Starting phenix.real_space_refine on Wed Dec 13 13:21:20 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w92_32359/12_2023/7w92_32359.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w92_32359/12_2023/7w92_32359.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w92_32359/12_2023/7w92_32359.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w92_32359/12_2023/7w92_32359.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w92_32359/12_2023/7w92_32359.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w92_32359/12_2023/7w92_32359.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.035 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 114 5.16 5 C 15986 2.51 5 N 4211 2.21 5 O 4760 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 53": "OD1" <-> "OD2" Residue "A PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 80": "OD1" <-> "OD2" Residue "A ASP 88": "OD1" <-> "OD2" Residue "A GLU 96": "OE1" <-> "OE2" Residue "A PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 138": "OD1" <-> "OD2" Residue "A PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 154": "OE1" <-> "OE2" Residue "A TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 180": "OE1" <-> "OE2" Residue "A PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 198": "OD1" <-> "OD2" Residue "A TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 287": "OD1" <-> "OD2" Residue "A ASP 290": "OD1" <-> "OD2" Residue "A ASP 294": "OD1" <-> "OD2" Residue "A GLU 309": "OE1" <-> "OE2" Residue "A TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 324": "OE1" <-> "OE2" Residue "A PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 340": "OE1" <-> "OE2" Residue "A TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 428": "OD1" <-> "OD2" Residue "A TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 451": "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 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 554": "OE1" <-> "OE2" Residue "A PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 571": "OD1" <-> "OD2" Residue "A ASP 586": "OD1" <-> "OD2" Residue "A PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 619": "OE1" <-> "OE2" Residue "A TYR 636": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 654": "OE1" <-> "OE2" Residue "A GLU 661": "OE1" <-> "OE2" Residue "A GLU 748": "OE1" <-> "OE2" Residue "A GLU 773": "OE1" <-> "OE2" Residue "A PHE 782": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 796": "OD1" <-> "OD2" Residue "A PHE 797": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 800": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 802": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 808": "OD1" <-> "OD2" Residue "A ASP 820": "OD1" <-> "OD2" Residue "A GLU 868": "OE1" <-> "OE2" 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 GLU 1017": "OE1" <-> "OE2" Residue "A TYR 1047": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1052": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1062": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1072": "OE1" <-> "OE2" Residue "A PHE 1075": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1089": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 96": "OE1" <-> "OE2" Residue "C PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 215": "OD1" <-> "OD2" Residue "C PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 287": "OD1" <-> "OD2" Residue "C PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 309": "OE1" <-> "OE2" Residue "C TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 324": "OE1" <-> "OE2" Residue "C PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 340": "OE1" <-> "OE2" Residue "C PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 427": "OD1" <-> "OD2" Residue "C ASP 428": "OD1" <-> "OD2" Residue "C ASP 442": "OD1" <-> "OD2" Residue "C TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 467": "OD1" <-> "OD2" Residue "C TYR 473": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 484": "OE1" <-> "OE2" Residue "C PHE 486": "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 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 554": "OE1" <-> "OE2" Residue "C ASP 568": "OD1" <-> "OD2" Residue "C ASP 578": "OD1" <-> "OD2" Residue "C PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 661": "OE1" <-> "OE2" Residue "C ASP 663": "OD1" <-> "OD2" Residue "C GLU 702": "OE1" <-> "OE2" Residue "C TYR 707": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 773": "OE1" <-> "OE2" Residue "C GLU 780": "OE1" <-> "OE2" 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 ASP 867": "OD1" <-> "OD2" Residue "C GLU 868": "OE1" <-> "OE2" Residue "C PHE 888": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 917": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 936": "OD1" <-> "OD2" Residue "C PHE 970": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 988": "OE1" <-> "OE2" Residue "C TYR 1047": "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 GLU 1092": "OE1" <-> "OE2" Residue "C PHE 1095": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1111": "OE1" <-> "OE2" Residue "C ASP 1127": "OD1" <-> "OD2" Residue "C ASP 1146": "OD1" <-> "OD2" Residue "B TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 53": "OD1" <-> "OD2" Residue "B PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 96": "OE1" <-> "OE2" Residue "B ASP 111": "OD1" <-> "OD2" Residue "B PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 138": "OD1" <-> "OD2" Residue "B TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 169": "OE1" <-> "OE2" Residue "B GLU 180": "OE1" <-> "OE2" Residue "B PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 281": "OE1" <-> "OE2" Residue "B ASP 294": "OD1" <-> "OD2" Residue "B GLU 309": "OE1" <-> "OE2" Residue "B TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 324": "OE1" <-> "OE2" Residue "B PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 364": "OD1" <-> "OD2" Residue "B TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 389": "OD1" <-> "OD2" Residue "B PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 406": "OE1" <-> "OE2" Residue "B ASP 428": "OD1" <-> "OD2" Residue "B ASP 442": "OD1" <-> "OD2" 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 GLU 465": "OE1" <-> "OE2" Residue "B ASP 467": "OD1" <-> "OD2" Residue "B TYR 489": "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 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 554": "OE1" <-> "OE2" Residue "B PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 578": "OD1" <-> "OD2" Residue "B GLU 583": "OE1" <-> "OE2" Residue "B ASP 586": "OD1" <-> "OD2" Residue "B PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 636": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 702": "OE1" <-> "OE2" Residue "B TYR 707": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 745": "OD1" <-> "OD2" Residue "B GLU 780": "OE1" <-> "OE2" Residue "B PHE 782": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 796": "OD1" <-> "OD2" Residue "B PHE 797": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 800": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 802": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 808": "OD1" <-> "OD2" Residue "B PHE 888": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 917": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 918": "OE1" <-> "OE2" Residue "B ASP 936": "OD1" <-> "OD2" Residue "B PHE 970": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 988": "OE1" <-> "OE2" Residue "B GLU 990": "OE1" <-> "OE2" Residue "B GLU 1017": "OE1" <-> "OE2" Residue "B ASP 1041": "OD1" <-> "OD2" 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 PHE 1075": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1084": "OD1" <-> "OD2" Residue "B PHE 1089": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1111": "OE1" <-> "OE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 25071 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 8382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1072, 8382 Classifications: {'peptide': 1072} Link IDs: {'PTRANS': 53, 'TRANS': 1018} Chain breaks: 6 Chain: "C" Number of atoms: 8296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1061, 8296 Classifications: {'peptide': 1061} Link IDs: {'PTRANS': 53, 'TRANS': 1007} Chain breaks: 6 Chain: "B" Number of atoms: 8393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1073, 8393 Classifications: {'peptide': 1073} Link IDs: {'PTRANS': 54, 'TRANS': 1018} Chain breaks: 7 Time building chain proxies: 13.05, per 1000 atoms: 0.52 Number of scatterers: 25071 At special positions: 0 Unit cell: (155.382, 141.987, 201.818, 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 114 16.00 O 4760 8.00 N 4211 7.00 C 15986 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.04 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.04 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.04 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 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 B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 9.13 Conformation dependent library (CDL) restraints added in 4.4 seconds 6326 Ramachandran restraints generated. 3163 Oldfield, 0 Emsley, 3163 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5994 Finding SS restraints... Secondary structure from input PDB file: 61 helices and 55 sheets defined 21.7% alpha, 21.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.55 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 removed outlier: 3.951A pdb=" N LYS A 300 " --> pdb=" O LEU A 296 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N THR A 302 " --> pdb=" O GLU A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 343 removed outlier: 4.049A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 removed outlier: 4.277A pdb=" N TYR A 369 " --> pdb=" O TYR A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 422 Processing helix chain 'A' and resid 438 through 443 removed outlier: 3.786A pdb=" N SER A 443 " --> pdb=" O ASN A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 506 removed outlier: 3.762A pdb=" N TYR A 505 " --> pdb=" O GLY A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 623 removed outlier: 4.002A pdb=" N VAL A 622 " --> pdb=" O THR A 618 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.819A pdb=" N ASN A 751 " --> pdb=" O THR A 747 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU A 754 " --> pdb=" O SER A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 782 removed outlier: 3.502A pdb=" N GLN A 762 " --> pdb=" O SER A 758 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU A 763 " --> pdb=" O PHE A 759 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASN A 764 " --> pdb=" O CYS A 760 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLN A 779 " --> pdb=" O ASP A 775 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL A 781 " --> pdb=" O ASN A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 823 removed outlier: 3.698A pdb=" N LEU A 821 " --> pdb=" O PHE A 817 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 884 removed outlier: 3.530A pdb=" N GLY A 880 " --> pdb=" O ALA A 876 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N THR A 883 " --> pdb=" O ALA A 879 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 907 removed outlier: 4.098A pdb=" N ALA A 903 " --> pdb=" O ALA A 899 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N TYR A 904 " --> pdb=" O MET A 900 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ASN A 907 " --> pdb=" O ALA A 903 " (cutoff:3.500A) Processing helix chain 'A' and resid 908 through 910 No H-bonds generated for 'chain 'A' and resid 908 through 910' Processing helix chain 'A' and resid 913 through 918 removed outlier: 3.977A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLU A 918 " --> pdb=" O ASN A 914 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 913 through 918' Processing helix chain 'A' and resid 919 through 939 removed outlier: 3.567A pdb=" N GLY A 932 " --> pdb=" O ASN A 928 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS A 933 " --> pdb=" O SER A 929 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ILE A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 941 through 944 removed outlier: 4.056A pdb=" N ALA A 944 " --> pdb=" O THR A 941 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 941 through 944' Processing helix chain 'A' and resid 945 through 965 removed outlier: 4.013A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU A 962 " --> pdb=" O ALA A 958 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.584A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N SER A 982 " --> pdb=" O ASN A 978 " (cutoff:3.500A) Processing helix chain 'A' and resid 989 through 1032 removed outlier: 3.555A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLN A1002 " --> pdb=" O THR A 998 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N SER A1003 " --> pdb=" O GLY A 999 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU A1004 " --> pdb=" O ARG A1000 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SER A1030 " --> pdb=" O ALA A1026 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 removed outlier: 3.662A pdb=" N THR C 302 " --> pdb=" O GLU C 298 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 386 through 389 removed outlier: 4.005A pdb=" N ASP C 389 " --> pdb=" O LYS C 386 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 386 through 389' Processing helix chain 'C' and resid 406 through 410 removed outlier: 3.723A pdb=" N ILE C 410 " --> pdb=" O VAL C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 422 removed outlier: 3.554A pdb=" N TYR C 421 " --> pdb=" O LYS C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 738 through 743 Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.647A pdb=" N SER C 750 " --> pdb=" O SER C 746 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ASN C 751 " --> pdb=" O THR C 747 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU C 754 " --> pdb=" O SER C 750 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 782 removed outlier: 3.754A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU C 767 " --> pdb=" O LEU C 763 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLN C 779 " --> pdb=" O ASP C 775 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL C 781 " --> pdb=" O ASN C 777 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N PHE C 782 " --> pdb=" O THR C 778 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 823 removed outlier: 3.532A pdb=" N LEU C 821 " --> pdb=" O PHE C 817 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 884 removed outlier: 3.549A pdb=" N TYR C 873 " --> pdb=" O MET C 869 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLY C 880 " --> pdb=" O ALA C 876 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ILE C 882 " --> pdb=" O LEU C 878 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N THR C 883 " --> pdb=" O ALA C 879 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 908 removed outlier: 3.760A pdb=" N MET C 902 " --> pdb=" O PHE C 898 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ALA C 903 " --> pdb=" O ALA C 899 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N TYR C 904 " --> pdb=" O MET C 900 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ASN C 907 " --> pdb=" O ALA C 903 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 918 Processing helix chain 'C' and resid 919 through 939 removed outlier: 3.885A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N SER C 939 " --> pdb=" O GLN C 935 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.047A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA C 958 " --> pdb=" O GLN C 954 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LEU C 959 " --> pdb=" O ASN C 955 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LEU C 962 " --> pdb=" O ALA C 958 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 982 removed outlier: 3.722A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU C 981 " --> pdb=" O LEU C 977 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER C 982 " --> pdb=" O ASN C 978 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 976 through 982' Processing helix chain 'C' and resid 985 through 1032 removed outlier: 3.568A pdb=" N GLU C 990 " --> pdb=" O PRO C 986 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N THR C 998 " --> pdb=" O ASP C 994 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N SER C1003 " --> pdb=" O GLY C 999 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N TYR C1007 " --> pdb=" O SER C1003 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ILE C1013 " --> pdb=" O THR C1009 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ARG C1014 " --> pdb=" O GLN C1010 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA C1016 " --> pdb=" O LEU C1012 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N SER C1030 " --> pdb=" O ALA C1026 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 303 removed outlier: 3.738A pdb=" N LYS B 300 " --> pdb=" O LEU B 296 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N CYS B 301 " --> pdb=" O SER B 297 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N THR B 302 " --> pdb=" O GLU B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 343 removed outlier: 3.765A pdb=" N PHE B 342 " --> pdb=" O PHE B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 371 removed outlier: 3.759A pdb=" N ASN B 370 " --> pdb=" O SER B 366 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N SER B 371 " --> pdb=" O VAL B 367 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 366 through 371' Processing helix chain 'B' and resid 384 through 388 removed outlier: 3.593A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 384 through 388' Processing helix chain 'B' and resid 502 through 506 Processing helix chain 'B' and resid 737 through 743 removed outlier: 3.808A pdb=" N ILE B 742 " --> pdb=" O CYS B 738 " (cutoff:3.500A) Processing helix chain 'B' and resid 746 through 754 removed outlier: 3.592A pdb=" N ASN B 751 " --> pdb=" O THR B 747 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU B 754 " --> pdb=" O SER B 750 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 780 removed outlier: 3.933A pdb=" N LEU B 763 " --> pdb=" O PHE B 759 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASN B 764 " --> pdb=" O CYS B 760 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU B 767 " --> pdb=" O LEU B 763 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALA B 771 " --> pdb=" O LEU B 767 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLN B 779 " --> pdb=" O ASP B 775 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 824 removed outlier: 3.691A pdb=" N ASN B 824 " --> pdb=" O ASP B 820 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 884 removed outlier: 3.508A pdb=" N TYR B 873 " --> pdb=" O MET B 869 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE B 882 " --> pdb=" O LEU B 878 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N THR B 883 " --> pdb=" O ALA B 879 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 908 removed outlier: 3.687A pdb=" N MET B 902 " --> pdb=" O PHE B 898 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ALA B 903 " --> pdb=" O ALA B 899 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N TYR B 904 " --> pdb=" O MET B 900 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 919 removed outlier: 3.586A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.719A pdb=" N GLY B 932 " --> pdb=" O ASN B 928 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LYS B 933 " --> pdb=" O SER B 929 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N SER B 940 " --> pdb=" O ASP B 936 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.215A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU B 959 " --> pdb=" O ASN B 955 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU B 962 " --> pdb=" O ALA B 958 " (cutoff:3.500A) 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 removed outlier: 3.629A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N SER B 982 " --> pdb=" O ASN B 978 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LEU B 984 " --> pdb=" O ILE B 980 " (cutoff:3.500A) Processing helix chain 'B' and resid 988 through 1032 removed outlier: 4.386A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ASP B 994 " --> pdb=" O GLU B 990 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLY B 999 " --> pdb=" O ARG B 995 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLN B1002 " --> pdb=" O THR B 998 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N SER B1003 " --> pdb=" O GLY B 999 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU B1004 " --> pdb=" O ARG B1000 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ALA B1016 " --> pdb=" O LEU B1012 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N SER B1030 " --> pdb=" O ALA B1026 " (cutoff:3.500A) Processing helix chain 'B' and resid 1143 through 1147 removed outlier: 3.500A pdb=" N ASP B1146 " --> pdb=" O PRO B1143 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N SER B1147 " --> pdb=" O GLU B1144 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1143 through 1147' Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31 removed outlier: 3.695A pdb=" N VAL A 62 " --> pdb=" O THR A 29 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N TYR A 265 " --> pdb=" O PHE A 65 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 4.025A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLY C 548 " --> pdb=" O PHE C 541 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 51 removed outlier: 6.517A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 54 through 55 Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.807A pdb=" N LEU A 84 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.807A pdb=" N LEU A 84 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 91 through 93 removed outlier: 3.699A pdb=" N THR A 208 " --> pdb=" O LEU A 189 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLU A 191 " --> pdb=" O LYS A 206 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LYS A 206 " --> pdb=" O GLU A 191 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VAL A 193 " --> pdb=" O TYR A 204 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N TYR A 204 " --> pdb=" O VAL A 193 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LYS A 195 " --> pdb=" O LYS A 202 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LYS A 202 " --> pdb=" O LYS A 195 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 119 through 121 removed outlier: 3.663A pdb=" N ILE A 128 " --> pdb=" O TYR A 170 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 311 through 317 removed outlier: 3.568A pdb=" N THR A 315 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL A 610 " --> pdb=" O ILE A 651 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 325 through 328 removed outlier: 3.705A pdb=" N GLY A 548 " --> pdb=" O PHE A 541 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU A 546 " --> pdb=" O PHE A 543 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N THR A 588 " --> pdb=" O VAL A 551 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ASP A 574 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.252A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N PHE A 400 " --> pdb=" O VAL A 510 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N VAL A 510 " --> pdb=" O PHE A 400 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ILE A 402 " --> pdb=" O TYR A 508 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N THR A 376 " --> pdb=" O ALA A 435 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.942A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 452 through 454 removed outlier: 3.606A pdb=" N GLN A 493 " --> pdb=" O TYR A 453 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.511A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.387A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.912A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N SER A 691 " --> pdb=" O GLN A 675 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLN A 675 " --> pdb=" O SER A 691 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILE A 664 " --> pdb=" O ALA A 672 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 712 through 715 removed outlier: 3.804A pdb=" N ILE A 712 " --> pdb=" O PHE A1075 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LYS A1073 " --> pdb=" O ILE A 714 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 718 through 722 Processing sheet with id=AB9, first strand: chain 'A' and resid 718 through 722 removed outlier: 3.503A pdb=" N GLY A1059 " --> pdb=" O ALA A1056 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ALA A1056 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.801A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 735 through 736 Processing sheet with id=AC2, first strand: chain 'A' and resid 787 through 788 Processing sheet with id=AC3, first strand: chain 'A' and resid 1122 through 1125 removed outlier: 5.432A pdb=" N GLY A1124 " --> pdb=" O ALA A1087 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AC5, first strand: chain 'C' and resid 28 through 30 removed outlier: 3.538A pdb=" N VAL C 62 " --> pdb=" O THR C 29 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.819A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N TYR C 266 " --> pdb=" O ALA C 93 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ALA C 93 " --> pdb=" O TYR C 266 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLY C 268 " --> pdb=" O TYR C 91 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N VAL C 90 " --> pdb=" O PHE C 194 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N PHE C 194 " --> pdb=" O VAL C 90 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU C 189 " --> pdb=" O THR C 208 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N THR C 208 " --> pdb=" O LEU C 189 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLU C 191 " --> pdb=" O LYS C 206 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LYS C 206 " --> pdb=" O GLU C 191 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL C 193 " --> pdb=" O TYR C 204 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N LYS C 195 " --> pdb=" O LYS C 202 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LYS C 202 " --> pdb=" O LYS C 195 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ILE C 197 " --> pdb=" O TYR C 200 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE C 203 " --> pdb=" O VAL C 227 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 42 through 43 removed outlier: 5.954A pdb=" N PHE C 43 " --> pdb=" O ARG B 567 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LEU B 585 " --> pdb=" O VAL B 576 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N THR B 553 " --> pdb=" O ASP B 586 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N THR B 588 " --> pdb=" O VAL B 551 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLY B 550 " --> pdb=" O VAL B 539 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL B 539 " --> pdb=" O GLY B 550 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.811A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ARG C 273 " --> pdb=" O ASP C 53 " (cutoff:3.500A) removed outlier: 7.955A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 84 through 85 removed outlier: 4.141A pdb=" N LEU C 84 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N LEU C 141 " --> pdb=" O LEU C 244 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 84 through 85 removed outlier: 4.141A pdb=" N LEU C 84 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU C 241 " --> pdb=" O GLY C 103 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASN C 121 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N TRP C 104 " --> pdb=" O ILE C 119 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N CYS C 131 " --> pdb=" O SER C 116 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N VAL C 120 " --> pdb=" O VAL C 127 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N TYR C 170 " --> pdb=" O ILE C 128 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.290A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.771A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 356 through 358 removed outlier: 3.937A pdb=" N LYS C 356 " --> pdb=" O ALA C 397 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N ALA C 397 " --> pdb=" O LYS C 356 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 391 through 392 removed outlier: 3.574A pdb=" N VAL C 524 " --> pdb=" O PHE C 392 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 400 through 402 Processing sheet with id=AD5, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AD6, first strand: chain 'C' and resid 473 through 474 removed outlier: 4.019A pdb=" N TYR C 473 " --> pdb=" O TYR C 489 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.263A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.778A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 711 through 713 removed outlier: 3.719A pdb=" N ILE C 712 " --> pdb=" O PHE C1075 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 718 through 719 Processing sheet with id=AE1, first strand: chain 'C' and resid 718 through 719 removed outlier: 3.530A pdb=" N GLY C1059 " --> pdb=" O ALA C1056 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AE3, first strand: chain 'C' and resid 1094 through 1097 Processing sheet with id=AE4, first strand: chain 'B' and resid 27 through 30 removed outlier: 4.241A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N THR B 63 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL B 267 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N TYR B 265 " --> pdb=" O PHE B 65 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.532A pdb=" N PHE B 275 " --> pdb=" O THR B 51 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ARG B 273 " --> pdb=" O ASP B 53 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLN B 271 " --> pdb=" O PHE B 55 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'B' and resid 84 through 85 removed outlier: 5.781A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.907A pdb=" N ILE B 105 " --> pdb=" O GLN B 239 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE B 128 " --> pdb=" O TYR B 170 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N TYR B 170 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N VAL B 130 " --> pdb=" O PHE B 168 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'B' and resid 91 through 96 removed outlier: 3.748A pdb=" N ASN B 188 " --> pdb=" O GLU B 96 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N TYR B 204 " --> pdb=" O VAL B 193 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LYS B 195 " --> pdb=" O LYS B 202 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LYS B 202 " --> pdb=" O LYS B 195 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'B' and resid 311 through 317 removed outlier: 7.310A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.887A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N SER B 399 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU B 513 " --> pdb=" O CYS B 432 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N CYS B 432 " --> pdb=" O LEU B 513 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AF3, first strand: chain 'B' and resid 473 through 474 removed outlier: 3.544A pdb=" N TYR B 473 " --> pdb=" O TYR B 489 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N TYR B 489 " --> pdb=" O TYR B 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF3 Processing sheet with id=AF4, first strand: chain 'B' and resid 654 through 655 removed outlier: 3.534A pdb=" N GLU B 654 " --> pdb=" O ILE B 692 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N SER B 691 " --> pdb=" O GLN B 675 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'B' and resid 711 through 713 Processing sheet with id=AF6, first strand: chain 'B' and resid 718 through 719 Processing sheet with id=AF7, first strand: chain 'B' and resid 718 through 719 removed outlier: 7.386A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.892A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N TYR B1047 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AF9, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AG1, first strand: chain 'B' and resid 1094 through 1097 657 hydrogen bonds defined for protein. 1830 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: 11.24 Time building geometry restraints manager: 9.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 8123 1.35 - 1.47: 6422 1.47 - 1.60: 10961 1.60 - 1.72: 0 1.72 - 1.84: 144 Bond restraints: 25650 Sorted by residual: bond pdb=" C GLN C 23 " pdb=" N LEU C 24 " ideal model delta sigma weight residual 1.331 1.373 -0.042 2.07e-02 2.33e+03 4.10e+00 bond pdb=" CA THR B 630 " pdb=" C THR B 630 " ideal model delta sigma weight residual 1.525 1.565 -0.040 2.10e-02 2.27e+03 3.56e+00 bond pdb=" CA GLU B 516 " pdb=" CB GLU B 516 " ideal model delta sigma weight residual 1.526 1.554 -0.028 1.70e-02 3.46e+03 2.64e+00 bond pdb=" C GLN C1142 " pdb=" N PRO C1143 " ideal model delta sigma weight residual 1.334 1.346 -0.013 8.40e-03 1.42e+04 2.35e+00 bond pdb=" CB ASP B 198 " pdb=" CG ASP B 198 " ideal model delta sigma weight residual 1.516 1.552 -0.036 2.50e-02 1.60e+03 2.09e+00 ... (remaining 25645 not shown) Histogram of bond angle deviations from ideal: 100.37 - 107.63: 916 107.63 - 114.88: 14770 114.88 - 122.14: 13828 122.14 - 129.40: 5272 129.40 - 136.66: 103 Bond angle restraints: 34889 Sorted by residual: angle pdb=" C ILE B 197 " pdb=" N ASP B 198 " pdb=" CA ASP B 198 " ideal model delta sigma weight residual 121.54 129.90 -8.36 1.91e+00 2.74e-01 1.92e+01 angle pdb=" N VAL C1128 " pdb=" CA VAL C1128 " pdb=" C VAL C1128 " ideal model delta sigma weight residual 112.96 108.96 4.00 1.00e+00 1.00e+00 1.60e+01 angle pdb=" C ALA B 570 " pdb=" N ASP B 571 " pdb=" CA ASP B 571 " ideal model delta sigma weight residual 122.46 128.03 -5.57 1.41e+00 5.03e-01 1.56e+01 angle pdb=" C ILE C 197 " pdb=" N ASP C 198 " pdb=" CA ASP C 198 " ideal model delta sigma weight residual 122.08 127.37 -5.29 1.47e+00 4.63e-01 1.30e+01 angle pdb=" N PRO C 986 " pdb=" CA PRO C 986 " pdb=" C PRO C 986 " ideal model delta sigma weight residual 110.70 114.92 -4.22 1.22e+00 6.72e-01 1.20e+01 ... (remaining 34884 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 13992 18.00 - 35.99: 1058 35.99 - 53.99: 181 53.99 - 71.99: 39 71.99 - 89.98: 27 Dihedral angle restraints: 15297 sinusoidal: 5979 harmonic: 9318 Sorted by residual: dihedral pdb=" CB CYS B 391 " pdb=" SG CYS B 391 " pdb=" SG CYS B 525 " pdb=" CB CYS B 525 " ideal model delta sinusoidal sigma weight residual -86.00 -3.44 -82.56 1 1.00e+01 1.00e-02 8.36e+01 dihedral pdb=" CB CYS A 538 " pdb=" SG CYS A 538 " pdb=" SG CYS A 590 " pdb=" CB CYS A 590 " ideal model delta sinusoidal sigma weight residual 93.00 175.38 -82.38 1 1.00e+01 1.00e-02 8.33e+01 dihedral pdb=" CB CYS C 662 " pdb=" SG CYS C 662 " pdb=" SG CYS C 671 " pdb=" CB CYS C 671 " ideal model delta sinusoidal sigma weight residual -86.00 -6.18 -79.82 1 1.00e+01 1.00e-02 7.90e+01 ... (remaining 15294 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 2911 0.046 - 0.092: 711 0.092 - 0.138: 282 0.138 - 0.183: 30 0.183 - 0.229: 4 Chirality restraints: 3938 Sorted by residual: chirality pdb=" CA ASP B 198 " pdb=" N ASP B 198 " pdb=" C ASP B 198 " pdb=" CB ASP B 198 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.31e+00 chirality pdb=" CB ILE A 434 " pdb=" CA ILE A 434 " pdb=" CG1 ILE A 434 " pdb=" CG2 ILE A 434 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.20 2.00e-01 2.50e+01 1.02e+00 chirality pdb=" CB ILE A 472 " pdb=" CA ILE A 472 " pdb=" CG1 ILE A 472 " pdb=" CG2 ILE A 472 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.19 2.00e-01 2.50e+01 9.05e-01 ... (remaining 3935 not shown) Planarity restraints: 4530 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO C 986 " 0.057 5.00e-02 4.00e+02 8.40e-02 1.13e+01 pdb=" N PRO C 987 " -0.145 5.00e-02 4.00e+02 pdb=" CA PRO C 987 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO C 987 " 0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO B 986 " -0.052 5.00e-02 4.00e+02 7.70e-02 9.50e+00 pdb=" N PRO B 987 " 0.133 5.00e-02 4.00e+02 pdb=" CA PRO B 987 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO B 987 " -0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 986 " -0.048 5.00e-02 4.00e+02 7.17e-02 8.22e+00 pdb=" N PRO A 987 " 0.124 5.00e-02 4.00e+02 pdb=" CA PRO A 987 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 987 " -0.041 5.00e-02 4.00e+02 ... (remaining 4527 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.82: 8060 2.82 - 3.34: 18859 3.34 - 3.86: 39193 3.86 - 4.38: 42873 4.38 - 4.90: 76730 Nonbonded interactions: 185715 Sorted by model distance: nonbonded pdb=" O THR A 393 " pdb=" OG1 THR A 523 " model vdw 2.306 2.440 nonbonded pdb=" O SER B 438 " pdb=" OG SER B 438 " model vdw 2.316 2.440 nonbonded pdb=" O SER B 151 " pdb=" OG SER B 151 " model vdw 2.334 2.440 nonbonded pdb=" O SER C 689 " pdb=" OG SER C 689 " model vdw 2.334 2.440 nonbonded pdb=" OG SER C 591 " pdb=" OE1 GLU C 619 " model vdw 2.336 2.440 ... (remaining 185710 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 14 through 621 or resid 641 through 1147)) selection = (chain 'B' and (resid 14 through 621 or resid 641 through 1147)) selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.040 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: 0.000 Extract box with map and model: 14.670 Check model and map are aligned: 0.380 Set scattering table: 0.220 Process input model: 68.770 Find NCS groups from input model: 2.140 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 97.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7296 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 : 0.003 0.046 25650 Z= 0.199 Angle : 0.665 11.663 34889 Z= 0.362 Chirality : 0.047 0.229 3938 Planarity : 0.006 0.084 4530 Dihedral : 13.050 89.983 9186 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 0.11 % Allowed : 4.79 % Favored : 95.10 % 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: -4.34 (0.11), residues: 3163 helix: -4.94 (0.05), residues: 602 sheet: -1.21 (0.19), residues: 597 loop : -2.87 (0.11), residues: 1964 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 152 HIS 0.006 0.001 HIS A 519 PHE 0.018 0.001 PHE B 400 TYR 0.014 0.001 TYR C 707 ARG 0.009 0.000 ARG A 408 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6326 Ramachandran restraints generated. 3163 Oldfield, 0 Emsley, 3163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6326 Ramachandran restraints generated. 3163 Oldfield, 0 Emsley, 3163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 606 residues out of total 2798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 603 time to evaluate : 2.782 Fit side-chains 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: 2 residues processed: 606 average time/residue: 0.4321 time to fit residues: 389.8087 Evaluate side-chains 488 residues out of total 2798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 486 time to evaluate : 3.081 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2350 time to fit residues: 5.0423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 270 optimal weight: 4.9990 chunk 242 optimal weight: 3.9990 chunk 134 optimal weight: 0.2980 chunk 82 optimal weight: 0.4980 chunk 163 optimal weight: 0.9990 chunk 129 optimal weight: 0.0770 chunk 250 optimal weight: 6.9990 chunk 97 optimal weight: 1.9990 chunk 152 optimal weight: 3.9990 chunk 186 optimal weight: 1.9990 chunk 290 optimal weight: 0.0470 overall best weight: 0.3838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN A 196 ASN A 207 HIS A 239 GLN A 360 ASN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 487 ASN A 519 HIS A 658 ASN A 762 GLN A 901 GLN A 949 GLN A 955 ASN A1002 GLN A1005 GLN A1071 GLN ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS C 211 ASN ** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 563 GLN C 955 ASN C1071 GLN B 137 ASN B 474 GLN B 493 GLN B1005 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7348 moved from start: 0.2008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 25650 Z= 0.169 Angle : 0.560 10.892 34889 Z= 0.286 Chirality : 0.043 0.195 3938 Planarity : 0.004 0.055 4530 Dihedral : 3.778 19.837 3437 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 1.50 % Allowed : 12.19 % Favored : 86.31 % 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: -2.98 (0.12), residues: 3163 helix: -2.38 (0.15), residues: 626 sheet: -0.58 (0.19), residues: 662 loop : -2.46 (0.12), residues: 1875 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP B 353 HIS 0.003 0.001 HIS B1048 PHE 0.026 0.001 PHE B 374 TYR 0.021 0.001 TYR B 453 ARG 0.006 0.000 ARG B 995 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6326 Ramachandran restraints generated. 3163 Oldfield, 0 Emsley, 3163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6326 Ramachandran restraints generated. 3163 Oldfield, 0 Emsley, 3163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 513 residues out of total 2798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 471 time to evaluate : 2.688 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 42 outliers final: 18 residues processed: 492 average time/residue: 0.4273 time to fit residues: 320.1464 Evaluate side-chains 462 residues out of total 2798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 444 time to evaluate : 2.853 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.2376 time to fit residues: 12.2868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 161 optimal weight: 4.9990 chunk 90 optimal weight: 1.9990 chunk 241 optimal weight: 2.9990 chunk 197 optimal weight: 1.9990 chunk 80 optimal weight: 0.6980 chunk 291 optimal weight: 2.9990 chunk 314 optimal weight: 1.9990 chunk 259 optimal weight: 3.9990 chunk 288 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 chunk 233 optimal weight: 0.8980 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 HIS ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 536 ASN A 644 GLN A1074 ASN A1088 HIS C 23 GLN C 66 HIS C 196 ASN C 207 HIS C 245 HIS ** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 493 GLN C 607 GLN C 613 GLN C 955 ASN B 437 ASN ** B 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 949 GLN B 965 GLN B1106 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 0.2960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 25650 Z= 0.349 Angle : 0.634 13.266 34889 Z= 0.326 Chirality : 0.046 0.172 3938 Planarity : 0.005 0.112 4530 Dihedral : 4.374 24.710 3437 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 2.39 % Allowed : 15.12 % Favored : 82.49 % 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: -2.30 (0.13), residues: 3163 helix: -0.84 (0.20), residues: 640 sheet: -0.47 (0.19), residues: 658 loop : -2.28 (0.12), residues: 1865 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B 353 HIS 0.006 0.001 HIS A1064 PHE 0.042 0.002 PHE A 342 TYR 0.023 0.002 TYR B 396 ARG 0.013 0.001 ARG A 457 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6326 Ramachandran restraints generated. 3163 Oldfield, 0 Emsley, 3163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6326 Ramachandran restraints generated. 3163 Oldfield, 0 Emsley, 3163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 551 residues out of total 2798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 484 time to evaluate : 3.322 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 67 outliers final: 35 residues processed: 522 average time/residue: 0.4337 time to fit residues: 344.7772 Evaluate side-chains 486 residues out of total 2798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 451 time to evaluate : 3.089 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 0 residues processed: 35 average time/residue: 0.2650 time to fit residues: 20.9917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 287 optimal weight: 0.0970 chunk 218 optimal weight: 0.7980 chunk 151 optimal weight: 0.0010 chunk 32 optimal weight: 2.9990 chunk 138 optimal weight: 0.9980 chunk 195 optimal weight: 0.5980 chunk 292 optimal weight: 1.9990 chunk 309 optimal weight: 0.3980 chunk 152 optimal weight: 4.9990 chunk 276 optimal weight: 1.9990 chunk 83 optimal weight: 0.0370 overall best weight: 0.2262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 658 ASN C 207 HIS C 542 ASN C 607 GLN C 613 GLN B 437 ASN ** B 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 919 ASN B1088 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7418 moved from start: 0.3106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 25650 Z= 0.139 Angle : 0.539 11.966 34889 Z= 0.270 Chirality : 0.043 0.197 3938 Planarity : 0.004 0.047 4530 Dihedral : 3.927 22.164 3437 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.36 % Allowed : 17.33 % Favored : 81.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.79 (0.14), residues: 3163 helix: 0.00 (0.21), residues: 632 sheet: -0.12 (0.19), residues: 691 loop : -2.16 (0.13), residues: 1840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 353 HIS 0.002 0.000 HIS B1088 PHE 0.025 0.001 PHE B 374 TYR 0.027 0.001 TYR A 351 ARG 0.006 0.000 ARG A 457 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6326 Ramachandran restraints generated. 3163 Oldfield, 0 Emsley, 3163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6326 Ramachandran restraints generated. 3163 Oldfield, 0 Emsley, 3163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 496 residues out of total 2798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 458 time to evaluate : 3.081 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 38 outliers final: 18 residues processed: 475 average time/residue: 0.4289 time to fit residues: 306.9506 Evaluate side-chains 452 residues out of total 2798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 434 time to evaluate : 2.694 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.2319 time to fit residues: 11.9802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 257 optimal weight: 8.9990 chunk 175 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 230 optimal weight: 3.9990 chunk 127 optimal weight: 1.9990 chunk 263 optimal weight: 6.9990 chunk 213 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 157 optimal weight: 4.9990 chunk 277 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 317 ASN ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1134 ASN ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS ** C 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 GLN C 955 ASN C 978 ASN B 134 GLN B 437 ASN ** B 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 919 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.3819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.067 25650 Z= 0.509 Angle : 0.724 15.979 34889 Z= 0.375 Chirality : 0.050 0.197 3938 Planarity : 0.005 0.062 4530 Dihedral : 4.925 27.691 3437 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.99 % Favored : 93.01 % Rotamer: Outliers : 2.86 % Allowed : 18.48 % Favored : 78.66 % 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: -2.01 (0.14), residues: 3163 helix: -0.20 (0.21), residues: 643 sheet: -0.46 (0.19), residues: 671 loop : -2.19 (0.13), residues: 1849 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP B 353 HIS 0.008 0.002 HIS B1048 PHE 0.042 0.003 PHE C 374 TYR 0.028 0.002 TYR B 396 ARG 0.009 0.001 ARG B 346 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6326 Ramachandran restraints generated. 3163 Oldfield, 0 Emsley, 3163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6326 Ramachandran restraints generated. 3163 Oldfield, 0 Emsley, 3163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 570 residues out of total 2798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 490 time to evaluate : 2.846 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 80 outliers final: 46 residues processed: 525 average time/residue: 0.4181 time to fit residues: 332.2210 Evaluate side-chains 512 residues out of total 2798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 466 time to evaluate : 2.762 Switching outliers to nearest non-outliers outliers start: 46 outliers final: 0 residues processed: 46 average time/residue: 0.2458 time to fit residues: 24.7559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 57.2681 > 50: distance: 22 - 28: 11.361 distance: 28 - 29: 17.110 distance: 28 - 34: 26.759 distance: 29 - 30: 22.874 distance: 29 - 32: 12.153 distance: 30 - 31: 15.061 distance: 30 - 35: 20.779 distance: 32 - 33: 43.087 distance: 33 - 34: 3.061 distance: 35 - 36: 13.974 distance: 36 - 39: 22.982 distance: 37 - 38: 7.024 distance: 37 - 41: 51.037 distance: 39 - 40: 35.006 distance: 41 - 42: 11.457 distance: 42 - 43: 11.891 distance: 42 - 45: 15.690 distance: 43 - 44: 18.124 distance: 43 - 50: 12.187 distance: 45 - 46: 9.097 distance: 46 - 47: 17.609 distance: 47 - 48: 29.080 distance: 48 - 49: 57.268 distance: 50 - 51: 11.953 distance: 50 - 56: 3.368 distance: 51 - 52: 20.135 distance: 51 - 54: 16.453 distance: 52 - 53: 8.696 distance: 52 - 57: 14.188 distance: 54 - 55: 10.006 distance: 55 - 56: 18.314 distance: 57 - 58: 13.452 distance: 58 - 59: 24.542 distance: 58 - 61: 7.525 distance: 59 - 60: 5.915 distance: 59 - 63: 14.893 distance: 61 - 62: 22.766 distance: 63 - 64: 23.011 distance: 64 - 65: 15.404 distance: 64 - 67: 22.575 distance: 65 - 66: 16.646 distance: 65 - 72: 19.982 distance: 67 - 68: 11.432 distance: 68 - 69: 15.453 distance: 69 - 70: 17.825 distance: 70 - 71: 21.822 distance: 72 - 73: 12.357 distance: 73 - 74: 11.722 distance: 73 - 76: 20.467 distance: 74 - 75: 6.737 distance: 74 - 83: 32.728 distance: 76 - 77: 14.853 distance: 77 - 78: 21.578 distance: 78 - 79: 16.550 distance: 79 - 80: 4.914 distance: 80 - 81: 5.191 distance: 80 - 82: 8.976 distance: 83 - 84: 12.987 distance: 84 - 85: 16.094 distance: 84 - 87: 13.022 distance: 85 - 86: 16.858 distance: 85 - 89: 7.347 distance: 86 - 117: 25.237 distance: 87 - 88: 7.323 distance: 89 - 90: 7.983 distance: 90 - 91: 21.492 distance: 90 - 93: 24.404 distance: 91 - 92: 16.441 distance: 91 - 100: 12.053 distance: 93 - 94: 15.111 distance: 94 - 95: 13.307 distance: 94 - 96: 14.212 distance: 95 - 97: 17.751 distance: 96 - 98: 8.308 distance: 97 - 99: 17.943 distance: 98 - 99: 13.469 distance: 100 - 101: 6.549 distance: 101 - 102: 7.476 distance: 101 - 104: 7.145 distance: 102 - 103: 8.191 distance: 102 - 108: 4.945 distance: 103 - 133: 10.981 distance: 104 - 105: 10.804 distance: 104 - 106: 26.929 distance: 105 - 107: 18.715