': 218} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 204} Chain breaks: 1 Chain: "H" Number of atoms: 3247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 3247 Classifications: {'peptide': 218} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 204} Chain breaks: 1 Chain: "K" Number of atoms: 3228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 3228 Classifications: {'peptide': 213} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 203} Chain: "L" Number of atoms: 3198 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 3198 Classifications: {'peptide': 211} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 201} Chain: "M" Number of atoms: 3247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 3247 Classifications: {'peptide': 218} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 204} Chain breaks: 1 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "N" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 3, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 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 chiralities: 2 Chain: "P" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 2, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 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 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 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 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 chiralities: 2 Chain: "U" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 2, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 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 chiralities: 2 Chain: "W" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "X" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 3, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 Chain: "Y" 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 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 chiralities: 8 Chain: "B" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 Chain: "C" 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 chiralities: 8 Time building chain proxies: 22.57, per 1000 atoms: 0.31 Number of scatterers: 71940 At special positions: 0 Unit cell: (186.208, 178.802, 213.716, 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 147 16.00 O 7309 8.00 N 6047 7.00 C 23369 6.00 H 35068 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=52, 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=2.12 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.02 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.05 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.09 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.06 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=2.05 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=1.88 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.04 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.16 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.00 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=2.12 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.02 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.05 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.09 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.06 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=2.05 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=1.88 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.04 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.16 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.00 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=2.02 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.02 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.05 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.10 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.02 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.04 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.06 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=2.04 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.02 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 92 " distance=2.26 Simple disulfide: pdb=" SG CYS D 142 " - pdb=" SG CYS D 208 " distance=2.04 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.10 Simple disulfide: pdb=" SG CYS E 134 " - pdb=" SG CYS E 194 " distance=2.06 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.13 Simple disulfide: pdb=" SG CYS F 134 " - pdb=" SG CYS F 194 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 92 " distance=2.06 Simple disulfide: pdb=" SG CYS G 142 " - pdb=" SG CYS G 208 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.26 Simple disulfide: pdb=" SG CYS H 142 " - pdb=" SG CYS H 208 " distance=2.04 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.10 Simple disulfide: pdb=" SG CYS K 134 " - pdb=" SG CYS K 194 " distance=2.06 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.13 Simple disulfide: pdb=" SG CYS L 134 " - pdb=" SG CYS L 194 " distance=2.03 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 92 " distance=2.06 Simple disulfide: pdb=" SG CYS M 142 " - pdb=" SG CYS M 208 " distance=2.04 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 ALPHA1-2 " MAN N 5 " - " MAN N 6 " " MAN X 5 " - " MAN X 6 " ALPHA1-3 " BMA J 3 " - " MAN J 4 " " BMA P 3 " - " MAN P 4 " " BMA U 3 " - " MAN U 4 " " BMA W 3 " - " MAN W 4 " ALPHA1-6 " BMA J 3 " - " MAN J 5 " " BMA N 3 " - " MAN N 4 " " MAN N 4 " - " MAN N 5 " " BMA W 3 " - " MAN W 5 " " BMA X 3 " - " MAN X 4 " " MAN X 4 " - " MAN X 5 " BETA1-3 " BMA N 3 " - " BMA N 8 " " MAN N 4 " - " BMA N 7 " " BMA X 3 " - " BMA X 8 " " MAN X 4 " - " BMA X 7 " BETA1-4 " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " 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 U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " BETA1-6 " BMA P 3 " - " BMA P 5 " " BMA U 3 " - " BMA U 5 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 331 " " NAG A1303 " - " ASN A 343 " " NAG A1304 " - " ASN A 603 " " NAG A1305 " - " ASN A1074 " " NAG A1306 " - " ASN A 657 " " NAG A1307 " - " ASN A 282 " " NAG A1308 " - " ASN A 616 " " NAG B1301 " - " ASN B 61 " " NAG B1303 " - " ASN B 343 " " NAG B1305 " - " ASN B1074 " " NAG B1306 " - " ASN B 657 " " NAG B1307 " - " ASN B 282 " " NAG B1308 " - " ASN B 616 " " NAG B1309 " - " ASN B 709 " " NAG C1201 " - " ASN C 657 " " NAG C1202 " - " ASN C1074 " " NAG C1203 " - " ASN C 61 " " NAG C1204 " - " ASN C 282 " " NAG C1205 " - " ASN C 331 " " NAG C1206 " - " ASN C 343 " " NAG C1207 " - " ASN C 603 " " NAG C1208 " - " ASN C 616 " " NAG I 1 " - " ASN A1134 " " NAG J 1 " - " ASN A 801 " " NAG N 1 " - " ASN A 717 " " NAG O 1 " - " ASN A1098 " " NAG P 1 " - " ASN A 709 " " NAG Q 1 " - " ASN C 717 " " NAG R 1 " - " ASN C 801 " " NAG S 1 " - " ASN C1098 " " NAG T 1 " - " ASN C1134 " " NAG U 1 " - " ASN C 709 " " NAG V 1 " - " ASN B1134 " " NAG Y 1 " - " ASN B1098 " Time building additional restraints: 45.75 Conformation dependent library (CDL) restraints added in 4.4 seconds 9080 Ramachandran restraints generated. 4540 Oldfield, 0 Emsley, 4540 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8652 Finding SS restraints... Secondary structure from input PDB file: 95 helices and 89 sheets defined 19.3% alpha, 38.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.77 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 349 through 353 removed outlier: 3.890A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 371 removed outlier: 4.569A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.228A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) 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 759 removed outlier: 6.975A pdb=" N SER A 758 " --> pdb=" O GLN A 755 " (cutoff:3.500A) Processing helix chain 'A' and resid 760 through 783 removed outlier: 4.198A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS A 776 " --> pdb=" O VAL A 772 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.901A 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 removed outlier: 3.577A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 removed outlier: 3.580A pdb=" N ALA A 903 " --> pdb=" O ALA A 899 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 918 removed outlier: 3.537A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.588A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) 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 965 Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 982 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.800A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N TYR A1007 " --> pdb=" O SER A1003 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1147 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.890A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 371 removed outlier: 4.569A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.230A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) 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: 6.975A pdb=" N SER B 758 " --> pdb=" O GLN B 755 " (cutoff:3.500A) Processing helix chain 'B' and resid 760 through 783 removed outlier: 4.198A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LYS B 776 " --> pdb=" O VAL B 772 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.900A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.577A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.581A pdb=" N ALA B 903 " --> pdb=" O ALA B 899 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 918 removed outlier: 3.538A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.588A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) 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 965 Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 982 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.799A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N TYR B1007 " --> pdb=" O SER B1003 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1147 Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.889A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 371 removed outlier: 4.569A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.227A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 759 removed outlier: 6.975A pdb=" N SER C 758 " --> pdb=" O GLN C 755 " (cutoff:3.500A) Processing helix chain 'C' and resid 760 through 783 removed outlier: 3.806A 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 Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 913 through 919 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: 3.914A 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 982 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.798A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1147 Processing helix chain 'D' and resid 52A through 55 Processing helix chain 'D' and resid 73 through 75 No H-bonds generated for 'chain 'D' and resid 73 through 75' Processing helix chain 'D' and resid 83 through 87 Processing helix chain 'D' and resid 163 through 165 No H-bonds generated for 'chain 'D' and resid 163 through 165' Processing helix chain 'D' and resid 196 through 199 removed outlier: 3.989A pdb=" N GLY D 199 " --> pdb=" O SER D 196 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 196 through 199' Processing helix chain 'E' and resid 79 through 83 removed outlier: 3.784A pdb=" N PHE E 83 " --> pdb=" O PHE E 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 121 through 127 removed outlier: 4.049A pdb=" N SER E 127 " --> pdb=" O GLU E 123 " (cutoff:3.500A) Processing helix chain 'E' and resid 183 through 187 Processing helix chain 'F' and resid 79 through 83 removed outlier: 3.503A pdb=" N PHE F 83 " --> pdb=" O PHE F 80 " (cutoff:3.500A) Processing helix chain 'F' and resid 121 through 127 Processing helix chain 'F' and resid 183 through 187 Processing helix chain 'G' and resid 28 through 32 removed outlier: 4.057A pdb=" N ALA G 31 " --> pdb=" O ARG G 28 " (cutoff:3.500A) Processing helix chain 'G' and resid 52A through 55 removed outlier: 3.629A pdb=" N THR G 55 " --> pdb=" O THR G 52A" (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 52A through 55' Processing helix chain 'G' and resid 83 through 87 Processing helix chain 'G' and resid 163 through 165 No H-bonds generated for 'chain 'G' and resid 163 through 165' Processing helix chain 'G' and resid 196 through 199 removed outlier: 4.179A pdb=" N GLY G 199 " --> pdb=" O SER G 196 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 196 through 199' Processing helix chain 'H' and resid 52A through 55 Processing helix chain 'H' and resid 73 through 75 No H-bonds generated for 'chain 'H' and resid 73 through 75' Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'H' and resid 163 through 165 No H-bonds generated for 'chain 'H' and resid 163 through 165' Processing helix chain 'H' and resid 196 through 199 removed outlier: 3.988A pdb=" N GLY H 199 " --> pdb=" O SER H 196 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 196 through 199' Processing helix chain 'K' and resid 79 through 83 removed outlier: 3.784A pdb=" N PHE K 83 " --> pdb=" O PHE K 80 " (cutoff:3.500A) Processing helix chain 'K' and resid 121 through 127 removed outlier: 4.049A pdb=" N SER K 127 " --> pdb=" O GLU K 123 " (cutoff:3.500A) Processing helix chain 'K' and resid 183 through 187 Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.502A pdb=" N PHE L 83 " --> pdb=" O PHE L 80 " (cutoff:3.500A) Processing helix chain 'L' and resid 121 through 127 Processing helix chain 'L' and resid 183 through 187 Processing helix chain 'M' and resid 28 through 32 removed outlier: 4.058A pdb=" N ALA M 31 " --> pdb=" O ARG M 28 " (cutoff:3.500A) Processing helix chain 'M' and resid 52A through 55 removed outlier: 3.628A pdb=" N THR M 55 " --> pdb=" O THR M 52A" (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 52A through 55' Processing helix chain 'M' and resid 83 through 87 Processing helix chain 'M' and resid 163 through 165 No H-bonds generated for 'chain 'M' and resid 163 through 165' Processing helix chain 'M' and resid 196 through 199 removed outlier: 4.180A pdb=" N GLY M 199 " --> pdb=" O SER M 196 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 196 through 199' Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.221A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.630A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.376A 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: 6.249A pdb=" N PHE A 43 " --> pdb=" O ARG C 567 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 4.210A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ARG A 273 " --> pdb=" O ASP A 53 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 83 through 85 removed outlier: 6.728A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 83 through 85 removed outlier: 6.529A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.602A 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: 5.268A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.294A 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: 5.540A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.123A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 391 through 392 Processing sheet with id=AB1, first strand: chain 'A' and resid 448 through 453 removed outlier: 5.845A pdb=" N TYR A 449 " --> pdb=" O PHE A 497 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N PHE A 497 " --> pdb=" O TYR A 449 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N TYR A 451 " --> pdb=" O TYR A 495 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.344A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 701 through 704 Processing sheet with id=AB4, first strand: chain 'A' and resid 718 through 728 removed outlier: 5.821A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB6, first strand: chain 'A' and resid 787 through 788 Processing sheet with id=AB7, first strand: chain 'A' and resid 1076 through 1078 removed outlier: 4.469A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1081 through 1083 removed outlier: 4.499A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 28 through 30 removed outlier: 8.220A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 47 through 55 removed outlier: 4.210A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ARG B 273 " --> pdb=" O ASP B 53 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 83 through 85 removed outlier: 6.729A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 83 through 85 removed outlier: 6.529A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.269A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 325 through 328 removed outlier: 5.539A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.124A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 391 through 392 Processing sheet with id=AC8, first strand: chain 'B' and resid 448 through 453 removed outlier: 5.844A pdb=" N TYR B 449 " --> pdb=" O PHE B 497 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N PHE B 497 " --> pdb=" O TYR B 449 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N TYR B 451 " --> pdb=" O TYR B 495 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.345A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 701 through 704 Processing sheet with id=AD2, first strand: chain 'B' and resid 712 through 715 removed outlier: 4.469A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 718 through 728 removed outlier: 5.821A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD5, first strand: chain 'B' and resid 1081 through 1083 removed outlier: 4.500A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 28 through 30 removed outlier: 8.007A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLU C 224 " --> pdb=" O SER C 205 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 47 through 55 removed outlier: 7.366A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 83 through 85 removed outlier: 6.728A pdb=" N LEU C 141 " --> pdb=" O LEU C 244 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 83 through 85 removed outlier: 6.530A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.240A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.121A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.725A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 448 through 453 removed outlier: 5.846A pdb=" N TYR C 449 " --> pdb=" O PHE C 497 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N PHE C 497 " --> pdb=" O TYR C 449 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N TYR C 451 " --> pdb=" O TYR C 495 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.024A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.408A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.631A 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 728 removed outlier: 6.403A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N ASN C 717 " --> pdb=" O ALA C1070 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.403A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N ASN C 717 " --> pdb=" O ALA C1070 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.496A 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: 4.690A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'D' and resid 3 through 7 Processing sheet with id=AF2, first strand: chain 'D' and resid 10 through 13 removed outlier: 6.605A pdb=" N GLY D 10 " --> pdb=" O THR D 110 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N SER D 112 " --> pdb=" O GLY D 10 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N VAL D 12 " --> pdb=" O SER D 112 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILE D 89 " --> pdb=" O ARG D 39 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N MET D 34 " --> pdb=" O SER D 50 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N SER D 50 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'D' and resid 10 through 13 removed outlier: 6.605A pdb=" N GLY D 10 " --> pdb=" O THR D 110 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N SER D 112 " --> pdb=" O GLY D 10 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N VAL D 12 " --> pdb=" O SER D 112 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ALA D 102 " --> pdb=" O ARG D 94 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'D' and resid 120 through 124 removed outlier: 6.209A pdb=" N TYR D 185 " --> pdb=" O ASP D 146 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'D' and resid 120 through 124 removed outlier: 6.209A pdb=" N TYR D 185 " --> pdb=" O ASP D 146 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'D' and resid 152 through 157 removed outlier: 3.865A pdb=" N TYR D 206 " --> pdb=" O VAL D 225 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'E' and resid 4 through 7 Processing sheet with id=AF8, first strand: chain 'E' and resid 10 through 13 removed outlier: 6.337A pdb=" N LEU E 33 " --> pdb=" O TYR E 49 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N TYR E 49 " --> pdb=" O LEU E 33 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N TRP E 35 " --> pdb=" O LEU E 47 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LYS E 50 " --> pdb=" O THR E 53 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'E' and resid 10 through 13 removed outlier: 3.565A pdb=" N SER E 95 " --> pdb=" O ALA E 92 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'E' and resid 115 through 118 removed outlier: 4.302A pdb=" N ASN E 138 " --> pdb=" O TYR E 173 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N TYR E 173 " --> pdb=" O ASN E 138 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N SER E 174 " --> pdb=" O THR E 164 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'E' and resid 153 through 154 Processing sheet with id=AG3, first strand: chain 'F' and resid 4 through 7 removed outlier: 3.691A pdb=" N GLU F 70 " --> pdb=" O SER F 67 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'F' and resid 10 through 13 removed outlier: 6.511A pdb=" N LEU F 33 " --> pdb=" O TYR F 49 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N TYR F 49 " --> pdb=" O LEU F 33 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N TRP F 35 " --> pdb=" O LEU F 47 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'F' and resid 10 through 13 Processing sheet with id=AG6, first strand: chain 'F' and resid 114 through 118 removed outlier: 5.622A pdb=" N TYR F 173 " --> pdb=" O ASN F 138 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'F' and resid 153 through 154 Processing sheet with id=AG8, first strand: chain 'G' and resid 3 through 7 Processing sheet with id=AG9, first strand: chain 'G' and resid 11 through 13 removed outlier: 6.674A pdb=" N VAL G 12 " --> pdb=" O SER G 112 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N MET G 34 " --> pdb=" O SER G 50 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N SER G 50 " --> pdb=" O MET G 34 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N TRP G 36 " --> pdb=" O VAL G 48 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'G' and resid 11 through 13 removed outlier: 6.674A pdb=" N VAL G 12 " --> pdb=" O SER G 112 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N ALA G 102 " --> pdb=" O ARG G 94 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'G' and resid 120 through 124 removed outlier: 6.148A pdb=" N TYR G 185 " --> pdb=" O ASP G 146 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'G' and resid 120 through 124 removed outlier: 6.148A pdb=" N TYR G 185 " --> pdb=" O ASP G 146 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'G' and resid 153 through 157 removed outlier: 4.279A pdb=" N TYR G 206 " --> pdb=" O VAL G 225 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AH6, first strand: chain 'H' and resid 10 through 13 removed outlier: 6.605A pdb=" N GLY H 10 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N SER H 112 " --> pdb=" O GLY H 10 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N VAL H 12 " --> pdb=" O SER H 112 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE H 89 " --> pdb=" O ARG H 39 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N MET H 34 " --> pdb=" O SER H 50 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N SER H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'H' and resid 10 through 13 removed outlier: 6.605A pdb=" N GLY H 10 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N SER H 112 " --> pdb=" O GLY H 10 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N VAL H 12 " --> pdb=" O SER H 112 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ALA H 102 " --> pdb=" O ARG H 94 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'H' and resid 120 through 124 removed outlier: 6.209A pdb=" N TYR H 185 " --> pdb=" O ASP H 146 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'H' and resid 120 through 124 removed outlier: 6.209A pdb=" N TYR H 185 " --> pdb=" O ASP H 146 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'H' and resid 152 through 157 removed outlier: 3.865A pdb=" N TYR H 206 " --> pdb=" O VAL H 225 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'K' and resid 4 through 7 Processing sheet with id=AI3, first strand: chain 'K' and resid 10 through 13 removed outlier: 6.337A pdb=" N LEU K 33 " --> pdb=" O TYR K 49 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N TYR K 49 " --> pdb=" O LEU K 33 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N TRP K 35 " --> pdb=" O LEU K 47 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LYS K 50 " --> pdb=" O THR K 53 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'K' and resid 10 through 13 removed outlier: 3.565A pdb=" N SER K 95 " --> pdb=" O ALA K 92 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'K' and resid 115 through 118 removed outlier: 4.303A pdb=" N ASN K 138 " --> pdb=" O TYR K 173 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N TYR K 173 " --> pdb=" O ASN K 138 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N SER K 174 " --> pdb=" O THR K 164 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'K' and resid 153 through 154 Processing sheet with id=AI7, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.691A pdb=" N GLU L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.512A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'L' and resid 10 through 13 Processing sheet with id=AJ1, first strand: chain 'L' and resid 114 through 118 removed outlier: 5.621A pdb=" N TYR L 173 " --> pdb=" O ASN L 138 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'L' and resid 153 through 154 Processing sheet with id=AJ3, first strand: chain 'M' and resid 3 through 7 Processing sheet with id=AJ4, first strand: chain 'M' and resid 11 through 13 removed outlier: 6.674A pdb=" N VAL M 12 " --> pdb=" O SER M 112 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N MET M 34 " --> pdb=" O SER M 50 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N SER M 50 " --> pdb=" O MET M 34 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N TRP M 36 " --> pdb=" O VAL M 48 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'M' and resid 11 through 13 removed outlier: 6.674A pdb=" N VAL M 12 " --> pdb=" O SER M 112 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N ALA M 102 " --> pdb=" O ARG M 94 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'M' and resid 120 through 124 removed outlier: 6.148A pdb=" N TYR M 185 " --> pdb=" O ASP M 146 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain 'M' and resid 120 through 124 removed outlier: 6.148A pdb=" N TYR M 185 " --> pdb=" O ASP M 146 " (cutoff:3.500A) Processing sheet with id=AJ8, first strand: chain 'M' and resid 153 through 157 removed outlier: 4.280A pdb=" N TYR M 206 " --> pdb=" O VAL M 225 " (cutoff:3.500A) 1656 hydrogen bonds defined for protein. 4446 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: 33.77 Time building geometry restraints manager: 48.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 35065 1.04 - 1.25: 5787 1.25 - 1.46: 12505 1.46 - 1.66: 19196 1.66 - 1.87: 187 Bond restraints: 72740 Sorted by residual: bond pdb=" C ILE B1081 " pdb=" O ILE B1081 " ideal model delta sigma weight residual 1.236 1.164 0.072 9.90e-03 1.02e+04 5.32e+01 bond pdb=" C ILE A1081 " pdb=" O ILE A1081 " ideal model delta sigma weight residual 1.236 1.165 0.071 9.90e-03 1.02e+04 5.16e+01 bond pdb=" C VAL H 144 " pdb=" O VAL H 144 " ideal model delta sigma weight residual 1.238 1.170 0.067 1.17e-02 7.31e+03 3.32e+01 bond pdb=" NE ARG A 454 " pdb=" CZ ARG A 454 " ideal model delta sigma weight residual 1.326 1.389 -0.063 1.10e-02 8.26e+03 3.26e+01 bond pdb=" C VAL D 144 " pdb=" O VAL D 144 " ideal model delta sigma weight residual 1.238 1.171 0.067 1.17e-02 7.31e+03 3.23e+01 ... (remaining 72735 not shown) Histogram of bond angle deviations from ideal: 72.36 - 87.82: 8 87.82 - 103.28: 387 103.28 - 118.75: 97475 118.75 - 134.21: 32759 134.21 - 149.67: 36 Bond angle restraints: 130665 Sorted by residual: angle pdb="HD21 ASN B 709 " pdb=" ND2 ASN B 709 " pdb="HD22 ASN B 709 " ideal model delta sigma weight residual 120.00 72.36 47.64 3.00e+00 1.11e-01 2.52e+02 angle pdb="HD21 ASN A1098 " pdb=" ND2 ASN A1098 " pdb="HD22 ASN A1098 " ideal model delta sigma weight residual 120.00 73.30 46.70 3.00e+00 1.11e-01 2.42e+02 angle pdb="HD21 ASN B1098 " pdb=" ND2 ASN B1098 " pdb="HD22 ASN B1098 " ideal model delta sigma weight residual 120.00 73.33 46.67 3.00e+00 1.11e-01 2.42e+02 angle pdb="HD21 ASN B 616 " pdb=" ND2 ASN B 616 " pdb="HD22 ASN B 616 " ideal model delta sigma weight residual 120.00 73.70 46.30 3.00e+00 1.11e-01 2.38e+02 angle pdb=" CG ASN B 709 " pdb=" ND2 ASN B 709 " pdb="HD22 ASN B 709 " ideal model delta sigma weight residual 120.00 74.53 45.47 3.00e+00 1.11e-01 2.30e+02 ... (remaining 130660 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.87: 27510 17.87 - 35.73: 1198 35.73 - 53.60: 238 53.60 - 71.46: 154 71.46 - 89.33: 69 Dihedral angle restraints: 29169 sinusoidal: 13175 harmonic: 15994 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 -173.00 87.00 1 1.00e+01 1.00e-02 9.10e+01 dihedral pdb=" CB CYS E 23 " pdb=" SG CYS E 23 " pdb=" SG CYS E 88 " pdb=" CB CYS E 88 " ideal model delta sinusoidal sigma weight residual -86.00 -0.23 -85.77 1 1.00e+01 1.00e-02 8.89e+01 dihedral pdb=" CB CYS K 23 " pdb=" SG CYS K 23 " pdb=" SG CYS K 88 " pdb=" CB CYS K 88 " ideal model delta sinusoidal sigma weight residual -86.00 -0.25 -85.75 1 1.00e+01 1.00e-02 8.89e+01 ... (remaining 29166 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.811: 6075 0.811 - 1.622: 3 1.622 - 2.433: 4 2.433 - 3.244: 1 3.244 - 4.055: 3 Chirality restraints: 6086 Sorted by residual: chirality pdb=" C1 MAN P 4 " pdb=" O3 BMA P 3 " pdb=" C2 MAN P 4 " pdb=" O5 MAN P 4 " both_signs ideal model delta sigma weight residual False 2.40 1.84 0.56 2.00e-02 2.50e+03 7.84e+02 chirality pdb=" C1 BMA P 3 " pdb=" O4 NAG P 2 " pdb=" C2 BMA P 3 " pdb=" O5 BMA P 3 " both_signs ideal model delta sigma weight residual False -2.40 -1.99 -0.41 2.00e-02 2.50e+03 4.13e+02 chirality pdb=" C1 NAG A1306 " pdb=" ND2 ASN A 657 " pdb=" C2 NAG A1306 " pdb=" O5 NAG A1306 " both_signs ideal model delta sigma weight residual False -2.40 1.65 -4.05 2.00e-01 2.50e+01 4.11e+02 ... (remaining 6083 not shown) Planarity restraints: 10855 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 709 " -0.182 2.00e-02 2.50e+03 3.85e-01 2.22e+03 pdb=" CG ASN A 709 " 0.102 2.00e-02 2.50e+03 pdb=" OD1 ASN A 709 " 0.085 2.00e-02 2.50e+03 pdb=" ND2 ASN A 709 " 0.163 2.00e-02 2.50e+03 pdb="HD21 ASN A 709 " 0.547 2.00e-02 2.50e+03 pdb="HD22 ASN A 709 " -0.716 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 801 " 0.184 2.00e-02 2.50e+03 3.85e-01 2.22e+03 pdb=" CG ASN A 801 " -0.114 2.00e-02 2.50e+03 pdb=" OD1 ASN A 801 " -0.082 2.00e-02 2.50e+03 pdb=" ND2 ASN A 801 " -0.170 2.00e-02 2.50e+03 pdb="HD21 ASN A 801 " -0.537 2.00e-02 2.50e+03 pdb="HD22 ASN A 801 " 0.719 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 717 " 0.177 2.00e-02 2.50e+03 3.85e-01 2.22e+03 pdb=" CG ASN A 717 " -0.110 2.00e-02 2.50e+03 pdb=" OD1 ASN A 717 " -0.088 2.00e-02 2.50e+03 pdb=" ND2 ASN A 717 " -0.161 2.00e-02 2.50e+03 pdb="HD21 ASN A 717 " -0.539 2.00e-02 2.50e+03 pdb="HD22 ASN A 717 " 0.721 2.00e-02 2.50e+03 ... (remaining 10852 not shown) Histogram of nonbonded interaction distances: 0.36 - 1.21: 9 1.21 - 2.05: 896 2.05 - 2.90: 179521 2.90 - 3.75: 298354 3.75 - 4.60: 527912 Warning: very small nonbonded interaction distances. Nonbonded interactions: 1006692 Sorted by model distance: nonbonded pdb="HD22 ASN B 801 " pdb=" C1 NAG W 1 " model vdw 0.358 2.750 nonbonded pdb="HD22 ASN B 717 " pdb=" C1 NAG X 1 " model vdw 0.386 2.750 nonbonded pdb=" OD2 ASP D 72 " pdb="HH12 ARG G 57 " model vdw 0.480 1.850 nonbonded pdb=" OD1 ASP D 72 " pdb="HH22 ARG G 57 " model vdw 1.027 1.850 nonbonded pdb="HH12 ARG H 57 " pdb=" OD2 ASP M 72 " model vdw 1.066 1.850 ... (remaining 1006687 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 69 or (resid 80 and (name N or name CA or name \ C or name O or name CB or name CG or name OD1 or name OD2 or name HA or name HB2 \ or name HB3)) or resid 81 through 121 or (resid 122 and (name N or name CA or n \ ame 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 name HD21)) or resid 123 through 143 or (resid 165 \ 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 HA or name HB2 or name HB3 or name HD21)) or resid 166 through \ 172 or (resid 186 and (name N or name CA or name C or name O or name CB or name \ CG or name CD1 or name CD2 or name CE1 or name CE2 or name CZ or name HA or nam \ e HB2 or name HB3 or name HD1 or name HD2 or name HE1 or name HE2 or name HZ )) \ or resid 187 through 233 or (resid 234 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 name HD21)) or resid 235 through 245 or (resid 263 and (name N o \ r name CA or name C or name O or name CB or name HA or name HB1 or name HB2 or n \ ame HB3)) or resid 264 through 330 or (resid 331 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 o \ r name HB2 or name HB3 or name HD21)) or resid 332 through 342 or (resid 343 and \ (name N or name CA or name C or name O or name CB or name CG or name OD1 or nam \ e ND2 or name H or name HA or name HB2 or name HB3 or name HD21)) or resid 344 t \ hrough 444 or (resid 447 and (name N or name CA or name C or name O or name HA2 \ or name HA3)) or resid 448 through 454 or (resid 462 and (name N or name CA or n \ ame C or name O or name CB or name CG or name CD or name CE or name NZ or name H \ A or name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name HD3 or nam \ e HE2 or name HE3 or name HZ1 or name HZ2 or name HZ3)) or resid 463 through 468 \ or (resid 489 and (name N or name CA or name C or name O or name CB or name CG \ or name CD1 or name CD2 or name CE1 or name CE2 or name CZ or name OH or name HA \ or name HB2 or name HB3 or name HD1 or name HD2 or name HE1 or name HE2 or name \ HH )) or resid 490 through 501 or (resid 503 and (name N or name CA or name C o \ r name O or name CB or name CG1 or name CG2 or name HA or name HB or name HG11 o \ r name HG12 or name HG13 or name HG21 or name HG22 or name HG23)) or resid 504 t \ hrough 602 or (resid 603 and (name N or name CA or name C or name O or name CB o \ r name CG or name OD1 or name ND2 or name H or name HA or name HB2 or name HB3 o \ r name HD21)) or resid 604 through 615 or (resid 616 and (name N or name CA or n \ ame 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 name HD21)) or resid 617 through 620 or (resid 641 \ 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 HA or name HB2 or name HB3 or name HD21 or name HD22)) or resi \ d 642 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 name HD21)) or resid 658 through 676 or (resid 689 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 name HB3 \ or name HG )) or resid 690 through 716 or (resid 717 and (name N or name CA or n \ ame 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 name HD21)) or resid 718 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 name HD21)) or resid 8 \ 02 through 827 or (resid 854 and (name N or name CA or name C or name O or name \ CB or name CG or name CD or name CE or name NZ or name HA or name HB2 or name HB \ 3 or name HG2 or name HG3 or name HD2 or name HD3 or name HE2 or name HE3 or nam \ e HZ1 or name HZ2 or name HZ3)) or resid 855 through 1097 or (resid 1098 and (na \ me N or name CA or name C or name O or name CB or name CG or name OD1 or name ND \ 2 or name H or name HA or name HB2 or name HB3 or name HD21)) or resid 1099 thro \ ugh 1147 or resid 1301 through 1308)) selection = (chain 'B' and (resid 27 through 69 or (resid 80 and (name N or name CA or name \ C or name O or name CB or name CG or name OD1 or name OD2 or name HA or name HB2 \ or name HB3)) or resid 81 through 121 or (resid 122 and (name N or name CA or n \ ame 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 name HD21)) or resid 123 through 143 or (resid 165 \ 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 HA or name HB2 or name HB3 or name HD21)) or resid 166 through \ 172 or (resid 186 and (name N or name CA or name C or name O or name CB or name \ CG or name CD1 or name CD2 or name CE1 or name CE2 or name CZ or name HA or nam \ e HB2 or name HB3 or name HD1 or name HD2 or name HE1 or name HE2 or name HZ )) \ or resid 187 through 233 or (resid 234 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 name HD21)) or resid 235 through 245 or (resid 263 and (name N o \ r name CA or name C or name O or name CB or name HA or name HB1 or name HB2 or n \ ame HB3)) or resid 264 through 330 or (resid 331 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 o \ r name HB2 or name HB3 or name HD21)) or resid 332 through 342 or (resid 343 and \ (name N or name CA or name C or name O or name CB or name CG or name OD1 or nam \ e ND2 or name H or name HA or name HB2 or name HB3 or name HD21)) or resid 344 t \ hrough 444 or (resid 447 and (name N or name CA or name C or name O or name HA2 \ or name HA3)) or resid 448 through 454 or (resid 462 and (name N or name CA or n \ ame C or name O or name CB or name CG or name CD or name CE or name NZ or name H \ A or name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name HD3 or nam \ e HE2 or name HE3 or name HZ1 or name HZ2 or name HZ3)) or resid 463 through 468 \ or (resid 489 and (name N or name CA or name C or name O or name CB or name CG \ or name CD1 or name CD2 or name CE1 or name CE2 or name CZ or name OH or name HA \ or name HB2 or name HB3 or name HD1 or name HD2 or name HE1 or name HE2 or name \ HH )) or resid 490 through 501 or (resid 503 and (name N or name CA or name C o \ r name O or name CB or name CG1 or name CG2 or name HA or name HB or name HG11 o \ r name HG12 or name HG13 or name HG21 or name HG22 or name HG23)) or resid 504 t \ hrough 602 or (resid 603 and (name N or name CA or name C or name O or name CB o \ r name CG or name OD1 or name ND2 or name H or name HA or name HB2 or name HB3 o \ r name HD21)) or resid 604 through 615 or (resid 616 and (name N or name CA or n \ ame 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 name HD21)) or resid 617 through 620 or (resid 641 \ 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 HA or name HB2 or name HB3 or name HD21 or name HD22)) or resi \ d 642 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 name HD21)) or resid 658 through 676 or (resid 689 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 name HB3 \ or name HG )) or resid 690 through 716 or (resid 717 and (name N or name CA or n \ ame 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 name HD21)) or resid 718 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 name HD21)) or resid 8 \ 02 through 827 or (resid 854 and (name N or name CA or name C or name O or name \ CB or name CG or name CD or name CE or name NZ or name HA or name HB2 or name HB \ 3 or name HG2 or name HG3 or name HD2 or name HD3 or name HE2 or name HE3 or nam \ e HZ1 or name HZ2 or name HZ3)) or resid 855 through 1097 or (resid 1098 and (na \ me N or name CA or name C or name O or name CB or name CG or name OD1 or name ND \ 2 or name H or name HA or name HB2 or name HB3 or name HD21)) or resid 1099 thro \ ugh 1147 or resid 1301 through 1308)) selection = (chain 'C' and (resid 27 through 60 or (resid 61 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 o \ r name HB2 or name HB3)) or resid 62 through 1133 or (resid 1134 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 nam \ e H or name HA or name HB2 or name HB3)) or resid 1135 through 1147 or resid 120 \ 1 through 1208)) } ncs_group { reference = chain 'D' selection = chain 'G' selection = chain 'H' selection = chain 'M' } ncs_group { reference = (chain 'E' and ((resid 2 and (name N or name CA or name C or name O or name CB o \ r name CG1 or name CG2 or name HA or name HB or name HG11 or name HG12 or name H \ G13 or name HG21 or name HG22 or name HG23)) or resid 3 through 212)) selection = chain 'F' selection = (chain 'K' and ((resid 2 and (name N or name CA or name C or name O or name CB o \ r name CG1 or name CG2 or name HA or name HB or name HG11 or name HG12 or name H \ G13 or name HG21 or name HG22 or name HG23)) or resid 3 through 212)) selection = chain 'L' } ncs_group { reference = chain 'I' selection = chain 'O' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'V' selection = chain 'Y' } ncs_group { reference = (chain 'J' and resid 1 through 4) selection = (chain 'P' and resid 1 through 4) selection = (chain 'U' and resid 1 through 4) selection = (chain 'W' and resid 1 through 4) } ncs_group { reference = chain 'N' selection = chain 'X' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 4.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.910 Extract box with map and model: 11.800 Check model and map are aligned: 0.810 Set scattering table: 0.500 Process input model: 183.420 Find NCS groups from input model: 2.910 Set up NCS constraints: 0.530 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:2.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 207.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7394 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 : 0.014 0.113 37672 Z= 0.905 Angle : 1.654 19.519 51237 Z= 1.122 Chirality : 0.148 4.055 6086 Planarity : 0.015 0.290 6466 Dihedral : 12.729 89.327 13067 Min Nonbonded Distance : 1.189 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer Outliers : 0.87 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.12), residues: 4540 helix: -1.06 (0.16), residues: 739 sheet: -0.01 (0.14), residues: 1298 loop : -0.28 (0.12), residues: 2503 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9080 Ramachandran restraints generated. 4540 Oldfield, 0 Emsley, 4540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9080 Ramachandran restraints generated. 4540 Oldfield, 0 Emsley, 4540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 530 residues out of total 4024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 495 time to evaluate : 4.374 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 outliers start: 35 outliers final: 13 residues processed: 528 average time/residue: 1.1461 time to fit residues: 909.1428 Evaluate side-chains 278 residues out of total 4024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 265 time to evaluate : 4.281 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 13 outliers final: 3 residues processed: 13 average time/residue: 0.7378 time to fit residues: 23.6696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 459 random chunks: chunk 387 optimal weight: 5.9990 chunk 347 optimal weight: 10.0000 chunk 193 optimal weight: 0.7980 chunk 118 optimal weight: 4.9990 chunk 234 optimal weight: 3.9990 chunk 185 optimal weight: 0.9990 chunk 359 optimal weight: 0.8980 chunk 139 optimal weight: 7.9990 chunk 218 optimal weight: 4.9990 chunk 267 optimal weight: 0.5980 chunk 416 optimal weight: 4.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 122 ASN A 234 ASN A 360 ASN A 784 GLN B 234 ASN B 603 ASN B1002 GLN C 764 ASN C 804 GLN C 935 GLN C1005 GLN D 32 HIS H 32 HIS ** M 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 81 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7475 moved from start: 0.2151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.075 37672 Z= 0.216 Angle : 0.664 9.511 51237 Z= 0.354 Chirality : 0.049 0.833 6086 Planarity : 0.004 0.096 6466 Dihedral : 5.654 26.378 4935 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer Outliers : 0.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.12), residues: 4540 helix: 0.42 (0.18), residues: 727 sheet: 0.05 (0.13), residues: 1443 loop : -0.11 (0.12), residues: 2370 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9080 Ramachandran restraints generated. 4540 Oldfield, 0 Emsley, 4540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9080 Ramachandran restraints generated. 4540 Oldfield, 0 Emsley, 4540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 4024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 274 time to evaluate : 4.359 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 outliers start: 32 outliers final: 21 residues processed: 296 average time/residue: 1.2027 time to fit residues: 536.5622 Evaluate side-chains 244 residues out of total 4024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 223 time to evaluate : 4.335 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 2 residues processed: 21 average time/residue: 0.8724 time to fit residues: 36.0113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 459 random chunks: chunk 231 optimal weight: 0.5980 chunk 129 optimal weight: 7.9990 chunk 346 optimal weight: 30.0000 chunk 283 optimal weight: 1.9990 chunk 114 optimal weight: 30.0000 chunk 417 optimal weight: 6.9990 chunk 451 optimal weight: 50.0000 chunk 371 optimal weight: 20.0000 chunk 414 optimal weight: 30.0000 chunk 142 optimal weight: 9.9990 chunk 334 optimal weight: 5.9990 overall best weight: 4.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS ** A 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 207 HIS A 644 GLN A 762 GLN A 804 GLN A 935 GLN A1106 GLN B 66 HIS B 207 HIS B 644 GLN ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1088 HIS ** C 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.3376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.149 37672 Z= 0.418 Angle : 0.682 9.116 51237 Z= 0.358 Chirality : 0.049 0.809 6086 Planarity : 0.005 0.077 6466 Dihedral : 5.267 25.749 4935 Min Nonbonded Distance : 1.698 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer Outliers : 1.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.12), residues: 4540 helix: 0.26 (0.19), residues: 724 sheet: -0.16 (0.13), residues: 1458 loop : -0.43 (0.13), residues: 2358 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9080 Ramachandran restraints generated. 4540 Oldfield, 0 Emsley, 4540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9080 Ramachandran restraints generated. 4540 Oldfield, 0 Emsley, 4540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 4024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 242 time to evaluate : 4.349 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 outliers start: 44 outliers final: 26 residues processed: 279 average time/residue: 1.0867 time to fit residues: 466.2210 Evaluate side-chains 234 residues out of total 4024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 208 time to evaluate : 4.315 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 3 residues processed: 26 average time/residue: 0.6969 time to fit residues: 38.0063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 459 random chunks: chunk 412 optimal weight: 20.0000 chunk 313 optimal weight: 20.0000 chunk 216 optimal weight: 6.9990 chunk 46 optimal weight: 10.0000 chunk 199 optimal weight: 10.0000 chunk 280 optimal weight: 0.8980 chunk 419 optimal weight: 20.0000 chunk 443 optimal weight: 8.9990 chunk 218 optimal weight: 0.6980 chunk 397 optimal weight: 20.0000 chunk 119 optimal weight: 5.9990 overall best weight: 4.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 GLN ** A 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1106 GLN ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 66 HIS C 655 HIS C1106 GLN ** M 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.3994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.086 37672 Z= 0.361 Angle : 0.618 8.974 51237 Z= 0.325 Chirality : 0.047 0.726 6086 Planarity : 0.004 0.070 6466 Dihedral : 5.100 26.574 4935 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.63 % Favored : 96.32 % Rotamer Outliers : 1.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.12), residues: 4540 helix: 0.29 (0.18), residues: 763 sheet: -0.22 (0.14), residues: 1454 loop : -0.54 (0.13), residues: 2323 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9080 Ramachandran restraints generated. 4540 Oldfield, 0 Emsley, 4540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9080 Ramachandran restraints generated. 4540 Oldfield, 0 Emsley, 4540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 4024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 213 time to evaluate : 4.363 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 outliers start: 41 outliers final: 26 residues processed: 243 average time/residue: 1.1773 time to fit residues: 437.9830 Evaluate side-chains 220 residues out of total 4024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 194 time to evaluate : 4.357 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 26 outliers final: 1 residues processed: 26 average time/residue: 0.7869 time to fit residues: 41.1504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 459 random chunks: chunk 369 optimal weight: 10.0000 chunk 251 optimal weight: 0.6980 chunk 6 optimal weight: 7.9990 chunk 330 optimal weight: 20.0000 chunk 183 optimal weight: 2.9990 chunk 378 optimal weight: 10.0000 chunk 306 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 226 optimal weight: 20.0000 chunk 398 optimal weight: 10.0000 chunk 111 optimal weight: 4.9990 overall best weight: 5.3390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 779 GLN ** A 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1002 GLN B 762 GLN ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN C 675 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.4586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.143 37672 Z= 0.443 Angle : 0.658 9.595 51237 Z= 0.342 Chirality : 0.048 0.734 6086 Planarity : 0.004 0.065 6466 Dihedral : 5.093 25.196 4935 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer Outliers : 0.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.12), residues: 4540 helix: 0.11 (0.18), residues: 762 sheet: -0.44 (0.14), residues: 1456 loop : -0.74 (0.13), residues: 2322 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9080 Ramachandran restraints generated. 4540 Oldfield, 0 Emsley, 4540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9080 Ramachandran restraints generated. 4540 Oldfield, 0 Emsley, 4540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 4024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 200 time to evaluate : 4.355 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 outliers start: 27 outliers final: 20 residues processed: 222 average time/residue: 1.0980 time to fit residues: 374.2079 Evaluate side-chains 208 residues out of total 4024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 188 time to evaluate : 4.378 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 20 outliers final: 1 residues processed: 20 average time/residue: 0.7043 time to fit residues: 30.5724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 459 random chunks: chunk 149 optimal weight: 1.9990 chunk 399 optimal weight: 9.9990 chunk 87 optimal weight: 0.9990 chunk 260 optimal weight: 0.5980 chunk 109 optimal weight: 20.0000 chunk 444 optimal weight: 1.9990 chunk 368 optimal weight: 40.0000 chunk 205 optimal weight: 20.0000 chunk 36 optimal weight: 5.9990 chunk 146 optimal weight: 3.9990 chunk 233 optimal weight: 9.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.4668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.074 37672 Z= 0.199 Angle : 0.544 8.413 51237 Z= 0.281 Chirality : 0.046 0.710 6086 Planarity : 0.003 0.068 6466 Dihedral : 4.809 24.752 4935 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer Outliers : 0.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.12), residues: 4540 helix: 0.66 (0.19), residues: 762 sheet: -0.30 (0.14), residues: 1463 loop : -0.56 (0.13), residues: 2315 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9080 Ramachandran restraints generated. 4540 Oldfield, 0 Emsley, 4540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9080 Ramachandran restraints generated. 4540 Oldfield, 0 Emsley, 4540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 4024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 201 time to evaluate : 4.484 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 outliers start: 13 outliers final: 10 residues processed: 208 average time/residue: 1.1210 time to fit residues: 359.6787 Evaluate side-chains 192 residues out of total 4024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 182 time to evaluate : 4.356 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 10 outliers final: 1 residues processed: 10 average time/residue: 0.6930 time to fit residues: 17.9167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 459 random chunks: chunk 428 optimal weight: 40.0000 chunk 50 optimal weight: 5.9990 chunk 253 optimal weight: 3.9990 chunk 324 optimal weight: 20.0000 chunk 251 optimal weight: 1.9990 chunk 373 optimal weight: 30.0000 chunk 247 optimal weight: 6.9990 chunk 442 optimal weight: 10.0000 chunk 276 optimal weight: 0.9980 chunk 269 optimal weight: 0.9990 chunk 204 optimal weight: 20.0000 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 913 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.4867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.118 37672 Z= 0.268 Angle : 0.553 7.929 51237 Z= 0.287 Chirality : 0.046 0.717 6086 Planarity : 0.004 0.070 6466 Dihedral : 4.701 24.227 4935 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer Outliers : 0.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.12), residues: 4540 helix: 0.76 (0.19), residues: 768 sheet: -0.31 (0.14), residues: 1445 loop : -0.57 (0.13), residues: 2327 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9080 Ramachandran restraints generated. 4540 Oldfield, 0 Emsley, 4540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9080 Ramachandran restraints generated. 4540 Oldfield, 0 Emsley, 4540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 4024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 190 time to evaluate : 4.497 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 outliers start: 15 outliers final: 8 residues processed: 202 average time/residue: 1.1099 time to fit residues: 347.1935 Evaluate side-chains 190 residues out of total 4024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 182 time to evaluate : 4.348 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 3 residues processed: 8 average time/residue: 0.7683 time to fit residues: 16.3028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 459 random chunks: chunk 273 optimal weight: 0.8980 chunk 176 optimal weight: 2.9990 chunk 264 optimal weight: 2.9990 chunk 133 optimal weight: 9.9990 chunk 86 optimal weight: 4.9990 chunk 85 optimal weight: 0.7980 chunk 281 optimal weight: 2.9990 chunk 301 optimal weight: 2.9990 chunk 218 optimal weight: 6.9990 chunk 41 optimal weight: 0.0370 chunk 347 optimal weight: 6.9990 overall best weight: 1.5462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1113 GLN ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.4964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.094 37672 Z= 0.174 Angle : 0.512 8.937 51237 Z= 0.264 Chirality : 0.045 0.706 6086 Planarity : 0.003 0.085 6466 Dihedral : 4.531 24.146 4935 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer Outliers : 0.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.12), residues: 4540 helix: 1.10 (0.19), residues: 768 sheet: -0.21 (0.14), residues: 1440 loop : -0.45 (0.13), residues: 2332 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9080 Ramachandran restraints generated. 4540 Oldfield, 0 Emsley, 4540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9080 Ramachandran restraints generated. 4540 Oldfield, 0 Emsley, 4540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 4024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 186 time to evaluate : 4.389 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 outliers start: 17 outliers final: 13 residues processed: 194 average time/residue: 1.0911 time to fit residues: 329.8456 Evaluate side-chains 192 residues out of total 4024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 179 time to evaluate : 4.370 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 5 residues processed: 13 average time/residue: 0.7345 time to fit residues: 22.5408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 459 random chunks: chunk 402 optimal weight: 20.0000 chunk 423 optimal weight: 30.0000 chunk 386 optimal weight: 9.9990 chunk 412 optimal weight: 3.9990 chunk 248 optimal weight: 5.9990 chunk 179 optimal weight: 2.9990 chunk 323 optimal weight: 0.0470 chunk 126 optimal weight: 9.9990 chunk 372 optimal weight: 20.0000 chunk 389 optimal weight: 50.0000 chunk 410 optimal weight: 5.9990 overall best weight: 3.8086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 641 ASN ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.5200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.095 37672 Z= 0.325 Angle : 0.565 9.178 51237 Z= 0.292 Chirality : 0.046 0.718 6086 Planarity : 0.004 0.075 6466 Dihedral : 4.600 24.360 4935 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer Outliers : 0.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.12), residues: 4540 helix: 0.84 (0.19), residues: 768 sheet: -0.29 (0.14), residues: 1412 loop : -0.60 (0.13), residues: 2360 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9080 Ramachandran restraints generated. 4540 Oldfield, 0 Emsley, 4540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9080 Ramachandran restraints generated. 4540 Oldfield, 0 Emsley, 4540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 4024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 184 time to evaluate : 4.381 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 outliers start: 14 outliers final: 10 residues processed: 191 average time/residue: 1.1011 time to fit residues: 328.2515 Evaluate side-chains 186 residues out of total 4024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 176 time to evaluate : 4.331 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 2 residues processed: 10 average time/residue: 0.7255 time to fit residues: 18.4082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 459 random chunks: chunk 270 optimal weight: 7.9990 chunk 435 optimal weight: 9.9990 chunk 266 optimal weight: 0.5980 chunk 206 optimal weight: 9.9990 chunk 303 optimal weight: 6.9990 chunk 457 optimal weight: 30.0000 chunk 420 optimal weight: 7.9990 chunk 364 optimal weight: 1.9990 chunk 37 optimal weight: 0.3980 chunk 281 optimal weight: 1.9990 chunk 223 optimal weight: 4.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 644 GLN ** A 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.5272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.067 37672 Z= 0.203 Angle : 0.525 13.758 51237 Z= 0.270 Chirality : 0.045 0.708 6086 Planarity : 0.004 0.074 6466 Dihedral : 4.515 24.289 4935 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer Outliers : 0.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.12), residues: 4540 helix: 1.07 (0.19), residues: 768 sheet: -0.25 (0.13), residues: 1440 loop : -0.49 (0.13), residues: 2332 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9080 Ramachandran restraints generated. 4540 Oldfield, 0 Emsley, 4540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9080 Ramachandran restraints generated. 4540 Oldfield, 0 Emsley, 4540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 4024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 175 time to evaluate : 4.400 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 outliers start: 4 outliers final: 3 residues processed: 178 average time/residue: 1.1146 time to fit residues: 308.6174 Evaluate side-chains 176 residues out of total 4024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 173 time to evaluate : 4.390 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 3 average time/residue: 0.7034 time to fit residues: 9.2493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 459 random chunks: chunk 289 optimal weight: 0.0870 chunk 387 optimal weight: 5.9990 chunk 111 optimal weight: 8.9990 chunk 335 optimal weight: 20.0000 chunk 53 optimal weight: 0.9990 chunk 101 optimal weight: 20.0000 chunk 364 optimal weight: 0.8980 chunk 152 optimal weight: 5.9990 chunk 374 optimal weight: 1.9990 chunk 46 optimal weight: 9.9990 chunk 67 optimal weight: 5.9990 overall best weight: 1.9964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 GLN ** 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 = 0.4516 r_free = 0.4516 target = 0.116653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.071091 restraints weight = 355555.252| |-----------------------------------------------------------------------------| r_work (start): 0.3608 rms_B_bonded: 3.62 r_work: 0.3469 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3323 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.5388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.067 37672 Z= 0.205 Angle : 0.513 8.006 51237 Z= 0.264 Chirality : 0.045 0.710 6086 Planarity : 0.003 0.072 6466 Dihedral : 4.416 24.629 4935 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer Outliers : 0.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.12), residues: 4540 helix: 1.21 (0.19), residues: 768 sheet: -0.16 (0.14), residues: 1416 loop : -0.48 (0.13), residues: 2356 =============================================================================== Job complete usr+sys time: 13071.95 seconds wall clock time: 228 minutes 37.17 seconds (13717.17 seconds total)