Starting phenix.real_space_refine (version: dev) on Wed Feb 22 03:53:37 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jjj_22354/02_2023/7jjj_22354.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jjj_22354/02_2023/7jjj_22354.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jjj_22354/02_2023/7jjj_22354.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jjj_22354/02_2023/7jjj_22354.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jjj_22354/02_2023/7jjj_22354.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jjj_22354/02_2023/7jjj_22354.pdb" } resolution = 4.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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 Process input model Symmetric amino acids flipped Residue "A PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 497": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 505": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 636": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 797": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 802": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 833": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 855": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 873": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 904": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 917": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 970": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1047": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1062": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1075": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1092": "OE1" <-> "OE2" Residue "A PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 96": "OE1" <-> "OE2" Residue "B PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 191": "OE1" <-> "OE2" Residue "B PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 490": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 497": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 505": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 636": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 782": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 797": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 802": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 833": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 855": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 873": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 904": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 917": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 970": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1047": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1052": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1062": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1075": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1089": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1092": "OE1" <-> "OE2" Residue "B PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 80": "OD1" <-> "OD2" Residue "C PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 497": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 505": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 636": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 759": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 782": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 797": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 802": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 855": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 873": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 888": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 904": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 906": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 917": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 970": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1052": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1062": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1075": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1089": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 497": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 505": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 636": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 797": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 802": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 833": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 855": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 873": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 904": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 917": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 970": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 1047": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 1062": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 1075": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 1092": "OE1" <-> "OE2" Residue "D PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 96": "OE1" <-> "OE2" Residue "E PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 191": "OE1" <-> "OE2" Residue "E PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 490": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 497": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 505": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 636": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 782": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 797": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 802": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 833": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 855": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 873": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 904": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 917": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 970": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 1047": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 1052": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 1062": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 1075": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 1089": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 1092": "OE1" <-> "OE2" Residue "E PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 80": "OD1" <-> "OD2" Residue "F PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 497": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 505": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 636": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 759": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 782": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 797": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 802": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 855": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 873": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 888": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 904": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 906": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 917": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 970": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 1052": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 1062": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 1075": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 1089": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 54614 Number of models: 1 Model: "" Number of chains: 92 Chain: "A" Number of atoms: 8739 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1120, 8739 Classifications: {'peptide': 1120} Link IDs: {'PTRANS': 55, 'TRANS': 1064} Chain breaks: 1 Chain: "B" Number of atoms: 8657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1109, 8657 Classifications: {'peptide': 1109} Link IDs: {'PTRANS': 53, 'TRANS': 1055} Chain breaks: 2 Chain: "C" Number of atoms: 8648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1108, 8648 Classifications: {'peptide': 1108} Link IDs: {'PTRANS': 53, 'TRANS': 1054} Chain breaks: 2 Chain: "D" Number of atoms: 8739 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1120, 8739 Classifications: {'peptide': 1120} Link IDs: {'PTRANS': 55, 'TRANS': 1064} Chain breaks: 1 Chain: "E" Number of atoms: 8657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1109, 8657 Classifications: {'peptide': 1109} Link IDs: {'PTRANS': 53, 'TRANS': 1055} Chain breaks: 2 Chain: "F" Number of atoms: 8648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1108, 8648 Classifications: {'peptide': 1108} Link IDs: {'PTRANS': 53, 'TRANS': 1054} Chain breaks: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen 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 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 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 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 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 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 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 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 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 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 chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 3 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "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 chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen 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 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 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 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 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 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 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 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 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 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 chiralities: 2 Chain: "r" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "s" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "t" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 4 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 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 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 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 chiralities: 2 Chain: "y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "0" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "1" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "2" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "3" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "4" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "5" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "6" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 3 Chain: "7" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "8" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "9" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "AA" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "BA" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "CA" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "DA" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "EA" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "FA" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "GA" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "HA" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "IA" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "JA" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "KA" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "LA" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "MA" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "NA" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "OA" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "PA" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "QA" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "RA" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "SA" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "TA" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "UA" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "VA" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "WA" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "XA" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 4 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "D" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 22.05, per 1000 atoms: 0.40 Number of scatterers: 54614 At special positions: 0 Unit cell: (205.85, 226.55, 172.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 240 16.00 O 10850 8.00 N 8886 7.00 C 34638 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=90, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.02 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=2.06 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.14 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.05 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=2.04 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A 840 " - pdb=" SG CYS A 851 " distance=2.02 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.02 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.02 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.04 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.17 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.05 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.02 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.02 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B 840 " - pdb=" SG CYS B 851 " distance=2.02 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.02 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.02 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.06 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.13 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.04 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.02 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=2.02 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 C 840 " - pdb=" SG CYS C 851 " 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 D 15 " - pdb=" SG CYS D 136 " distance=2.03 Simple disulfide: pdb=" SG CYS D 131 " - pdb=" SG CYS D 166 " distance=2.02 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=2.06 Simple disulfide: pdb=" SG CYS D 379 " - pdb=" SG CYS D 432 " distance=2.14 Simple disulfide: pdb=" SG CYS D 391 " - pdb=" SG CYS D 525 " distance=2.05 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=2.03 Simple disulfide: pdb=" SG CYS D 738 " - pdb=" SG CYS D 760 " distance=2.04 Simple disulfide: pdb=" SG CYS D 743 " - pdb=" SG CYS D 749 " distance=2.03 Simple disulfide: pdb=" SG CYS D 840 " - pdb=" SG CYS D 851 " distance=2.02 Simple disulfide: pdb=" SG CYS D1032 " - pdb=" SG CYS D1043 " distance=2.02 Simple disulfide: pdb=" SG CYS D1082 " - pdb=" SG CYS D1126 " distance=2.03 Simple disulfide: pdb=" SG CYS E 15 " - pdb=" SG CYS E 136 " distance=2.02 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 166 " distance=2.03 Simple disulfide: pdb=" SG CYS E 291 " - pdb=" SG CYS E 301 " distance=2.03 Simple disulfide: pdb=" SG CYS E 336 " - pdb=" SG CYS E 361 " distance=2.04 Simple disulfide: pdb=" SG CYS E 379 " - pdb=" SG CYS E 432 " distance=2.17 Simple disulfide: pdb=" SG CYS E 391 " - pdb=" SG CYS E 525 " distance=2.05 Simple disulfide: pdb=" SG CYS E 480 " - pdb=" SG CYS E 488 " distance=2.02 Simple disulfide: pdb=" SG CYS E 538 " - pdb=" SG CYS E 590 " distance=2.03 Simple disulfide: pdb=" SG CYS E 617 " - pdb=" SG CYS E 649 " distance=2.02 Simple disulfide: pdb=" SG CYS E 662 " - pdb=" SG CYS E 671 " distance=2.03 Simple disulfide: pdb=" SG CYS E 738 " - pdb=" SG CYS E 760 " distance=2.03 Simple disulfide: pdb=" SG CYS E 743 " - pdb=" SG CYS E 749 " distance=2.03 Simple disulfide: pdb=" SG CYS E 840 " - pdb=" SG CYS E 851 " distance=2.02 Simple disulfide: pdb=" SG CYS E1032 " - pdb=" SG CYS E1043 " distance=2.02 Simple disulfide: pdb=" SG CYS E1082 " - pdb=" SG CYS E1126 " distance=2.03 Simple disulfide: pdb=" SG CYS F 15 " - pdb=" SG CYS F 136 " distance=2.02 Simple disulfide: pdb=" SG CYS F 131 " - pdb=" SG CYS F 166 " distance=2.03 Simple disulfide: pdb=" SG CYS F 291 " - pdb=" SG CYS F 301 " distance=2.03 Simple disulfide: pdb=" SG CYS F 336 " - pdb=" SG CYS F 361 " distance=2.06 Simple disulfide: pdb=" SG CYS F 379 " - pdb=" SG CYS F 432 " distance=2.13 Simple disulfide: pdb=" SG CYS F 391 " - pdb=" SG CYS F 525 " distance=2.04 Simple disulfide: pdb=" SG CYS F 480 " - pdb=" SG CYS F 488 " distance=2.02 Simple disulfide: pdb=" SG CYS F 538 " - pdb=" SG CYS F 590 " distance=2.03 Simple disulfide: pdb=" SG CYS F 617 " - pdb=" SG CYS F 649 " distance=2.02 Simple disulfide: pdb=" SG CYS F 662 " - pdb=" SG CYS F 671 " distance=2.03 Simple disulfide: pdb=" SG CYS F 738 " - pdb=" SG CYS F 760 " distance=2.02 Simple disulfide: pdb=" SG CYS F 743 " - pdb=" SG CYS F 749 " distance=2.03 Simple disulfide: pdb=" SG CYS F 840 " - pdb=" SG CYS F 851 " distance=2.03 Simple disulfide: pdb=" SG CYS F1032 " - pdb=" SG CYS F1043 " distance=2.02 Simple disulfide: pdb=" SG CYS F1082 " - pdb=" SG CYS F1126 " distance=2.02 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 0 1 " - " NAG 0 2 " " NAG 1 1 " - " NAG 1 2 " " NAG 2 1 " - " NAG 2 2 " " NAG 3 1 " - " NAG 3 2 " " NAG 4 1 " - " NAG 4 2 " " NAG 5 1 " - " NAG 5 2 " " NAG 6 1 " - " NAG 6 2 " " NAG 7 1 " - " NAG 7 2 " " NAG 8 1 " - " NAG 8 2 " " NAG 9 1 " - " NAG 9 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG 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 Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " " NAG 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 t 2 " - " BMA t 3 " " 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 y 1 " - " NAG y 2 " " NAG z 1 " - " NAG z 2 " " NAGAA 1 " - " NAGAA 2 " " NAGBA 1 " - " NAGBA 2 " " NAGCA 1 " - " NAGCA 2 " " NAGDA 1 " - " NAGDA 2 " " NAGEA 1 " - " NAGEA 2 " " NAGFA 1 " - " NAGFA 2 " " NAGGA 1 " - " NAGGA 2 " " NAGHA 1 " - " NAGHA 2 " " NAGIA 1 " - " NAGIA 2 " " NAGJA 1 " - " NAGJA 2 " " NAGKA 1 " - " NAGKA 2 " " NAGLA 1 " - " NAGLA 2 " " NAGMA 1 " - " NAGMA 2 " " NAGNA 1 " - " NAGNA 2 " " NAGOA 1 " - " NAGOA 2 " " NAGPA 1 " - " NAGPA 2 " " NAGQA 1 " - " NAGQA 2 " " NAGRA 1 " - " NAGRA 2 " " NAGSA 1 " - " NAGSA 2 " " NAGTA 1 " - " NAGTA 2 " " NAGUA 1 " - " NAGUA 2 " " NAGVA 1 " - " NAGVA 2 " " NAGWA 1 " - " NAGWA 2 " " NAGXA 1 " - " NAGXA 2 " " NAGXA 2 " - " BMAXA 3 " BETA1-6 " NAG 6 1 " - " FUC 6 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG S 1 " - " FUC S 3 " " NAG t 1 " - " FUC t 4 " " NAGXA 1 " - " FUCXA 4 " NAG-ASN " NAG 0 1 " - " ASN D 122 " " NAG 1 1 " - " ASN D 234 " " NAG 2 1 " - " ASN D 282 " " NAG 3 1 " - " ASN D 165 " " NAG 4 1 " - " ASN D 17 " " NAG 5 1 " - " ASN D 149 " " NAG 6 1 " - " ASN D 616 " " NAG 7 1 " - " ASN E 61 " " NAG 8 1 " - " ASN E 616 " " NAG 9 1 " - " ASN E 343 " " NAG A1301 " - " ASN A 331 " " NAG A1302 " - " ASN A 709 " " NAG A1303 " - " ASN A1134 " " NAG B1301 " - " ASN B 331 " " NAG B1302 " - " ASN B 282 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 331 " " NAG C1303 " - " ASN C 343 " " NAG D1301 " - " ASN D 331 " " NAG D1302 " - " ASN D 709 " " NAG D1303 " - " ASN D1134 " " NAG E1301 " - " ASN E 331 " " NAG E1302 " - " ASN E 282 " " NAG F1301 " - " ASN F 61 " " NAG F1302 " - " ASN F 331 " " NAG F1303 " - " ASN F 343 " " NAG G 1 " - " ASN A 61 " " NAG H 1 " - " ASN A 343 " " NAG I 1 " - " ASN A 717 " " NAG J 1 " - " ASN A 801 " " NAG K 1 " - " ASN A1074 " " NAG L 1 " - " ASN A1098 " " NAG M 1 " - " ASN A 122 " " NAG N 1 " - " ASN A 234 " " NAG O 1 " - " ASN A 282 " " NAG P 1 " - " ASN A 165 " " NAG Q 1 " - " ASN A 17 " " NAG R 1 " - " ASN A 149 " " NAG S 1 " - " ASN A 616 " " NAG T 1 " - " ASN B 61 " " NAG U 1 " - " ASN B 616 " " NAG V 1 " - " ASN B 343 " " NAG W 1 " - " ASN B 709 " " NAG X 1 " - " ASN B 717 " " NAG Y 1 " - " ASN B 801 " " NAG Z 1 " - " ASN B1074 " " NAG a 1 " - " ASN B1098 " " NAG b 1 " - " ASN B1134 " " NAG c 1 " - " ASN B 122 " " NAG d 1 " - " ASN B 234 " " NAG e 1 " - " ASN B 165 " " NAG f 1 " - " ASN B 17 " " NAG g 1 " - " ASN B 149 " " NAG h 1 " - " ASN C 616 " " NAG i 1 " - " ASN C 709 " " NAG j 1 " - " ASN C 717 " " NAG k 1 " - " ASN C 801 " " NAG l 1 " - " ASN C1074 " " NAG m 1 " - " ASN C1098 " " NAG n 1 " - " ASN C1134 " " NAG o 1 " - " ASN C 122 " " NAG p 1 " - " ASN C 234 " " NAG q 1 " - " ASN C 165 " " NAG r 1 " - " ASN C 17 " " NAG s 1 " - " ASN C 149 " " NAG t 1 " - " ASN C 282 " " NAG u 1 " - " ASN D 61 " " NAG v 1 " - " ASN D 343 " " NAG w 1 " - " ASN D 717 " " NAG x 1 " - " ASN D 801 " " NAG y 1 " - " ASN D1074 " " NAG z 1 " - " ASN D1098 " " NAGAA 1 " - " ASN E 709 " " NAGBA 1 " - " ASN E 717 " " NAGCA 1 " - " ASN E 801 " " NAGDA 1 " - " ASN E1074 " " NAGEA 1 " - " ASN E1098 " " NAGFA 1 " - " ASN E1134 " " NAGGA 1 " - " ASN E 122 " " NAGHA 1 " - " ASN E 234 " " NAGIA 1 " - " ASN E 165 " " NAGJA 1 " - " ASN E 17 " " NAGKA 1 " - " ASN E 149 " " NAGLA 1 " - " ASN F 616 " " NAGMA 1 " - " ASN F 709 " " NAGNA 1 " - " ASN F 717 " " NAGOA 1 " - " ASN F 801 " " NAGPA 1 " - " ASN F1074 " " NAGQA 1 " - " ASN F1098 " " NAGRA 1 " - " ASN F1134 " " NAGSA 1 " - " ASN F 122 " " NAGTA 1 " - " ASN F 234 " " NAGUA 1 " - " ASN F 165 " " NAGVA 1 " - " ASN F 17 " " NAGWA 1 " - " ASN F 149 " " NAGXA 1 " - " ASN F 282 " Time building additional restraints: 20.03 Conformation dependent library (CDL) restraints added in 6.2 seconds 13284 Ramachandran restraints generated. 6642 Oldfield, 0 Emsley, 6642 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 12460 Finding SS restraints... Secondary structure from input PDB file: 156 helices and 100 sheets defined 25.7% alpha, 30.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.41 Creating SS restraints... Processing helix chain 'A' and resid 253 through 258 removed outlier: 3.679A pdb=" N TRP A 258 " --> pdb=" O SER A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.819A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 369 Processing helix chain 'A' and resid 383 through 389 removed outlier: 4.768A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.478A 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 737 through 744 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 757 through 783 removed outlier: 3.719A 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 836 through 841 Processing helix chain 'A' and resid 842 through 847 Processing helix chain 'A' and resid 848 through 855 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 885 through 889 removed outlier: 3.522A pdb=" N GLY A 889 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 910 Processing helix chain 'A' and resid 913 through 919 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 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 3.990A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1146 Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 337 through 343 Processing helix chain 'B' and resid 349 through 353 Processing helix chain 'B' and resid 364 through 371 removed outlier: 4.038A pdb=" N ASN B 370 " --> pdb=" O VAL B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 389 removed outlier: 4.721A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.105A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 739 through 744 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 756 through 783 removed outlier: 3.919A pdb=" N CYS B 760 " --> pdb=" O TYR B 756 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 836 through 841 Processing helix chain 'B' and resid 842 through 847 Processing helix chain 'B' and resid 848 through 855 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 897 through 910 Processing helix chain 'B' and resid 912 through 919 removed outlier: 3.952A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 3.958A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 337 through 343 Processing helix chain 'C' and resid 351 through 353 No H-bonds generated for 'chain 'C' and resid 351 through 353' Processing helix chain 'C' and resid 364 through 366 No H-bonds generated for 'chain 'C' and resid 364 through 366' Processing helix chain 'C' and resid 367 through 372 removed outlier: 4.472A pdb=" N SER C 371 " --> pdb=" O VAL C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 389 removed outlier: 4.743A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) 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 754 Processing helix chain 'C' and resid 756 through 783 removed outlier: 3.815A pdb=" N CYS C 760 " --> pdb=" O TYR C 756 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 836 through 841 Processing helix chain 'C' and resid 842 through 847 Processing helix chain 'C' and resid 848 through 855 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 885 through 889 removed outlier: 3.506A pdb=" N GLY C 889 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 910 Processing helix chain 'C' and resid 913 through 919 Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 3.961A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1146 Processing helix chain 'D' and resid 253 through 258 removed outlier: 3.679A pdb=" N TRP D 258 " --> pdb=" O SER D 254 " (cutoff:3.500A) Processing helix chain 'D' and resid 294 through 303 Processing helix chain 'D' and resid 337 through 343 Processing helix chain 'D' and resid 349 through 353 removed outlier: 3.819A pdb=" N TRP D 353 " --> pdb=" O VAL D 350 " (cutoff:3.500A) Processing helix chain 'D' and resid 364 through 369 Processing helix chain 'D' and resid 383 through 389 removed outlier: 4.768A pdb=" N ASN D 388 " --> pdb=" O THR D 385 " (cutoff:3.500A) Processing helix chain 'D' and resid 405 through 410 removed outlier: 4.478A 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 737 through 744 Processing helix chain 'D' and resid 746 through 754 Processing helix chain 'D' and resid 757 through 783 removed outlier: 3.719A 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 836 through 841 Processing helix chain 'D' and resid 842 through 847 Processing helix chain 'D' and resid 848 through 855 Processing helix chain 'D' and resid 866 through 884 Processing helix chain 'D' and resid 885 through 889 removed outlier: 3.522A pdb=" N GLY D 889 " --> pdb=" O TRP D 886 " (cutoff:3.500A) Processing helix chain 'D' and resid 897 through 910 Processing helix chain 'D' and resid 913 through 919 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 984 Processing helix chain 'D' and resid 985 through 1033 removed outlier: 3.990A pdb=" N VAL D 991 " --> pdb=" O PRO D 987 " (cutoff:3.500A) Processing helix chain 'D' and resid 1141 through 1146 Processing helix chain 'E' and resid 294 through 303 Processing helix chain 'E' and resid 337 through 343 Processing helix chain 'E' and resid 349 through 353 Processing helix chain 'E' and resid 364 through 371 removed outlier: 4.038A pdb=" N ASN E 370 " --> pdb=" O VAL E 367 " (cutoff:3.500A) Processing helix chain 'E' and resid 383 through 389 removed outlier: 4.721A pdb=" N ASN E 388 " --> pdb=" O THR E 385 " (cutoff:3.500A) Processing helix chain 'E' and resid 405 through 410 removed outlier: 4.105A pdb=" N ARG E 408 " --> pdb=" O ASP E 405 " (cutoff:3.500A) Processing helix chain 'E' and resid 416 through 422 Processing helix chain 'E' and resid 502 through 505 Processing helix chain 'E' and resid 739 through 744 Processing helix chain 'E' and resid 746 through 754 Processing helix chain 'E' and resid 756 through 783 removed outlier: 3.919A pdb=" N CYS E 760 " --> pdb=" O TYR E 756 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ASP E 775 " --> pdb=" O ALA E 771 " (cutoff:3.500A) Processing helix chain 'E' and resid 816 through 826 Processing helix chain 'E' and resid 836 through 841 Processing helix chain 'E' and resid 842 through 847 Processing helix chain 'E' and resid 848 through 855 Processing helix chain 'E' and resid 866 through 884 Processing helix chain 'E' and resid 897 through 910 Processing helix chain 'E' and resid 912 through 919 removed outlier: 3.952A pdb=" N LEU E 916 " --> pdb=" O THR E 912 " (cutoff:3.500A) Processing helix chain 'E' and resid 919 through 941 Processing helix chain 'E' and resid 942 through 944 No H-bonds generated for 'chain 'E' and resid 942 through 944' Processing helix chain 'E' and resid 945 through 965 Processing helix chain 'E' and resid 966 through 968 No H-bonds generated for 'chain 'E' and resid 966 through 968' Processing helix chain 'E' and resid 976 through 984 Processing helix chain 'E' and resid 985 through 1033 removed outlier: 3.958A pdb=" N VAL E 991 " --> pdb=" O PRO E 987 " (cutoff:3.500A) Processing helix chain 'F' and resid 294 through 303 Processing helix chain 'F' and resid 337 through 343 Processing helix chain 'F' and resid 351 through 353 No H-bonds generated for 'chain 'F' and resid 351 through 353' Processing helix chain 'F' and resid 364 through 366 No H-bonds generated for 'chain 'F' and resid 364 through 366' Processing helix chain 'F' and resid 367 through 372 removed outlier: 4.472A pdb=" N SER F 371 " --> pdb=" O VAL F 367 " (cutoff:3.500A) Processing helix chain 'F' and resid 383 through 389 removed outlier: 4.743A pdb=" N ASN F 388 " --> pdb=" O THR F 385 " (cutoff:3.500A) Processing helix chain 'F' and resid 405 through 410 removed outlier: 4.722A pdb=" N ARG F 408 " --> pdb=" O ASP F 405 " (cutoff:3.500A) Processing helix chain 'F' and resid 416 through 422 Processing helix chain 'F' and resid 502 through 505 Processing helix chain 'F' and resid 739 through 744 Processing helix chain 'F' and resid 746 through 754 Processing helix chain 'F' and resid 756 through 783 removed outlier: 3.815A pdb=" N CYS F 760 " --> pdb=" O TYR F 756 " (cutoff:3.500A) Processing helix chain 'F' and resid 816 through 826 Processing helix chain 'F' and resid 836 through 841 Processing helix chain 'F' and resid 842 through 847 Processing helix chain 'F' and resid 848 through 855 Processing helix chain 'F' and resid 866 through 884 Processing helix chain 'F' and resid 885 through 889 removed outlier: 3.506A pdb=" N GLY F 889 " --> pdb=" O TRP F 886 " (cutoff:3.500A) Processing helix chain 'F' and resid 897 through 910 Processing helix chain 'F' and resid 913 through 919 Processing helix chain 'F' and resid 919 through 941 Processing helix chain 'F' and resid 942 through 944 No H-bonds generated for 'chain 'F' and resid 942 through 944' Processing helix chain 'F' and resid 945 through 965 Processing helix chain 'F' and resid 966 through 968 No H-bonds generated for 'chain 'F' and resid 966 through 968' Processing helix chain 'F' and resid 976 through 984 Processing helix chain 'F' and resid 985 through 1033 removed outlier: 3.961A pdb=" N VAL F 991 " --> pdb=" O PRO F 987 " (cutoff:3.500A) Processing helix chain 'F' and resid 1140 through 1146 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 7.977A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 9.010A pdb=" N HIS A 207 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 9.761A pdb=" N LEU A 223 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 27 through 30 Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 7.487A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 83 through 85 removed outlier: 3.609A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N VAL A 126 " --> pdb=" O VAL A 171 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N VAL A 171 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N ILE A 128 " --> pdb=" O GLU A 169 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N GLU A 169 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N GLU A 132 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N ASN A 165 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N GLN A 134 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N ALA A 163 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 152 through 154 Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 315 removed outlier: 4.520A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N CYS A 649 " --> pdb=" O TYR A 612 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 325 through 328 Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 357 removed outlier: 3.579A pdb=" N VAL A 524 " --> pdb=" O PHE A 392 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 354 through 357 removed outlier: 5.453A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (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: 6.191A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.537A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 8.825A pdb=" N VAL A 656 " --> pdb=" O THR A 696 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 701 through 703 removed outlier: 6.587A pdb=" N ALA A 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.859A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.716A 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: 6.859A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 4.435A 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: 4.530A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 787 through 789 Processing sheet with id=AB9, first strand: chain 'A' and resid 1120 through 1123 Processing sheet with id=AC1, first strand: chain 'B' and resid 27 through 30 removed outlier: 7.646A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.371A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 10.088A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.922A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 27 through 30 Processing sheet with id=AC3, first strand: chain 'B' and resid 47 through 55 removed outlier: 7.339A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 83 through 85 removed outlier: 13.076A pdb=" N PHE B 135 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 12.976A pdb=" N THR B 240 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 10.437A pdb=" N ASN B 137 " --> pdb=" O THR B 240 " (cutoff:3.500A) removed outlier: 10.492A pdb=" N LEU B 242 " --> pdb=" O ASN B 137 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N LEU B 244 " --> pdb=" O PRO B 139 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N SER B 162 " --> pdb=" O GLN B 134 " (cutoff:3.500A) removed outlier: 5.935A pdb=" N CYS B 136 " --> pdb=" O TYR B 160 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N TYR B 160 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N ASP B 138 " --> pdb=" O ARG B 158 " (cutoff:3.500A) removed outlier: 8.199A pdb=" N ARG B 158 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N PHE B 140 " --> pdb=" O GLU B 156 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N GLU B 156 " --> pdb=" O PHE B 140 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 83 through 85 removed outlier: 4.275A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ASN B 121 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N VAL B 126 " --> pdb=" O VAL B 171 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N VAL B 171 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N ILE B 128 " --> pdb=" O GLU B 169 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N GLU B 169 " --> pdb=" O ILE B 128 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 311 through 315 removed outlier: 4.573A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 325 through 328 Processing sheet with id=AC8, first strand: chain 'B' and resid 354 through 357 removed outlier: 3.567A pdb=" N VAL B 524 " --> pdb=" O PHE B 392 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 354 through 357 removed outlier: 5.549A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N GLU B 516 " --> pdb=" O ASN B 394 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD2, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD3, first strand: chain 'B' and resid 654 through 660 removed outlier: 6.267A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.690A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 8.849A pdb=" N VAL B 656 " --> pdb=" O THR B 696 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 711 through 714 removed outlier: 4.312A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 717 through 728 removed outlier: 6.012A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD7, first strand: chain 'B' and resid 787 through 790 Processing sheet with id=AD8, first strand: chain 'B' and resid 1120 through 1123 Processing sheet with id=AD9, first strand: chain 'C' and resid 27 through 30 removed outlier: 7.619A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 47 through 55 removed outlier: 7.356A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 83 through 85 removed outlier: 6.883A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N VAL C 126 " --> pdb=" O TYR C 170 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N TYR C 170 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N ILE C 128 " --> pdb=" O PHE C 168 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N PHE C 168 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N VAL C 130 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N CYS C 166 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N SER C 162 " --> pdb=" O GLN C 134 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N CYS C 136 " --> pdb=" O TYR C 160 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N TYR C 160 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N ASP C 138 " --> pdb=" O ARG C 158 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N ARG C 158 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N PHE C 140 " --> pdb=" O GLU C 156 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N GLU C 156 " --> pdb=" O PHE C 140 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N GLY C 142 " --> pdb=" O GLU C 154 " (cutoff:3.500A) removed outlier: 5.124A pdb=" N GLU C 154 " --> pdb=" O GLY C 142 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 83 through 85 removed outlier: 13.249A pdb=" N PHE C 238 " --> pdb=" O PHE C 133 " (cutoff:3.500A) removed outlier: 12.921A pdb=" N PHE C 135 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 12.888A pdb=" N THR C 240 " --> pdb=" O PHE C 135 " (cutoff:3.500A) removed outlier: 10.670A pdb=" N ASN C 137 " --> pdb=" O THR C 240 " (cutoff:3.500A) removed outlier: 10.808A pdb=" N LEU C 242 " --> pdb=" O ASN C 137 " (cutoff:3.500A) removed outlier: 7.875A pdb=" N LEU C 244 " --> pdb=" O PRO C 139 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N LEU C 141 " --> pdb=" O LEU C 244 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N VAL C 126 " --> pdb=" O TYR C 170 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N TYR C 170 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N ILE C 128 " --> pdb=" O PHE C 168 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N PHE C 168 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N VAL C 130 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N CYS C 166 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N SER C 162 " --> pdb=" O GLN C 134 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N CYS C 136 " --> pdb=" O TYR C 160 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N TYR C 160 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N ASP C 138 " --> pdb=" O ARG C 158 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N ARG C 158 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N PHE C 140 " --> pdb=" O GLU C 156 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N GLU C 156 " --> pdb=" O PHE C 140 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N GLY C 142 " --> pdb=" O GLU C 154 " (cutoff:3.500A) removed outlier: 5.124A pdb=" N GLU C 154 " --> pdb=" O GLY C 142 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 311 through 315 removed outlier: 4.611A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 325 through 328 Processing sheet with id=AE6, first strand: chain 'C' and resid 348 through 349 removed outlier: 7.148A pdb=" N ALA C 348 " --> pdb=" O VAL C 401 " (cutoff:3.500A) removed outlier: 9.409A pdb=" N ARG C 403 " --> pdb=" O ALA C 348 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N VAL C 524 " --> pdb=" O PHE C 392 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 354 through 357 removed outlier: 5.414A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE9, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AF1, first strand: chain 'C' and resid 654 through 660 removed outlier: 6.244A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.672A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 8.663A pdb=" N VAL C 656 " --> pdb=" O THR C 696 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 711 through 714 removed outlier: 4.201A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 717 through 728 removed outlier: 6.005A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.551A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 1120 through 1123 removed outlier: 3.671A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'D' and resid 27 through 30 removed outlier: 7.977A pdb=" N ASN D 61 " --> pdb=" O TYR D 269 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N TYR D 269 " --> pdb=" O ASN D 61 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N SER D 205 " --> pdb=" O PRO D 225 " (cutoff:3.500A) removed outlier: 9.010A pdb=" N HIS D 207 " --> pdb=" O LEU D 223 " (cutoff:3.500A) removed outlier: 9.761A pdb=" N LEU D 223 " --> pdb=" O HIS D 207 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N VAL D 36 " --> pdb=" O LEU D 223 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'D' and resid 27 through 30 Processing sheet with id=AF8, first strand: chain 'D' and resid 48 through 55 removed outlier: 7.487A pdb=" N THR D 274 " --> pdb=" O ASP D 290 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N ASP D 290 " --> pdb=" O THR D 274 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N LEU D 276 " --> pdb=" O ALA D 288 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N ALA D 288 " --> pdb=" O LEU D 276 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N LYS D 278 " --> pdb=" O THR D 286 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'D' and resid 83 through 85 removed outlier: 3.609A pdb=" N GLY D 103 " --> pdb=" O LEU D 241 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ALA D 243 " --> pdb=" O ILE D 101 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N ILE D 101 " --> pdb=" O ALA D 243 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N ARG D 102 " --> pdb=" O ASN D 121 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N VAL D 126 " --> pdb=" O VAL D 171 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N VAL D 171 " --> pdb=" O VAL D 126 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N ILE D 128 " --> pdb=" O GLU D 169 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N GLU D 169 " --> pdb=" O ILE D 128 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N GLU D 132 " --> pdb=" O ASN D 165 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N ASN D 165 " --> pdb=" O GLU D 132 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N GLN D 134 " --> pdb=" O ALA D 163 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N ALA D 163 " --> pdb=" O GLN D 134 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'D' and resid 152 through 154 Processing sheet with id=AG2, first strand: chain 'D' and resid 311 through 315 removed outlier: 4.520A pdb=" N VAL D 595 " --> pdb=" O THR D 315 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N CYS D 649 " --> pdb=" O TYR D 612 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'D' and resid 325 through 328 Processing sheet with id=AG4, first strand: chain 'D' and resid 354 through 357 removed outlier: 3.579A pdb=" N VAL D 524 " --> pdb=" O PHE D 392 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N CYS D 361 " --> pdb=" O CYS D 525 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'D' and resid 354 through 357 removed outlier: 5.453A pdb=" N ASN D 394 " --> pdb=" O GLU D 516 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N GLU D 516 " --> pdb=" O ASN D 394 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'D' and resid 452 through 454 Processing sheet with id=AG7, first strand: chain 'D' and resid 473 through 474 Processing sheet with id=AG8, first strand: chain 'D' and resid 654 through 660 removed outlier: 6.191A pdb=" N GLU D 654 " --> pdb=" O ALA D 694 " (cutoff:3.500A) removed outlier: 8.537A pdb=" N THR D 696 " --> pdb=" O GLU D 654 " (cutoff:3.500A) removed outlier: 8.825A pdb=" N VAL D 656 " --> pdb=" O THR D 696 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'D' and resid 701 through 703 removed outlier: 6.587A pdb=" N ALA D 701 " --> pdb=" O ILE F 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG9 Processing sheet with id=AH1, first strand: chain 'D' and resid 711 through 728 removed outlier: 6.859A pdb=" N GLN D1071 " --> pdb=" O THR D 716 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N PHE D 718 " --> pdb=" O PRO D1069 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N ILE D 720 " --> pdb=" O TYR D1067 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N TYR D1067 " --> pdb=" O ILE D 720 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N VAL D 722 " --> pdb=" O VAL D1065 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N VAL D1065 " --> pdb=" O VAL D 722 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N THR D 724 " --> pdb=" O LEU D1063 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N LEU D1063 " --> pdb=" O THR D 724 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N ILE D 726 " --> pdb=" O VAL D1061 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N VAL D1061 " --> pdb=" O ILE D 726 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N GLY D1059 " --> pdb=" O PRO D 728 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N TYR D1067 " --> pdb=" O HIS D1048 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N HIS D1048 " --> pdb=" O TYR D1067 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'D' and resid 711 through 728 removed outlier: 6.859A pdb=" N GLN D1071 " --> pdb=" O THR D 716 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N PHE D 718 " --> pdb=" O PRO D1069 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N ILE D 720 " --> pdb=" O TYR D1067 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N TYR D1067 " --> pdb=" O ILE D 720 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N VAL D 722 " --> pdb=" O VAL D1065 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N VAL D1065 " --> pdb=" O VAL D 722 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N THR D 724 " --> pdb=" O LEU D1063 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N LEU D1063 " --> pdb=" O THR D 724 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N ILE D 726 " --> pdb=" O VAL D1061 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N VAL D1061 " --> pdb=" O ILE D 726 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N GLY D1059 " --> pdb=" O PRO D 728 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N PHE D1095 " --> pdb=" O ALA D1078 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'D' and resid 733 through 736 removed outlier: 4.530A pdb=" N LYS D 733 " --> pdb=" O LEU D 861 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'D' and resid 787 through 789 Processing sheet with id=AH5, first strand: chain 'D' and resid 1120 through 1123 Processing sheet with id=AH6, first strand: chain 'E' and resid 27 through 30 removed outlier: 7.646A pdb=" N ASN E 61 " --> pdb=" O TYR E 269 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N TYR E 269 " --> pdb=" O ASN E 61 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N SER E 205 " --> pdb=" O PRO E 225 " (cutoff:3.500A) removed outlier: 9.371A pdb=" N HIS E 207 " --> pdb=" O LEU E 223 " (cutoff:3.500A) removed outlier: 10.088A pdb=" N LEU E 223 " --> pdb=" O HIS E 207 " (cutoff:3.500A) removed outlier: 7.922A pdb=" N VAL E 36 " --> pdb=" O LEU E 223 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'E' and resid 27 through 30 Processing sheet with id=AH8, first strand: chain 'E' and resid 47 through 55 removed outlier: 7.339A pdb=" N THR E 274 " --> pdb=" O ASP E 290 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N ASP E 290 " --> pdb=" O THR E 274 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N LEU E 276 " --> pdb=" O ALA E 288 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N ALA E 288 " --> pdb=" O LEU E 276 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N LYS E 278 " --> pdb=" O THR E 286 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'E' and resid 83 through 85 removed outlier: 13.076A pdb=" N PHE E 135 " --> pdb=" O PHE E 238 " (cutoff:3.500A) removed outlier: 12.976A pdb=" N THR E 240 " --> pdb=" O PHE E 135 " (cutoff:3.500A) removed outlier: 10.437A pdb=" N ASN E 137 " --> pdb=" O THR E 240 " (cutoff:3.500A) removed outlier: 10.492A pdb=" N LEU E 242 " --> pdb=" O ASN E 137 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N LEU E 244 " --> pdb=" O PRO E 139 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N LEU E 141 " --> pdb=" O LEU E 244 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N SER E 162 " --> pdb=" O GLN E 134 " (cutoff:3.500A) removed outlier: 5.935A pdb=" N CYS E 136 " --> pdb=" O TYR E 160 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N TYR E 160 " --> pdb=" O CYS E 136 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N ASP E 138 " --> pdb=" O ARG E 158 " (cutoff:3.500A) removed outlier: 8.199A pdb=" N ARG E 158 " --> pdb=" O ASP E 138 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N PHE E 140 " --> pdb=" O GLU E 156 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N GLU E 156 " --> pdb=" O PHE E 140 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'E' and resid 83 through 85 removed outlier: 4.275A pdb=" N GLY E 103 " --> pdb=" O LEU E 241 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N ALA E 243 " --> pdb=" O ILE E 101 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N ILE E 101 " --> pdb=" O ALA E 243 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N ARG E 102 " --> pdb=" O ASN E 121 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ASN E 121 " --> pdb=" O ARG E 102 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N VAL E 126 " --> pdb=" O VAL E 171 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N VAL E 171 " --> pdb=" O VAL E 126 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N ILE E 128 " --> pdb=" O GLU E 169 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N GLU E 169 " --> pdb=" O ILE E 128 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'E' and resid 311 through 315 removed outlier: 4.573A pdb=" N VAL E 595 " --> pdb=" O THR E 315 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'E' and resid 325 through 328 Processing sheet with id=AI4, first strand: chain 'E' and resid 354 through 357 removed outlier: 3.567A pdb=" N VAL E 524 " --> pdb=" O PHE E 392 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N CYS E 361 " --> pdb=" O CYS E 525 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'E' and resid 354 through 357 removed outlier: 5.549A pdb=" N ASN E 394 " --> pdb=" O GLU E 516 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N GLU E 516 " --> pdb=" O ASN E 394 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'E' and resid 452 through 454 Processing sheet with id=AI7, first strand: chain 'E' and resid 473 through 474 Processing sheet with id=AI8, first strand: chain 'E' and resid 654 through 660 removed outlier: 6.267A pdb=" N GLU E 654 " --> pdb=" O ALA E 694 " (cutoff:3.500A) removed outlier: 8.690A pdb=" N THR E 696 " --> pdb=" O GLU E 654 " (cutoff:3.500A) removed outlier: 8.849A pdb=" N VAL E 656 " --> pdb=" O THR E 696 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'E' and resid 711 through 714 removed outlier: 4.312A pdb=" N PHE E1095 " --> pdb=" O ALA E1078 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'E' and resid 717 through 728 removed outlier: 6.012A pdb=" N TYR E1067 " --> pdb=" O HIS E1048 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N HIS E1048 " --> pdb=" O TYR E1067 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'E' and resid 734 through 736 Processing sheet with id=AJ3, first strand: chain 'E' and resid 787 through 790 Processing sheet with id=AJ4, first strand: chain 'E' and resid 1120 through 1123 Processing sheet with id=AJ5, first strand: chain 'F' and resid 27 through 30 removed outlier: 7.619A pdb=" N ASN F 61 " --> pdb=" O TYR F 269 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N TYR F 269 " --> pdb=" O ASN F 61 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N SER F 205 " --> pdb=" O PRO F 225 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'F' and resid 47 through 55 removed outlier: 7.356A pdb=" N THR F 274 " --> pdb=" O ASP F 290 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N ASP F 290 " --> pdb=" O THR F 274 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N LEU F 276 " --> pdb=" O ALA F 288 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N ALA F 288 " --> pdb=" O LEU F 276 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N LYS F 278 " --> pdb=" O THR F 286 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain 'F' and resid 83 through 85 removed outlier: 6.883A pdb=" N ALA F 243 " --> pdb=" O ILE F 101 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N ILE F 101 " --> pdb=" O ALA F 243 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N ARG F 102 " --> pdb=" O ASN F 121 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N VAL F 126 " --> pdb=" O TYR F 170 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N TYR F 170 " --> pdb=" O VAL F 126 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N ILE F 128 " --> pdb=" O PHE F 168 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N PHE F 168 " --> pdb=" O ILE F 128 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N VAL F 130 " --> pdb=" O CYS F 166 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N CYS F 166 " --> pdb=" O VAL F 130 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N SER F 162 " --> pdb=" O GLN F 134 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N CYS F 136 " --> pdb=" O TYR F 160 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N TYR F 160 " --> pdb=" O CYS F 136 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N ASP F 138 " --> pdb=" O ARG F 158 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N ARG F 158 " --> pdb=" O ASP F 138 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N PHE F 140 " --> pdb=" O GLU F 156 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N GLU F 156 " --> pdb=" O PHE F 140 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N GLY F 142 " --> pdb=" O GLU F 154 " (cutoff:3.500A) removed outlier: 5.124A pdb=" N GLU F 154 " --> pdb=" O GLY F 142 " (cutoff:3.500A) Processing sheet with id=AJ8, first strand: chain 'F' and resid 83 through 85 removed outlier: 13.249A pdb=" N PHE F 238 " --> pdb=" O PHE F 133 " (cutoff:3.500A) removed outlier: 12.921A pdb=" N PHE F 135 " --> pdb=" O PHE F 238 " (cutoff:3.500A) removed outlier: 12.888A pdb=" N THR F 240 " --> pdb=" O PHE F 135 " (cutoff:3.500A) removed outlier: 10.670A pdb=" N ASN F 137 " --> pdb=" O THR F 240 " (cutoff:3.500A) removed outlier: 10.808A pdb=" N LEU F 242 " --> pdb=" O ASN F 137 " (cutoff:3.500A) removed outlier: 7.875A pdb=" N LEU F 244 " --> pdb=" O PRO F 139 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N LEU F 141 " --> pdb=" O LEU F 244 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N VAL F 126 " --> pdb=" O TYR F 170 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N TYR F 170 " --> pdb=" O VAL F 126 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N ILE F 128 " --> pdb=" O PHE F 168 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N PHE F 168 " --> pdb=" O ILE F 128 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N VAL F 130 " --> pdb=" O CYS F 166 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N CYS F 166 " --> pdb=" O VAL F 130 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N SER F 162 " --> pdb=" O GLN F 134 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N CYS F 136 " --> pdb=" O TYR F 160 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N TYR F 160 " --> pdb=" O CYS F 136 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N ASP F 138 " --> pdb=" O ARG F 158 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N ARG F 158 " --> pdb=" O ASP F 138 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N PHE F 140 " --> pdb=" O GLU F 156 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N GLU F 156 " --> pdb=" O PHE F 140 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N GLY F 142 " --> pdb=" O GLU F 154 " (cutoff:3.500A) removed outlier: 5.124A pdb=" N GLU F 154 " --> pdb=" O GLY F 142 " (cutoff:3.500A) Processing sheet with id=AJ9, first strand: chain 'F' and resid 311 through 315 removed outlier: 4.611A pdb=" N VAL F 595 " --> pdb=" O THR F 315 " (cutoff:3.500A) Processing sheet with id=AK1, first strand: chain 'F' and resid 325 through 328 Processing sheet with id=AK2, first strand: chain 'F' and resid 348 through 349 removed outlier: 7.148A pdb=" N ALA F 348 " --> pdb=" O VAL F 401 " (cutoff:3.500A) removed outlier: 9.409A pdb=" N ARG F 403 " --> pdb=" O ALA F 348 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N VAL F 524 " --> pdb=" O PHE F 392 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N CYS F 361 " --> pdb=" O CYS F 525 " (cutoff:3.500A) Processing sheet with id=AK3, first strand: chain 'F' and resid 354 through 357 removed outlier: 5.414A pdb=" N ASN F 394 " --> pdb=" O GLU F 516 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N GLU F 516 " --> pdb=" O ASN F 394 " (cutoff:3.500A) Processing sheet with id=AK4, first strand: chain 'F' and resid 452 through 454 Processing sheet with id=AK5, first strand: chain 'F' and resid 473 through 474 Processing sheet with id=AK6, first strand: chain 'F' and resid 654 through 660 removed outlier: 6.244A pdb=" N GLU F 654 " --> pdb=" O ALA F 694 " (cutoff:3.500A) removed outlier: 8.672A pdb=" N THR F 696 " --> pdb=" O GLU F 654 " (cutoff:3.500A) removed outlier: 8.663A pdb=" N VAL F 656 " --> pdb=" O THR F 696 " (cutoff:3.500A) Processing sheet with id=AK7, first strand: chain 'F' and resid 711 through 714 removed outlier: 4.201A pdb=" N PHE F1095 " --> pdb=" O ALA F1078 " (cutoff:3.500A) Processing sheet with id=AK8, first strand: chain 'F' and resid 717 through 728 removed outlier: 6.005A pdb=" N TYR F1067 " --> pdb=" O HIS F1048 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N HIS F1048 " --> pdb=" O TYR F1067 " (cutoff:3.500A) Processing sheet with id=AK9, first strand: chain 'F' and resid 733 through 736 removed outlier: 4.551A pdb=" N LYS F 733 " --> pdb=" O LEU F 861 " (cutoff:3.500A) Processing sheet with id=AL1, first strand: chain 'F' and resid 1120 through 1123 removed outlier: 3.671A pdb=" N ALA F1087 " --> pdb=" O SER F1123 " (cutoff:3.500A) 2224 hydrogen bonds defined for protein. 5910 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: 23.72 Time building geometry restraints manager: 21.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 11884 1.32 - 1.46: 18834 1.46 - 1.60: 24782 1.60 - 1.74: 42 1.74 - 1.88: 292 Bond restraints: 55834 Sorted by residual: bond pdb=" C3 NAG 3 1 " pdb=" C4 NAG 3 1 " ideal model delta sigma weight residual 1.523 1.591 -0.068 1.00e-02 1.00e+04 4.68e+01 bond pdb=" C3 NAG P 1 " pdb=" C4 NAG P 1 " ideal model delta sigma weight residual 1.523 1.591 -0.068 1.00e-02 1.00e+04 4.68e+01 bond pdb=" C3 NAG l 1 " pdb=" C4 NAG l 1 " ideal model delta sigma weight residual 1.523 1.588 -0.065 1.00e-02 1.00e+04 4.19e+01 bond pdb=" C3 NAGPA 1 " pdb=" C4 NAGPA 1 " ideal model delta sigma weight residual 1.523 1.588 -0.065 1.00e-02 1.00e+04 4.19e+01 bond pdb=" C3 NAG K 1 " pdb=" C4 NAG K 1 " ideal model delta sigma weight residual 1.523 1.588 -0.065 1.00e-02 1.00e+04 4.17e+01 ... (remaining 55829 not shown) Histogram of bond angle deviations from ideal: 95.36 - 108.64: 6720 108.64 - 121.93: 58081 121.93 - 135.21: 11201 135.21 - 148.50: 0 148.50 - 161.78: 4 Bond angle restraints: 76006 Sorted by residual: angle pdb=" C2 NAG C1302 " pdb=" N2 NAG C1302 " pdb=" C7 NAG C1302 " ideal model delta sigma weight residual 123.12 161.78 -38.66 1.28e+00 6.08e-01 9.08e+02 angle pdb=" C2 NAG F1302 " pdb=" N2 NAG F1302 " pdb=" C7 NAG F1302 " ideal model delta sigma weight residual 123.12 161.78 -38.66 1.28e+00 6.08e-01 9.08e+02 angle pdb=" C2 NAG A1301 " pdb=" N2 NAG A1301 " pdb=" C7 NAG A1301 " ideal model delta sigma weight residual 123.12 161.20 -38.08 1.28e+00 6.08e-01 8.81e+02 angle pdb=" C2 NAG D1301 " pdb=" N2 NAG D1301 " pdb=" C7 NAG D1301 " ideal model delta sigma weight residual 123.12 161.20 -38.08 1.28e+00 6.08e-01 8.81e+02 angle pdb=" C8 NAGKA 2 " pdb=" C7 NAGKA 2 " pdb=" N2 NAGKA 2 " ideal model delta sigma weight residual 116.06 126.82 -10.76 9.90e-01 1.02e+00 1.18e+02 ... (remaining 76001 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 31760 17.88 - 35.77: 792 35.77 - 53.65: 206 53.65 - 71.53: 100 71.53 - 89.42: 34 Dihedral angle restraints: 32892 sinusoidal: 13480 harmonic: 19412 Sorted by residual: dihedral pdb=" CB CYS D 15 " pdb=" SG CYS D 15 " pdb=" SG CYS D 136 " pdb=" CB CYS D 136 " ideal model delta sinusoidal sigma weight residual 93.00 158.28 -65.28 1 1.00e+01 1.00e-02 5.58e+01 dihedral pdb=" CB CYS A 15 " pdb=" SG CYS A 15 " pdb=" SG CYS A 136 " pdb=" CB CYS A 136 " ideal model delta sinusoidal sigma weight residual 93.00 158.28 -65.28 1 1.00e+01 1.00e-02 5.58e+01 dihedral pdb=" CB CYS F 840 " pdb=" SG CYS F 840 " pdb=" SG CYS F 851 " pdb=" CB CYS F 851 " ideal model delta sinusoidal sigma weight residual 93.00 153.60 -60.60 1 1.00e+01 1.00e-02 4.89e+01 ... (remaining 32889 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.110: 6400 0.110 - 0.221: 1976 0.221 - 0.331: 458 0.331 - 0.442: 188 0.442 - 0.552: 90 Chirality restraints: 9112 Sorted by residual: chirality pdb=" C1 NAG S 2 " pdb=" O4 NAG S 1 " pdb=" C2 NAG S 2 " pdb=" O5 NAG S 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.03 -0.37 2.00e-02 2.50e+03 3.43e+02 chirality pdb=" C1 NAG 6 2 " pdb=" O4 NAG 6 1 " pdb=" C2 NAG 6 2 " pdb=" O5 NAG 6 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.03 -0.37 2.00e-02 2.50e+03 3.37e+02 chirality pdb=" C1 NAG 0 2 " pdb=" O4 NAG 0 1 " pdb=" C2 NAG 0 2 " pdb=" O5 NAG 0 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.65 0.25 2.00e-02 2.50e+03 1.55e+02 ... (remaining 9109 not shown) Planarity restraints: 9716 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG S 2 " -0.149 2.00e-02 2.50e+03 1.23e-01 1.90e+02 pdb=" C7 NAG S 2 " 0.037 2.00e-02 2.50e+03 pdb=" C8 NAG S 2 " -0.109 2.00e-02 2.50e+03 pdb=" N2 NAG S 2 " 0.201 2.00e-02 2.50e+03 pdb=" O7 NAG S 2 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG 6 2 " 0.149 2.00e-02 2.50e+03 1.23e-01 1.90e+02 pdb=" C7 NAG 6 2 " -0.037 2.00e-02 2.50e+03 pdb=" C8 NAG 6 2 " 0.109 2.00e-02 2.50e+03 pdb=" N2 NAG 6 2 " -0.201 2.00e-02 2.50e+03 pdb=" O7 NAG 6 2 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN E 122 " 0.089 2.00e-02 2.50e+03 9.76e-02 1.19e+02 pdb=" CG ASN E 122 " -0.033 2.00e-02 2.50e+03 pdb=" OD1 ASN E 122 " -0.017 2.00e-02 2.50e+03 pdb=" ND2 ASN E 122 " -0.156 2.00e-02 2.50e+03 pdb=" C1 NAGGA 1 " 0.118 2.00e-02 2.50e+03 ... (remaining 9713 not shown) Histogram of nonbonded interaction distances: 2.38 - 2.88: 20848 2.88 - 3.39: 51504 3.39 - 3.89: 95628 3.89 - 4.40: 110095 4.40 - 4.90: 174467 Nonbonded interactions: 452542 Sorted by model distance: nonbonded pdb=" N PRO E 600 " pdb=" O PRO E 600 " model vdw 2.377 2.496 nonbonded pdb=" N PRO B 600 " pdb=" O PRO B 600 " model vdw 2.377 2.496 nonbonded pdb=" N ASP F 843 " pdb=" OD1 ASP F 843 " model vdw 2.383 2.520 nonbonded pdb=" N ASP C 843 " pdb=" OD1 ASP C 843 " model vdw 2.383 2.520 nonbonded pdb=" N ASP E 663 " pdb=" O ASP E 663 " model vdw 2.415 2.496 ... (remaining 452537 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 '0' selection = chain '1' selection = chain '2' selection = chain '3' selection = chain '4' selection = chain '5' selection = chain '7' selection = chain '8' selection = chain '9' selection = chain 'AA' selection = chain 'BA' selection = chain 'CA' selection = chain 'DA' selection = chain 'EA' selection = chain 'FA' selection = chain 'G' selection = chain 'GA' selection = chain 'H' selection = chain 'HA' selection = chain 'I' selection = chain 'IA' selection = chain 'J' selection = chain 'JA' selection = chain 'K' selection = chain 'KA' selection = chain 'L' selection = chain 'LA' selection = chain 'M' selection = chain 'MA' selection = chain 'N' selection = chain 'NA' selection = chain 'O' selection = chain 'OA' selection = chain 'P' selection = chain 'PA' selection = chain 'Q' selection = chain 'QA' selection = chain 'R' selection = chain 'RA' selection = chain 'SA' selection = chain 'T' selection = chain 'TA' selection = chain 'U' selection = chain 'UA' selection = chain 'V' selection = chain 'VA' selection = chain 'W' selection = chain 'WA' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = 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 'u' selection = chain 'v' selection = chain 'w' selection = chain 'x' selection = chain 'y' selection = chain 'z' } ncs_group { reference = chain '6' selection = chain 'S' } ncs_group { reference = (chain 'A' and (resid 14 through 618 or resid 632 through 1146 or resid 1301 thr \ ough 1302)) selection = (chain 'B' and (resid 14 through 689 or resid 692 through 1146 or resid 1301 thr \ ough 1302)) selection = (chain 'C' and (resid 14 through 676 or resid 690 through 1146 or resid 1301 thr \ ough 1302)) selection = (chain 'D' and (resid 14 through 618 or resid 632 through 1146 or resid 1301 thr \ ough 1302)) selection = (chain 'E' and (resid 14 through 689 or resid 692 through 1146 or resid 1301 thr \ ough 1302)) selection = (chain 'F' and (resid 14 through 676 or resid 690 through 1146 or resid 1301 thr \ ough 1302)) } ncs_group { reference = chain 'XA' selection = chain 't' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 240 5.16 5 C 34638 2.51 5 N 8886 2.21 5 O 10850 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.650 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: 0.030 Extract box with map and model: 23.000 Check model and map are aligned: 0.600 Process input model: 116.790 Find NCS groups from input model: 5.200 Set up NCS constraints: 1.300 Set refine NCS operators: 0.010 Set scattering table: 0.390 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 154.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 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 0.156 55834 Z= 1.282 Angle : 1.773 38.664 76006 Z= 1.242 Chirality : 0.129 0.552 9112 Planarity : 0.009 0.123 9620 Dihedral : 9.938 89.416 20162 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 0.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer Outliers : 0.07 % 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: 0.68 (0.09), residues: 6642 helix: 0.46 (0.12), residues: 1366 sheet: 1.20 (0.14), residues: 1252 loop : 0.32 (0.09), residues: 4024 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13284 Ramachandran restraints generated. 6642 Oldfield, 0 Emsley, 6642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13284 Ramachandran restraints generated. 6642 Oldfield, 0 Emsley, 6642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1093 residues out of total 5800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 1089 time to evaluate : 4.845 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 1093 average time/residue: 0.5258 time to fit residues: 971.2166 Evaluate side-chains 424 residues out of total 5800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 422 time to evaluate : 4.842 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.3900 time to fit residues: 7.9014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 664 random chunks: chunk 560 optimal weight: 3.9990 chunk 503 optimal weight: 2.9990 chunk 279 optimal weight: 20.0000 chunk 171 optimal weight: 2.9990 chunk 339 optimal weight: 6.9990 chunk 268 optimal weight: 5.9990 chunk 520 optimal weight: 6.9990 chunk 201 optimal weight: 0.9990 chunk 316 optimal weight: 0.9990 chunk 387 optimal weight: 0.9990 chunk 602 optimal weight: 2.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 HIS A 317 ASN A 641 ASN A 914 ASN ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 GLN ** A1071 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 926 GLN B 955 ASN B1054 GLN C 146 HIS C 188 ASN ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 928 ASN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 957 GLN C1010 GLN C1023 ASN D 69 HIS D 317 ASN D 641 ASN D 914 ASN ** D 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1005 GLN ** D1071 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 926 GLN E 955 ASN E1054 GLN F 146 HIS F 188 ASN ** F 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 928 ASN ** F 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 957 GLN F1010 GLN F1023 ASN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.2672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.053 55834 Z= 0.244 Angle : 0.668 10.336 76006 Z= 0.374 Chirality : 0.049 0.565 9112 Planarity : 0.004 0.066 9620 Dihedral : 5.645 25.714 8292 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer Outliers : 0.24 % 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: 0.80 (0.10), residues: 6642 helix: 1.88 (0.14), residues: 1336 sheet: 0.99 (0.15), residues: 1192 loop : -0.02 (0.09), residues: 4114 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13284 Ramachandran restraints generated. 6642 Oldfield, 0 Emsley, 6642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13284 Ramachandran restraints generated. 6642 Oldfield, 0 Emsley, 6642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 609 residues out of total 5800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 595 time to evaluate : 5.178 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 outliers start: 14 outliers final: 6 residues processed: 607 average time/residue: 0.5114 time to fit residues: 535.6999 Evaluate side-chains 326 residues out of total 5800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 320 time to evaluate : 5.112 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.4304 time to fit residues: 11.3618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 664 random chunks: chunk 335 optimal weight: 9.9990 chunk 187 optimal weight: 9.9990 chunk 501 optimal weight: 5.9990 chunk 410 optimal weight: 0.8980 chunk 166 optimal weight: 10.0000 chunk 604 optimal weight: 6.9990 chunk 652 optimal weight: 10.0000 chunk 537 optimal weight: 0.9990 chunk 599 optimal weight: 9.9990 chunk 205 optimal weight: 0.5980 chunk 484 optimal weight: 8.9990 overall best weight: 3.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 317 ASN A 536 ASN A 658 ASN A 914 ASN ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1048 HIS A1058 HIS ** A1071 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 388 ASN B 926 GLN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN B1048 HIS ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 957 GLN D 66 HIS ** D 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 317 ASN D 536 ASN D 658 ASN D 914 ASN ** D 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1048 HIS D1058 HIS ** D1071 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 388 ASN E 926 GLN ** E 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1048 HIS ** F 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 957 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.3473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.077 55834 Z= 0.286 Angle : 0.638 8.287 76006 Z= 0.353 Chirality : 0.048 0.505 9112 Planarity : 0.004 0.070 9620 Dihedral : 5.575 25.715 8292 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer Outliers : 0.14 % 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: 0.38 (0.10), residues: 6642 helix: 1.74 (0.14), residues: 1362 sheet: 0.58 (0.14), residues: 1296 loop : -0.37 (0.09), residues: 3984 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13284 Ramachandran restraints generated. 6642 Oldfield, 0 Emsley, 6642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13284 Ramachandran restraints generated. 6642 Oldfield, 0 Emsley, 6642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 5800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 426 time to evaluate : 4.893 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 outliers start: 8 outliers final: 6 residues processed: 432 average time/residue: 0.5092 time to fit residues: 386.2483 Evaluate side-chains 284 residues out of total 5800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 278 time to evaluate : 4.796 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.3842 time to fit residues: 10.8073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 664 random chunks: chunk 596 optimal weight: 10.0000 chunk 454 optimal weight: 8.9990 chunk 313 optimal weight: 5.9990 chunk 66 optimal weight: 10.0000 chunk 288 optimal weight: 5.9990 chunk 405 optimal weight: 0.8980 chunk 606 optimal weight: 5.9990 chunk 641 optimal weight: 9.9990 chunk 316 optimal weight: 0.8980 chunk 574 optimal weight: 1.9990 chunk 172 optimal weight: 8.9990 overall best weight: 3.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 HIS ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 536 ASN A 901 GLN ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1071 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 185 ASN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 957 GLN D 69 HIS ** D 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 901 GLN ** D 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1071 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 185 ASN ** E 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 957 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.4025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.070 55834 Z= 0.271 Angle : 0.601 8.368 76006 Z= 0.329 Chirality : 0.047 0.485 9112 Planarity : 0.004 0.054 9620 Dihedral : 5.525 25.867 8292 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer Outliers : 0.10 % 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: 0.17 (0.10), residues: 6642 helix: 1.66 (0.14), residues: 1370 sheet: 0.57 (0.14), residues: 1288 loop : -0.60 (0.09), residues: 3984 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13284 Ramachandran restraints generated. 6642 Oldfield, 0 Emsley, 6642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13284 Ramachandran restraints generated. 6642 Oldfield, 0 Emsley, 6642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 5800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 396 time to evaluate : 4.897 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 outliers start: 6 outliers final: 4 residues processed: 402 average time/residue: 0.5060 time to fit residues: 358.5624 Evaluate side-chains 266 residues out of total 5800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 262 time to evaluate : 4.886 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.4197 time to fit residues: 9.4349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 664 random chunks: chunk 534 optimal weight: 20.0000 chunk 364 optimal weight: 3.9990 chunk 9 optimal weight: 10.0000 chunk 477 optimal weight: 3.9990 chunk 264 optimal weight: 6.9990 chunk 547 optimal weight: 8.9990 chunk 443 optimal weight: 9.9990 chunk 0 optimal weight: 30.0000 chunk 327 optimal weight: 0.9990 chunk 576 optimal weight: 0.9980 chunk 161 optimal weight: 3.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 ASN ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1071 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 644 GLN B 784 GLN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1058 HIS ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 957 GLN D 148 ASN ** D 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1005 GLN ** D1071 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1106 GLN E 644 GLN E 784 GLN ** E 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1002 GLN ** E1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1058 HIS ** F 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 183 GLN ** F 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 957 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.4359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.066 55834 Z= 0.247 Angle : 0.587 8.927 76006 Z= 0.322 Chirality : 0.047 0.553 9112 Planarity : 0.004 0.067 9620 Dihedral : 5.467 27.384 8292 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer Outliers : 0.05 % 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: 0.12 (0.10), residues: 6642 helix: 1.72 (0.14), residues: 1370 sheet: 0.44 (0.14), residues: 1246 loop : -0.63 (0.09), residues: 4026 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13284 Ramachandran restraints generated. 6642 Oldfield, 0 Emsley, 6642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13284 Ramachandran restraints generated. 6642 Oldfield, 0 Emsley, 6642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 5800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 382 time to evaluate : 4.835 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 outliers start: 3 outliers final: 3 residues processed: 385 average time/residue: 0.5235 time to fit residues: 360.1379 Evaluate side-chains 263 residues out of total 5800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 260 time to evaluate : 4.836 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.5609 time to fit residues: 9.3338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 664 random chunks: chunk 215 optimal weight: 2.9990 chunk 577 optimal weight: 8.9990 chunk 126 optimal weight: 5.9990 chunk 376 optimal weight: 6.9990 chunk 158 optimal weight: 0.0570 chunk 642 optimal weight: 2.9990 chunk 533 optimal weight: 9.9990 chunk 297 optimal weight: 6.9990 chunk 53 optimal weight: 1.9990 chunk 212 optimal weight: 9.9990 chunk 337 optimal weight: 1.9990 overall best weight: 2.0106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 GLN ** A1071 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1106 GLN B 185 ASN B1002 GLN ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 183 GLN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1071 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1106 GLN E 185 ASN E1002 GLN ** E1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.4603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.056 55834 Z= 0.196 Angle : 0.545 7.903 76006 Z= 0.297 Chirality : 0.046 0.435 9112 Planarity : 0.004 0.066 9620 Dihedral : 5.316 30.427 8292 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer Outliers : 0.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.10), residues: 6642 helix: 1.91 (0.14), residues: 1360 sheet: 0.45 (0.14), residues: 1250 loop : -0.60 (0.09), residues: 4032 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13284 Ramachandran restraints generated. 6642 Oldfield, 0 Emsley, 6642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13284 Ramachandran restraints generated. 6642 Oldfield, 0 Emsley, 6642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 5800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 390 time to evaluate : 4.908 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 outliers start: 1 outliers final: 1 residues processed: 391 average time/residue: 0.5150 time to fit residues: 358.6760 Evaluate side-chains 252 residues out of total 5800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 251 time to evaluate : 4.805 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.4730 time to fit residues: 7.3174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 664 random chunks: chunk 619 optimal weight: 9.9990 chunk 72 optimal weight: 1.9990 chunk 366 optimal weight: 1.9990 chunk 469 optimal weight: 2.9990 chunk 363 optimal weight: 5.9990 chunk 540 optimal weight: 5.9990 chunk 358 optimal weight: 7.9990 chunk 639 optimal weight: 2.9990 chunk 400 optimal weight: 7.9990 chunk 390 optimal weight: 0.3980 chunk 295 optimal weight: 10.0000 overall best weight: 2.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1071 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1106 GLN ** B1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 690 GLN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1036 GLN ** D 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 690 GLN ** D1071 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1106 GLN ** E 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1002 GLN ** E1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 690 GLN ** F 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F1036 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.4837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.057 55834 Z= 0.198 Angle : 0.541 7.729 76006 Z= 0.296 Chirality : 0.046 0.435 9112 Planarity : 0.004 0.064 9620 Dihedral : 5.258 26.381 8292 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer Outliers : 0.00 % 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: 0.22 (0.10), residues: 6642 helix: 1.94 (0.14), residues: 1372 sheet: 0.39 (0.14), residues: 1250 loop : -0.57 (0.09), residues: 4020 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13284 Ramachandran restraints generated. 6642 Oldfield, 0 Emsley, 6642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13284 Ramachandran restraints generated. 6642 Oldfield, 0 Emsley, 6642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 5800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 370 time to evaluate : 5.234 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 outliers start: 0 outliers final: 0 residues processed: 370 average time/residue: 0.5030 time to fit residues: 330.6003 Evaluate side-chains 259 residues out of total 5800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 259 time to evaluate : 4.837 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 6.4308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 664 random chunks: chunk 395 optimal weight: 1.9990 chunk 255 optimal weight: 2.9990 chunk 382 optimal weight: 10.0000 chunk 192 optimal weight: 0.7980 chunk 125 optimal weight: 0.9990 chunk 123 optimal weight: 5.9990 chunk 406 optimal weight: 6.9990 chunk 436 optimal weight: 7.9990 chunk 316 optimal weight: 3.9990 chunk 59 optimal weight: 8.9990 chunk 503 optimal weight: 9.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 HIS A1054 GLN ** A1071 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1106 GLN ** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1036 GLN ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 69 HIS D 690 GLN D1054 GLN ** D1071 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1106 GLN ** E 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1002 GLN ** E1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1036 GLN ** F 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.5004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.059 55834 Z= 0.202 Angle : 0.548 8.088 76006 Z= 0.298 Chirality : 0.046 0.426 9112 Planarity : 0.004 0.063 9620 Dihedral : 5.221 25.711 8292 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer Outliers : 0.00 % 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: 0.20 (0.10), residues: 6642 helix: 1.94 (0.14), residues: 1372 sheet: 0.37 (0.14), residues: 1270 loop : -0.59 (0.09), residues: 4000 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13284 Ramachandran restraints generated. 6642 Oldfield, 0 Emsley, 6642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13284 Ramachandran restraints generated. 6642 Oldfield, 0 Emsley, 6642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 5800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 360 time to evaluate : 4.789 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 outliers start: 0 outliers final: 0 residues processed: 360 average time/residue: 0.5013 time to fit residues: 322.6840 Evaluate side-chains 261 residues out of total 5800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 261 time to evaluate : 4.841 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 6.4208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 664 random chunks: chunk 582 optimal weight: 0.0970 chunk 613 optimal weight: 8.9990 chunk 559 optimal weight: 9.9990 chunk 596 optimal weight: 6.9990 chunk 612 optimal weight: 4.9990 chunk 358 optimal weight: 6.9990 chunk 259 optimal weight: 0.1980 chunk 468 optimal weight: 10.0000 chunk 183 optimal weight: 9.9990 chunk 538 optimal weight: 0.8980 chunk 564 optimal weight: 4.9990 overall best weight: 2.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1071 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1106 GLN ** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1071 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1106 GLN ** E 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.5219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.064 55834 Z= 0.204 Angle : 0.560 9.421 76006 Z= 0.302 Chirality : 0.046 0.411 9112 Planarity : 0.004 0.062 9620 Dihedral : 5.220 25.736 8292 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer Outliers : 0.00 % 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: 0.17 (0.10), residues: 6642 helix: 1.91 (0.14), residues: 1392 sheet: 0.34 (0.14), residues: 1276 loop : -0.62 (0.09), residues: 3974 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13284 Ramachandran restraints generated. 6642 Oldfield, 0 Emsley, 6642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13284 Ramachandran restraints generated. 6642 Oldfield, 0 Emsley, 6642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 5800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 347 time to evaluate : 4.876 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 outliers start: 0 outliers final: 0 residues processed: 347 average time/residue: 0.5077 time to fit residues: 312.2652 Evaluate side-chains 247 residues out of total 5800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 247 time to evaluate : 4.831 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 6.3835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 664 random chunks: chunk 594 optimal weight: 0.9990 chunk 391 optimal weight: 5.9990 chunk 630 optimal weight: 5.9990 chunk 384 optimal weight: 0.9990 chunk 299 optimal weight: 4.9990 chunk 438 optimal weight: 0.8980 chunk 661 optimal weight: 0.7980 chunk 608 optimal weight: 10.0000 chunk 526 optimal weight: 10.0000 chunk 54 optimal weight: 5.9990 chunk 406 optimal weight: 3.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 317 ASN ** A1071 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 317 ASN ** D1071 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.5362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.049 55834 Z= 0.170 Angle : 0.530 7.679 76006 Z= 0.287 Chirality : 0.045 0.400 9112 Planarity : 0.004 0.063 9620 Dihedral : 5.102 24.987 8292 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer Outliers : 0.00 % 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: 0.22 (0.10), residues: 6642 helix: 2.03 (0.14), residues: 1382 sheet: 0.35 (0.14), residues: 1278 loop : -0.60 (0.09), residues: 3982 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13284 Ramachandran restraints generated. 6642 Oldfield, 0 Emsley, 6642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13284 Ramachandran restraints generated. 6642 Oldfield, 0 Emsley, 6642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 5800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 339 time to evaluate : 5.193 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 outliers start: 0 outliers final: 0 residues processed: 339 average time/residue: 0.5107 time to fit residues: 307.9140 Evaluate side-chains 263 residues out of total 5800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 263 time to evaluate : 4.839 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 6.3942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 664 random chunks: chunk 322 optimal weight: 9.9990 chunk 418 optimal weight: 0.9990 chunk 561 optimal weight: 7.9990 chunk 161 optimal weight: 6.9990 chunk 485 optimal weight: 10.0000 chunk 77 optimal weight: 1.9990 chunk 146 optimal weight: 10.0000 chunk 527 optimal weight: 9.9990 chunk 220 optimal weight: 0.7980 chunk 541 optimal weight: 5.9990 chunk 66 optimal weight: 6.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 317 ASN A 474 GLN ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1071 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1106 GLN ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 920 GLN ** C 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 317 ASN D 474 GLN ** D 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1071 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1106 GLN ** E 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 920 GLN ** E1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.062817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.052271 restraints weight = 259536.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.053584 restraints weight = 154729.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.054501 restraints weight = 105097.169| |-----------------------------------------------------------------------------| r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.5559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.086 55834 Z= 0.269 Angle : 0.586 10.407 76006 Z= 0.317 Chirality : 0.046 0.410 9112 Planarity : 0.004 0.061 9620 Dihedral : 5.317 26.897 8292 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer Outliers : 0.00 % 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: 0.03 (0.10), residues: 6642 helix: 1.88 (0.14), residues: 1378 sheet: 0.23 (0.15), residues: 1268 loop : -0.73 (0.09), residues: 3996 =============================================================================== Job complete usr+sys time: 8184.03 seconds wall clock time: 148 minutes 5.49 seconds (8885.49 seconds total)