Starting phenix.real_space_refine on Sun Mar 10 14:44:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kkl_22910/03_2024/7kkl_22910_trim.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kkl_22910/03_2024/7kkl_22910.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.85 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kkl_22910/03_2024/7kkl_22910.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kkl_22910/03_2024/7kkl_22910.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kkl_22910/03_2024/7kkl_22910_trim.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kkl_22910/03_2024/7kkl_22910_trim.pdb" } resolution = 2.85 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.011 sd= 0.385 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 117 5.16 5 C 17160 2.51 5 N 4437 2.21 5 O 5310 1.98 5 H 25437 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 PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 138": "OD1" <-> "OD2" Residue "A PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 224": "OE1" <-> "OE2" 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 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 TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 421": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 449": "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 484": "OE1" <-> "OE2" Residue "A PHE 486": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 489": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 516": "OE1" <-> "OE2" Residue "A PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 718": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 756": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 1072": "OE1" <-> "OE2" Residue "A PHE 1089": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 1095": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 138": "OD1" <-> "OD2" Residue "C PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 224": "OE1" <-> "OE2" 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 TYR 313": "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 TYR 351": "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 TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 421": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 449": "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 484": "OE1" <-> "OE2" Residue "C PHE 486": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 489": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 516": "OE1" <-> "OE2" Residue "C PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 718": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 756": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 1072": "OE1" <-> "OE2" Residue "C PHE 1089": "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 "E PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 138": "OD1" <-> "OD2" Residue "D PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 224": "OE1" <-> "OE2" Residue "D PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 421": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 484": "OE1" <-> "OE2" Residue "D PHE 486": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 489": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 516": "OE1" <-> "OE2" Residue "D PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 718": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 756": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 1072": "OE1" <-> "OE2" Residue "D PHE 1089": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 1095": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 52461 Number of models: 1 Model: "" Number of chains: 27 Chain: "A" Number of atoms: 15441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1002, 15441 Classifications: {'peptide': 1002} Link IDs: {'PTRANS': 49, 'TRANS': 952} Chain breaks: 7 Chain: "B" Number of atoms: 1752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 1752 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 4, 'TRANS': 113} Chain: "C" Number of atoms: 15441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1002, 15441 Classifications: {'peptide': 1002} Link IDs: {'PTRANS': 49, 'TRANS': 952} Chain breaks: 7 Chain: "E" Number of atoms: 1752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 1752 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 4, 'TRANS': 113} Chain: "D" Number of atoms: 15441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1002, 15441 Classifications: {'peptide': 1002} Link IDs: {'PTRANS': 49, 'TRANS': 952} Chain breaks: 7 Chain: "F" Number of atoms: 1752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 1752 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 4, 'TRANS': 113} Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 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 dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "C" 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 dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "D" 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 dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Time building chain proxies: 17.53, per 1000 atoms: 0.33 Number of scatterers: 52461 At special positions: 0 Unit cell: (140.946, 140.946, 192.654, 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 117 16.00 O 5310 8.00 N 4437 7.00 C 17160 6.00 H 25437 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, 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=2.02 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.08 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.04 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.02 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.02 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.02 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 96 " distance=2.04 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.02 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.09 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.04 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.02 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.02 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.02 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.04 Simple disulfide: pdb=" SG CYS D 131 " - pdb=" SG CYS D 166 " distance=2.03 Simple disulfide: pdb=" SG CYS D 291 " - pdb=" SG CYS D 301 " distance=2.02 Simple disulfide: pdb=" SG CYS D 336 " - pdb=" SG CYS D 361 " distance=2.03 Simple disulfide: pdb=" SG CYS D 379 " - pdb=" SG CYS D 432 " distance=2.03 Simple disulfide: pdb=" SG CYS D 391 " - pdb=" SG CYS D 525 " distance=2.08 Simple disulfide: pdb=" SG CYS D 480 " - pdb=" SG CYS D 488 " distance=2.03 Simple disulfide: pdb=" SG CYS D 538 " - pdb=" SG CYS D 590 " distance=2.03 Simple disulfide: pdb=" SG CYS D 617 " - pdb=" SG CYS D 649 " distance=2.04 Simple disulfide: pdb=" SG CYS D 662 " - pdb=" SG CYS D 671 " distance=2.02 Simple disulfide: pdb=" SG CYS D 738 " - pdb=" SG CYS D 760 " distance=2.03 Simple disulfide: pdb=" SG CYS D 743 " - pdb=" SG CYS D 749 " distance=2.03 Simple disulfide: pdb=" SG CYS D1032 " - pdb=" SG CYS D1043 " distance=2.02 Simple disulfide: pdb=" SG CYS D1082 " - pdb=" SG CYS D1126 " distance=2.02 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 282 " " NAG A1303 " - " ASN A 603 " " NAG A1304 " - " ASN A 616 " " NAG A1305 " - " ASN A 657 " " NAG A1306 " - " ASN A 709 " " NAG A1307 " - " ASN A1074 " " NAG A1308 " - " ASN A 165 " " NAG A1309 " - " ASN A 331 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 282 " " NAG C1303 " - " ASN C 603 " " NAG C1304 " - " ASN C 616 " " NAG C1305 " - " ASN C 657 " " NAG C1306 " - " ASN C 709 " " NAG C1307 " - " ASN C1074 " " NAG C1308 " - " ASN C 165 " " NAG C1309 " - " ASN C 331 " " NAG D1301 " - " ASN D 61 " " NAG D1302 " - " ASN D 282 " " NAG D1303 " - " ASN D 603 " " NAG D1304 " - " ASN D 616 " " NAG D1305 " - " ASN D 657 " " NAG D1306 " - " ASN D 709 " " NAG D1307 " - " ASN D1074 " " NAG D1308 " - " ASN D 165 " " NAG D1309 " - " ASN D 331 " " NAG G 1 " - " ASN A 234 " " NAG H 1 " - " ASN A 717 " " NAG I 1 " - " ASN A 801 " " NAG J 1 " - " ASN A1098 " " NAG K 1 " - " ASN A1134 " " NAG L 1 " - " ASN A 343 " " NAG M 1 " - " ASN C 234 " " NAG N 1 " - " ASN C 717 " " NAG O 1 " - " ASN C 801 " " NAG P 1 " - " ASN C1098 " " NAG Q 1 " - " ASN C1134 " " NAG R 1 " - " ASN C 343 " " NAG S 1 " - " ASN D 234 " " NAG T 1 " - " ASN D 717 " " NAG U 1 " - " ASN D 801 " " NAG V 1 " - " ASN D1098 " " NAG W 1 " - " ASN D1134 " " NAG X 1 " - " ASN D 343 " Time building additional restraints: 32.81 Conformation dependent library (CDL) restraints added in 4.2 seconds 6612 Ramachandran restraints generated. 3306 Oldfield, 0 Emsley, 3306 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6252 Finding SS restraints... Secondary structure from input PDB file: 87 helices and 54 sheets defined 25.4% alpha, 33.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.66 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.910A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.590A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 386 through 389 Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.709A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 739 through 744 Processing helix chain 'A' and resid 746 through 753 Processing helix chain 'A' and resid 754 through 757 Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.822A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 885 removed outlier: 3.539A pdb=" N GLY A 885 " --> pdb=" O THR A 881 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 913 through 918 Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 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: 4.793A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 4.122A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 30 Processing helix chain 'B' and resid 62 through 65 Processing helix chain 'B' and resid 74 through 76 No H-bonds generated for 'chain 'B' and resid 74 through 76' Processing helix chain 'B' and resid 87 through 91 Processing helix chain 'B' and resid 102 through 106 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: 3.592A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 386 through 389 Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.722A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 739 through 744 Processing helix chain 'C' and resid 746 through 753 Processing helix chain 'C' and resid 754 through 757 Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.823A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 885 removed outlier: 3.537A pdb=" N GLY C 885 " --> pdb=" O THR C 881 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 913 through 918 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 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: 4.863A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1147 removed outlier: 4.122A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'E' and resid 25 through 30 Processing helix chain 'E' and resid 62 through 65 Processing helix chain 'E' and resid 74 through 76 No H-bonds generated for 'chain 'E' and resid 74 through 76' Processing helix chain 'E' and resid 87 through 91 Processing helix chain 'E' and resid 102 through 106 Processing helix chain 'D' and resid 294 through 303 Processing helix chain 'D' and resid 337 through 343 removed outlier: 3.916A pdb=" N VAL D 341 " --> pdb=" O PRO D 337 " (cutoff:3.500A) Processing helix chain 'D' and resid 349 through 353 removed outlier: 3.590A pdb=" N TRP D 353 " --> pdb=" O VAL D 350 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 370 Processing helix chain 'D' and resid 386 through 390 Processing helix chain 'D' and resid 405 through 410 removed outlier: 4.719A pdb=" N ARG D 408 " --> pdb=" O ASP D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 422 Processing helix chain 'D' and resid 502 through 505 Processing helix chain 'D' and resid 739 through 744 Processing helix chain 'D' and resid 746 through 753 Processing helix chain 'D' and resid 754 through 757 Processing helix chain 'D' and resid 758 through 783 removed outlier: 3.825A pdb=" N ASP D 775 " --> pdb=" O ALA D 771 " (cutoff:3.500A) Processing helix chain 'D' and resid 816 through 826 Processing helix chain 'D' and resid 866 through 885 removed outlier: 3.537A pdb=" N GLY D 885 " --> pdb=" O THR D 881 " (cutoff:3.500A) Processing helix chain 'D' and resid 886 through 890 Processing helix chain 'D' and resid 897 through 908 Processing helix chain 'D' and resid 913 through 918 Processing helix chain 'D' and resid 919 through 941 Processing helix chain 'D' and resid 942 through 944 No H-bonds generated for 'chain 'D' and resid 942 through 944' Processing helix chain 'D' and resid 945 through 965 Processing helix chain 'D' and resid 966 through 968 No H-bonds generated for 'chain 'D' and resid 966 through 968' Processing helix chain 'D' and resid 976 through 982 Processing helix chain 'D' and resid 985 through 1033 removed outlier: 4.865A pdb=" N VAL D 991 " --> pdb=" O PRO D 987 " (cutoff:3.500A) Processing helix chain 'D' and resid 1140 through 1147 removed outlier: 4.120A pdb=" N GLU D1144 " --> pdb=" O PRO D1140 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 30 Processing helix chain 'F' and resid 62 through 65 Processing helix chain 'F' and resid 74 through 76 No H-bonds generated for 'chain 'F' and resid 74 through 76' Processing helix chain 'F' and resid 87 through 91 Processing helix chain 'F' and resid 102 through 106 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.538A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 6.504A pdb=" N GLY D 566 " --> pdb=" O ASP D 574 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N ASP D 574 " --> pdb=" O ILE D 587 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLU D 324 " --> pdb=" O CYS D 538 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 7.817A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.762A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.324A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.934A 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: 5.446A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 324 through 328 removed outlier: 3.695A pdb=" N GLU A 324 " --> pdb=" O CYS A 538 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N PHE A 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA9, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.377A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB2, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 660 removed outlier: 4.995A pdb=" N THR A 696 " --> pdb=" O VAL A 656 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N ASN A 658 " --> pdb=" O THR A 696 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 702 through 704 Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.402A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N ASN A 717 " --> pdb=" O ALA A1070 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.402A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N ASN A 717 " --> pdb=" O ALA A1070 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.485A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 788 through 790 removed outlier: 6.206A pdb=" N ILE A 788 " --> pdb=" O ASN D 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.496A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 4 through 7 removed outlier: 6.395A pdb=" N GLY B 16 " --> pdb=" O SER B 85 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 10 through 13 removed outlier: 6.382A pdb=" N GLY B 10 " --> pdb=" O THR B 116 " (cutoff:3.500A) removed outlier: 7.702A pdb=" N SER B 118 " --> pdb=" O GLY B 10 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N VAL B 12 " --> pdb=" O SER B 118 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N MET B 34 " --> pdb=" O GLY B 50 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N GLY B 50 " --> pdb=" O MET B 34 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N TRP B 36 " --> pdb=" O VAL B 48 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 28 through 30 removed outlier: 8.569A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 47 through 55 removed outlier: 7.817A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 84 through 85 removed outlier: 6.764A pdb=" N LEU C 141 " --> pdb=" O LEU C 244 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 84 through 85 removed outlier: 6.321A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.444A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.322A 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: 6.688A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 324 through 328 removed outlier: 3.693A pdb=" N GLU C 324 " --> pdb=" O CYS C 538 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N PHE C 565 " --> pdb=" O PHE D 43 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 354 through 358 Processing sheet with id=AD1, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.371A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AD3, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AD4, first strand: chain 'C' and resid 654 through 660 removed outlier: 4.993A pdb=" N THR C 696 " --> pdb=" O VAL C 656 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N ASN C 658 " --> pdb=" O THR C 696 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 702 through 704 Processing sheet with id=AD6, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.406A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 7.033A 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: 6.093A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N ASN C 717 " --> pdb=" O ALA C1070 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.406A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 7.033A 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: 6.093A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N ASN C 717 " --> pdb=" O ALA C1070 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.484A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.498A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'E' and resid 4 through 7 removed outlier: 6.393A pdb=" N GLY E 16 " --> pdb=" O SER E 85 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'E' and resid 10 through 13 removed outlier: 6.379A pdb=" N GLY E 10 " --> pdb=" O THR E 116 " (cutoff:3.500A) removed outlier: 7.698A pdb=" N SER E 118 " --> pdb=" O GLY E 10 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N VAL E 12 " --> pdb=" O SER E 118 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N MET E 34 " --> pdb=" O GLY E 50 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N GLY E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 28 through 30 removed outlier: 8.572A pdb=" N ASN D 61 " --> pdb=" O TYR D 269 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N TYR D 269 " --> pdb=" O ASN D 61 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ALA D 264 " --> pdb=" O THR D 95 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N PHE D 201 " --> pdb=" O ASP D 228 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N ASP D 228 " --> pdb=" O PHE D 201 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N ILE D 203 " --> pdb=" O LEU D 226 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N HIS D 207 " --> pdb=" O ALA D 222 " (cutoff:3.500A) removed outlier: 9.925A pdb=" N ALA D 222 " --> pdb=" O HIS D 207 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N VAL D 36 " --> pdb=" O LEU D 223 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 47 through 55 removed outlier: 7.806A pdb=" N THR D 274 " --> pdb=" O ASP D 290 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N ASP D 290 " --> pdb=" O THR D 274 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N LEU D 276 " --> pdb=" O ALA D 288 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N ALA D 288 " --> pdb=" O LEU D 276 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N LYS D 278 " --> pdb=" O THR D 286 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 84 through 85 removed outlier: 6.735A pdb=" N LEU D 141 " --> pdb=" O LEU D 244 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 84 through 85 removed outlier: 6.311A pdb=" N ALA D 243 " --> pdb=" O ILE D 101 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N ILE D 101 " --> pdb=" O ALA D 243 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N ARG D 102 " --> pdb=" O ASN D 121 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 311 through 319 removed outlier: 5.472A pdb=" N ILE D 312 " --> pdb=" O THR D 599 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N THR D 599 " --> pdb=" O ILE D 312 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N GLN D 314 " --> pdb=" O VAL D 597 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N VAL D 597 " --> pdb=" O GLN D 314 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 354 through 358 Processing sheet with id=AE9, first strand: chain 'D' and resid 361 through 362 removed outlier: 6.376A pdb=" N CYS D 361 " --> pdb=" O CYS D 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE9 Processing sheet with id=AF1, first strand: chain 'D' and resid 452 through 454 Processing sheet with id=AF2, first strand: chain 'D' and resid 473 through 474 Processing sheet with id=AF3, first strand: chain 'D' and resid 654 through 660 removed outlier: 4.993A pdb=" N THR D 696 " --> pdb=" O VAL D 656 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N ASN D 658 " --> pdb=" O THR D 696 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ILE D 670 " --> pdb=" O ILE D 666 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'D' and resid 711 through 728 removed outlier: 6.407A pdb=" N SER D 711 " --> pdb=" O THR D1076 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N THR D1076 " --> pdb=" O SER D 711 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N ALA D 713 " --> pdb=" O ASN D1074 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N ASN D1074 " --> pdb=" O ALA D 713 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N GLU D1072 " --> pdb=" O PRO D 715 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N ASN D 717 " --> pdb=" O ALA D1070 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N TYR D1067 " --> pdb=" O HIS D1048 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N HIS D1048 " --> pdb=" O TYR D1067 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'D' and resid 711 through 728 removed outlier: 6.407A pdb=" N SER D 711 " --> pdb=" O THR D1076 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N THR D1076 " --> pdb=" O SER D 711 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N ALA D 713 " --> pdb=" O ASN D1074 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N ASN D1074 " --> pdb=" O ALA D 713 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N GLU D1072 " --> pdb=" O PRO D 715 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N ASN D 717 " --> pdb=" O ALA D1070 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ALA D1078 " --> pdb=" O PHE D1095 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N PHE D1095 " --> pdb=" O ALA D1078 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'D' and resid 733 through 736 removed outlier: 4.483A pdb=" N LYS D 733 " --> pdb=" O LEU D 861 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'D' and resid 1120 through 1125 removed outlier: 4.496A pdb=" N ALA D1087 " --> pdb=" O SER D1123 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'F' and resid 4 through 7 removed outlier: 6.399A pdb=" N GLY F 16 " --> pdb=" O SER F 85 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'F' and resid 10 through 13 removed outlier: 6.377A pdb=" N GLY F 10 " --> pdb=" O THR F 116 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N SER F 118 " --> pdb=" O GLY F 10 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N VAL F 12 " --> pdb=" O SER F 118 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N MET F 34 " --> pdb=" O GLY F 50 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N GLY F 50 " --> pdb=" O MET F 34 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N TRP F 36 " --> pdb=" O VAL F 48 " (cutoff:3.500A) 1205 hydrogen bonds defined for protein. 3213 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: 23.02 Time building geometry restraints manager: 34.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.95 - 1.13: 25433 1.13 - 1.31: 4748 1.31 - 1.49: 12514 1.49 - 1.67: 10201 1.67 - 1.86: 147 Bond restraints: 53043 Sorted by residual: bond pdb=" N GLU C1072 " pdb=" H GLU C1072 " ideal model delta sigma weight residual 0.860 1.188 -0.328 2.00e-02 2.50e+03 2.69e+02 bond pdb=" NH1 ARG C1091 " pdb="HH12 ARG C1091 " ideal model delta sigma weight residual 0.860 1.048 -0.188 2.00e-02 2.50e+03 8.85e+01 bond pdb=" NH1 ARG D1091 " pdb="HH12 ARG D1091 " ideal model delta sigma weight residual 0.860 1.048 -0.188 2.00e-02 2.50e+03 8.85e+01 bond pdb=" NH1 ARG A1091 " pdb="HH12 ARG A1091 " ideal model delta sigma weight residual 0.860 1.048 -0.188 2.00e-02 2.50e+03 8.83e+01 bond pdb=" NH2 ARG C 355 " pdb="HH21 ARG C 355 " ideal model delta sigma weight residual 0.860 1.047 -0.187 2.00e-02 2.50e+03 8.74e+01 ... (remaining 53038 not shown) Histogram of bond angle deviations from ideal: 87.14 - 96.58: 6 96.58 - 106.01: 1344 106.01 - 115.44: 61514 115.44 - 124.87: 31421 124.87 - 134.30: 851 Bond angle restraints: 95136 Sorted by residual: angle pdb=" N GLN A1071 " pdb=" CA GLN A1071 " pdb=" C GLN A1071 " ideal model delta sigma weight residual 110.80 87.14 23.66 2.13e+00 2.20e-01 1.23e+02 angle pdb=" N GLN D1071 " pdb=" CA GLN D1071 " pdb=" C GLN D1071 " ideal model delta sigma weight residual 110.80 87.84 22.96 2.13e+00 2.20e-01 1.16e+02 angle pdb=" N VAL C1040 " pdb=" CA VAL C1040 " pdb=" C VAL C1040 " ideal model delta sigma weight residual 110.42 119.60 -9.18 9.60e-01 1.09e+00 9.14e+01 angle pdb=" N VAL A1040 " pdb=" CA VAL A1040 " pdb=" C VAL A1040 " ideal model delta sigma weight residual 110.42 119.58 -9.16 9.60e-01 1.09e+00 9.10e+01 angle pdb=" N VAL D1040 " pdb=" CA VAL D1040 " pdb=" C VAL D1040 " ideal model delta sigma weight residual 110.42 119.57 -9.15 9.60e-01 1.09e+00 9.08e+01 ... (remaining 95131 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.31: 25038 17.31 - 34.62: 867 34.62 - 51.93: 289 51.93 - 69.24: 139 69.24 - 86.55: 25 Dihedral angle restraints: 26358 sinusoidal: 14697 harmonic: 11661 Sorted by residual: dihedral pdb=" CA GLN A1071 " pdb=" C GLN A1071 " pdb=" N GLU A1072 " pdb=" CA GLU A1072 " ideal model delta harmonic sigma weight residual 180.00 154.62 25.38 0 5.00e+00 4.00e-02 2.58e+01 dihedral pdb=" CA GLN D1071 " pdb=" C GLN D1071 " pdb=" N GLU D1072 " pdb=" CA GLU D1072 " ideal model delta harmonic sigma weight residual 180.00 155.27 24.73 0 5.00e+00 4.00e-02 2.45e+01 dihedral pdb=" CB CYS E 22 " pdb=" SG CYS E 22 " pdb=" SG CYS E 96 " pdb=" CB CYS E 96 " ideal model delta sinusoidal sigma weight residual 93.00 53.86 39.14 1 1.00e+01 1.00e-02 2.15e+01 ... (remaining 26355 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.107: 3165 0.107 - 0.214: 908 0.214 - 0.321: 229 0.321 - 0.428: 90 0.428 - 0.535: 42 Chirality restraints: 4434 Sorted by residual: chirality pdb=" C1 NAG I 2 " pdb=" O4 NAG I 1 " pdb=" C2 NAG I 2 " pdb=" O5 NAG I 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.63 0.23 2.00e-02 2.50e+03 1.36e+02 chirality pdb=" C1 NAG U 2 " pdb=" O4 NAG U 1 " pdb=" C2 NAG U 2 " pdb=" O5 NAG U 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.63 0.23 2.00e-02 2.50e+03 1.33e+02 chirality pdb=" C1 NAG O 2 " pdb=" O4 NAG O 1 " pdb=" C2 NAG O 2 " pdb=" O5 NAG O 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.63 0.23 2.00e-02 2.50e+03 1.32e+02 ... (remaining 4431 not shown) Planarity restraints: 8001 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN C1071 " 0.116 2.00e-02 2.50e+03 1.91e-01 3.65e+02 pdb=" N GLU C1072 " -0.331 2.00e-02 2.50e+03 pdb=" CA GLU C1072 " 0.112 2.00e-02 2.50e+03 pdb=" H GLU C1072 " 0.103 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN A1071 " 0.049 2.00e-02 2.50e+03 8.98e-02 8.07e+01 pdb=" N GLU A1072 " -0.156 2.00e-02 2.50e+03 pdb=" CA GLU A1072 " 0.050 2.00e-02 2.50e+03 pdb=" H GLU A1072 " 0.056 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN D1071 " -0.048 2.00e-02 2.50e+03 8.80e-02 7.74e+01 pdb=" N GLU D1072 " 0.152 2.00e-02 2.50e+03 pdb=" CA GLU D1072 " -0.049 2.00e-02 2.50e+03 pdb=" H GLU D1072 " -0.055 2.00e-02 2.50e+03 ... (remaining 7998 not shown) Histogram of nonbonded interaction distances: 1.64 - 2.23: 5393 2.23 - 2.82: 103179 2.82 - 3.42: 143187 3.42 - 4.01: 197081 4.01 - 4.60: 289134 Nonbonded interactions: 737974 Sorted by model distance: nonbonded pdb=" HA PRO A 715 " pdb=" O GLN A1071 " model vdw 1.641 2.620 nonbonded pdb=" HA PRO D 715 " pdb=" O GLN D1071 " model vdw 1.648 2.620 nonbonded pdb=" HB1 ALA A 372 " pdb=" HG SER F 102 " model vdw 1.678 2.270 nonbonded pdb=" HA PRO C 715 " pdb=" O GLN C1071 " model vdw 1.689 2.620 nonbonded pdb=" H ASN D 360 " pdb="HG22 THR D 523 " model vdw 1.692 2.270 ... (remaining 737969 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' selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' 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: 0.000 Normalize map: mean=0, sd=1: 2.130 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: 0.590 Extract box with map and model: 13.360 Check model and map are aligned: 0.600 Set scattering table: 0.380 Process input model: 132.350 Find NCS groups from input model: 2.240 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:11.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 163.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 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 : 0.020 0.133 27606 Z= 1.323 Angle : 1.691 23.656 37545 Z= 1.134 Chirality : 0.123 0.535 4434 Planarity : 0.008 0.048 4782 Dihedral : 9.889 86.551 10860 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 0.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 0.41 % Allowed : 0.10 % Favored : 99.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.96 (0.14), residues: 3306 helix: 0.14 (0.18), residues: 657 sheet: 1.36 (0.17), residues: 870 loop : 0.61 (0.14), residues: 1779 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.008 TRP D 64 HIS 0.012 0.003 HIS D1048 PHE 0.029 0.005 PHE D 58 TYR 0.048 0.007 TYR A 489 ARG 0.008 0.001 ARG B 67 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6612 Ramachandran restraints generated. 3306 Oldfield, 0 Emsley, 3306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6612 Ramachandran restraints generated. 3306 Oldfield, 0 Emsley, 3306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 506 residues out of total 2898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 494 time to evaluate : 3.684 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: A 115 GLN cc_start: 0.7664 (mm-40) cc_final: 0.7268 (mm-40) REVERT: A 200 TYR cc_start: 0.8121 (m-80) cc_final: 0.7878 (m-10) REVERT: A 603 ASN cc_start: 0.7917 (OUTLIER) cc_final: 0.7706 (t0) REVERT: B 37 TYR cc_start: 0.8109 (m-80) cc_final: 0.7570 (m-80) REVERT: B 107 ASP cc_start: 0.8546 (m-30) cc_final: 0.8238 (m-30) REVERT: B 116 THR cc_start: 0.8581 (m) cc_final: 0.8320 (p) REVERT: C 115 GLN cc_start: 0.7698 (mm-40) cc_final: 0.7316 (mm-40) REVERT: C 140 PHE cc_start: 0.8507 (p90) cc_final: 0.8266 (p90) REVERT: C 365 TYR cc_start: 0.8958 (m-80) cc_final: 0.8463 (m-80) REVERT: C 603 ASN cc_start: 0.7887 (OUTLIER) cc_final: 0.7656 (t0) REVERT: E 37 TYR cc_start: 0.8170 (m-80) cc_final: 0.7657 (m-80) REVERT: E 47 LEU cc_start: 0.8741 (tp) cc_final: 0.8538 (tm) REVERT: E 76 LYS cc_start: 0.9244 (mtmm) cc_final: 0.8991 (mmmm) REVERT: E 107 ASP cc_start: 0.8419 (m-30) cc_final: 0.8176 (m-30) REVERT: E 108 TYR cc_start: 0.8707 (m-80) cc_final: 0.8448 (m-80) REVERT: E 116 THR cc_start: 0.8664 (m) cc_final: 0.8390 (p) REVERT: D 115 GLN cc_start: 0.7794 (mm-40) cc_final: 0.7470 (mm-40) REVERT: D 133 PHE cc_start: 0.7734 (m-80) cc_final: 0.7485 (m-80) REVERT: D 200 TYR cc_start: 0.8136 (m-80) cc_final: 0.7894 (m-10) REVERT: D 603 ASN cc_start: 0.7865 (OUTLIER) cc_final: 0.7628 (t0) REVERT: F 37 TYR cc_start: 0.8043 (m-80) cc_final: 0.7814 (m-80) REVERT: F 107 ASP cc_start: 0.8440 (m-30) cc_final: 0.8227 (m-30) REVERT: F 116 THR cc_start: 0.8787 (m) cc_final: 0.8511 (p) outliers start: 12 outliers final: 1 residues processed: 506 average time/residue: 2.2923 time to fit residues: 1359.7919 Evaluate side-chains 264 residues out of total 2898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 260 time to evaluate : 3.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain D residue 603 ASN Chi-restraints excluded: chain D residue 945 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 281 optimal weight: 0.8980 chunk 252 optimal weight: 1.9990 chunk 140 optimal weight: 2.9990 chunk 86 optimal weight: 0.7980 chunk 170 optimal weight: 0.9990 chunk 134 optimal weight: 2.9990 chunk 261 optimal weight: 5.9990 chunk 101 optimal weight: 8.9990 chunk 158 optimal weight: 0.9990 chunk 194 optimal weight: 0.8980 chunk 302 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 ASN A 218 GLN A 784 GLN ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 GLN C 188 ASN ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 544 ASN C 784 GLN C1002 GLN E 39 GLN D 188 ASN D 784 GLN D1002 GLN D1005 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.2674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 27606 Z= 0.231 Angle : 0.677 9.255 37545 Z= 0.363 Chirality : 0.050 0.514 4434 Planarity : 0.005 0.069 4782 Dihedral : 6.060 53.290 4940 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 1.55 % Allowed : 8.66 % Favored : 89.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.03 (0.14), residues: 3306 helix: 1.65 (0.20), residues: 639 sheet: 0.83 (0.16), residues: 933 loop : 0.35 (0.14), residues: 1734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 109 HIS 0.004 0.001 HIS C 519 PHE 0.014 0.001 PHE C 486 TYR 0.016 0.001 TYR D1067 ARG 0.011 0.001 ARG D 646 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6612 Ramachandran restraints generated. 3306 Oldfield, 0 Emsley, 3306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6612 Ramachandran restraints generated. 3306 Oldfield, 0 Emsley, 3306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 2898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 313 time to evaluate : 3.211 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: A 115 GLN cc_start: 0.7569 (mm-40) cc_final: 0.7327 (mm110) REVERT: A 603 ASN cc_start: 0.7871 (OUTLIER) cc_final: 0.7588 (t0) REVERT: A 950 ASP cc_start: 0.8536 (t70) cc_final: 0.8321 (t0) REVERT: B 107 ASP cc_start: 0.8395 (m-30) cc_final: 0.8110 (m-30) REVERT: C 115 GLN cc_start: 0.7603 (mm-40) cc_final: 0.7325 (mm-40) REVERT: C 365 TYR cc_start: 0.8826 (m-80) cc_final: 0.8214 (m-80) REVERT: C 603 ASN cc_start: 0.7936 (OUTLIER) cc_final: 0.7621 (t0) REVERT: E 13 GLN cc_start: 0.8016 (pp30) cc_final: 0.7598 (pp30) REVERT: E 37 TYR cc_start: 0.7823 (m-80) cc_final: 0.7569 (m-80) REVERT: E 107 ASP cc_start: 0.8285 (m-30) cc_final: 0.8067 (m-30) REVERT: D 115 GLN cc_start: 0.7698 (mm-40) cc_final: 0.7433 (mm-40) REVERT: D 133 PHE cc_start: 0.7988 (m-80) cc_final: 0.7725 (m-80) REVERT: F 37 TYR cc_start: 0.7776 (m-80) cc_final: 0.7402 (m-80) REVERT: F 47 LEU cc_start: 0.9161 (tt) cc_final: 0.8957 (tm) REVERT: F 107 ASP cc_start: 0.8372 (m-30) cc_final: 0.8032 (m-30) outliers start: 45 outliers final: 18 residues processed: 341 average time/residue: 1.8681 time to fit residues: 774.7222 Evaluate side-chains 261 residues out of total 2898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 241 time to evaluate : 3.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 TRP Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain C residue 104 TRP Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain D residue 104 TRP Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 323 THR Chi-restraints excluded: chain D residue 326 ILE Chi-restraints excluded: chain D residue 619 GLU Chi-restraints excluded: chain D residue 858 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 168 optimal weight: 3.9990 chunk 93 optimal weight: 3.9990 chunk 251 optimal weight: 4.9990 chunk 205 optimal weight: 2.9990 chunk 83 optimal weight: 0.9980 chunk 302 optimal weight: 0.6980 chunk 327 optimal weight: 7.9990 chunk 269 optimal weight: 4.9990 chunk 300 optimal weight: 3.9990 chunk 103 optimal weight: 9.9990 chunk 243 optimal weight: 2.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 ASN ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 218 GLN C 394 ASN D1002 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.3255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 27606 Z= 0.289 Angle : 0.592 9.212 37545 Z= 0.314 Chirality : 0.046 0.341 4434 Planarity : 0.004 0.056 4782 Dihedral : 5.719 50.042 4936 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.86 % Allowed : 9.97 % Favored : 88.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.78 (0.14), residues: 3306 helix: 1.75 (0.20), residues: 639 sheet: 0.58 (0.17), residues: 843 loop : 0.13 (0.14), residues: 1824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 104 HIS 0.003 0.001 HIS A 519 PHE 0.015 0.001 PHE A 32 TYR 0.017 0.001 TYR D1067 ARG 0.006 0.001 ARG B 45 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6612 Ramachandran restraints generated. 3306 Oldfield, 0 Emsley, 3306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6612 Ramachandran restraints generated. 3306 Oldfield, 0 Emsley, 3306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 2898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 235 time to evaluate : 3.173 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: A 115 GLN cc_start: 0.7769 (mm-40) cc_final: 0.7446 (mm-40) REVERT: A 516 GLU cc_start: 0.7751 (mt-10) cc_final: 0.7543 (mt-10) REVERT: A 603 ASN cc_start: 0.7953 (OUTLIER) cc_final: 0.7673 (t0) REVERT: B 87 LYS cc_start: 0.7556 (ptpp) cc_final: 0.7096 (ptpt) REVERT: B 90 ASP cc_start: 0.8607 (m-30) cc_final: 0.8357 (m-30) REVERT: B 108 TYR cc_start: 0.8598 (m-80) cc_final: 0.8240 (m-80) REVERT: C 115 GLN cc_start: 0.7786 (mm-40) cc_final: 0.7535 (mm-40) REVERT: C 365 TYR cc_start: 0.8997 (m-80) cc_final: 0.8463 (m-80) REVERT: C 603 ASN cc_start: 0.7986 (OUTLIER) cc_final: 0.7723 (t0) REVERT: E 37 TYR cc_start: 0.7814 (m-80) cc_final: 0.7596 (m-80) REVERT: E 73 ASP cc_start: 0.5162 (p0) cc_final: 0.4440 (p0) REVERT: E 107 ASP cc_start: 0.8357 (m-30) cc_final: 0.8074 (m-30) REVERT: D 115 GLN cc_start: 0.7940 (mm-40) cc_final: 0.7670 (mm-40) REVERT: D 133 PHE cc_start: 0.8041 (m-80) cc_final: 0.7769 (m-80) REVERT: F 37 TYR cc_start: 0.7756 (m-80) cc_final: 0.7411 (m-80) REVERT: F 107 ASP cc_start: 0.8418 (m-30) cc_final: 0.8086 (m-30) outliers start: 54 outliers final: 27 residues processed: 264 average time/residue: 1.8304 time to fit residues: 591.3410 Evaluate side-chains 243 residues out of total 2898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 214 time to evaluate : 3.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 TRP Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain C residue 104 TRP Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain D residue 104 TRP Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 323 THR Chi-restraints excluded: chain D residue 503 VAL Chi-restraints excluded: chain D residue 603 ASN Chi-restraints excluded: chain D residue 619 GLU Chi-restraints excluded: chain D residue 760 CYS Chi-restraints excluded: chain D residue 856 ASN Chi-restraints excluded: chain D residue 858 LEU Chi-restraints excluded: chain D residue 1010 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 299 optimal weight: 1.9990 chunk 227 optimal weight: 5.9990 chunk 157 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 144 optimal weight: 3.9990 chunk 203 optimal weight: 2.9990 chunk 304 optimal weight: 3.9990 chunk 321 optimal weight: 1.9990 chunk 158 optimal weight: 2.9990 chunk 288 optimal weight: 0.9980 chunk 86 optimal weight: 2.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 388 ASN C 394 ASN D 388 ASN ** D1142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.3612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 27606 Z= 0.256 Angle : 0.545 8.988 37545 Z= 0.288 Chirality : 0.045 0.328 4434 Planarity : 0.003 0.054 4782 Dihedral : 5.566 49.956 4936 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 1.62 % Allowed : 10.39 % Favored : 87.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.66 (0.14), residues: 3306 helix: 1.77 (0.20), residues: 645 sheet: 0.55 (0.17), residues: 828 loop : -0.03 (0.14), residues: 1833 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 104 HIS 0.004 0.001 HIS A 655 PHE 0.016 0.001 PHE C 140 TYR 0.016 0.001 TYR D1067 ARG 0.006 0.000 ARG B 45 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6612 Ramachandran restraints generated. 3306 Oldfield, 0 Emsley, 3306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6612 Ramachandran restraints generated. 3306 Oldfield, 0 Emsley, 3306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 2898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 236 time to evaluate : 3.206 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: A 133 PHE cc_start: 0.7843 (m-80) cc_final: 0.7542 (m-80) REVERT: A 603 ASN cc_start: 0.8009 (OUTLIER) cc_final: 0.7783 (t0) REVERT: B 87 LYS cc_start: 0.7461 (ptpp) cc_final: 0.7061 (ptpt) REVERT: B 90 ASP cc_start: 0.8474 (m-30) cc_final: 0.8225 (m-30) REVERT: B 108 TYR cc_start: 0.8577 (m-80) cc_final: 0.8230 (m-80) REVERT: C 115 GLN cc_start: 0.7885 (mm-40) cc_final: 0.7654 (mm-40) REVERT: C 140 PHE cc_start: 0.8136 (p90) cc_final: 0.7936 (p90) REVERT: C 198 ASP cc_start: 0.7828 (m-30) cc_final: 0.7550 (m-30) REVERT: C 365 TYR cc_start: 0.9016 (m-80) cc_final: 0.8559 (m-80) REVERT: C 603 ASN cc_start: 0.7998 (OUTLIER) cc_final: 0.7791 (t0) REVERT: E 73 ASP cc_start: 0.4625 (p0) cc_final: 0.4368 (p0) REVERT: E 87 LYS cc_start: 0.8165 (ptpp) cc_final: 0.7338 (ptpp) REVERT: E 90 ASP cc_start: 0.8613 (m-30) cc_final: 0.7862 (m-30) REVERT: E 107 ASP cc_start: 0.8424 (m-30) cc_final: 0.8164 (m-30) REVERT: D 115 GLN cc_start: 0.7962 (mm-40) cc_final: 0.7723 (mm-40) REVERT: D 133 PHE cc_start: 0.8043 (m-80) cc_final: 0.7750 (m-80) REVERT: D 902 MET cc_start: 0.9133 (mmt) cc_final: 0.8718 (mmt) REVERT: D 950 ASP cc_start: 0.8460 (t70) cc_final: 0.8239 (t0) REVERT: F 6 GLU cc_start: 0.8177 (mt-10) cc_final: 0.7734 (mt-10) REVERT: F 37 TYR cc_start: 0.7570 (m-80) cc_final: 0.7335 (m-80) REVERT: F 90 ASP cc_start: 0.8663 (m-30) cc_final: 0.7955 (m-30) REVERT: F 107 ASP cc_start: 0.8469 (m-30) cc_final: 0.8149 (m-30) outliers start: 47 outliers final: 23 residues processed: 263 average time/residue: 1.8527 time to fit residues: 597.6290 Evaluate side-chains 237 residues out of total 2898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 212 time to evaluate : 3.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 TRP Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain C residue 104 TRP Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain D residue 104 TRP Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 323 THR Chi-restraints excluded: chain D residue 503 VAL Chi-restraints excluded: chain D residue 603 ASN Chi-restraints excluded: chain D residue 619 GLU Chi-restraints excluded: chain D residue 856 ASN Chi-restraints excluded: chain D residue 858 LEU Chi-restraints excluded: chain D residue 1010 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 268 optimal weight: 3.9990 chunk 182 optimal weight: 1.9990 chunk 4 optimal weight: 0.0770 chunk 239 optimal weight: 7.9990 chunk 132 optimal weight: 2.9990 chunk 274 optimal weight: 3.9990 chunk 222 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 chunk 164 optimal weight: 3.9990 chunk 288 optimal weight: 3.9990 chunk 81 optimal weight: 2.9990 overall best weight: 2.4146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 394 ASN ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1101 HIS ** D 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 moved from start: 0.3878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 27606 Z= 0.286 Angle : 0.542 9.320 37545 Z= 0.286 Chirality : 0.045 0.314 4434 Planarity : 0.003 0.059 4782 Dihedral : 5.664 48.947 4936 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.36 % Favored : 97.55 % Rotamer: Outliers : 1.55 % Allowed : 10.63 % Favored : 87.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.60 (0.14), residues: 3306 helix: 1.80 (0.20), residues: 645 sheet: 0.45 (0.17), residues: 828 loop : -0.07 (0.14), residues: 1833 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 104 HIS 0.004 0.001 HIS A1064 PHE 0.020 0.001 PHE D 140 TYR 0.016 0.001 TYR D1067 ARG 0.005 0.000 ARG B 45 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6612 Ramachandran restraints generated. 3306 Oldfield, 0 Emsley, 3306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6612 Ramachandran restraints generated. 3306 Oldfield, 0 Emsley, 3306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 2898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 223 time to evaluate : 3.219 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: A 242 LEU cc_start: 0.8768 (OUTLIER) cc_final: 0.8253 (mt) REVERT: B 90 ASP cc_start: 0.8493 (m-30) cc_final: 0.8243 (m-30) REVERT: B 108 TYR cc_start: 0.8606 (m-80) cc_final: 0.8243 (m-80) REVERT: C 115 GLN cc_start: 0.7894 (mm-40) cc_final: 0.7685 (mm-40) REVERT: C 140 PHE cc_start: 0.8080 (p90) cc_final: 0.7872 (p90) REVERT: C 365 TYR cc_start: 0.9017 (m-80) cc_final: 0.8578 (m-80) REVERT: E 77 ASN cc_start: 0.8568 (m-40) cc_final: 0.8340 (m-40) REVERT: E 90 ASP cc_start: 0.8184 (m-30) cc_final: 0.7847 (m-30) REVERT: E 107 ASP cc_start: 0.8480 (m-30) cc_final: 0.8179 (m-30) REVERT: D 133 PHE cc_start: 0.8092 (m-80) cc_final: 0.7792 (m-80) REVERT: D 950 ASP cc_start: 0.8454 (t70) cc_final: 0.8226 (t0) REVERT: F 6 GLU cc_start: 0.8159 (mt-10) cc_final: 0.7679 (mt-10) REVERT: F 37 TYR cc_start: 0.7678 (m-80) cc_final: 0.7392 (m-80) REVERT: F 90 ASP cc_start: 0.8236 (m-30) cc_final: 0.7763 (m-30) REVERT: F 107 ASP cc_start: 0.8554 (m-30) cc_final: 0.8220 (m-30) outliers start: 45 outliers final: 24 residues processed: 249 average time/residue: 2.0503 time to fit residues: 624.8794 Evaluate side-chains 229 residues out of total 2898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 204 time to evaluate : 3.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 TRP Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain C residue 104 TRP Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 115 VAL Chi-restraints excluded: chain D residue 104 TRP Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 323 THR Chi-restraints excluded: chain D residue 503 VAL Chi-restraints excluded: chain D residue 603 ASN Chi-restraints excluded: chain D residue 619 GLU Chi-restraints excluded: chain D residue 856 ASN Chi-restraints excluded: chain D residue 858 LEU Chi-restraints excluded: chain D residue 1010 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 108 optimal weight: 10.0000 chunk 289 optimal weight: 3.9990 chunk 63 optimal weight: 3.9990 chunk 188 optimal weight: 1.9990 chunk 79 optimal weight: 6.9990 chunk 322 optimal weight: 0.9980 chunk 267 optimal weight: 5.9990 chunk 149 optimal weight: 8.9990 chunk 26 optimal weight: 6.9990 chunk 106 optimal weight: 2.9990 chunk 169 optimal weight: 0.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 804 GLN C 394 ASN ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.4051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 27606 Z= 0.258 Angle : 0.529 9.218 37545 Z= 0.278 Chirality : 0.045 0.313 4434 Planarity : 0.003 0.063 4782 Dihedral : 5.610 52.595 4932 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.30 % Favored : 97.61 % Rotamer: Outliers : 1.45 % Allowed : 10.87 % Favored : 87.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.14), residues: 3306 helix: 1.86 (0.20), residues: 645 sheet: 0.50 (0.18), residues: 813 loop : -0.13 (0.14), residues: 1848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 886 HIS 0.003 0.001 HIS A 655 PHE 0.009 0.001 PHE C 718 TYR 0.021 0.001 TYR B 95 ARG 0.007 0.000 ARG F 45 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6612 Ramachandran restraints generated. 3306 Oldfield, 0 Emsley, 3306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6612 Ramachandran restraints generated. 3306 Oldfield, 0 Emsley, 3306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 2898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 220 time to evaluate : 3.150 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: A 133 PHE cc_start: 0.8053 (m-80) cc_final: 0.7797 (m-80) REVERT: A 242 LEU cc_start: 0.8783 (OUTLIER) cc_final: 0.8263 (mt) REVERT: A 950 ASP cc_start: 0.8415 (t70) cc_final: 0.8188 (t0) REVERT: B 87 LYS cc_start: 0.7380 (ptpp) cc_final: 0.7116 (ptpp) REVERT: B 90 ASP cc_start: 0.8487 (m-30) cc_final: 0.8235 (m-30) REVERT: B 108 TYR cc_start: 0.8585 (m-80) cc_final: 0.8248 (m-80) REVERT: C 115 GLN cc_start: 0.7917 (mm-40) cc_final: 0.7682 (mm110) REVERT: C 140 PHE cc_start: 0.8086 (p90) cc_final: 0.7820 (p90) REVERT: C 365 TYR cc_start: 0.9031 (m-80) cc_final: 0.8590 (m-80) REVERT: C 1142 GLN cc_start: 0.8188 (tp40) cc_final: 0.7910 (tp-100) REVERT: E 107 ASP cc_start: 0.8492 (m-30) cc_final: 0.8137 (m-30) REVERT: D 133 PHE cc_start: 0.8108 (m-80) cc_final: 0.7804 (m-80) REVERT: D 950 ASP cc_start: 0.8423 (t70) cc_final: 0.8198 (t0) REVERT: F 6 GLU cc_start: 0.8204 (mt-10) cc_final: 0.7747 (mt-10) REVERT: F 37 TYR cc_start: 0.7681 (m-80) cc_final: 0.7415 (m-80) REVERT: F 107 ASP cc_start: 0.8537 (m-30) cc_final: 0.8190 (m-30) outliers start: 42 outliers final: 26 residues processed: 244 average time/residue: 1.9254 time to fit residues: 568.2062 Evaluate side-chains 231 residues out of total 2898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 204 time to evaluate : 3.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 TRP Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain C residue 104 TRP Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 619 GLU Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 115 VAL Chi-restraints excluded: chain D residue 104 TRP Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 323 THR Chi-restraints excluded: chain D residue 503 VAL Chi-restraints excluded: chain D residue 603 ASN Chi-restraints excluded: chain D residue 619 GLU Chi-restraints excluded: chain D residue 856 ASN Chi-restraints excluded: chain D residue 858 LEU Chi-restraints excluded: chain D residue 1010 GLN Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain F residue 115 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 310 optimal weight: 1.9990 chunk 36 optimal weight: 7.9990 chunk 183 optimal weight: 1.9990 chunk 235 optimal weight: 4.9990 chunk 182 optimal weight: 2.9990 chunk 271 optimal weight: 5.9990 chunk 179 optimal weight: 2.9990 chunk 320 optimal weight: 0.9980 chunk 200 optimal weight: 2.9990 chunk 195 optimal weight: 3.9990 chunk 148 optimal weight: 0.6980 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 69 HIS C 394 ASN C 762 GLN ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.4162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 27606 Z= 0.220 Angle : 0.516 9.128 37545 Z= 0.271 Chirality : 0.045 0.293 4434 Planarity : 0.003 0.067 4782 Dihedral : 5.599 54.397 4932 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.51 % Favored : 97.40 % Rotamer: Outliers : 1.24 % Allowed : 10.90 % Favored : 87.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.56 (0.14), residues: 3306 helix: 1.79 (0.20), residues: 663 sheet: 0.43 (0.17), residues: 855 loop : -0.14 (0.14), residues: 1788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 104 HIS 0.003 0.001 HIS A 655 PHE 0.021 0.001 PHE A 140 TYR 0.014 0.001 TYR D1067 ARG 0.008 0.000 ARG F 45 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6612 Ramachandran restraints generated. 3306 Oldfield, 0 Emsley, 3306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6612 Ramachandran restraints generated. 3306 Oldfield, 0 Emsley, 3306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 2898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 224 time to evaluate : 3.215 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: A 133 PHE cc_start: 0.8018 (m-80) cc_final: 0.7752 (m-80) REVERT: A 242 LEU cc_start: 0.8775 (OUTLIER) cc_final: 0.8229 (mt) REVERT: A 950 ASP cc_start: 0.8385 (t70) cc_final: 0.8157 (t0) REVERT: B 87 LYS cc_start: 0.7362 (ptpp) cc_final: 0.7116 (ptpp) REVERT: B 90 ASP cc_start: 0.8496 (m-30) cc_final: 0.8256 (m-30) REVERT: B 108 TYR cc_start: 0.8582 (m-80) cc_final: 0.8238 (m-80) REVERT: C 115 GLN cc_start: 0.7915 (mm-40) cc_final: 0.7703 (mm110) REVERT: C 140 PHE cc_start: 0.8093 (p90) cc_final: 0.7845 (p90) REVERT: C 365 TYR cc_start: 0.9036 (m-80) cc_final: 0.8613 (m-80) REVERT: E 89 GLU cc_start: 0.7197 (pp20) cc_final: 0.6905 (pp20) REVERT: E 107 ASP cc_start: 0.8494 (m-30) cc_final: 0.8148 (m-30) REVERT: E 117 VAL cc_start: 0.7633 (OUTLIER) cc_final: 0.7414 (t) REVERT: D 133 PHE cc_start: 0.8072 (m-80) cc_final: 0.7765 (m-80) REVERT: D 950 ASP cc_start: 0.8388 (t70) cc_final: 0.8162 (t0) REVERT: F 6 GLU cc_start: 0.8215 (mt-10) cc_final: 0.7752 (mt-10) REVERT: F 37 TYR cc_start: 0.7688 (m-80) cc_final: 0.7444 (m-80) REVERT: F 90 ASP cc_start: 0.8008 (m-30) cc_final: 0.7289 (m-30) REVERT: F 107 ASP cc_start: 0.8550 (m-30) cc_final: 0.8201 (m-30) outliers start: 36 outliers final: 24 residues processed: 244 average time/residue: 1.9702 time to fit residues: 582.0298 Evaluate side-chains 232 residues out of total 2898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 206 time to evaluate : 3.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 TRP Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1082 CYS Chi-restraints excluded: chain C residue 104 TRP Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 619 GLU Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 115 VAL Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain D residue 104 TRP Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 323 THR Chi-restraints excluded: chain D residue 603 ASN Chi-restraints excluded: chain D residue 619 GLU Chi-restraints excluded: chain D residue 856 ASN Chi-restraints excluded: chain D residue 858 LEU Chi-restraints excluded: chain D residue 1010 GLN Chi-restraints excluded: chain F residue 4 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 198 optimal weight: 2.9990 chunk 128 optimal weight: 7.9990 chunk 191 optimal weight: 1.9990 chunk 96 optimal weight: 2.9990 chunk 63 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 chunk 204 optimal weight: 0.9990 chunk 218 optimal weight: 10.0000 chunk 158 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 252 optimal weight: 2.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 HIS A 675 GLN ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 69 HIS D 675 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8637 moved from start: 0.4327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 27606 Z= 0.262 Angle : 0.526 9.377 37545 Z= 0.276 Chirality : 0.044 0.294 4434 Planarity : 0.003 0.078 4782 Dihedral : 5.739 59.985 4932 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.06 % Favored : 96.85 % Rotamer: Outliers : 1.38 % Allowed : 11.04 % Favored : 87.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.50 (0.14), residues: 3306 helix: 1.74 (0.20), residues: 666 sheet: 0.43 (0.17), residues: 870 loop : -0.20 (0.14), residues: 1770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 886 HIS 0.004 0.001 HIS A1064 PHE 0.014 0.001 PHE C 342 TYR 0.027 0.001 TYR F 95 ARG 0.009 0.000 ARG F 45 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6612 Ramachandran restraints generated. 3306 Oldfield, 0 Emsley, 3306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6612 Ramachandran restraints generated. 3306 Oldfield, 0 Emsley, 3306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 2898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 212 time to evaluate : 3.402 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: A 133 PHE cc_start: 0.8033 (m-80) cc_final: 0.7749 (m-80) REVERT: A 242 LEU cc_start: 0.8792 (OUTLIER) cc_final: 0.8223 (mt) REVERT: A 950 ASP cc_start: 0.8400 (t70) cc_final: 0.8184 (t0) REVERT: B 87 LYS cc_start: 0.7356 (ptpp) cc_final: 0.7120 (ptpp) REVERT: B 90 ASP cc_start: 0.8471 (m-30) cc_final: 0.8211 (m-30) REVERT: B 108 TYR cc_start: 0.8558 (m-80) cc_final: 0.8235 (m-80) REVERT: C 115 GLN cc_start: 0.7928 (mm-40) cc_final: 0.7699 (mm110) REVERT: C 140 PHE cc_start: 0.8100 (p90) cc_final: 0.7697 (p90) REVERT: C 365 TYR cc_start: 0.9051 (m-80) cc_final: 0.8644 (m-80) REVERT: C 1142 GLN cc_start: 0.8235 (tp40) cc_final: 0.7970 (tp-100) REVERT: D 133 PHE cc_start: 0.8095 (m-80) cc_final: 0.7839 (m-80) REVERT: D 950 ASP cc_start: 0.8409 (t70) cc_final: 0.8181 (t0) REVERT: F 6 GLU cc_start: 0.8275 (mt-10) cc_final: 0.7793 (mt-10) REVERT: F 37 TYR cc_start: 0.7703 (m-80) cc_final: 0.7459 (m-80) REVERT: F 107 ASP cc_start: 0.8566 (m-30) cc_final: 0.8201 (m-30) outliers start: 40 outliers final: 24 residues processed: 237 average time/residue: 1.9474 time to fit residues: 558.7015 Evaluate side-chains 230 residues out of total 2898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 205 time to evaluate : 3.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 TRP Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 619 GLU Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 104 TRP Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 619 GLU Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain D residue 104 TRP Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 323 THR Chi-restraints excluded: chain D residue 603 ASN Chi-restraints excluded: chain D residue 619 GLU Chi-restraints excluded: chain D residue 856 ASN Chi-restraints excluded: chain D residue 858 LEU Chi-restraints excluded: chain D residue 1010 GLN Chi-restraints excluded: chain F residue 4 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 291 optimal weight: 0.6980 chunk 307 optimal weight: 2.9990 chunk 280 optimal weight: 3.9990 chunk 299 optimal weight: 1.9990 chunk 180 optimal weight: 0.1980 chunk 130 optimal weight: 0.7980 chunk 234 optimal weight: 4.9990 chunk 91 optimal weight: 2.9990 chunk 270 optimal weight: 0.0770 chunk 282 optimal weight: 0.5980 chunk 298 optimal weight: 0.9980 overall best weight: 0.4738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.4402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 27606 Z= 0.143 Angle : 0.498 8.824 37545 Z= 0.259 Chirality : 0.045 0.570 4434 Planarity : 0.003 0.078 4782 Dihedral : 5.545 59.522 4932 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.24 % Favored : 97.67 % Rotamer: Outliers : 0.83 % Allowed : 11.46 % Favored : 87.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.64 (0.14), residues: 3306 helix: 1.96 (0.20), residues: 663 sheet: 0.45 (0.17), residues: 870 loop : -0.12 (0.14), residues: 1773 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 886 HIS 0.003 0.001 HIS C 655 PHE 0.023 0.001 PHE A 140 TYR 0.015 0.001 TYR F 95 ARG 0.009 0.000 ARG F 45 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6612 Ramachandran restraints generated. 3306 Oldfield, 0 Emsley, 3306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6612 Ramachandran restraints generated. 3306 Oldfield, 0 Emsley, 3306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 2898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 224 time to evaluate : 3.261 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: A 133 PHE cc_start: 0.7993 (m-80) cc_final: 0.7708 (m-80) REVERT: A 950 ASP cc_start: 0.8235 (t70) cc_final: 0.8007 (t0) REVERT: B 87 LYS cc_start: 0.7348 (ptpp) cc_final: 0.7122 (ptpp) REVERT: B 90 ASP cc_start: 0.8510 (m-30) cc_final: 0.8284 (m-30) REVERT: B 108 TYR cc_start: 0.8566 (m-80) cc_final: 0.8250 (m-80) REVERT: C 140 PHE cc_start: 0.8091 (p90) cc_final: 0.7801 (p90) REVERT: C 1142 GLN cc_start: 0.8226 (tp40) cc_final: 0.7960 (tp-100) REVERT: E 107 ASP cc_start: 0.8500 (m-30) cc_final: 0.8172 (m-30) REVERT: D 133 PHE cc_start: 0.8033 (m-80) cc_final: 0.7778 (m-80) REVERT: D 140 PHE cc_start: 0.8306 (p90) cc_final: 0.8012 (p90) REVERT: D 950 ASP cc_start: 0.8277 (t70) cc_final: 0.8055 (t0) REVERT: F 6 GLU cc_start: 0.8254 (mt-10) cc_final: 0.7878 (mt-10) REVERT: F 37 TYR cc_start: 0.7683 (m-80) cc_final: 0.7440 (m-80) REVERT: F 54 ARG cc_start: 0.8678 (ppp80) cc_final: 0.8180 (ptp90) REVERT: F 107 ASP cc_start: 0.8556 (m-30) cc_final: 0.8200 (m-30) outliers start: 24 outliers final: 18 residues processed: 237 average time/residue: 1.9608 time to fit residues: 566.7766 Evaluate side-chains 219 residues out of total 2898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 201 time to evaluate : 3.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 TRP Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 619 GLU Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain C residue 104 TRP Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain D residue 104 TRP Chi-restraints excluded: chain D residue 323 THR Chi-restraints excluded: chain D residue 603 ASN Chi-restraints excluded: chain D residue 856 ASN Chi-restraints excluded: chain D residue 858 LEU Chi-restraints excluded: chain D residue 1010 GLN Chi-restraints excluded: chain F residue 4 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 196 optimal weight: 2.9990 chunk 316 optimal weight: 0.2980 chunk 193 optimal weight: 0.5980 chunk 150 optimal weight: 9.9990 chunk 219 optimal weight: 10.0000 chunk 331 optimal weight: 0.9990 chunk 305 optimal weight: 0.7980 chunk 264 optimal weight: 0.8980 chunk 27 optimal weight: 6.9990 chunk 204 optimal weight: 3.9990 chunk 161 optimal weight: 0.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 675 GLN ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.4511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 27606 Z= 0.148 Angle : 0.497 8.762 37545 Z= 0.257 Chirality : 0.044 0.413 4434 Planarity : 0.004 0.079 4782 Dihedral : 5.304 57.464 4932 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.33 % Favored : 97.58 % Rotamer: Outliers : 0.79 % Allowed : 11.90 % Favored : 87.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.71 (0.14), residues: 3306 helix: 2.01 (0.20), residues: 684 sheet: 0.48 (0.17), residues: 870 loop : -0.09 (0.14), residues: 1752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 104 HIS 0.002 0.001 HIS A 207 PHE 0.019 0.001 PHE D 140 TYR 0.014 0.001 TYR F 95 ARG 0.011 0.000 ARG B 45 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6612 Ramachandran restraints generated. 3306 Oldfield, 0 Emsley, 3306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6612 Ramachandran restraints generated. 3306 Oldfield, 0 Emsley, 3306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 2898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 217 time to evaluate : 3.231 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: A 133 PHE cc_start: 0.7985 (m-80) cc_final: 0.7704 (m-80) REVERT: A 950 ASP cc_start: 0.8200 (t70) cc_final: 0.7992 (t0) REVERT: B 87 LYS cc_start: 0.7322 (ptpp) cc_final: 0.7098 (ptpp) REVERT: B 90 ASP cc_start: 0.8512 (m-30) cc_final: 0.8288 (m-30) REVERT: B 108 TYR cc_start: 0.8557 (m-80) cc_final: 0.8246 (m-80) REVERT: C 140 PHE cc_start: 0.8102 (p90) cc_final: 0.7664 (p90) REVERT: C 365 TYR cc_start: 0.8883 (m-80) cc_final: 0.8425 (m-80) REVERT: C 574 ASP cc_start: 0.8442 (t0) cc_final: 0.7911 (t0) REVERT: C 1142 GLN cc_start: 0.8253 (tp40) cc_final: 0.7983 (tp-100) REVERT: E 3 GLN cc_start: 0.6301 (tp40) cc_final: 0.5879 (tp40) REVERT: E 107 ASP cc_start: 0.8452 (m-30) cc_final: 0.8143 (m-30) REVERT: D 133 PHE cc_start: 0.8011 (m-80) cc_final: 0.7728 (m-80) REVERT: D 140 PHE cc_start: 0.8309 (p90) cc_final: 0.8026 (p90) REVERT: D 902 MET cc_start: 0.9154 (mmt) cc_final: 0.8771 (mmt) REVERT: D 950 ASP cc_start: 0.8258 (t70) cc_final: 0.8036 (t0) REVERT: F 6 GLU cc_start: 0.8247 (mt-10) cc_final: 0.7885 (mt-10) REVERT: F 37 TYR cc_start: 0.7669 (m-80) cc_final: 0.7375 (m-80) REVERT: F 54 ARG cc_start: 0.8672 (ppp80) cc_final: 0.8171 (ptp90) REVERT: F 107 ASP cc_start: 0.8559 (m-30) cc_final: 0.8223 (m-30) outliers start: 23 outliers final: 20 residues processed: 230 average time/residue: 2.0418 time to fit residues: 578.9978 Evaluate side-chains 222 residues out of total 2898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 202 time to evaluate : 3.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 TRP Chi-restraints excluded: chain A residue 140 PHE Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 619 GLU Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain C residue 104 TRP Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 675 GLN Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain D residue 104 TRP Chi-restraints excluded: chain D residue 323 THR Chi-restraints excluded: chain D residue 603 ASN Chi-restraints excluded: chain D residue 856 ASN Chi-restraints excluded: chain D residue 858 LEU Chi-restraints excluded: chain D residue 1010 GLN Chi-restraints excluded: chain F residue 4 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 64, in __init__ weight = self.w, xray_structure = self.xray_structure) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 69.7109 > 50: distance: 1485 - 1729: 3.008 distance: 1607 - 1617: 4.348 distance: 1618 - 1619: 19.793 distance: 1618 - 1621: 3.587 distance: 1618 - 1624: 6.024 distance: 1619 - 1620: 34.270 distance: 1619 - 1631: 19.046 distance: 1621 - 1625: 3.493 distance: 1621 - 1626: 4.201 distance: 1631 - 1632: 55.453 distance: 1631 - 1642: 38.259 distance: 1632 - 1633: 47.602 distance: 1632 - 1635: 57.058 distance: 1632 - 1643: 47.727 distance: 1633 - 1634: 37.281 distance: 1633 - 1651: 27.954 distance: 1635 - 1636: 56.161 distance: 1635 - 1644: 46.487 distance: 1635 - 1645: 54.257 distance: 1636 - 1637: 69.060 distance: 1636 - 1638: 48.084 distance: 1637 - 1639: 46.064 distance: 1637 - 1646: 51.536 distance: 1638 - 1640: 19.880 distance: 1638 - 1647: 21.231 distance: 1639 - 1641: 21.559 distance: 1639 - 1648: 26.606 distance: 1640 - 1641: 11.110 distance: 1640 - 1649: 10.404 distance: 1651 - 1652: 17.435 distance: 1651 - 1659: 20.431 distance: 1652 - 1653: 3.790 distance: 1652 - 1655: 5.640 distance: 1652 - 1660: 3.085 distance: 1655 - 1656: 6.665 distance: 1655 - 1661: 3.836 distance: 1655 - 1662: 5.234 distance: 1656 - 1657: 3.225 distance: 2786 - 2795: 3.254 distance: 7315 - 7840: 3.115 distance: 9557 - 9875: 3.597 distance: 12375 - 12436: 3.007 distance: 12984 - 13037: 3.016 distance: 13024 - 13085: 3.060 distance: 13088 - 13161: 3.016 distance: 13396 - 13456: 3.009 distance: 14357 - 14668: 3.021 distance: 18452 - 18694: 3.072 distance: 22664 - 23874: 3.003 distance: 24505 - 25036: 3.013 distance: 25976 - 25977: 3.095 distance: 25977 - 25978: 6.666 distance: 25977 - 25980: 3.201 distance: 25978 - 25979: 7.620 distance: 25978 - 25997: 16.480 distance: 25997 - 25998: 21.111 distance: 25997 - 26006: 18.665 distance: 25997 - 26059: 22.995 distance: 25998 - 25999: 21.342 distance: 25998 - 26001: 37.217 distance: 25998 - 26007: 23.289 distance: 25999 - 26000: 17.192 distance: 25999 - 26014: 12.868 distance: 26000 - 26056: 18.207 distance: 26001 - 26002: 69.154 distance: 26001 - 26008: 47.368 distance: 26001 - 26009: 42.001 distance: 26002 - 26010: 66.919 distance: 26002 - 26011: 41.334 distance: 26003 - 26004: 63.872 distance: 26003 - 26005: 58.664 distance: 26005 - 26012: 43.753 distance: 26005 - 26013: 17.069 distance: 26014 - 26015: 5.479 distance: 26014 - 26021: 3.289 distance: 30217 - 30278: 3.068 distance: 30281 - 30354: 3.006 distance: 31550 - 31861: 3.021 distance: 41698 - 42229: 3.011 distance: 46761 - 46822: 3.005 distance: 47370 - 47423: 3.005 distance: 47410 - 47471: 3.055 distance: 47474 - 47547: 3.012 distance: 48743 - 49054: 3.031 distance: 50818 - 50827: 3.634 distance: 50925 - 50928: 4.268 distance: 50928 - 50931: 9.867 distance: 50928 - 50932: 7.336 distance: 50928 - 50933: 3.942 distance: 50941 - 50942: 5.366 distance: 50942 - 50953: 7.934 distance: 50942 - 50954: 8.944 distance: 50942 - 50955: 9.710 distance: 51061 - 51068: 5.004 distance: 51589 - 51593: 5.748 distance: 51593 - 51594: 5.693 distance: 51593 - 51604: 5.762 distance: 51666 - 51673: 3.772 distance: 51673 - 51677: 11.570 distance: 51677 - 51678: 11.394 distance: 51677 - 51688: 11.646 distance: 51678 - 51679: 3.444 distance: 51678 - 51685: 3.427 distance: 51681 - 51688: 3.681 distance: 51694 - 51701: 8.290 distance: 51701 - 51705: 21.056 distance: 51705 - 51706: 20.420 distance: 51705 - 51716: 21.139 distance: 51706 - 51707: 6.492 distance: 51706 - 51713: 6.532 distance: 51709 - 51716: 7.042 distance: 51729 - 51733: 7.630 distance: 51733 - 51734: 7.480 distance: 51733 - 51744: 7.584 distance: 51757 - 51761: 4.920 distance: 51761 - 51762: 4.887 distance: 51761 - 51772: 4.924 distance: 51778 - 51785: 6.128 distance: 51785 - 51789: 19.024 distance: 51789 - 51790: 18.448 distance: 51789 - 51800: 19.026 distance: 51790 - 51791: 5.956 distance: 51790 - 51797: 6.088 distance: 51793 - 51800: 6.439 distance: 51841 - 51845: 3.056 distance: 51845 - 51856: 3.066 distance: 51862 - 51869: 9.376 distance: 51869 - 51873: 32.852 distance: 51873 - 51874: 31.226 distance: 51873 - 51884: 32.564 distance: 51874 - 51875: 9.737 distance: 51874 - 51881: 9.711 distance: 51877 - 51884: 10.759 distance: 51897 - 51901: 6.669 distance: 51901 - 51902: 6.533 distance: 51901 - 51912: 6.627 distance: 51918 - 51925: 4.413 distance: 51925 - 51929: 13.443 distance: 51929 - 51930: 13.092 distance: 51929 - 51940: 13.566 distance: 51930 - 51931: 4.510 distance: 51930 - 51937: 4.453 distance: 51933 - 51940: 4.787 distance: 52065 - 52069: 5.344 distance: 52069 - 52070: 5.268 distance: 52069 - 52080: 5.311