Starting phenix.real_space_refine on Tue Mar 19 18:42:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w92_32359/03_2024/7w92_32359.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w92_32359/03_2024/7w92_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_32359/03_2024/7w92_32359.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w92_32359/03_2024/7w92_32359.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w92_32359/03_2024/7w92_32359.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w92_32359/03_2024/7w92_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-dev-5265/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: 13.60, per 1000 atoms: 0.54 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: 7.97 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: 3.20 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: 11.10 Time building geometry restraints manager: 8.98 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: 3.620 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: 0.020 Extract box with map and model: 14.200 Check model and map are aligned: 0.400 Set scattering table: 0.250 Process input model: 65.640 Find NCS groups from input model: 2.130 Set up NCS constraints: 0.110 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:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 89.190 ------------------------------------------------------------------------------- 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 : 2.835 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: A 52 GLN cc_start: 0.8123 (tm-30) cc_final: 0.7806 (tm-30) REVERT: A 86 PHE cc_start: 0.7493 (t80) cc_final: 0.7131 (t80) REVERT: A 153 MET cc_start: -0.4908 (tpt) cc_final: -0.5183 (tpt) REVERT: A 296 LEU cc_start: 0.8293 (tp) cc_final: 0.7955 (tp) REVERT: A 515 PHE cc_start: 0.6586 (p90) cc_final: 0.6032 (p90) REVERT: A 539 VAL cc_start: 0.7778 (t) cc_final: 0.7525 (m) REVERT: A 580 GLN cc_start: 0.7633 (mm-40) cc_final: 0.7380 (mm-40) REVERT: A 606 ASN cc_start: 0.8525 (m-40) cc_final: 0.8272 (t0) REVERT: A 790 LYS cc_start: 0.8397 (mttt) cc_final: 0.7689 (mttm) REVERT: C 140 PHE cc_start: 0.7705 (p90) cc_final: 0.7462 (p90) REVERT: C 206 LYS cc_start: 0.8222 (tptt) cc_final: 0.7861 (tppt) REVERT: C 603 ASN cc_start: 0.7866 (p0) cc_final: 0.7533 (p0) REVERT: C 702 GLU cc_start: 0.6734 (tp30) cc_final: 0.6502 (mm-30) REVERT: C 1073 LYS cc_start: 0.8325 (tttt) cc_final: 0.8065 (tttm) REVERT: C 1118 ASP cc_start: 0.6397 (p0) cc_final: 0.6194 (p0) REVERT: B 191 GLU cc_start: 0.5954 (tt0) cc_final: 0.4023 (mt-10) REVERT: B 296 LEU cc_start: 0.8506 (tp) cc_final: 0.8071 (tp) REVERT: B 368 LEU cc_start: 0.8580 (mt) cc_final: 0.8305 (mp) REVERT: B 369 TYR cc_start: 0.4795 (m-80) cc_final: 0.4347 (m-80) REVERT: B 449 TYR cc_start: 0.6887 (m-80) cc_final: 0.6566 (m-80) REVERT: B 453 TYR cc_start: 0.7257 (p90) cc_final: 0.6796 (p90) REVERT: B 455 LEU cc_start: 0.7222 (tp) cc_final: 0.6845 (tp) REVERT: B 826 VAL cc_start: 0.7507 (m) cc_final: 0.7290 (t) REVERT: B 883 THR cc_start: 0.8405 (m) cc_final: 0.8166 (p) REVERT: B 994 ASP cc_start: 0.7445 (t0) cc_final: 0.6946 (t0) outliers start: 3 outliers final: 2 residues processed: 606 average time/residue: 0.4129 time to fit residues: 373.8236 Evaluate side-chains 488 residues out of total 2798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 486 time to evaluate : 2.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain B residue 130 VAL 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: 0.0980 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: 0.6980 overall best weight: 0.5182 ------------------------------------------------------------------------------- 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 A1088 HIS ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 606 ASN B1005 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7366 moved from start: 0.2038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 25650 Z= 0.182 Angle : 0.561 11.072 34889 Z= 0.288 Chirality : 0.043 0.190 3938 Planarity : 0.004 0.052 4530 Dihedral : 3.850 20.181 3439 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 1.57 % Allowed : 11.83 % Favored : 86.60 % 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: -3.00 (0.13), residues: 3163 helix: -2.41 (0.15), residues: 631 sheet: -0.61 (0.19), residues: 670 loop : -2.47 (0.12), residues: 1862 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP B 353 HIS 0.003 0.001 HIS B1048 PHE 0.028 0.001 PHE B 374 TYR 0.015 0.001 TYR C 660 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 521 residues out of total 2798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 477 time to evaluate : 2.662 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 PHE cc_start: 0.7384 (t80) cc_final: 0.7105 (t80) REVERT: A 177 MET cc_start: -0.0564 (mtt) cc_final: -0.1067 (mtt) REVERT: A 457 ARG cc_start: 0.5394 (OUTLIER) cc_final: 0.4719 (ttm-80) REVERT: A 462 LYS cc_start: 0.8754 (mmmt) cc_final: 0.8497 (mmtm) REVERT: A 580 GLN cc_start: 0.7767 (mm-40) cc_final: 0.7534 (mm-40) REVERT: A 597 VAL cc_start: 0.8488 (t) cc_final: 0.8279 (p) REVERT: A 606 ASN cc_start: 0.8556 (m-40) cc_final: 0.8251 (t0) REVERT: A 790 LYS cc_start: 0.8460 (mttt) cc_final: 0.7593 (mttm) REVERT: A 964 LYS cc_start: 0.8658 (mtpp) cc_final: 0.8433 (ttmm) REVERT: A 995 ARG cc_start: 0.7310 (mtt-85) cc_final: 0.7086 (ttt-90) REVERT: C 99 ASN cc_start: 0.8636 (OUTLIER) cc_final: 0.8266 (p0) REVERT: C 290 ASP cc_start: 0.7508 (t0) cc_final: 0.7245 (m-30) REVERT: C 603 ASN cc_start: 0.8010 (p0) cc_final: 0.7745 (p0) REVERT: C 702 GLU cc_start: 0.6835 (tp30) cc_final: 0.6497 (mm-30) REVERT: C 933 LYS cc_start: 0.8241 (ttmt) cc_final: 0.8020 (ttmm) REVERT: C 1029 MET cc_start: 0.8712 (tpp) cc_final: 0.8386 (tpp) REVERT: C 1073 LYS cc_start: 0.8298 (tttt) cc_final: 0.8050 (tttm) REVERT: B 191 GLU cc_start: 0.5919 (tt0) cc_final: 0.3680 (mt-10) REVERT: B 202 LYS cc_start: 0.7402 (tptt) cc_final: 0.7069 (tptt) REVERT: B 225 PRO cc_start: 0.7919 (Cg_exo) cc_final: 0.7455 (Cg_endo) REVERT: B 296 LEU cc_start: 0.8244 (tp) cc_final: 0.8031 (tt) REVERT: B 883 THR cc_start: 0.8619 (m) cc_final: 0.6992 (t) REVERT: B 994 ASP cc_start: 0.7351 (t0) cc_final: 0.7135 (t0) outliers start: 44 outliers final: 21 residues processed: 500 average time/residue: 0.4019 time to fit residues: 304.2028 Evaluate side-chains 473 residues out of total 2798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 450 time to evaluate : 2.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 457 ARG Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 532 ASN Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain C residue 99 ASN Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 820 ASP Chi-restraints excluded: chain B residue 1118 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 161 optimal weight: 2.9990 chunk 90 optimal weight: 0.9990 chunk 241 optimal weight: 2.9990 chunk 197 optimal weight: 1.9990 chunk 80 optimal weight: 0.7980 chunk 291 optimal weight: 2.9990 chunk 314 optimal weight: 1.9990 chunk 259 optimal weight: 4.9990 chunk 288 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 233 optimal weight: 3.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- 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 C 23 GLN ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 ASN C 207 HIS C 245 HIS ** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 487 ASN C 493 GLN C 607 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 965 GLN B1106 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 moved from start: 0.2941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 25650 Z= 0.353 Angle : 0.623 15.183 34889 Z= 0.320 Chirality : 0.046 0.173 3938 Planarity : 0.004 0.054 4530 Dihedral : 4.367 25.773 3438 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 2.93 % Allowed : 15.05 % Favored : 82.02 % 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: -2.33 (0.13), residues: 3163 helix: -0.89 (0.20), residues: 640 sheet: -0.52 (0.19), residues: 645 loop : -2.26 (0.12), residues: 1878 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 353 HIS 0.007 0.001 HIS A1064 PHE 0.036 0.002 PHE A 342 TYR 0.020 0.002 TYR B 396 ARG 0.006 0.001 ARG B 995 *********************** 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 571 residues out of total 2798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 489 time to evaluate : 2.807 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: A 52 GLN cc_start: 0.7996 (tm-30) cc_final: 0.7700 (tm-30) REVERT: A 86 PHE cc_start: 0.7482 (t80) cc_final: 0.7144 (t80) REVERT: A 153 MET cc_start: -0.4453 (tpt) cc_final: -0.5468 (tpp) REVERT: A 177 MET cc_start: -0.0407 (mtt) cc_final: -0.3129 (mtt) REVERT: A 304 LYS cc_start: 0.8626 (tppp) cc_final: 0.8356 (tppp) REVERT: A 580 GLN cc_start: 0.7853 (mm-40) cc_final: 0.7583 (mm-40) REVERT: C 48 LEU cc_start: 0.8403 (mm) cc_final: 0.8089 (mp) REVERT: C 99 ASN cc_start: 0.8769 (OUTLIER) cc_final: 0.8423 (p0) REVERT: C 177 MET cc_start: -0.2795 (mmt) cc_final: -0.3836 (mmt) REVERT: C 556 ASN cc_start: 0.8225 (t0) cc_final: 0.7993 (t0) REVERT: C 902 MET cc_start: 0.7918 (mmm) cc_final: 0.7644 (mmt) REVERT: C 933 LYS cc_start: 0.8276 (ttmt) cc_final: 0.8046 (ttmm) REVERT: C 1029 MET cc_start: 0.8720 (tpp) cc_final: 0.8447 (tpp) REVERT: C 1107 ARG cc_start: 0.7902 (mtm110) cc_final: 0.6365 (tpt90) REVERT: B 41 LYS cc_start: 0.7691 (mtpt) cc_final: 0.7452 (mtpt) REVERT: B 192 PHE cc_start: 0.7303 (m-80) cc_final: 0.7043 (m-10) REVERT: B 203 ILE cc_start: 0.8507 (mt) cc_final: 0.8293 (mp) REVERT: B 298 GLU cc_start: 0.7726 (tp30) cc_final: 0.7516 (tp30) REVERT: B 346 ARG cc_start: 0.5331 (mmm160) cc_final: 0.5085 (mmm160) REVERT: B 429 PHE cc_start: 0.8028 (t80) cc_final: 0.7517 (t80) REVERT: B 1107 ARG cc_start: 0.6948 (mtt-85) cc_final: 0.5763 (tpt170) outliers start: 82 outliers final: 54 residues processed: 534 average time/residue: 0.3964 time to fit residues: 321.0697 Evaluate side-chains 513 residues out of total 2798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 458 time to evaluate : 2.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ASN Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 428 ASP Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 457 ARG Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 578 ASP Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 673 SER Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 895 GLN Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 99 ASN Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 493 GLN Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 532 ASN Chi-restraints excluded: chain C residue 535 LYS Chi-restraints excluded: chain C residue 605 SER Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 914 ASN Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 342 PHE Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 693 ILE Chi-restraints excluded: chain B residue 703 ASN Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 1111 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 287 optimal weight: 0.8980 chunk 218 optimal weight: 0.7980 chunk 151 optimal weight: 0.0670 chunk 32 optimal weight: 5.9990 chunk 138 optimal weight: 4.9990 chunk 195 optimal weight: 0.8980 chunk 292 optimal weight: 0.9990 chunk 309 optimal weight: 0.9980 chunk 152 optimal weight: 0.8980 chunk 276 optimal weight: 2.9990 chunk 83 optimal weight: 0.0770 overall best weight: 0.5476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS 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 919 ASN B1088 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7464 moved from start: 0.3090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 25650 Z= 0.171 Angle : 0.548 13.054 34889 Z= 0.276 Chirality : 0.043 0.228 3938 Planarity : 0.004 0.047 4530 Dihedral : 4.059 23.818 3438 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.36 % Allowed : 17.55 % Favored : 80.09 % 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: -1.88 (0.14), residues: 3163 helix: -0.15 (0.21), residues: 639 sheet: -0.18 (0.19), residues: 664 loop : -2.16 (0.13), residues: 1860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 353 HIS 0.003 0.001 HIS A1064 PHE 0.027 0.001 PHE B 374 TYR 0.025 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 525 residues out of total 2798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 459 time to evaluate : 2.723 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: A 86 PHE cc_start: 0.7518 (t80) cc_final: 0.7243 (t80) REVERT: A 153 MET cc_start: -0.4562 (tpt) cc_final: -0.5612 (tpp) REVERT: A 177 MET cc_start: -0.0571 (mtt) cc_final: -0.2704 (mtt) REVERT: A 304 LYS cc_start: 0.8565 (tppp) cc_final: 0.8322 (tppp) REVERT: A 473 TYR cc_start: 0.8040 (t80) cc_final: 0.7803 (t80) REVERT: A 580 GLN cc_start: 0.7799 (mm-40) cc_final: 0.7526 (mm-40) REVERT: A 697 MET cc_start: 0.8034 (OUTLIER) cc_final: 0.7798 (ptm) REVERT: C 48 LEU cc_start: 0.8391 (mm) cc_final: 0.8119 (mp) REVERT: C 52 GLN cc_start: 0.7296 (tm-30) cc_final: 0.7053 (tm-30) REVERT: C 92 PHE cc_start: 0.6720 (t80) cc_final: 0.6439 (t80) REVERT: C 98 SER cc_start: 0.8964 (OUTLIER) cc_final: 0.8733 (p) REVERT: C 99 ASN cc_start: 0.8829 (OUTLIER) cc_final: 0.8477 (p0) REVERT: C 177 MET cc_start: -0.2721 (mmt) cc_final: -0.3886 (mmt) REVERT: C 324 GLU cc_start: 0.7508 (mp0) cc_final: 0.6945 (mp0) REVERT: C 518 LEU cc_start: 0.5266 (tp) cc_final: 0.4983 (tt) REVERT: C 535 LYS cc_start: 0.8504 (OUTLIER) cc_final: 0.8238 (mptt) REVERT: C 549 THR cc_start: 0.8687 (m) cc_final: 0.8400 (m) REVERT: C 556 ASN cc_start: 0.8179 (t0) cc_final: 0.7954 (t0) REVERT: C 574 ASP cc_start: 0.7718 (p0) cc_final: 0.7037 (t0) REVERT: C 823 PHE cc_start: 0.7901 (t80) cc_final: 0.7677 (t80) REVERT: C 1107 ARG cc_start: 0.7834 (mtm110) cc_final: 0.6359 (tpt170) REVERT: B 202 LYS cc_start: 0.7389 (tptt) cc_final: 0.6939 (tptt) REVERT: B 225 PRO cc_start: 0.7913 (Cg_exo) cc_final: 0.7536 (Cg_endo) REVERT: B 298 GLU cc_start: 0.7586 (tp30) cc_final: 0.7380 (tp30) REVERT: B 429 PHE cc_start: 0.7987 (t80) cc_final: 0.7540 (t80) REVERT: B 883 THR cc_start: 0.8720 (m) cc_final: 0.8130 (p) outliers start: 66 outliers final: 37 residues processed: 498 average time/residue: 0.4044 time to fit residues: 306.2407 Evaluate side-chains 489 residues out of total 2798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 448 time to evaluate : 2.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 428 ASP Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 99 ASN Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 493 GLN Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 535 LYS Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 607 GLN Chi-restraints excluded: chain C residue 673 SER Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 703 ASN Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1111 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 257 optimal weight: 5.9990 chunk 175 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 230 optimal weight: 3.9990 chunk 127 optimal weight: 0.0570 chunk 263 optimal weight: 6.9990 chunk 213 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 157 optimal weight: 3.9990 chunk 277 optimal weight: 0.0980 chunk 78 optimal weight: 1.9990 overall best weight: 1.6304 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 66 HIS ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS C 493 GLN C 506 GLN C 542 ASN C 613 GLN C 955 ASN C 978 ASN B 134 GLN ** B 450 ASN ** 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: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.3505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 25650 Z= 0.362 Angle : 0.621 13.997 34889 Z= 0.318 Chirality : 0.046 0.199 3938 Planarity : 0.004 0.052 4530 Dihedral : 4.454 25.722 3438 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 3.90 % Allowed : 17.87 % Favored : 78.23 % 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: -1.84 (0.14), residues: 3163 helix: -0.00 (0.21), residues: 644 sheet: -0.30 (0.19), residues: 657 loop : -2.11 (0.13), residues: 1862 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 353 HIS 0.007 0.001 HIS A1064 PHE 0.036 0.002 PHE C 374 TYR 0.020 0.002 TYR C 28 ARG 0.006 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 581 residues out of total 2798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 472 time to evaluate : 2.872 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 PHE cc_start: 0.7636 (t80) cc_final: 0.7352 (t80) REVERT: A 153 MET cc_start: -0.4055 (tpt) cc_final: -0.5395 (tpp) REVERT: A 177 MET cc_start: -0.0329 (mtt) cc_final: -0.1293 (mtt) REVERT: A 304 LYS cc_start: 0.8625 (tppp) cc_final: 0.8364 (tppp) REVERT: C 48 LEU cc_start: 0.8434 (mm) cc_final: 0.8186 (mp) REVERT: C 98 SER cc_start: 0.9001 (OUTLIER) cc_final: 0.8754 (p) REVERT: C 99 ASN cc_start: 0.8938 (OUTLIER) cc_final: 0.8569 (p0) REVERT: C 177 MET cc_start: -0.2833 (mmt) cc_final: -0.4121 (mmt) REVERT: C 206 LYS cc_start: 0.8333 (tptt) cc_final: 0.7981 (tptp) REVERT: C 290 ASP cc_start: 0.7716 (t0) cc_final: 0.7402 (m-30) REVERT: C 324 GLU cc_start: 0.7567 (mp0) cc_final: 0.7096 (mp0) REVERT: C 544 ASN cc_start: 0.7995 (OUTLIER) cc_final: 0.7717 (p0) REVERT: C 564 GLN cc_start: 0.7827 (mp10) cc_final: 0.7578 (mp10) REVERT: C 574 ASP cc_start: 0.7725 (p0) cc_final: 0.7102 (t0) REVERT: C 823 PHE cc_start: 0.8027 (t80) cc_final: 0.7804 (t80) REVERT: C 902 MET cc_start: 0.7845 (mmm) cc_final: 0.7642 (mmt) REVERT: C 1073 LYS cc_start: 0.8476 (mtpt) cc_final: 0.8230 (mtpp) REVERT: C 1107 ARG cc_start: 0.8044 (mtm110) cc_final: 0.6598 (tpt170) REVERT: B 190 ARG cc_start: 0.6880 (mtp180) cc_final: 0.6326 (mtp180) REVERT: B 213 VAL cc_start: 0.7579 (OUTLIER) cc_final: 0.7376 (t) REVERT: B 429 PHE cc_start: 0.8064 (t80) cc_final: 0.7506 (t80) REVERT: B 1107 ARG cc_start: 0.6995 (mtt-85) cc_final: 0.5939 (tpt170) outliers start: 109 outliers final: 73 residues processed: 530 average time/residue: 0.3952 time to fit residues: 317.4771 Evaluate side-chains 532 residues out of total 2798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 455 time to evaluate : 2.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 30 ASN Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 334 ASN Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 428 ASP Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 436 TRP Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 457 ARG Chi-restraints excluded: chain A residue 501 ASN Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 578 ASP Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 895 GLN Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 99 ASN Chi-restraints excluded: chain C residue 125 ASN Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 281 GLU Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 544 ASN Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 607 GLN Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 673 SER Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 914 ASN Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 342 PHE Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 440 ASN Chi-restraints excluded: chain B residue 498 GLN Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 693 ILE Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 703 ASN Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 820 ASP Chi-restraints excluded: chain B residue 964 LYS Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1111 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 104 optimal weight: 0.6980 chunk 278 optimal weight: 2.9990 chunk 61 optimal weight: 0.9980 chunk 181 optimal weight: 0.0020 chunk 76 optimal weight: 4.9990 chunk 309 optimal weight: 0.9990 chunk 257 optimal weight: 6.9990 chunk 143 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 102 optimal weight: 0.7980 chunk 162 optimal weight: 1.9990 overall best weight: 0.6990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS C 607 GLN C 613 GLN C 955 ASN ** B 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 moved from start: 0.3572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 25650 Z= 0.195 Angle : 0.573 13.570 34889 Z= 0.288 Chirality : 0.044 0.192 3938 Planarity : 0.004 0.050 4530 Dihedral : 4.212 24.506 3438 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 2.79 % Allowed : 19.91 % Favored : 77.31 % 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: -1.58 (0.14), residues: 3163 helix: 0.42 (0.22), residues: 638 sheet: -0.13 (0.19), residues: 659 loop : -2.04 (0.13), residues: 1866 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 436 HIS 0.004 0.001 HIS A1064 PHE 0.039 0.001 PHE C 374 TYR 0.026 0.001 TYR A 351 ARG 0.007 0.000 ARG C1019 *********************** REFINEMENT MACRO_CYCLE 6 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 535 residues out of total 2798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 457 time to evaluate : 2.235 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 PHE cc_start: 0.7581 (t80) cc_final: 0.7342 (t80) REVERT: A 153 MET cc_start: -0.4121 (tpt) cc_final: -0.5484 (tpp) REVERT: A 177 MET cc_start: -0.0325 (mtt) cc_final: -0.1899 (mtt) REVERT: A 304 LYS cc_start: 0.8590 (tppp) cc_final: 0.8319 (tppp) REVERT: A 515 PHE cc_start: 0.7692 (OUTLIER) cc_final: 0.5899 (p90) REVERT: C 48 LEU cc_start: 0.8407 (mm) cc_final: 0.8179 (mp) REVERT: C 98 SER cc_start: 0.8958 (OUTLIER) cc_final: 0.8710 (p) REVERT: C 99 ASN cc_start: 0.8819 (OUTLIER) cc_final: 0.8461 (p0) REVERT: C 177 MET cc_start: -0.2796 (mmt) cc_final: -0.4108 (mmt) REVERT: C 206 LYS cc_start: 0.8240 (tptt) cc_final: 0.8012 (tptp) REVERT: C 290 ASP cc_start: 0.7696 (t0) cc_final: 0.7367 (m-30) REVERT: C 324 GLU cc_start: 0.7528 (mp0) cc_final: 0.6870 (mp0) REVERT: C 564 GLN cc_start: 0.7813 (mp10) cc_final: 0.7574 (mp10) REVERT: C 574 ASP cc_start: 0.7633 (p0) cc_final: 0.7104 (t0) REVERT: C 790 LYS cc_start: 0.8721 (mtpp) cc_final: 0.8412 (mmtm) REVERT: C 823 PHE cc_start: 0.8022 (t80) cc_final: 0.7793 (t80) REVERT: C 902 MET cc_start: 0.7758 (mmm) cc_final: 0.7543 (mmt) REVERT: C 1107 ARG cc_start: 0.7940 (mtm110) cc_final: 0.6483 (tpt170) REVERT: B 190 ARG cc_start: 0.6811 (mtp180) cc_final: 0.6309 (mtp180) REVERT: B 202 LYS cc_start: 0.7212 (tptt) cc_final: 0.6824 (tptt) REVERT: B 213 VAL cc_start: 0.7572 (OUTLIER) cc_final: 0.7370 (t) REVERT: B 225 PRO cc_start: 0.7907 (Cg_exo) cc_final: 0.7565 (Cg_endo) REVERT: B 429 PHE cc_start: 0.7935 (t80) cc_final: 0.7428 (t80) REVERT: B 1107 ARG cc_start: 0.6958 (mtt-85) cc_final: 0.5904 (tpt170) outliers start: 78 outliers final: 55 residues processed: 505 average time/residue: 0.3897 time to fit residues: 299.6323 Evaluate side-chains 505 residues out of total 2798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 446 time to evaluate : 2.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 334 ASN Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 428 ASP Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 578 ASP Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 99 ASN Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 281 GLU Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 532 ASN Chi-restraints excluded: chain C residue 607 GLN Chi-restraints excluded: chain C residue 619 GLU Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 673 SER Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 914 ASN Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 440 ASN Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 703 ASN Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 820 ASP Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1111 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 298 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 176 optimal weight: 2.9990 chunk 226 optimal weight: 9.9990 chunk 175 optimal weight: 1.9990 chunk 260 optimal weight: 0.5980 chunk 172 optimal weight: 0.7980 chunk 308 optimal weight: 2.9990 chunk 193 optimal weight: 0.9990 chunk 188 optimal weight: 0.3980 chunk 142 optimal weight: 4.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 657 ASN ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS C 607 GLN C 613 GLN C 955 ASN ** B 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 moved from start: 0.3716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 25650 Z= 0.238 Angle : 0.578 13.140 34889 Z= 0.292 Chirality : 0.044 0.218 3938 Planarity : 0.004 0.075 4530 Dihedral : 4.239 25.358 3438 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 3.25 % Allowed : 19.91 % Favored : 76.84 % 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: -1.52 (0.14), residues: 3163 helix: 0.56 (0.22), residues: 638 sheet: -0.09 (0.19), residues: 659 loop : -2.03 (0.13), residues: 1866 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.002 TRP A 436 HIS 0.004 0.001 HIS A1064 PHE 0.036 0.001 PHE C 374 TYR 0.021 0.001 TYR A1138 ARG 0.007 0.000 ARG B 995 *********************** REFINEMENT MACRO_CYCLE 7 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 548 residues out of total 2798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 457 time to evaluate : 2.613 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 PHE cc_start: 0.7590 (t80) cc_final: 0.7361 (t80) REVERT: A 121 ASN cc_start: 0.7055 (OUTLIER) cc_final: 0.6810 (p0) REVERT: A 153 MET cc_start: -0.4256 (tpt) cc_final: -0.5650 (tpp) REVERT: A 177 MET cc_start: -0.0298 (mtt) cc_final: -0.1471 (mtt) REVERT: A 515 PHE cc_start: 0.7817 (OUTLIER) cc_final: 0.5765 (p90) REVERT: A 564 GLN cc_start: 0.7640 (mp10) cc_final: 0.7419 (mp10) REVERT: A 1091 ARG cc_start: 0.7193 (mtm-85) cc_final: 0.6981 (ttp-170) REVERT: C 48 LEU cc_start: 0.8403 (mm) cc_final: 0.8172 (mp) REVERT: C 98 SER cc_start: 0.8996 (OUTLIER) cc_final: 0.8736 (m) REVERT: C 99 ASN cc_start: 0.8914 (OUTLIER) cc_final: 0.8604 (p0) REVERT: C 177 MET cc_start: -0.2733 (mmt) cc_final: -0.4046 (mmt) REVERT: C 202 LYS cc_start: 0.8335 (mptt) cc_final: 0.7818 (mptt) REVERT: C 564 GLN cc_start: 0.7823 (mp10) cc_final: 0.7594 (mp10) REVERT: C 574 ASP cc_start: 0.7635 (p0) cc_final: 0.7126 (t0) REVERT: C 790 LYS cc_start: 0.8719 (mtpp) cc_final: 0.8406 (mmtm) REVERT: C 823 PHE cc_start: 0.8008 (t80) cc_final: 0.7800 (t80) REVERT: C 1107 ARG cc_start: 0.7957 (mtm110) cc_final: 0.6479 (tpt170) REVERT: B 64 TRP cc_start: 0.7259 (t-100) cc_final: 0.7006 (t60) REVERT: B 140 PHE cc_start: 0.7524 (m-10) cc_final: 0.7227 (m-10) REVERT: B 190 ARG cc_start: 0.6791 (mtp180) cc_final: 0.6317 (mtp180) REVERT: B 202 LYS cc_start: 0.7284 (tptt) cc_final: 0.6921 (tptt) REVERT: B 213 VAL cc_start: 0.7606 (OUTLIER) cc_final: 0.7404 (t) REVERT: B 225 PRO cc_start: 0.7885 (Cg_exo) cc_final: 0.7549 (Cg_endo) REVERT: B 317 ASN cc_start: 0.7676 (m-40) cc_final: 0.7462 (m-40) REVERT: B 429 PHE cc_start: 0.7964 (t80) cc_final: 0.7429 (t80) REVERT: B 567 ARG cc_start: 0.7843 (mtm-85) cc_final: 0.7630 (mtt180) REVERT: B 1107 ARG cc_start: 0.6975 (mtt-85) cc_final: 0.5918 (tpt170) outliers start: 91 outliers final: 68 residues processed: 513 average time/residue: 0.3900 time to fit residues: 306.6078 Evaluate side-chains 522 residues out of total 2798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 449 time to evaluate : 2.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 30 ASN Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 266 TYR Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 334 ASN Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 428 ASP Chi-restraints excluded: chain A residue 436 TRP Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 457 ARG Chi-restraints excluded: chain A residue 501 ASN Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 578 ASP Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 646 ARG Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 663 ASP Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 99 ASN Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 281 GLU Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 607 GLN Chi-restraints excluded: chain C residue 619 GLU Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 673 SER Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 914 ASN Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1123 SER Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 440 ASN Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 703 ASN Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 820 ASP Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1111 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 190 optimal weight: 0.8980 chunk 123 optimal weight: 8.9990 chunk 184 optimal weight: 0.9990 chunk 92 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 59 optimal weight: 0.7980 chunk 196 optimal weight: 0.9980 chunk 210 optimal weight: 0.6980 chunk 152 optimal weight: 7.9990 chunk 28 optimal weight: 2.9990 chunk 242 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS C 955 ASN ** B 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 moved from start: 0.3798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 25650 Z= 0.225 Angle : 0.583 12.417 34889 Z= 0.293 Chirality : 0.044 0.222 3938 Planarity : 0.004 0.061 4530 Dihedral : 4.260 27.377 3438 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 3.25 % Allowed : 20.23 % Favored : 76.52 % 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: -1.45 (0.14), residues: 3163 helix: 0.73 (0.22), residues: 638 sheet: -0.10 (0.19), residues: 659 loop : -2.01 (0.13), residues: 1866 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.002 TRP A 436 HIS 0.004 0.001 HIS A1064 PHE 0.028 0.001 PHE C 374 TYR 0.021 0.001 TYR A1138 ARG 0.007 0.000 ARG B 995 *********************** REFINEMENT MACRO_CYCLE 8 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 549 residues out of total 2798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 458 time to evaluate : 2.576 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 PHE cc_start: 0.7597 (t80) cc_final: 0.7384 (t80) REVERT: A 153 MET cc_start: -0.4133 (tpt) cc_final: -0.5510 (tpp) REVERT: A 177 MET cc_start: -0.0385 (mtt) cc_final: -0.1279 (mtt) REVERT: A 508 TYR cc_start: 0.6870 (m-80) cc_final: 0.6038 (m-80) REVERT: A 515 PHE cc_start: 0.7850 (OUTLIER) cc_final: 0.5874 (p90) REVERT: A 564 GLN cc_start: 0.7682 (mp10) cc_final: 0.7417 (mp10) REVERT: A 1091 ARG cc_start: 0.7203 (mtm-85) cc_final: 0.6988 (ttp-170) REVERT: C 48 LEU cc_start: 0.8392 (mm) cc_final: 0.8166 (mp) REVERT: C 98 SER cc_start: 0.8991 (OUTLIER) cc_final: 0.8723 (m) REVERT: C 99 ASN cc_start: 0.8895 (OUTLIER) cc_final: 0.8591 (p0) REVERT: C 173 GLN cc_start: 0.5632 (pm20) cc_final: 0.5307 (pp30) REVERT: C 177 MET cc_start: -0.2561 (mmt) cc_final: -0.3867 (mmt) REVERT: C 202 LYS cc_start: 0.8323 (mptt) cc_final: 0.7794 (mptt) REVERT: C 206 LYS cc_start: 0.8308 (tptt) cc_final: 0.7975 (tptp) REVERT: C 290 ASP cc_start: 0.7649 (t0) cc_final: 0.7344 (m-30) REVERT: C 544 ASN cc_start: 0.7939 (OUTLIER) cc_final: 0.7681 (p0) REVERT: C 564 GLN cc_start: 0.7824 (mp10) cc_final: 0.7592 (mp10) REVERT: C 574 ASP cc_start: 0.7623 (p0) cc_final: 0.7127 (t0) REVERT: C 790 LYS cc_start: 0.8723 (mtpp) cc_final: 0.8398 (mmtm) REVERT: C 1107 ARG cc_start: 0.7949 (mtm110) cc_final: 0.6486 (tpt170) REVERT: B 64 TRP cc_start: 0.7223 (t-100) cc_final: 0.7000 (t60) REVERT: B 190 ARG cc_start: 0.6761 (mtp180) cc_final: 0.6319 (mtp180) REVERT: B 202 LYS cc_start: 0.7307 (tptt) cc_final: 0.7092 (tptt) REVERT: B 213 VAL cc_start: 0.7589 (OUTLIER) cc_final: 0.7383 (t) REVERT: B 225 PRO cc_start: 0.7964 (Cg_exo) cc_final: 0.7621 (Cg_endo) REVERT: B 317 ASN cc_start: 0.7658 (m-40) cc_final: 0.7410 (m-40) REVERT: B 429 PHE cc_start: 0.7991 (t80) cc_final: 0.7444 (t80) REVERT: B 567 ARG cc_start: 0.7860 (mtm-85) cc_final: 0.7636 (mtt180) REVERT: B 1107 ARG cc_start: 0.6978 (mtt-85) cc_final: 0.5856 (tpt170) outliers start: 91 outliers final: 74 residues processed: 509 average time/residue: 0.3945 time to fit residues: 305.1242 Evaluate side-chains 531 residues out of total 2798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 452 time to evaluate : 2.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 30 ASN Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 266 TYR Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 334 ASN Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 428 ASP Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 436 TRP Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 457 ARG Chi-restraints excluded: chain A residue 501 ASN Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 578 ASP Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 646 ARG Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 663 ASP Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 895 GLN Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 99 ASN Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 281 GLU Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 532 ASN Chi-restraints excluded: chain C residue 544 ASN Chi-restraints excluded: chain C residue 619 GLU Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 673 SER Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 914 ASN Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1123 SER Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 304 LYS Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 440 ASN Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 703 ASN Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 820 ASP Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1111 GLU Chi-restraints excluded: chain B residue 1118 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 280 optimal weight: 2.9990 chunk 295 optimal weight: 0.9980 chunk 269 optimal weight: 0.9980 chunk 287 optimal weight: 0.0870 chunk 172 optimal weight: 0.6980 chunk 125 optimal weight: 3.9990 chunk 225 optimal weight: 0.0050 chunk 88 optimal weight: 0.9980 chunk 259 optimal weight: 0.7980 chunk 271 optimal weight: 0.9980 chunk 286 optimal weight: 0.6980 overall best weight: 0.4572 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 544 ASN ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS C 607 GLN C 955 ASN ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 moved from start: 0.3831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 25650 Z= 0.171 Angle : 0.574 12.635 34889 Z= 0.290 Chirality : 0.044 0.355 3938 Planarity : 0.004 0.065 4530 Dihedral : 4.097 27.209 3438 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 2.61 % Allowed : 21.05 % Favored : 76.34 % 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: -1.30 (0.14), residues: 3163 helix: 0.98 (0.22), residues: 638 sheet: -0.06 (0.20), residues: 662 loop : -1.93 (0.13), residues: 1863 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.001 TRP A 436 HIS 0.003 0.001 HIS A1064 PHE 0.034 0.001 PHE C 823 TYR 0.021 0.001 TYR A1138 ARG 0.007 0.000 ARG B 995 *********************** REFINEMENT MACRO_CYCLE 9 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 527 residues out of total 2798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 454 time to evaluate : 3.039 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: -0.4150 (tpt) cc_final: -0.5502 (tpp) REVERT: A 177 MET cc_start: -0.0404 (mtt) cc_final: -0.0969 (mtt) REVERT: A 422 ASN cc_start: 0.7273 (m-40) cc_final: 0.6164 (m-40) REVERT: A 508 TYR cc_start: 0.6733 (m-80) cc_final: 0.5996 (m-80) REVERT: A 515 PHE cc_start: 0.7873 (OUTLIER) cc_final: 0.5790 (p90) REVERT: A 564 GLN cc_start: 0.7610 (mp10) cc_final: 0.7356 (mp10) REVERT: A 1091 ARG cc_start: 0.7179 (mtm-85) cc_final: 0.6969 (ttp-170) REVERT: C 48 LEU cc_start: 0.8369 (mm) cc_final: 0.8145 (mp) REVERT: C 98 SER cc_start: 0.8994 (OUTLIER) cc_final: 0.8727 (m) REVERT: C 99 ASN cc_start: 0.8892 (OUTLIER) cc_final: 0.8598 (p0) REVERT: C 177 MET cc_start: -0.2657 (mmt) cc_final: -0.3998 (mmt) REVERT: C 202 LYS cc_start: 0.8319 (mptt) cc_final: 0.7817 (mptt) REVERT: C 206 LYS cc_start: 0.8292 (tptt) cc_final: 0.7956 (tptp) REVERT: C 290 ASP cc_start: 0.7652 (t0) cc_final: 0.7326 (m-30) REVERT: C 549 THR cc_start: 0.8684 (m) cc_final: 0.8450 (m) REVERT: C 564 GLN cc_start: 0.7788 (mp10) cc_final: 0.7551 (mp10) REVERT: C 574 ASP cc_start: 0.7574 (p0) cc_final: 0.7175 (t0) REVERT: C 790 LYS cc_start: 0.8721 (mtpp) cc_final: 0.8411 (mmtm) REVERT: C 1107 ARG cc_start: 0.7893 (mtm110) cc_final: 0.6444 (tpt170) REVERT: B 64 TRP cc_start: 0.7213 (t-100) cc_final: 0.6994 (t60) REVERT: B 168 PHE cc_start: 0.7150 (t80) cc_final: 0.6776 (t80) REVERT: B 190 ARG cc_start: 0.6764 (mtp180) cc_final: 0.6289 (mtp180) REVERT: B 202 LYS cc_start: 0.7296 (tptt) cc_final: 0.7061 (tptt) REVERT: B 213 VAL cc_start: 0.7579 (OUTLIER) cc_final: 0.7373 (t) REVERT: B 225 PRO cc_start: 0.7948 (Cg_exo) cc_final: 0.7597 (Cg_endo) REVERT: B 357 ARG cc_start: 0.6868 (ttm-80) cc_final: 0.6621 (ttm170) REVERT: B 429 PHE cc_start: 0.7988 (t80) cc_final: 0.7469 (t80) REVERT: B 498 GLN cc_start: 0.7950 (pt0) cc_final: 0.7740 (pp30) REVERT: B 567 ARG cc_start: 0.7886 (mtm-85) cc_final: 0.7656 (mtt180) REVERT: B 1107 ARG cc_start: 0.6968 (mtt-85) cc_final: 0.5853 (tpt170) outliers start: 73 outliers final: 64 residues processed: 496 average time/residue: 0.3906 time to fit residues: 296.3509 Evaluate side-chains 512 residues out of total 2798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 444 time to evaluate : 2.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 266 TYR Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 334 ASN Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 428 ASP Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 457 ARG Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 663 ASP Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 99 ASN Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 281 GLU Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 532 ASN Chi-restraints excluded: chain C residue 607 GLN Chi-restraints excluded: chain C residue 619 GLU Chi-restraints excluded: chain C residue 673 SER Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 914 ASN Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1123 SER Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 304 LYS Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 440 ASN Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 703 ASN Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 820 ASP Chi-restraints excluded: chain B residue 933 LYS Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1111 GLU Chi-restraints excluded: chain B residue 1118 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 188 optimal weight: 0.9980 chunk 303 optimal weight: 1.9990 chunk 185 optimal weight: 0.0670 chunk 144 optimal weight: 8.9990 chunk 211 optimal weight: 0.6980 chunk 318 optimal weight: 2.9990 chunk 293 optimal weight: 0.3980 chunk 253 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 196 optimal weight: 0.0040 chunk 155 optimal weight: 5.9990 overall best weight: 0.4330 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A1134 ASN C 207 HIS C 607 GLN C 955 ASN ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 moved from start: 0.3896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 25650 Z= 0.170 Angle : 0.575 11.881 34889 Z= 0.290 Chirality : 0.043 0.281 3938 Planarity : 0.004 0.049 4530 Dihedral : 4.020 29.516 3438 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 2.64 % Allowed : 21.09 % Favored : 76.27 % 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: -1.17 (0.15), residues: 3163 helix: 1.17 (0.22), residues: 638 sheet: -0.01 (0.20), residues: 668 loop : -1.88 (0.13), residues: 1857 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 436 HIS 0.003 0.000 HIS A1064 PHE 0.033 0.001 PHE C 823 TYR 0.021 0.001 TYR A1138 ARG 0.009 0.000 ARG A 509 ********************** REFINEMENT MACRO_CYCLE 10 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 522 residues out of total 2798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 448 time to evaluate : 2.540 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 VAL cc_start: 0.5927 (OUTLIER) cc_final: 0.5687 (t) REVERT: A 153 MET cc_start: -0.4173 (tpt) cc_final: -0.5543 (tpp) REVERT: A 177 MET cc_start: -0.0228 (mtt) cc_final: -0.1253 (mtt) REVERT: A 422 ASN cc_start: 0.7294 (m-40) cc_final: 0.6220 (m-40) REVERT: A 508 TYR cc_start: 0.6826 (m-80) cc_final: 0.6031 (m-80) REVERT: A 515 PHE cc_start: 0.7853 (OUTLIER) cc_final: 0.5861 (p90) REVERT: A 564 GLN cc_start: 0.7591 (mp10) cc_final: 0.7320 (mp10) REVERT: A 580 GLN cc_start: 0.7705 (mm-40) cc_final: 0.7258 (mm110) REVERT: A 1091 ARG cc_start: 0.7168 (mtm-85) cc_final: 0.6954 (ttp-170) REVERT: C 48 LEU cc_start: 0.8368 (mm) cc_final: 0.8131 (mp) REVERT: C 98 SER cc_start: 0.8977 (OUTLIER) cc_final: 0.8754 (p) REVERT: C 99 ASN cc_start: 0.8888 (OUTLIER) cc_final: 0.8553 (p0) REVERT: C 177 MET cc_start: -0.2804 (mmt) cc_final: -0.4168 (mmt) REVERT: C 202 LYS cc_start: 0.8304 (mptt) cc_final: 0.7820 (mptt) REVERT: C 206 LYS cc_start: 0.8291 (tptt) cc_final: 0.7909 (tptp) REVERT: C 290 ASP cc_start: 0.7657 (t0) cc_final: 0.7324 (m-30) REVERT: C 549 THR cc_start: 0.8678 (m) cc_final: 0.8460 (m) REVERT: C 564 GLN cc_start: 0.7769 (mp10) cc_final: 0.7531 (mp10) REVERT: C 574 ASP cc_start: 0.7517 (p0) cc_final: 0.7210 (t0) REVERT: C 702 GLU cc_start: 0.7069 (tm-30) cc_final: 0.6843 (tm-30) REVERT: C 790 LYS cc_start: 0.8720 (mtpp) cc_final: 0.8411 (mmtm) REVERT: C 1107 ARG cc_start: 0.7860 (mtm110) cc_final: 0.6387 (tpt170) REVERT: B 64 TRP cc_start: 0.7185 (t-100) cc_final: 0.6969 (t60) REVERT: B 190 ARG cc_start: 0.6757 (mtp180) cc_final: 0.6228 (mtp180) REVERT: B 213 VAL cc_start: 0.7537 (OUTLIER) cc_final: 0.7330 (t) REVERT: B 225 PRO cc_start: 0.7950 (Cg_exo) cc_final: 0.7584 (Cg_endo) REVERT: B 329 PHE cc_start: 0.7668 (m-80) cc_final: 0.7447 (m-80) REVERT: B 357 ARG cc_start: 0.6799 (ttm-80) cc_final: 0.6507 (ttm170) REVERT: B 429 PHE cc_start: 0.7999 (t80) cc_final: 0.7512 (t80) REVERT: B 567 ARG cc_start: 0.7869 (mtm-85) cc_final: 0.7629 (mtt180) REVERT: B 796 ASP cc_start: 0.6952 (p0) cc_final: 0.6701 (p0) REVERT: B 1107 ARG cc_start: 0.6958 (mtt-85) cc_final: 0.5828 (tpt170) outliers start: 74 outliers final: 62 residues processed: 493 average time/residue: 0.4162 time to fit residues: 318.5221 Evaluate side-chains 508 residues out of total 2798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 441 time to evaluate : 2.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 266 TYR Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 334 ASN Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 428 ASP Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 457 ARG Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 578 ASP Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 99 ASN Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 281 GLU Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 532 ASN Chi-restraints excluded: chain C residue 607 GLN Chi-restraints excluded: chain C residue 619 GLU Chi-restraints excluded: chain C residue 673 SER Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 914 ASN Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1123 SER Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 304 LYS Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 440 ASN Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 703 ASN Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 820 ASP Chi-restraints excluded: chain B residue 933 LYS Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1118 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 201 optimal weight: 0.7980 chunk 270 optimal weight: 3.9990 chunk 77 optimal weight: 4.9990 chunk 234 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 70 optimal weight: 2.9990 chunk 254 optimal weight: 6.9990 chunk 106 optimal weight: 1.9990 chunk 261 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 46 optimal weight: 10.0000 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1134 ASN ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS C 607 GLN C 955 ASN B 30 ASN B 394 ASN ** B 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 804 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.145339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.114360 restraints weight = 48255.115| |-----------------------------------------------------------------------------| r_work (start): 0.3622 rms_B_bonded: 3.22 r_work: 0.3514 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.4076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 25650 Z= 0.321 Angle : 0.639 11.749 34889 Z= 0.327 Chirality : 0.046 0.253 3938 Planarity : 0.005 0.063 4530 Dihedral : 4.408 28.002 3438 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 2.89 % Allowed : 21.37 % Favored : 75.73 % 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: -1.34 (0.14), residues: 3163 helix: 0.93 (0.22), residues: 638 sheet: -0.11 (0.20), residues: 657 loop : -1.94 (0.13), residues: 1868 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 436 HIS 0.006 0.001 HIS A1064 PHE 0.034 0.002 PHE C 823 TYR 0.022 0.002 TYR A1138 ARG 0.011 0.001 ARG A1019 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6620.14 seconds wall clock time: 119 minutes 14.45 seconds (7154.45 seconds total)