Starting phenix.real_space_refine on Fri Aug 9 05:39:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w94_32360/08_2024/7w94_32360.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w94_32360/08_2024/7w94_32360.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w94_32360/08_2024/7w94_32360.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w94_32360/08_2024/7w94_32360.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w94_32360/08_2024/7w94_32360.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w94_32360/08_2024/7w94_32360.cif" } resolution = 3.4 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 15993 2.51 5 N 4214 2.21 5 O 4761 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 96": "OE1" <-> "OE2" Residue "B PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 135": "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 PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 180": "OE1" <-> "OE2" Residue "B PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 198": "OD1" <-> "OD2" Residue "B ASP 228": "OD1" <-> "OD2" Residue "B PHE 238": "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 287": "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 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 340": "OE1" <-> "OE2" Residue "B PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 398": "OD1" <-> "OD2" Residue "B ASP 405": "OD1" <-> "OD2" Residue "B TYR 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 427": "OD1" <-> "OD2" Residue "B TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 467": "OD1" <-> "OD2" Residue "B GLU 471": "OE1" <-> "OE2" Residue "B TYR 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 490": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 554": "OE1" <-> "OE2" Residue "B PHE 559": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 568": "OD1" <-> "OD2" Residue "B ASP 571": "OD1" <-> "OD2" Residue "B PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 636": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 654": "OE1" <-> "OE2" Residue "B TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 661": "OE1" <-> "OE2" 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 PHE 782": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 797": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 802": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 808": "OD1" <-> "OD2" Residue "B GLU 819": "OE1" <-> "OE2" Residue "B PHE 855": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 867": "OD1" <-> "OD2" Residue "B GLU 868": "OE1" <-> "OE2" Residue "B PHE 888": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 917": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 918": "OE1" <-> "OE2" Residue "B PHE 970": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 988": "OE1" <-> "OE2" Residue "B ASP 994": "OD1" <-> "OD2" Residue "B GLU 1017": "OE1" <-> "OE2" 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 PHE 1089": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1092": "OE1" <-> "OE2" Residue "B PHE 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1127": "OD1" <-> "OD2" Residue "B ASP 1146": "OD1" <-> "OD2" Residue "C TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 40": "OD1" <-> "OD2" 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 TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 169": "OE1" <-> "OE2" Residue "C ASP 178": "OD1" <-> "OD2" Residue "C GLU 180": "OE1" <-> "OE2" Residue "C PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 281": "OE1" <-> "OE2" Residue "C TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 340": "OE1" <-> "OE2" Residue "C TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 389": "OD1" <-> "OD2" Residue "C PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 398": "OD1" <-> "OD2" Residue "C PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 420": "OD1" <-> "OD2" Residue "C TYR 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 428": "OD1" <-> "OD2" Residue "C TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 465": "OE1" <-> "OE2" Residue "C TYR 473": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 505": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 516": "OE1" <-> "OE2" Residue "C PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 554": "OE1" <-> "OE2" Residue "C PHE 559": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 568": "OD1" <-> "OD2" Residue "C ASP 571": "OD1" <-> "OD2" Residue "C GLU 583": "OE1" <-> "OE2" Residue "C ASP 586": "OD1" <-> "OD2" Residue "C TYR 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 619": "OE1" <-> "OE2" Residue "C TYR 636": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 654": "OE1" <-> "OE2" Residue "C TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 661": "OE1" <-> "OE2" Residue "C TYR 707": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 748": "OE1" <-> "OE2" Residue "C ASP 775": "OD1" <-> "OD2" Residue "C PHE 782": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 796": "OD1" <-> "OD2" Residue "C PHE 797": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 800": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 802": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 808": "OD1" <-> "OD2" Residue "C GLU 868": "OE1" <-> "OE2" Residue "C PHE 888": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 904": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 917": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 970": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 979": "OD1" <-> "OD2" Residue "C GLU 988": "OE1" <-> "OE2" Residue "C GLU 990": "OE1" <-> "OE2" Residue "C TYR 1047": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1052": "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 GLU 1111": "OE1" <-> "OE2" Residue "C ASP 1127": "OD1" <-> "OD2" Residue "C ASP 1139": "OD1" <-> "OD2" Residue "A PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 37": "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 88": "OD1" <-> "OD2" Residue "A PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 138": "OD1" <-> "OD2" Residue "A PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 198": "OD1" <-> "OD2" Residue "A PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 281": "OE1" <-> "OE2" 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 PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 389": "OD1" <-> "OD2" Residue "A TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 420": "OD1" <-> "OD2" Residue "A TYR 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 427": "OD1" <-> "OD2" Residue "A ASP 428": "OD1" <-> "OD2" Residue "A TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 467": "OD1" <-> "OD2" Residue "A TYR 505": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 516": "OE1" <-> "OE2" 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 559": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 583": "OE1" <-> "OE2" Residue "A PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 619": "OE1" <-> "OE2" Residue "A TYR 636": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 725": "OE1" <-> "OE2" Residue "A ASP 745": "OD1" <-> "OD2" Residue "A PHE 759": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 773": "OE1" <-> "OE2" Residue "A GLU 780": "OE1" <-> "OE2" Residue "A PHE 782": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 789": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 PHE 817": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 855": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 867": "OD1" <-> "OD2" Residue "A PHE 888": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 904": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 917": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 936": "OD1" <-> "OD2" Residue "A PHE 970": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 979": "OD1" <-> "OD2" Residue "A GLU 988": "OE1" <-> "OE2" Residue "A GLU 990": "OE1" <-> "OE2" Residue "A GLU 1017": "OE1" <-> "OE2" Residue "A ASP 1041": "OD1" <-> "OD2" 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 GLU 1092": "OE1" <-> "OE2" Residue "A PHE 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1118": "OD1" <-> "OD2" Residue "A ASP 1127": "OD1" <-> "OD2" Residue "A ASP 1139": "OD1" <-> "OD2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 25082 Number of models: 1 Model: "" Number of chains: 3 Chain: "B" Number of atoms: 8356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1068, 8356 Classifications: {'peptide': 1068} Link IDs: {'PTRANS': 52, 'TRANS': 1015} Chain breaks: 6 Chain: "C" Number of atoms: 8356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1068, 8356 Classifications: {'peptide': 1068} Link IDs: {'PTRANS': 52, 'TRANS': 1015} Chain breaks: 6 Chain: "A" Number of atoms: 8370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1070, 8370 Classifications: {'peptide': 1070} Link IDs: {'PTRANS': 53, 'TRANS': 1016} Chain breaks: 6 Time building chain proxies: 13.56, per 1000 atoms: 0.54 Number of scatterers: 25082 At special positions: 0 Unit cell: (157.168, 144.666, 181.279, 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 4761 8.00 N 4214 7.00 C 15993 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 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=2.04 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=2.04 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 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=2.04 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 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 A 131 " - pdb=" SG CYS A 166 " distance=2.03 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=2.03 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 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: 8.10 Conformation dependent library (CDL) restraints added in 4.3 seconds 6328 Ramachandran restraints generated. 3164 Oldfield, 0 Emsley, 3164 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5992 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 49 sheets defined 21.9% alpha, 22.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.50 Creating SS restraints... Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 341 removed outlier: 4.233A pdb=" N GLU B 340 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 371 removed outlier: 3.524A pdb=" N SER B 371 " --> pdb=" O VAL B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 387 removed outlier: 4.004A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 removed outlier: 4.100A pdb=" N TYR B 421 " --> pdb=" O LYS B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 removed outlier: 3.636A pdb=" N TYR B 741 " --> pdb=" O ASP B 737 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ILE B 742 " --> pdb=" O CYS B 738 " (cutoff:3.500A) Processing helix chain 'B' and resid 746 through 754 removed outlier: 3.662A pdb=" N SER B 750 " --> pdb=" O SER B 746 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) removed outlier: 3.733A 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 782 removed outlier: 3.809A pdb=" N LEU B 763 " --> pdb=" O PHE B 759 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ASN B 764 " --> pdb=" O CYS B 760 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N GLN B 779 " --> pdb=" O ASP B 775 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N VAL B 781 " --> pdb=" O ASN B 777 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N PHE B 782 " --> pdb=" O THR B 778 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 824 removed outlier: 3.820A pdb=" N ASN B 824 " --> pdb=" O ASP B 820 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 883 removed outlier: 3.504A pdb=" N TYR B 873 " --> pdb=" O MET B 869 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 908 removed outlier: 3.870A pdb=" N MET B 902 " --> pdb=" O PHE B 898 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N ALA B 903 " --> pdb=" O ALA B 899 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N TYR B 904 " --> pdb=" O MET B 900 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 918 removed outlier: 3.608A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLU B 918 " --> pdb=" O ASN B 914 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 913 through 918' Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.678A pdb=" N ASN B 925 " --> pdb=" O LYS B 921 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LYS B 933 " --> pdb=" O SER B 929 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N SER B 939 " --> pdb=" O GLN B 935 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N SER B 940 " --> pdb=" O ASP B 936 " (cutoff:3.500A) Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.587A pdb=" N GLN B 949 " --> pdb=" O LEU B 945 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLN B 954 " --> pdb=" O ASN B 950 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ALA B 958 " --> pdb=" O GLN B 954 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU B 959 " --> pdb=" O ASN B 955 " (cutoff:3.500A) removed outlier: 3.555A 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: 3.609A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N SER B 982 " --> pdb=" O ASN B 978 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1032 removed outlier: 4.181A pdb=" N GLU B 990 " --> pdb=" O PRO B 986 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLY B 999 " --> pdb=" O ARG B 995 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLN B1002 " --> pdb=" O THR B 998 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N SER B1003 " --> pdb=" O GLY B 999 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ALA B1016 " --> pdb=" O LEU B1012 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLU B1017 " --> pdb=" O ILE B1013 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE B1018 " --> pdb=" O ARG B1014 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU B1024 " --> pdb=" O ALA B1020 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N SER B1030 " --> pdb=" O ALA B1026 " (cutoff:3.500A) Processing helix chain 'B' and resid 1142 through 1147 removed outlier: 4.149A pdb=" N ASP B1146 " --> pdb=" O GLN B1142 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N SER B1147 " --> pdb=" O PRO B1143 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1142 through 1147' Processing helix chain 'C' and resid 294 through 304 removed outlier: 3.838A pdb=" N LYS C 300 " --> pdb=" O LEU C 296 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N THR C 302 " --> pdb=" O GLU C 298 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 removed outlier: 3.944A pdb=" N TYR C 421 " --> pdb=" O LYS C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 506 removed outlier: 3.512A pdb=" N GLN C 506 " --> pdb=" O VAL C 503 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 removed outlier: 3.575A pdb=" N TYR C 741 " --> pdb=" O ASP C 737 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ILE C 742 " --> pdb=" O CYS C 738 " (cutoff:3.500A) Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.571A pdb=" N ASN C 751 " --> pdb=" O THR C 747 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU C 753 " --> pdb=" O CYS C 749 " (cutoff:3.500A) removed outlier: 3.867A 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: 3.597A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N LEU C 763 " --> pdb=" O PHE C 759 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ASN C 764 " --> pdb=" O CYS C 760 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU C 767 " --> pdb=" O LEU C 763 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLY C 769 " --> pdb=" O ARG C 765 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE C 770 " --> pdb=" O ALA C 766 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLN C 779 " --> pdb=" O ASP C 775 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL C 781 " --> pdb=" O ASN C 777 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N PHE C 782 " --> pdb=" O THR C 778 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.506A pdb=" N LEU C 821 " --> pdb=" O PHE C 817 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ASN C 824 " --> pdb=" O ASP C 820 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LYS C 825 " --> pdb=" O LEU C 821 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 884 removed outlier: 3.504A pdb=" N ALA C 871 " --> pdb=" O ASP C 867 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLN C 872 " --> pdb=" O GLU C 868 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ILE C 882 " --> pdb=" O LEU C 878 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N THR C 883 " --> pdb=" O ALA C 879 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 891 removed outlier: 4.180A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 906 removed outlier: 3.584A pdb=" N MET C 902 " --> pdb=" O PHE C 898 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N ALA C 903 " --> pdb=" O ALA C 899 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N TYR C 904 " --> pdb=" O MET C 900 " (cutoff:3.500A) Processing helix chain 'C' and resid 907 through 909 No H-bonds generated for 'chain 'C' and resid 907 through 909' Processing helix chain 'C' and resid 913 through 918 removed outlier: 3.577A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLU C 918 " --> pdb=" O ASN C 914 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 913 through 918' Processing helix chain 'C' and resid 919 through 938 removed outlier: 3.507A pdb=" N ILE C 931 " --> pdb=" O PHE C 927 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLY C 932 " --> pdb=" O ASN C 928 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LYS C 933 " --> pdb=" O SER C 929 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (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: 3.910A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU C 959 " --> pdb=" O ASN C 955 " (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 984 removed outlier: 3.787A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LEU C 981 " --> pdb=" O LEU C 977 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ARG C 983 " --> pdb=" O ASP C 979 " (cutoff:3.500A) Processing helix chain 'C' and resid 989 through 1032 removed outlier: 3.663A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLN C1002 " --> pdb=" O THR C 998 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N SER C1003 " --> pdb=" O GLY C 999 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N TYR C1007 " --> pdb=" O SER C1003 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ALA C1016 " --> pdb=" O LEU C1012 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA C1020 " --> pdb=" O ALA C1016 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N SER C1030 " --> pdb=" O ALA C1026 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1146 removed outlier: 3.808A pdb=" N ASP C1146 " --> pdb=" O GLN C1142 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 304 removed outlier: 3.729A pdb=" N LYS A 300 " --> pdb=" O LEU A 296 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LYS A 304 " --> pdb=" O LYS A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 removed outlier: 3.553A pdb=" N TYR A 369 " --> pdb=" O TYR A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 389 removed outlier: 3.808A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ASP A 389 " --> pdb=" O LYS A 386 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 384 through 389' Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.994A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLN A 409 " --> pdb=" O GLU A 406 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE A 410 " --> pdb=" O VAL A 407 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 405 through 410' Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 502 through 505 removed outlier: 3.641A pdb=" N TYR A 505 " --> pdb=" O GLY A 502 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 502 through 505' Processing helix chain 'A' and resid 737 through 743 removed outlier: 3.812A pdb=" N TYR A 741 " --> pdb=" O ASP A 737 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ILE A 742 " --> pdb=" O CYS A 738 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.539A pdb=" N ASN A 751 " --> pdb=" O THR A 747 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU A 753 " --> pdb=" O CYS A 749 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LEU A 754 " --> pdb=" O SER A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 760 through 782 removed outlier: 3.683A pdb=" N ASN A 764 " --> pdb=" O CYS A 760 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLU A 773 " --> pdb=" O GLY A 769 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLN A 779 " --> pdb=" O ASP A 775 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL A 781 " --> pdb=" O ASN A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 824 removed outlier: 3.907A pdb=" N ASN A 824 " --> pdb=" O ASP A 820 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 884 removed outlier: 3.763A pdb=" N ALA A 871 " --> pdb=" O ASP A 867 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLN A 872 " --> pdb=" O GLU A 868 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N THR A 881 " --> pdb=" O LEU A 877 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILE A 882 " --> pdb=" O LEU A 878 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N THR A 883 " --> pdb=" O ALA A 879 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 908 removed outlier: 3.612A pdb=" N MET A 902 " --> pdb=" O PHE A 898 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ALA A 903 " --> pdb=" O ALA A 899 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N TYR A 904 " --> pdb=" O MET A 900 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 919 removed outlier: 3.812A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.585A pdb=" N ASN A 925 " --> pdb=" O LYS A 921 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLY A 932 " --> pdb=" O ASN A 928 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LYS A 933 " --> pdb=" O SER A 929 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ILE A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N SER A 937 " --> pdb=" O LYS A 933 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N SER A 939 " --> pdb=" O GLN A 935 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N THR A 941 " --> pdb=" O SER A 937 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.921A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLN A 965 " --> pdb=" O THR A 961 " (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 982 Processing helix chain 'A' and resid 985 through 1032 removed outlier: 3.816A pdb=" N GLU A 990 " --> pdb=" O PRO A 986 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ASP A 994 " --> pdb=" O GLU A 990 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLY A 999 " --> pdb=" O ARG A 995 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLN A1002 " --> pdb=" O THR A 998 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N SER A1003 " --> pdb=" O GLY A 999 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU A1004 " --> pdb=" O ARG A1000 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ALA A1016 " --> pdb=" O LEU A1012 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLU A1017 " --> pdb=" O ILE A1013 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1146 removed outlier: 3.693A pdb=" N LEU A1145 " --> pdb=" O LEU A1141 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ASP A1146 " --> pdb=" O GLN A1142 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1141 through 1146' Processing sheet with id=AA1, first strand: chain 'B' and resid 28 through 30 Processing sheet with id=AA2, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.901A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ARG B 273 " --> pdb=" O ASP B 53 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N VAL B 289 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 67 through 68 removed outlier: 4.125A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N THR B 95 " --> pdb=" O ALA B 264 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N PHE B 194 " --> pdb=" O VAL B 90 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ASN B 188 " --> pdb=" O GLU B 96 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU B 189 " --> pdb=" O THR B 208 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N THR B 208 " --> pdb=" O LEU B 189 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL B 193 " --> pdb=" O TYR B 204 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N TYR B 204 " --> pdb=" O VAL B 193 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N LYS B 195 " --> pdb=" O LYS B 202 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N LYS B 202 " --> pdb=" O LYS B 195 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.921A pdb=" N LEU B 84 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) removed outlier: 7.885A pdb=" N ARG B 246 " --> pdb=" O LEU B 141 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N VAL B 143 " --> pdb=" O ARG B 246 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.921A pdb=" N LEU B 84 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ILE B 105 " --> pdb=" O GLN B 239 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N TRP B 104 " --> pdb=" O ILE B 119 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ILE B 128 " --> pdb=" O TYR B 170 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N TYR B 170 " --> pdb=" O ILE B 128 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 311 through 317 removed outlier: 5.298A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.523A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLN B 613 " --> pdb=" O GLY B 594 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 325 through 328 removed outlier: 3.792A pdb=" N PHE B 541 " --> pdb=" O GLY B 548 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLY B 548 " --> pdb=" O PHE B 541 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.112A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N SER B 399 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE B 358 " --> pdb=" O VAL B 395 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ILE B 402 " --> pdb=" O TYR B 508 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N CYS B 432 " --> pdb=" O LEU B 513 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 452 through 453 Processing sheet with id=AB1, first strand: chain 'B' and resid 575 through 577 Processing sheet with id=AB2, first strand: chain 'B' and resid 654 through 660 removed outlier: 3.540A pdb=" N GLU B 654 " --> pdb=" O ILE B 692 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N THR B 696 " --> pdb=" O VAL B 656 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N ASN B 658 " --> pdb=" O THR B 696 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N SER B 691 " --> pdb=" O GLN B 675 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLN B 675 " --> pdb=" O SER B 691 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N TYR B 695 " --> pdb=" O CYS B 671 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ILE B 664 " --> pdb=" O ALA B 672 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 701 through 702 removed outlier: 6.528A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'B' and resid 711 through 713 Processing sheet with id=AB5, first strand: chain 'B' and resid 718 through 719 removed outlier: 6.993A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N TYR B1047 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 725 through 728 removed outlier: 3.627A pdb=" N GLU B 725 " --> pdb=" O PHE B1062 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLY B1059 " --> pdb=" O ALA B1056 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ALA B1056 " --> pdb=" O GLY B1059 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 735 through 736 Processing sheet with id=AB8, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.535A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AC1, first strand: chain 'C' and resid 28 through 31 removed outlier: 3.684A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA C 93 " --> pdb=" O TYR C 266 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ASN C 188 " --> pdb=" O GLU C 96 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N LEU C 212 " --> pdb=" O PHE C 186 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N ASN C 188 " --> pdb=" O ILE C 210 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N ILE C 210 " --> pdb=" O ASN C 188 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N ARG C 190 " --> pdb=" O THR C 208 " (cutoff:3.500A) removed outlier: 8.288A pdb=" N THR C 208 " --> pdb=" O ARG C 190 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 28 through 31 removed outlier: 3.684A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA C 93 " --> pdb=" O TYR C 266 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ASN C 188 " --> pdb=" O GLU C 96 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N VAL C 193 " --> pdb=" O TYR C 204 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N TYR C 204 " --> pdb=" O VAL C 193 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N LYS C 195 " --> pdb=" O LYS C 202 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 48 through 49 removed outlier: 3.566A pdb=" N LYS C 278 " --> pdb=" O ASP C 287 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 54 through 55 Processing sheet with id=AC5, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.507A pdb=" N GLY C 107 " --> pdb=" O ARG C 237 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 5.759A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ILE C 128 " --> pdb=" O TYR C 170 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N TYR C 170 " --> pdb=" O ILE C 128 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 311 through 317 removed outlier: 5.705A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL C 610 " --> pdb=" O ILE C 651 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE C 651 " --> pdb=" O VAL C 610 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N CYS C 649 " --> pdb=" O TYR C 612 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 325 through 328 removed outlier: 6.653A pdb=" N ILE C 326 " --> pdb=" O ASN C 542 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLY C 548 " --> pdb=" O PHE C 541 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N PHE C 543 " --> pdb=" O LEU C 546 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N THR C 588 " --> pdb=" O VAL C 551 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N THR C 553 " --> pdb=" O ASP C 586 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N PHE C 565 " --> pdb=" O PHE A 43 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 356 through 358 removed outlier: 3.707A pdb=" N VAL C 512 " --> pdb=" O ASP C 398 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AD1, first strand: chain 'C' and resid 654 through 660 removed outlier: 6.176A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.480A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 8.768A pdb=" N VAL C 656 " --> pdb=" O THR C 696 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N SER C 691 " --> pdb=" O GLN C 675 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 712 through 713 Processing sheet with id=AD3, first strand: chain 'C' and resid 718 through 719 Processing sheet with id=AD4, first strand: chain 'C' and resid 722 through 728 removed outlier: 3.518A pdb=" N GLY C1059 " --> pdb=" O ALA C1056 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 734 through 735 Processing sheet with id=AD6, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 3.725A pdb=" N SER C1123 " --> pdb=" O ALA C1087 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 1094 through 1097 Processing sheet with id=AD8, first strand: chain 'A' and resid 28 through 31 removed outlier: 3.504A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N THR A 95 " --> pdb=" O ALA A 264 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ALA A 93 " --> pdb=" O TYR A 266 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N TYR A 91 " --> pdb=" O GLY A 268 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N VAL A 90 " --> pdb=" O PHE A 194 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N PHE A 194 " --> pdb=" O VAL A 90 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ASN A 188 " --> pdb=" O GLU A 96 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LEU A 189 " --> pdb=" O THR A 208 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N THR A 208 " --> pdb=" O LEU A 189 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LYS A 206 " --> pdb=" O GLU A 191 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL A 193 " --> pdb=" O TYR A 204 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ILE A 197 " --> pdb=" O TYR A 200 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.978A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ARG A 273 " --> pdb=" O ASP A 53 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'A' and resid 84 through 85 removed outlier: 4.278A pdb=" N LEU A 84 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASN A 121 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N VAL A 120 " --> pdb=" O VAL A 127 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL A 127 " --> pdb=" O VAL A 120 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N VAL A 130 " --> pdb=" O PHE A 168 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'A' and resid 141 through 143 removed outlier: 3.752A pdb=" N LEU A 141 " --> pdb=" O LEU A 242 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'A' and resid 311 through 317 removed outlier: 5.539A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL A 610 " --> pdb=" O ILE A 651 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.151A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N SER A 514 " --> pdb=" O TYR A 396 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LYS A 378 " --> pdb=" O VAL A 433 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA A 435 " --> pdb=" O THR A 376 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'A' and resid 452 through 453 Processing sheet with id=AE6, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AE7, first strand: chain 'A' and resid 539 through 543 removed outlier: 3.633A pdb=" N GLY A 550 " --> pdb=" O VAL A 539 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLY A 548 " --> pdb=" O PHE A 541 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N THR A 588 " --> pdb=" O VAL A 551 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N THR A 553 " --> pdb=" O ASP A 586 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'A' and resid 654 through 660 removed outlier: 5.656A pdb=" N THR A 696 " --> pdb=" O VAL A 656 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N ASN A 658 " --> pdb=" O THR A 696 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N SER A 691 " --> pdb=" O GLN A 675 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLN A 675 " --> pdb=" O SER A 691 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N TYR A 695 " --> pdb=" O CYS A 671 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ILE A 664 " --> pdb=" O ALA A 672 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'A' and resid 712 through 722 removed outlier: 6.688A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ASN A 717 " --> pdb=" O ALA A1070 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N SER A 721 " --> pdb=" O THR A1066 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'A' and resid 712 through 722 removed outlier: 6.688A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ASN A 717 " --> pdb=" O ALA A1070 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N SER A 721 " --> pdb=" O THR A1066 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ALA A1056 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'A' and resid 735 through 736 Processing sheet with id=AF3, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.806A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N CYS A1082 " --> pdb=" O VAL A1133 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'A' and resid 1094 through 1097 676 hydrogen bonds defined for protein. 1848 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: 10.02 Time building geometry restraints manager: 9.04 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: 8122 1.35 - 1.47: 6304 1.47 - 1.59: 11092 1.59 - 1.71: 0 1.71 - 1.83: 144 Bond restraints: 25662 Sorted by residual: bond pdb=" CA ILE B 210 " pdb=" CB ILE B 210 " ideal model delta sigma weight residual 1.544 1.566 -0.022 1.42e-02 4.96e+03 2.40e+00 bond pdb=" N TRP B 152 " pdb=" CA TRP B 152 " ideal model delta sigma weight residual 1.460 1.480 -0.020 1.54e-02 4.22e+03 1.72e+00 bond pdb=" N ASP B 198 " pdb=" CA ASP B 198 " ideal model delta sigma weight residual 1.462 1.482 -0.020 1.54e-02 4.22e+03 1.69e+00 bond pdb=" C GLY B 744 " pdb=" N ASP B 745 " ideal model delta sigma weight residual 1.328 1.344 -0.016 1.30e-02 5.92e+03 1.53e+00 bond pdb=" N ASP B 745 " pdb=" CA ASP B 745 " ideal model delta sigma weight residual 1.460 1.477 -0.017 1.42e-02 4.96e+03 1.45e+00 ... (remaining 25657 not shown) Histogram of bond angle deviations from ideal: 100.51 - 107.30: 845 107.30 - 114.08: 14140 114.08 - 120.87: 10891 120.87 - 127.65: 8864 127.65 - 134.44: 162 Bond angle restraints: 34902 Sorted by residual: angle pdb=" CA LEU A 518 " pdb=" CB LEU A 518 " pdb=" CG LEU A 518 " ideal model delta sigma weight residual 116.30 132.57 -16.27 3.50e+00 8.16e-02 2.16e+01 angle pdb=" CA LEU B 517 " pdb=" CB LEU B 517 " pdb=" CG LEU B 517 " ideal model delta sigma weight residual 116.30 131.59 -15.29 3.50e+00 8.16e-02 1.91e+01 angle pdb=" CA LEU A 110 " pdb=" CB LEU A 110 " pdb=" CG LEU A 110 " ideal model delta sigma weight residual 116.30 131.05 -14.75 3.50e+00 8.16e-02 1.78e+01 angle pdb=" C LEU A 517 " pdb=" N LEU A 518 " pdb=" CA LEU A 518 " ideal model delta sigma weight residual 122.08 127.83 -5.75 1.47e+00 4.63e-01 1.53e+01 angle pdb=" C LYS A 150 " pdb=" N SER A 151 " pdb=" CA SER A 151 " ideal model delta sigma weight residual 121.54 128.59 -7.05 1.91e+00 2.74e-01 1.36e+01 ... (remaining 34897 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.09: 13916 18.09 - 36.18: 1119 36.18 - 54.27: 187 54.27 - 72.35: 42 72.35 - 90.44: 31 Dihedral angle restraints: 15295 sinusoidal: 5977 harmonic: 9318 Sorted by residual: dihedral pdb=" CB CYS B 538 " pdb=" SG CYS B 538 " pdb=" SG CYS B 590 " pdb=" CB CYS B 590 " ideal model delta sinusoidal sigma weight residual -86.00 -175.71 89.71 1 1.00e+01 1.00e-02 9.55e+01 dihedral pdb=" CB CYS B 291 " pdb=" SG CYS B 291 " pdb=" SG CYS B 301 " pdb=" CB CYS B 301 " ideal model delta sinusoidal sigma weight residual -86.00 -0.46 -85.54 1 1.00e+01 1.00e-02 8.85e+01 dihedral pdb=" CB CYS A 662 " pdb=" SG CYS A 662 " pdb=" SG CYS A 671 " pdb=" CB CYS A 671 " ideal model delta sinusoidal sigma weight residual -86.00 -1.32 -84.68 1 1.00e+01 1.00e-02 8.71e+01 ... (remaining 15292 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 3229 0.061 - 0.122: 619 0.122 - 0.183: 83 0.183 - 0.244: 2 0.244 - 0.305: 3 Chirality restraints: 3936 Sorted by residual: chirality pdb=" CB ILE C 410 " pdb=" CA ILE C 410 " pdb=" CG1 ILE C 410 " pdb=" CG2 ILE C 410 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.30 2.00e-01 2.50e+01 2.32e+00 chirality pdb=" CB ILE C 119 " pdb=" CA ILE C 119 " pdb=" CG1 ILE C 119 " pdb=" CG2 ILE C 119 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.27 2.00e-01 2.50e+01 1.76e+00 chirality pdb=" CB ILE B 410 " pdb=" CA ILE B 410 " pdb=" CG1 ILE B 410 " pdb=" CG2 ILE B 410 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.25 2.00e-01 2.50e+01 1.51e+00 ... (remaining 3933 not shown) Planarity restraints: 4529 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO B 986 " -0.059 5.00e-02 4.00e+02 8.88e-02 1.26e+01 pdb=" N PRO B 987 " 0.153 5.00e-02 4.00e+02 pdb=" CA PRO B 987 " -0.044 5.00e-02 4.00e+02 pdb=" CD PRO B 987 " -0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO C 986 " 0.058 5.00e-02 4.00e+02 8.59e-02 1.18e+01 pdb=" N PRO C 987 " -0.148 5.00e-02 4.00e+02 pdb=" CA PRO C 987 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO C 987 " 0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 986 " -0.055 5.00e-02 4.00e+02 8.22e-02 1.08e+01 pdb=" N PRO A 987 " 0.142 5.00e-02 4.00e+02 pdb=" CA PRO A 987 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO A 987 " -0.046 5.00e-02 4.00e+02 ... (remaining 4526 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 7409 2.81 - 3.33: 18966 3.33 - 3.86: 39595 3.86 - 4.38: 42927 4.38 - 4.90: 75730 Nonbonded interactions: 184627 Sorted by model distance: nonbonded pdb=" OG1 THR C 430 " pdb=" O PHE C 515 " model vdw 2.288 3.040 nonbonded pdb=" OG1 THR B 20 " pdb=" O LYS B 77 " model vdw 2.292 3.040 nonbonded pdb=" O GLN B 607 " pdb=" OH TYR B 674 " model vdw 2.309 3.040 nonbonded pdb=" OG1 THR B 33 " pdb=" O GLY B 219 " model vdw 2.313 3.040 nonbonded pdb=" OG SER B 349 " pdb=" O ARG B 452 " model vdw 2.320 3.040 ... (remaining 184622 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 14 through 620 or resid 633 through 1147)) selection = chain 'B' 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: 4.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.040 Check model and map are aligned: 0.160 Set scattering table: 0.230 Process input model: 63.400 Find NCS groups from input model: 1.140 Set up NCS constraints: 0.090 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:2.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 73.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7219 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 0.041 25662 Z= 0.188 Angle : 0.668 16.267 34902 Z= 0.361 Chirality : 0.049 0.305 3936 Planarity : 0.005 0.089 4529 Dihedral : 13.569 90.443 9186 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 0.14 % Allowed : 5.11 % Favored : 94.75 % 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: -4.24 (0.11), residues: 3164 helix: -4.98 (0.05), residues: 565 sheet: -1.34 (0.19), residues: 642 loop : -2.78 (0.11), residues: 1957 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 152 HIS 0.003 0.000 HIS A 519 PHE 0.015 0.001 PHE B 592 TYR 0.024 0.001 TYR C 451 ARG 0.008 0.000 ARG C 408 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6328 Ramachandran restraints generated. 3164 Oldfield, 0 Emsley, 3164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6328 Ramachandran restraints generated. 3164 Oldfield, 0 Emsley, 3164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 660 residues out of total 2798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 656 time to evaluate : 2.612 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 52 GLN cc_start: 0.8559 (tm-30) cc_final: 0.8351 (tm-30) REVERT: B 133 PHE cc_start: 0.7080 (m-80) cc_final: 0.6868 (m-80) REVERT: B 138 ASP cc_start: 0.8240 (m-30) cc_final: 0.7991 (m-30) REVERT: B 177 MET cc_start: -0.4190 (mmp) cc_final: -0.4582 (mmp) REVERT: B 353 TRP cc_start: 0.5899 (p90) cc_final: 0.5528 (p90) REVERT: B 641 ASN cc_start: 0.6793 (m110) cc_final: 0.5956 (p0) REVERT: B 726 ILE cc_start: 0.8755 (mp) cc_final: 0.8539 (mt) REVERT: B 773 GLU cc_start: 0.7609 (tt0) cc_final: 0.7148 (tt0) REVERT: B 804 GLN cc_start: 0.8285 (mm-40) cc_final: 0.8053 (mm110) REVERT: B 820 ASP cc_start: 0.7970 (t0) cc_final: 0.7597 (t0) REVERT: B 1127 ASP cc_start: 0.7021 (t0) cc_final: 0.6608 (t0) REVERT: C 99 ASN cc_start: 0.8048 (m-40) cc_final: 0.7465 (p0) REVERT: C 140 PHE cc_start: 0.6860 (m-80) cc_final: 0.6535 (m-80) REVERT: C 190 ARG cc_start: 0.8015 (mtt180) cc_final: 0.7551 (mtt180) REVERT: C 238 PHE cc_start: 0.6930 (p90) cc_final: 0.6552 (p90) REVERT: C 303 LEU cc_start: 0.8836 (tp) cc_final: 0.8450 (tt) REVERT: C 347 PHE cc_start: 0.4448 (m-10) cc_final: 0.2576 (m-10) REVERT: C 358 ILE cc_start: 0.5947 (mt) cc_final: 0.5715 (pt) REVERT: C 368 LEU cc_start: 0.8316 (pt) cc_final: 0.7937 (pt) REVERT: C 441 LEU cc_start: 0.6822 (mt) cc_final: 0.6165 (tt) REVERT: C 646 ARG cc_start: 0.7863 (mpp80) cc_final: 0.7660 (ttm-80) REVERT: C 748 GLU cc_start: 0.7761 (mp0) cc_final: 0.7558 (mp0) REVERT: C 758 SER cc_start: 0.8117 (p) cc_final: 0.7845 (p) REVERT: C 776 LYS cc_start: 0.8713 (ttmt) cc_final: 0.8333 (ttmt) REVERT: C 960 ASN cc_start: 0.8315 (t0) cc_final: 0.7956 (t0) REVERT: A 40 ASP cc_start: 0.7358 (t70) cc_final: 0.7096 (t70) REVERT: A 55 PHE cc_start: 0.7187 (m-80) cc_final: 0.6800 (m-80) REVERT: A 86 PHE cc_start: 0.7882 (t80) cc_final: 0.7519 (t80) REVERT: A 133 PHE cc_start: 0.5969 (m-80) cc_final: 0.5109 (m-80) REVERT: A 189 LEU cc_start: 0.8657 (tp) cc_final: 0.8409 (tp) REVERT: A 196 ASN cc_start: 0.7476 (p0) cc_final: 0.6637 (p0) REVERT: A 239 GLN cc_start: 0.7093 (tp-100) cc_final: 0.6647 (mm-40) REVERT: A 355 ARG cc_start: 0.7044 (ttp80) cc_final: 0.6820 (ttp80) REVERT: A 400 PHE cc_start: 0.7204 (p90) cc_final: 0.6857 (p90) REVERT: A 528 LYS cc_start: 0.7979 (mmtm) cc_final: 0.7747 (mptt) REVERT: A 556 ASN cc_start: 0.7561 (t0) cc_final: 0.7315 (t0) REVERT: A 578 ASP cc_start: 0.7322 (t0) cc_final: 0.6911 (t0) REVERT: A 606 ASN cc_start: 0.8486 (m-40) cc_final: 0.8270 (m-40) REVERT: A 607 GLN cc_start: 0.8003 (mp10) cc_final: 0.7409 (mp10) REVERT: A 675 GLN cc_start: 0.7215 (tm-30) cc_final: 0.6695 (tm-30) REVERT: A 790 LYS cc_start: 0.7832 (mtpt) cc_final: 0.7112 (mtpt) REVERT: A 973 ILE cc_start: 0.9059 (tt) cc_final: 0.8779 (mt) REVERT: A 994 ASP cc_start: 0.7748 (t0) cc_final: 0.7472 (t0) outliers start: 4 outliers final: 1 residues processed: 659 average time/residue: 0.4056 time to fit residues: 409.9718 Evaluate side-chains 523 residues out of total 2798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 522 time to evaluate : 2.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 391 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 269 optimal weight: 0.0470 chunk 241 optimal weight: 0.9990 chunk 134 optimal weight: 0.6980 chunk 82 optimal weight: 2.9990 chunk 163 optimal weight: 0.5980 chunk 129 optimal weight: 4.9990 chunk 250 optimal weight: 1.9990 chunk 96 optimal weight: 2.9990 chunk 152 optimal weight: 3.9990 chunk 186 optimal weight: 2.9990 chunk 289 optimal weight: 4.9990 overall best weight: 0.8682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 23 GLN B 49 HIS B 66 HIS B 99 ASN B 196 ASN B 239 GLN B 360 ASN ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 519 HIS B 655 HIS B 690 GLN B 709 ASN B 774 GLN B 969 ASN B1023 ASN B1106 GLN B1135 ASN C 121 ASN C 137 ASN C 343 ASN C 544 ASN C 563 GLN C 655 HIS C 657 ASN C 965 GLN A 149 ASN A 370 ASN A 422 ASN A1002 GLN A1074 ASN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7336 moved from start: 0.2193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 25662 Z= 0.219 Angle : 0.607 11.463 34902 Z= 0.310 Chirality : 0.046 0.351 3936 Planarity : 0.005 0.067 4529 Dihedral : 4.140 24.945 3441 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 1.97 % Allowed : 12.01 % Favored : 86.03 % 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: -3.10 (0.12), residues: 3164 helix: -2.82 (0.15), residues: 613 sheet: -0.88 (0.19), residues: 645 loop : -2.31 (0.12), residues: 1906 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 104 HIS 0.007 0.001 HIS B1083 PHE 0.027 0.002 PHE C 55 TYR 0.021 0.001 TYR B 91 ARG 0.012 0.001 ARG B 102 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6328 Ramachandran restraints generated. 3164 Oldfield, 0 Emsley, 3164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6328 Ramachandran restraints generated. 3164 Oldfield, 0 Emsley, 3164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 593 residues out of total 2798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 538 time to evaluate : 2.784 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: B 52 GLN cc_start: 0.8425 (tm-30) cc_final: 0.8213 (tm-30) REVERT: B 91 TYR cc_start: 0.8292 (OUTLIER) cc_final: 0.8088 (t80) REVERT: B 177 MET cc_start: -0.4566 (mmp) cc_final: -0.4910 (mmp) REVERT: B 277 LEU cc_start: 0.8432 (mm) cc_final: 0.8149 (mp) REVERT: B 353 TRP cc_start: 0.5935 (p90) cc_final: 0.5666 (p90) REVERT: B 355 ARG cc_start: 0.7387 (mpp-170) cc_final: 0.7117 (ttp80) REVERT: B 432 CYS cc_start: 0.2522 (OUTLIER) cc_final: 0.1367 (m) REVERT: B 498 GLN cc_start: 0.6729 (mm110) cc_final: 0.6182 (tp40) REVERT: B 773 GLU cc_start: 0.7470 (tt0) cc_final: 0.6707 (tt0) REVERT: B 820 ASP cc_start: 0.8139 (t0) cc_final: 0.7807 (t0) REVERT: B 902 MET cc_start: 0.7399 (OUTLIER) cc_final: 0.7138 (mmm) REVERT: B 1127 ASP cc_start: 0.7141 (t0) cc_final: 0.6725 (t0) REVERT: C 99 ASN cc_start: 0.8064 (m-40) cc_final: 0.7714 (p0) REVERT: C 140 PHE cc_start: 0.6985 (m-80) cc_final: 0.6681 (m-80) REVERT: C 238 PHE cc_start: 0.6805 (p90) cc_final: 0.6540 (p90) REVERT: C 239 GLN cc_start: 0.6875 (mm-40) cc_final: 0.6512 (mm-40) REVERT: C 324 GLU cc_start: 0.5856 (pp20) cc_final: 0.5584 (pp20) REVERT: C 353 TRP cc_start: 0.4779 (p-90) cc_final: 0.4563 (p-90) REVERT: C 355 ARG cc_start: 0.6177 (tpp-160) cc_final: 0.5618 (tpp-160) REVERT: C 441 LEU cc_start: 0.6708 (mt) cc_final: 0.6014 (tt) REVERT: C 515 PHE cc_start: 0.7059 (p90) cc_final: 0.6576 (p90) REVERT: C 559 PHE cc_start: 0.7092 (m-80) cc_final: 0.6680 (m-80) REVERT: C 646 ARG cc_start: 0.8008 (mpp80) cc_final: 0.7783 (ttm-80) REVERT: C 745 ASP cc_start: 0.6584 (t0) cc_final: 0.6220 (t0) REVERT: C 776 LYS cc_start: 0.8646 (ttmt) cc_final: 0.8312 (ttmt) REVERT: C 804 GLN cc_start: 0.8424 (mm-40) cc_final: 0.8105 (mm110) REVERT: C 960 ASN cc_start: 0.8087 (t0) cc_final: 0.7847 (t0) REVERT: C 1017 GLU cc_start: 0.8007 (tm-30) cc_final: 0.7792 (tm-30) REVERT: C 1073 LYS cc_start: 0.8235 (tmtt) cc_final: 0.8033 (mtpt) REVERT: A 34 ARG cc_start: 0.5810 (mtp85) cc_final: 0.5588 (mmt90) REVERT: A 40 ASP cc_start: 0.7378 (t70) cc_final: 0.7118 (t0) REVERT: A 53 ASP cc_start: 0.7457 (t0) cc_final: 0.6920 (t0) REVERT: A 55 PHE cc_start: 0.7335 (m-80) cc_final: 0.6991 (m-80) REVERT: A 86 PHE cc_start: 0.7698 (t80) cc_final: 0.7408 (t80) REVERT: A 133 PHE cc_start: 0.6152 (m-80) cc_final: 0.5317 (m-80) REVERT: A 177 MET cc_start: -0.3541 (mtp) cc_final: -0.4184 (mtt) REVERT: A 189 LEU cc_start: 0.8731 (tp) cc_final: 0.8494 (tp) REVERT: A 190 ARG cc_start: 0.6523 (mtt180) cc_final: 0.5911 (mtt180) REVERT: A 196 ASN cc_start: 0.7910 (p0) cc_final: 0.7698 (p0) REVERT: A 201 PHE cc_start: 0.6725 (t80) cc_final: 0.6006 (t80) REVERT: A 356 LYS cc_start: 0.8470 (OUTLIER) cc_final: 0.8266 (tttm) REVERT: A 390 LEU cc_start: 0.8217 (pp) cc_final: 0.7843 (pp) REVERT: A 400 PHE cc_start: 0.6943 (p90) cc_final: 0.6599 (p90) REVERT: A 528 LYS cc_start: 0.8205 (mmtm) cc_final: 0.7969 (mptt) REVERT: A 556 ASN cc_start: 0.7577 (t0) cc_final: 0.7329 (t0) REVERT: A 606 ASN cc_start: 0.8538 (m-40) cc_final: 0.8325 (m-40) REVERT: A 607 GLN cc_start: 0.8021 (mp10) cc_final: 0.7416 (mp10) REVERT: A 643 PHE cc_start: 0.8278 (t80) cc_final: 0.8055 (t80) REVERT: A 646 ARG cc_start: 0.7531 (mpp80) cc_final: 0.7103 (mpp80) REVERT: A 651 ILE cc_start: 0.8697 (tt) cc_final: 0.8473 (pt) REVERT: A 675 GLN cc_start: 0.7302 (tm-30) cc_final: 0.7081 (tm-30) REVERT: A 779 GLN cc_start: 0.8033 (OUTLIER) cc_final: 0.7461 (mp10) REVERT: A 820 ASP cc_start: 0.7841 (m-30) cc_final: 0.7630 (m-30) REVERT: A 869 MET cc_start: 0.8250 (mtt) cc_final: 0.7994 (mtt) REVERT: A 900 MET cc_start: 0.8353 (mtm) cc_final: 0.8112 (mtm) REVERT: A 918 GLU cc_start: 0.7936 (OUTLIER) cc_final: 0.7681 (mp0) REVERT: A 973 ILE cc_start: 0.9145 (tt) cc_final: 0.8891 (pt) REVERT: A 1030 SER cc_start: 0.8867 (m) cc_final: 0.8612 (t) REVERT: A 1111 GLU cc_start: 0.7667 (pm20) cc_final: 0.6876 (pm20) outliers start: 55 outliers final: 24 residues processed: 563 average time/residue: 0.4163 time to fit residues: 357.6661 Evaluate side-chains 521 residues out of total 2798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 491 time to evaluate : 2.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 91 TYR Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 196 ASN Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 974 SER Chi-restraints excluded: chain B residue 1101 HIS Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 895 GLN Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 356 LYS Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 779 GLN Chi-restraints excluded: chain A residue 918 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 160 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 241 optimal weight: 0.6980 chunk 197 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 290 optimal weight: 0.9980 chunk 313 optimal weight: 0.8980 chunk 258 optimal weight: 6.9990 chunk 287 optimal weight: 2.9990 chunk 98 optimal weight: 0.8980 chunk 232 optimal weight: 2.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 394 ASN B 563 GLN B 969 ASN B1023 ASN C 239 GLN C 657 ASN C 764 ASN C 901 GLN C 928 ASN C1002 GLN A 99 ASN ** A 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 448 ASN A 450 ASN A1083 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7394 moved from start: 0.2776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 25662 Z= 0.240 Angle : 0.575 12.180 34902 Z= 0.294 Chirality : 0.045 0.290 3936 Planarity : 0.004 0.052 4529 Dihedral : 4.137 20.902 3440 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.68 % Allowed : 14.94 % Favored : 82.38 % 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: -2.43 (0.13), residues: 3164 helix: -1.25 (0.20), residues: 615 sheet: -0.76 (0.19), residues: 669 loop : -2.14 (0.12), residues: 1880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 258 HIS 0.006 0.001 HIS B1083 PHE 0.025 0.002 PHE B 374 TYR 0.031 0.001 TYR A 421 ARG 0.008 0.001 ARG A1091 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6328 Ramachandran restraints generated. 3164 Oldfield, 0 Emsley, 3164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6328 Ramachandran restraints generated. 3164 Oldfield, 0 Emsley, 3164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 589 residues out of total 2798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 514 time to evaluate : 2.583 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 52 GLN cc_start: 0.8506 (tm-30) cc_final: 0.8267 (tm-30) REVERT: B 177 MET cc_start: -0.4369 (mmp) cc_final: -0.4902 (mmp) REVERT: B 244 LEU cc_start: 0.2950 (OUTLIER) cc_final: 0.2437 (pt) REVERT: B 277 LEU cc_start: 0.8470 (mm) cc_final: 0.8178 (mp) REVERT: B 353 TRP cc_start: 0.6195 (p90) cc_final: 0.5769 (p90) REVERT: B 355 ARG cc_start: 0.7581 (mpp-170) cc_final: 0.7038 (ttp80) REVERT: B 432 CYS cc_start: 0.2379 (OUTLIER) cc_final: 0.1149 (m) REVERT: B 498 GLN cc_start: 0.6767 (mm110) cc_final: 0.6288 (tp-100) REVERT: B 560 LEU cc_start: 0.8230 (tp) cc_final: 0.7871 (tp) REVERT: B 820 ASP cc_start: 0.8185 (t0) cc_final: 0.7901 (t0) REVERT: B 902 MET cc_start: 0.7503 (OUTLIER) cc_final: 0.7232 (mmm) REVERT: B 1127 ASP cc_start: 0.7183 (t0) cc_final: 0.6777 (t0) REVERT: C 99 ASN cc_start: 0.7999 (m-40) cc_final: 0.7742 (p0) REVERT: C 140 PHE cc_start: 0.7083 (m-80) cc_final: 0.6808 (m-80) REVERT: C 192 PHE cc_start: 0.7080 (m-80) cc_final: 0.6746 (m-80) REVERT: C 238 PHE cc_start: 0.6758 (p90) cc_final: 0.6499 (p90) REVERT: C 239 GLN cc_start: 0.6769 (OUTLIER) cc_final: 0.6410 (mm-40) REVERT: C 441 LEU cc_start: 0.6680 (mt) cc_final: 0.6037 (tt) REVERT: C 497 PHE cc_start: 0.3095 (m-80) cc_final: 0.2676 (m-80) REVERT: C 646 ARG cc_start: 0.8012 (mpp80) cc_final: 0.7800 (ttm-80) REVERT: C 745 ASP cc_start: 0.6746 (t0) cc_final: 0.6399 (t0) REVERT: C 776 LYS cc_start: 0.8593 (ttmt) cc_final: 0.8326 (ttpp) REVERT: C 779 GLN cc_start: 0.8130 (tt0) cc_final: 0.7883 (tm-30) REVERT: C 804 GLN cc_start: 0.8471 (mm-40) cc_final: 0.8082 (mm110) REVERT: C 896 ILE cc_start: 0.8313 (mt) cc_final: 0.7996 (tt) REVERT: C 960 ASN cc_start: 0.8144 (t0) cc_final: 0.7944 (t0) REVERT: C 1005 GLN cc_start: 0.8004 (mm-40) cc_final: 0.7649 (mt0) REVERT: C 1073 LYS cc_start: 0.8240 (tmtt) cc_final: 0.7995 (mtpt) REVERT: A 34 ARG cc_start: 0.5929 (mtp85) cc_final: 0.5716 (mmt90) REVERT: A 40 ASP cc_start: 0.7527 (t70) cc_final: 0.7248 (t0) REVERT: A 86 PHE cc_start: 0.7879 (t80) cc_final: 0.7595 (t80) REVERT: A 104 TRP cc_start: 0.7606 (m-90) cc_final: 0.7351 (m-90) REVERT: A 177 MET cc_start: -0.3647 (mtp) cc_final: -0.4341 (mtt) REVERT: A 189 LEU cc_start: 0.8754 (tp) cc_final: 0.8521 (tp) REVERT: A 190 ARG cc_start: 0.6578 (mtt180) cc_final: 0.5964 (mtt180) REVERT: A 195 LYS cc_start: 0.7533 (mmmt) cc_final: 0.7084 (mmmt) REVERT: A 196 ASN cc_start: 0.7751 (p0) cc_final: 0.7501 (p0) REVERT: A 201 PHE cc_start: 0.6713 (t80) cc_final: 0.5936 (t80) REVERT: A 390 LEU cc_start: 0.8299 (OUTLIER) cc_final: 0.8020 (pp) REVERT: A 400 PHE cc_start: 0.7019 (p90) cc_final: 0.6641 (p90) REVERT: A 495 TYR cc_start: 0.7603 (m-80) cc_final: 0.7299 (t80) REVERT: A 513 LEU cc_start: 0.7785 (mt) cc_final: 0.7496 (mp) REVERT: A 556 ASN cc_start: 0.7692 (t0) cc_final: 0.7456 (t0) REVERT: A 607 GLN cc_start: 0.8084 (mp10) cc_final: 0.7500 (mp10) REVERT: A 900 MET cc_start: 0.8451 (mtm) cc_final: 0.8161 (mtm) REVERT: A 918 GLU cc_start: 0.7893 (OUTLIER) cc_final: 0.7607 (mp0) REVERT: A 994 ASP cc_start: 0.7824 (t0) cc_final: 0.7525 (t0) outliers start: 75 outliers final: 45 residues processed: 553 average time/residue: 0.3828 time to fit residues: 326.0148 Evaluate side-chains 546 residues out of total 2798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 495 time to evaluate : 2.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 ASN Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 721 SER Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 779 GLN Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 239 GLN Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 451 TYR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 816 SER Chi-restraints excluded: chain C residue 895 GLN Chi-restraints excluded: chain C residue 933 LYS Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 306 PHE Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 356 LYS Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 535 LYS Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 918 GLU Chi-restraints excluded: chain A residue 1083 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 286 optimal weight: 0.9990 chunk 218 optimal weight: 0.5980 chunk 150 optimal weight: 9.9990 chunk 32 optimal weight: 3.9990 chunk 138 optimal weight: 6.9990 chunk 194 optimal weight: 2.9990 chunk 291 optimal weight: 0.9980 chunk 308 optimal weight: 2.9990 chunk 152 optimal weight: 2.9990 chunk 276 optimal weight: 0.9980 chunk 83 optimal weight: 0.8980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 422 ASN B 544 ASN B 787 GLN B 969 ASN C 655 HIS C 928 ASN C 955 ASN ** A 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 655 HIS A 969 ASN A1005 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7398 moved from start: 0.3093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 25662 Z= 0.206 Angle : 0.553 9.113 34902 Z= 0.283 Chirality : 0.045 0.264 3936 Planarity : 0.004 0.049 4529 Dihedral : 4.119 18.550 3440 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 2.50 % Allowed : 16.76 % Favored : 80.74 % 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: -2.08 (0.14), residues: 3164 helix: -0.59 (0.21), residues: 623 sheet: -0.60 (0.19), residues: 667 loop : -2.04 (0.13), residues: 1874 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 258 HIS 0.009 0.001 HIS A1083 PHE 0.020 0.001 PHE A 643 TYR 0.028 0.001 TYR C1138 ARG 0.016 0.001 ARG C 190 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6328 Ramachandran restraints generated. 3164 Oldfield, 0 Emsley, 3164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6328 Ramachandran restraints generated. 3164 Oldfield, 0 Emsley, 3164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 580 residues out of total 2798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 510 time to evaluate : 2.656 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: B 52 GLN cc_start: 0.8508 (tm-30) cc_final: 0.8264 (tm-30) REVERT: B 177 MET cc_start: -0.4318 (mmp) cc_final: -0.4885 (mmt) REVERT: B 244 LEU cc_start: 0.3232 (OUTLIER) cc_final: 0.2804 (pt) REVERT: B 277 LEU cc_start: 0.8480 (mm) cc_final: 0.8188 (mp) REVERT: B 353 TRP cc_start: 0.6118 (p90) cc_final: 0.5704 (p90) REVERT: B 355 ARG cc_start: 0.7653 (mpp-170) cc_final: 0.7222 (ttp80) REVERT: B 432 CYS cc_start: 0.2112 (OUTLIER) cc_final: 0.0831 (m) REVERT: B 498 GLN cc_start: 0.6740 (mm110) cc_final: 0.6127 (tp-100) REVERT: B 773 GLU cc_start: 0.7916 (tp30) cc_final: 0.7424 (tp30) REVERT: B 776 LYS cc_start: 0.8428 (ttpp) cc_final: 0.8044 (ttpp) REVERT: B 820 ASP cc_start: 0.8184 (t0) cc_final: 0.7929 (t0) REVERT: B 1127 ASP cc_start: 0.7159 (t0) cc_final: 0.6740 (t0) REVERT: C 99 ASN cc_start: 0.8027 (m-40) cc_final: 0.7793 (p0) REVERT: C 120 VAL cc_start: 0.8607 (m) cc_final: 0.8222 (p) REVERT: C 192 PHE cc_start: 0.7015 (m-80) cc_final: 0.6780 (m-80) REVERT: C 238 PHE cc_start: 0.6891 (p90) cc_final: 0.6551 (p90) REVERT: C 353 TRP cc_start: 0.5013 (p-90) cc_final: 0.4618 (p-90) REVERT: C 355 ARG cc_start: 0.6367 (tpp-160) cc_final: 0.5578 (tpp80) REVERT: C 441 LEU cc_start: 0.6539 (mt) cc_final: 0.5868 (tt) REVERT: C 497 PHE cc_start: 0.3231 (m-80) cc_final: 0.3008 (m-80) REVERT: C 646 ARG cc_start: 0.8020 (mpp80) cc_final: 0.7803 (ttm-80) REVERT: C 745 ASP cc_start: 0.6932 (t0) cc_final: 0.6595 (t0) REVERT: C 776 LYS cc_start: 0.8618 (ttmt) cc_final: 0.8345 (ttpp) REVERT: C 779 GLN cc_start: 0.8186 (tt0) cc_final: 0.7926 (tm-30) REVERT: C 804 GLN cc_start: 0.8424 (mm-40) cc_final: 0.8072 (mm-40) REVERT: C 896 ILE cc_start: 0.8325 (mt) cc_final: 0.7999 (tt) REVERT: C 1005 GLN cc_start: 0.7933 (mm-40) cc_final: 0.7642 (mt0) REVERT: C 1073 LYS cc_start: 0.8236 (tmtt) cc_final: 0.7997 (mtpt) REVERT: C 1139 ASP cc_start: 0.7771 (t0) cc_final: 0.7519 (t0) REVERT: A 40 ASP cc_start: 0.7561 (t70) cc_final: 0.7345 (t0) REVERT: A 53 ASP cc_start: 0.7514 (t0) cc_final: 0.7286 (t70) REVERT: A 55 PHE cc_start: 0.7513 (m-80) cc_final: 0.7093 (m-80) REVERT: A 86 PHE cc_start: 0.7816 (t80) cc_final: 0.7526 (t80) REVERT: A 133 PHE cc_start: 0.6317 (m-80) cc_final: 0.5197 (m-80) REVERT: A 177 MET cc_start: -0.3598 (mtp) cc_final: -0.4261 (mtt) REVERT: A 189 LEU cc_start: 0.8680 (tp) cc_final: 0.8460 (tp) REVERT: A 190 ARG cc_start: 0.6574 (mtt180) cc_final: 0.6087 (mtt180) REVERT: A 195 LYS cc_start: 0.7500 (mmmt) cc_final: 0.7296 (mmmt) REVERT: A 196 ASN cc_start: 0.7746 (p0) cc_final: 0.7377 (p0) REVERT: A 201 PHE cc_start: 0.6691 (t80) cc_final: 0.5969 (t80) REVERT: A 390 LEU cc_start: 0.8288 (OUTLIER) cc_final: 0.7913 (pp) REVERT: A 400 PHE cc_start: 0.6943 (p90) cc_final: 0.6621 (p90) REVERT: A 495 TYR cc_start: 0.7499 (m-80) cc_final: 0.7258 (t80) REVERT: A 513 LEU cc_start: 0.7761 (mt) cc_final: 0.7481 (mp) REVERT: A 556 ASN cc_start: 0.7750 (t0) cc_final: 0.7504 (t0) REVERT: A 607 GLN cc_start: 0.8044 (mp10) cc_final: 0.7429 (mp10) REVERT: A 900 MET cc_start: 0.8479 (mtm) cc_final: 0.8198 (mtm) REVERT: A 994 ASP cc_start: 0.7715 (t0) cc_final: 0.7470 (t0) outliers start: 70 outliers final: 46 residues processed: 551 average time/residue: 0.3847 time to fit residues: 326.8768 Evaluate side-chains 535 residues out of total 2798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 486 time to evaluate : 2.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 ASN Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 563 GLN Chi-restraints excluded: chain B residue 721 SER Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 451 TYR Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 654 GLU Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 895 GLN Chi-restraints excluded: chain C residue 933 LYS Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 306 PHE Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 409 GLN Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 973 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 256 optimal weight: 3.9990 chunk 175 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 229 optimal weight: 0.0270 chunk 127 optimal weight: 3.9990 chunk 263 optimal weight: 0.8980 chunk 213 optimal weight: 0.0370 chunk 0 optimal weight: 9.9990 chunk 157 optimal weight: 0.0060 chunk 276 optimal weight: 0.6980 chunk 77 optimal weight: 4.9990 overall best weight: 0.3332 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 690 GLN B 709 ASN B1106 GLN ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 928 ASN A 125 ASN A 914 ASN A 969 ASN A1005 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7360 moved from start: 0.3240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 25662 Z= 0.142 Angle : 0.543 14.394 34902 Z= 0.274 Chirality : 0.044 0.242 3936 Planarity : 0.004 0.052 4529 Dihedral : 3.986 20.294 3440 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.86 % Allowed : 17.55 % Favored : 79.59 % 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: -1.74 (0.14), residues: 3164 helix: 0.02 (0.22), residues: 611 sheet: -0.45 (0.19), residues: 654 loop : -1.90 (0.13), residues: 1899 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 104 HIS 0.005 0.001 HIS A 655 PHE 0.023 0.001 PHE A 374 TYR 0.026 0.001 TYR C1138 ARG 0.012 0.001 ARG C 190 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6328 Ramachandran restraints generated. 3164 Oldfield, 0 Emsley, 3164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6328 Ramachandran restraints generated. 3164 Oldfield, 0 Emsley, 3164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 560 residues out of total 2798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 480 time to evaluate : 2.734 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 52 GLN cc_start: 0.8469 (tm-30) cc_final: 0.8262 (tm-30) REVERT: B 177 MET cc_start: -0.4348 (mmp) cc_final: -0.4907 (mmt) REVERT: B 277 LEU cc_start: 0.8469 (mm) cc_final: 0.8166 (mp) REVERT: B 353 TRP cc_start: 0.5868 (p90) cc_final: 0.5449 (p90) REVERT: B 355 ARG cc_start: 0.7620 (mpp-170) cc_final: 0.7209 (ttp80) REVERT: B 432 CYS cc_start: 0.2179 (OUTLIER) cc_final: 0.0751 (m) REVERT: B 498 GLN cc_start: 0.6717 (mm110) cc_final: 0.6103 (tp-100) REVERT: B 760 CYS cc_start: 0.5542 (m) cc_final: 0.5138 (m) REVERT: B 773 GLU cc_start: 0.7846 (tp30) cc_final: 0.7317 (tp30) REVERT: B 776 LYS cc_start: 0.8403 (ttpp) cc_final: 0.8044 (ttpp) REVERT: B 820 ASP cc_start: 0.8193 (t0) cc_final: 0.7933 (t0) REVERT: B 1127 ASP cc_start: 0.7105 (t0) cc_final: 0.6656 (t0) REVERT: C 99 ASN cc_start: 0.8057 (m-40) cc_final: 0.7818 (p0) REVERT: C 120 VAL cc_start: 0.8615 (m) cc_final: 0.8392 (p) REVERT: C 192 PHE cc_start: 0.6998 (m-80) cc_final: 0.6720 (m-80) REVERT: C 238 PHE cc_start: 0.6775 (p90) cc_final: 0.6524 (p90) REVERT: C 353 TRP cc_start: 0.5029 (p-90) cc_final: 0.4637 (p-90) REVERT: C 441 LEU cc_start: 0.6498 (mt) cc_final: 0.5844 (tt) REVERT: C 497 PHE cc_start: 0.3227 (m-80) cc_final: 0.2983 (m-80) REVERT: C 646 ARG cc_start: 0.8015 (mpp80) cc_final: 0.7779 (ttm-80) REVERT: C 745 ASP cc_start: 0.6964 (t0) cc_final: 0.6625 (t0) REVERT: C 776 LYS cc_start: 0.8605 (ttmt) cc_final: 0.8332 (ttpp) REVERT: C 779 GLN cc_start: 0.8210 (tt0) cc_final: 0.7942 (tm-30) REVERT: C 896 ILE cc_start: 0.8295 (mt) cc_final: 0.7967 (tt) REVERT: C 1005 GLN cc_start: 0.7873 (mm-40) cc_final: 0.7621 (mt0) REVERT: C 1073 LYS cc_start: 0.8225 (tmtt) cc_final: 0.7978 (mtpt) REVERT: C 1139 ASP cc_start: 0.7755 (t0) cc_final: 0.7466 (t0) REVERT: A 40 ASP cc_start: 0.7515 (t70) cc_final: 0.7299 (t0) REVERT: A 55 PHE cc_start: 0.7418 (m-80) cc_final: 0.6923 (m-80) REVERT: A 86 PHE cc_start: 0.7809 (t80) cc_final: 0.7546 (t80) REVERT: A 133 PHE cc_start: 0.6282 (m-80) cc_final: 0.5147 (m-80) REVERT: A 177 MET cc_start: -0.3637 (mtp) cc_final: -0.4189 (mtt) REVERT: A 190 ARG cc_start: 0.6523 (mtt180) cc_final: 0.6034 (mtt180) REVERT: A 201 PHE cc_start: 0.6635 (t80) cc_final: 0.5950 (t80) REVERT: A 281 GLU cc_start: 0.7267 (pm20) cc_final: 0.6887 (pp20) REVERT: A 390 LEU cc_start: 0.8242 (OUTLIER) cc_final: 0.8011 (pp) REVERT: A 400 PHE cc_start: 0.6857 (p90) cc_final: 0.6524 (p90) REVERT: A 900 MET cc_start: 0.8449 (mtm) cc_final: 0.8171 (mtm) REVERT: A 994 ASP cc_start: 0.7624 (t0) cc_final: 0.7389 (t0) outliers start: 80 outliers final: 53 residues processed: 530 average time/residue: 0.3941 time to fit residues: 323.2930 Evaluate side-chains 525 residues out of total 2798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 470 time to evaluate : 2.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 ASN Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 563 GLN Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 451 TYR Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 610 VAL Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 895 GLN Chi-restraints excluded: chain C residue 933 LYS Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 306 PHE Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 356 LYS Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 409 GLN Chi-restraints excluded: chain A residue 490 PHE Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 973 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 103 optimal weight: 2.9990 chunk 277 optimal weight: 3.9990 chunk 60 optimal weight: 0.0470 chunk 181 optimal weight: 0.7980 chunk 76 optimal weight: 2.9990 chunk 308 optimal weight: 0.7980 chunk 256 optimal weight: 0.7980 chunk 142 optimal weight: 8.9990 chunk 25 optimal weight: 5.9990 chunk 102 optimal weight: 0.5980 chunk 162 optimal weight: 2.9990 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 969 ASN ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 928 ASN A 969 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7374 moved from start: 0.3412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 25662 Z= 0.166 Angle : 0.540 8.465 34902 Z= 0.274 Chirality : 0.044 0.235 3936 Planarity : 0.004 0.042 4529 Dihedral : 3.920 20.766 3440 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 2.57 % Allowed : 18.37 % Favored : 79.06 % 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: -1.60 (0.14), residues: 3164 helix: 0.27 (0.22), residues: 619 sheet: -0.41 (0.20), residues: 640 loop : -1.84 (0.13), residues: 1905 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 258 HIS 0.010 0.001 HIS A 655 PHE 0.033 0.001 PHE C 306 TYR 0.023 0.001 TYR C1138 ARG 0.008 0.001 ARG C 190 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6328 Ramachandran restraints generated. 3164 Oldfield, 0 Emsley, 3164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6328 Ramachandran restraints generated. 3164 Oldfield, 0 Emsley, 3164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 555 residues out of total 2798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 483 time to evaluate : 2.859 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 52 GLN cc_start: 0.8458 (tm-30) cc_final: 0.8253 (tm-30) REVERT: B 177 MET cc_start: -0.4207 (mmp) cc_final: -0.4834 (mmt) REVERT: B 277 LEU cc_start: 0.8487 (mm) cc_final: 0.8190 (mp) REVERT: B 324 GLU cc_start: 0.7806 (mm-30) cc_final: 0.7583 (mm-30) REVERT: B 353 TRP cc_start: 0.5922 (p90) cc_final: 0.5569 (p90) REVERT: B 355 ARG cc_start: 0.7685 (mpp-170) cc_final: 0.7260 (ttp80) REVERT: B 400 PHE cc_start: 0.8142 (p90) cc_final: 0.7769 (p90) REVERT: B 432 CYS cc_start: 0.2350 (OUTLIER) cc_final: 0.0846 (m) REVERT: B 498 GLN cc_start: 0.6693 (mm110) cc_final: 0.5991 (tp40) REVERT: B 760 CYS cc_start: 0.5589 (m) cc_final: 0.5221 (m) REVERT: B 773 GLU cc_start: 0.7820 (tp30) cc_final: 0.7364 (tp30) REVERT: B 776 LYS cc_start: 0.8376 (ttpp) cc_final: 0.8018 (ttpp) REVERT: B 820 ASP cc_start: 0.8180 (t0) cc_final: 0.7950 (t0) REVERT: B 1127 ASP cc_start: 0.7147 (t0) cc_final: 0.6701 (t0) REVERT: C 99 ASN cc_start: 0.8075 (m-40) cc_final: 0.7855 (p0) REVERT: C 120 VAL cc_start: 0.8634 (m) cc_final: 0.8290 (p) REVERT: C 238 PHE cc_start: 0.6691 (p90) cc_final: 0.6471 (p90) REVERT: C 441 LEU cc_start: 0.6385 (mt) cc_final: 0.5750 (tt) REVERT: C 497 PHE cc_start: 0.3353 (m-80) cc_final: 0.3083 (m-80) REVERT: C 646 ARG cc_start: 0.8027 (mpp80) cc_final: 0.7790 (ttm-80) REVERT: C 745 ASP cc_start: 0.7085 (t0) cc_final: 0.6742 (t0) REVERT: C 779 GLN cc_start: 0.8216 (tt0) cc_final: 0.7950 (tm-30) REVERT: C 896 ILE cc_start: 0.8316 (mt) cc_final: 0.7976 (tt) REVERT: C 1005 GLN cc_start: 0.7876 (mm-40) cc_final: 0.7640 (mt0) REVERT: C 1073 LYS cc_start: 0.8226 (tmtt) cc_final: 0.7982 (mtpt) REVERT: C 1139 ASP cc_start: 0.7802 (t0) cc_final: 0.7514 (t0) REVERT: A 40 ASP cc_start: 0.7625 (t70) cc_final: 0.7376 (t0) REVERT: A 133 PHE cc_start: 0.6447 (m-80) cc_final: 0.5320 (m-80) REVERT: A 195 LYS cc_start: 0.7520 (mmmt) cc_final: 0.6755 (mmmt) REVERT: A 201 PHE cc_start: 0.6579 (t80) cc_final: 0.5856 (t80) REVERT: A 281 GLU cc_start: 0.7436 (pm20) cc_final: 0.7017 (pp20) REVERT: A 390 LEU cc_start: 0.8275 (OUTLIER) cc_final: 0.8021 (pp) REVERT: A 400 PHE cc_start: 0.6898 (p90) cc_final: 0.6544 (p90) REVERT: A 495 TYR cc_start: 0.6917 (OUTLIER) cc_final: 0.6272 (t80) REVERT: A 580 GLN cc_start: 0.6403 (tp40) cc_final: 0.5873 (tp40) REVERT: A 607 GLN cc_start: 0.7985 (mp10) cc_final: 0.7323 (mp10) REVERT: A 814 LYS cc_start: 0.8306 (mmtt) cc_final: 0.7815 (mmmt) REVERT: A 900 MET cc_start: 0.8481 (mtm) cc_final: 0.8170 (mtm) REVERT: A 994 ASP cc_start: 0.7613 (t0) cc_final: 0.7384 (t0) outliers start: 72 outliers final: 59 residues processed: 526 average time/residue: 0.3689 time to fit residues: 299.6745 Evaluate side-chains 534 residues out of total 2798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 472 time to evaluate : 2.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 ASN Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 563 GLN Chi-restraints excluded: chain B residue 721 SER Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 1101 HIS Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 451 TYR Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 610 VAL Chi-restraints excluded: chain C residue 651 ILE Chi-restraints excluded: chain C residue 654 GLU Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 819 GLU Chi-restraints excluded: chain C residue 895 GLN Chi-restraints excluded: chain C residue 933 LYS Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 306 PHE Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 409 GLN Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 973 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 297 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 175 optimal weight: 0.8980 chunk 225 optimal weight: 5.9990 chunk 174 optimal weight: 0.0970 chunk 259 optimal weight: 0.4980 chunk 172 optimal weight: 0.9990 chunk 307 optimal weight: 0.0670 chunk 192 optimal weight: 2.9990 chunk 187 optimal weight: 0.8980 chunk 141 optimal weight: 0.9980 overall best weight: 0.4916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 969 ASN ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 928 ASN A 99 ASN A 655 HIS A 779 GLN A 969 ASN A1002 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7365 moved from start: 0.3559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 25662 Z= 0.155 Angle : 0.544 14.154 34902 Z= 0.273 Chirality : 0.044 0.217 3936 Planarity : 0.004 0.040 4529 Dihedral : 3.830 21.071 3440 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 2.68 % Allowed : 19.09 % 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: -1.44 (0.14), residues: 3164 helix: 0.60 (0.22), residues: 618 sheet: -0.35 (0.19), residues: 641 loop : -1.79 (0.13), residues: 1905 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A 104 HIS 0.005 0.001 HIS A 655 PHE 0.028 0.001 PHE C 306 TYR 0.020 0.001 TYR C1138 ARG 0.008 0.001 ARG A 995 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6328 Ramachandran restraints generated. 3164 Oldfield, 0 Emsley, 3164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6328 Ramachandran restraints generated. 3164 Oldfield, 0 Emsley, 3164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 558 residues out of total 2798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 483 time to evaluate : 2.518 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 159 VAL cc_start: 0.7518 (OUTLIER) cc_final: 0.7272 (m) REVERT: B 177 MET cc_start: -0.4248 (mmp) cc_final: -0.4871 (mmt) REVERT: B 277 LEU cc_start: 0.8508 (mm) cc_final: 0.8208 (mp) REVERT: B 353 TRP cc_start: 0.5850 (p90) cc_final: 0.5501 (p90) REVERT: B 355 ARG cc_start: 0.7661 (mpp-170) cc_final: 0.7223 (ttp80) REVERT: B 400 PHE cc_start: 0.8111 (p90) cc_final: 0.7772 (p90) REVERT: B 432 CYS cc_start: 0.2484 (OUTLIER) cc_final: 0.0930 (m) REVERT: B 498 GLN cc_start: 0.6678 (mm110) cc_final: 0.5981 (tp40) REVERT: B 760 CYS cc_start: 0.5540 (m) cc_final: 0.5196 (m) REVERT: B 773 GLU cc_start: 0.7818 (tp30) cc_final: 0.7244 (tp30) REVERT: B 776 LYS cc_start: 0.8351 (ttpp) cc_final: 0.7943 (ttpp) REVERT: B 820 ASP cc_start: 0.8153 (t0) cc_final: 0.7951 (t0) REVERT: B 979 ASP cc_start: 0.7829 (t0) cc_final: 0.7626 (t0) REVERT: B 1127 ASP cc_start: 0.7069 (t0) cc_final: 0.6658 (t0) REVERT: C 99 ASN cc_start: 0.8104 (m-40) cc_final: 0.7898 (p0) REVERT: C 102 ARG cc_start: 0.7263 (mmm160) cc_final: 0.6798 (mmm160) REVERT: C 120 VAL cc_start: 0.8658 (m) cc_final: 0.8332 (p) REVERT: C 294 ASP cc_start: 0.7101 (p0) cc_final: 0.6346 (p0) REVERT: C 353 TRP cc_start: 0.5037 (p-90) cc_final: 0.4560 (p-90) REVERT: C 441 LEU cc_start: 0.6318 (mt) cc_final: 0.5680 (tt) REVERT: C 497 PHE cc_start: 0.3505 (m-80) cc_final: 0.3189 (m-80) REVERT: C 646 ARG cc_start: 0.8012 (mpp80) cc_final: 0.7783 (ttm-80) REVERT: C 745 ASP cc_start: 0.7078 (t0) cc_final: 0.6770 (t0) REVERT: C 779 GLN cc_start: 0.8215 (tt0) cc_final: 0.7948 (tm-30) REVERT: C 896 ILE cc_start: 0.8316 (mt) cc_final: 0.7975 (tt) REVERT: C 1005 GLN cc_start: 0.7887 (mm-40) cc_final: 0.7632 (mt0) REVERT: C 1073 LYS cc_start: 0.8234 (tmtt) cc_final: 0.8013 (mtpt) REVERT: C 1092 GLU cc_start: 0.7198 (pm20) cc_final: 0.6986 (pm20) REVERT: C 1139 ASP cc_start: 0.7797 (t0) cc_final: 0.7519 (t0) REVERT: A 55 PHE cc_start: 0.7292 (m-80) cc_final: 0.7052 (m-10) REVERT: A 104 TRP cc_start: 0.7532 (m-90) cc_final: 0.7267 (m-90) REVERT: A 133 PHE cc_start: 0.6412 (m-80) cc_final: 0.5325 (m-80) REVERT: A 195 LYS cc_start: 0.7432 (mmmt) cc_final: 0.7065 (mmmt) REVERT: A 201 PHE cc_start: 0.6548 (t80) cc_final: 0.5821 (t80) REVERT: A 281 GLU cc_start: 0.7557 (pm20) cc_final: 0.7071 (pp20) REVERT: A 390 LEU cc_start: 0.8308 (OUTLIER) cc_final: 0.8029 (pp) REVERT: A 400 PHE cc_start: 0.6879 (p90) cc_final: 0.6508 (p90) REVERT: A 495 TYR cc_start: 0.6973 (OUTLIER) cc_final: 0.6228 (t80) REVERT: A 580 GLN cc_start: 0.6433 (tp40) cc_final: 0.5963 (tp40) REVERT: A 607 GLN cc_start: 0.7964 (mp10) cc_final: 0.7359 (mp10) REVERT: A 814 LYS cc_start: 0.8318 (mmtt) cc_final: 0.7803 (mmmt) REVERT: A 896 ILE cc_start: 0.7663 (mt) cc_final: 0.7450 (tt) REVERT: A 900 MET cc_start: 0.8490 (mtm) cc_final: 0.8206 (mtm) REVERT: A 1002 GLN cc_start: 0.7687 (OUTLIER) cc_final: 0.7454 (mp10) outliers start: 75 outliers final: 59 residues processed: 526 average time/residue: 0.3827 time to fit residues: 312.7177 Evaluate side-chains 536 residues out of total 2798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 472 time to evaluate : 2.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 ASN Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 721 SER Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 974 SER Chi-restraints excluded: chain B residue 1101 HIS Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 451 TYR Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 610 VAL Chi-restraints excluded: chain C residue 651 ILE Chi-restraints excluded: chain C residue 654 GLU Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 819 GLU Chi-restraints excluded: chain C residue 895 GLN Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 1051 SER Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 306 PHE Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 1002 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 190 optimal weight: 2.9990 chunk 122 optimal weight: 10.0000 chunk 183 optimal weight: 4.9990 chunk 92 optimal weight: 1.9990 chunk 60 optimal weight: 0.7980 chunk 59 optimal weight: 2.9990 chunk 195 optimal weight: 2.9990 chunk 209 optimal weight: 1.9990 chunk 152 optimal weight: 6.9990 chunk 28 optimal weight: 0.0000 chunk 241 optimal weight: 0.1980 overall best weight: 0.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 787 GLN C 928 ASN ** A 655 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 969 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7415 moved from start: 0.3723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 25662 Z= 0.222 Angle : 0.577 12.701 34902 Z= 0.293 Chirality : 0.045 0.209 3936 Planarity : 0.004 0.052 4529 Dihedral : 3.973 21.056 3440 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 2.61 % Allowed : 19.59 % Favored : 77.81 % 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: -1.42 (0.14), residues: 3164 helix: 0.67 (0.22), residues: 619 sheet: -0.38 (0.19), residues: 647 loop : -1.79 (0.13), residues: 1898 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 353 HIS 0.004 0.001 HIS C1064 PHE 0.026 0.001 PHE C 306 TYR 0.028 0.001 TYR C1138 ARG 0.007 0.001 ARG C 190 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6328 Ramachandran restraints generated. 3164 Oldfield, 0 Emsley, 3164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6328 Ramachandran restraints generated. 3164 Oldfield, 0 Emsley, 3164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 556 residues out of total 2798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 483 time to evaluate : 2.458 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: B 159 VAL cc_start: 0.7634 (OUTLIER) cc_final: 0.7377 (m) REVERT: B 177 MET cc_start: -0.4110 (mmp) cc_final: -0.4821 (mmt) REVERT: B 277 LEU cc_start: 0.8528 (mm) cc_final: 0.8241 (mp) REVERT: B 353 TRP cc_start: 0.6081 (p90) cc_final: 0.5671 (p90) REVERT: B 400 PHE cc_start: 0.8167 (p90) cc_final: 0.7834 (p90) REVERT: B 432 CYS cc_start: 0.2487 (OUTLIER) cc_final: 0.0808 (m) REVERT: B 498 GLN cc_start: 0.6671 (mm110) cc_final: 0.6468 (mm-40) REVERT: B 563 GLN cc_start: 0.5201 (OUTLIER) cc_final: 0.4957 (tp40) REVERT: B 1127 ASP cc_start: 0.7167 (t0) cc_final: 0.6718 (t0) REVERT: C 99 ASN cc_start: 0.8137 (m-40) cc_final: 0.7931 (p0) REVERT: C 102 ARG cc_start: 0.7274 (mmm160) cc_final: 0.6820 (mmm160) REVERT: C 120 VAL cc_start: 0.8676 (m) cc_final: 0.8343 (p) REVERT: C 238 PHE cc_start: 0.6997 (p90) cc_final: 0.6537 (p90) REVERT: C 294 ASP cc_start: 0.6976 (p0) cc_final: 0.6257 (p0) REVERT: C 441 LEU cc_start: 0.6566 (mt) cc_final: 0.5880 (tt) REVERT: C 497 PHE cc_start: 0.3481 (m-80) cc_final: 0.3159 (m-80) REVERT: C 779 GLN cc_start: 0.8261 (tt0) cc_final: 0.7977 (tm-30) REVERT: C 1005 GLN cc_start: 0.7978 (mm-40) cc_final: 0.7692 (mt0) REVERT: C 1073 LYS cc_start: 0.8224 (tmtt) cc_final: 0.7963 (mtpt) REVERT: C 1139 ASP cc_start: 0.7768 (t0) cc_final: 0.7533 (t0) REVERT: A 104 TRP cc_start: 0.7590 (m-90) cc_final: 0.7171 (m-90) REVERT: A 133 PHE cc_start: 0.6500 (m-80) cc_final: 0.5365 (m-80) REVERT: A 190 ARG cc_start: 0.6655 (mtt180) cc_final: 0.6299 (mtt-85) REVERT: A 195 LYS cc_start: 0.7313 (mmmt) cc_final: 0.6413 (mmmt) REVERT: A 201 PHE cc_start: 0.6561 (t80) cc_final: 0.5825 (t80) REVERT: A 390 LEU cc_start: 0.8336 (OUTLIER) cc_final: 0.8056 (pp) REVERT: A 400 PHE cc_start: 0.6976 (p90) cc_final: 0.6599 (p90) REVERT: A 495 TYR cc_start: 0.7071 (OUTLIER) cc_final: 0.6337 (t80) REVERT: A 580 GLN cc_start: 0.6485 (tp40) cc_final: 0.6005 (tp40) REVERT: A 607 GLN cc_start: 0.8030 (mp10) cc_final: 0.7430 (mp10) REVERT: A 900 MET cc_start: 0.8540 (mtm) cc_final: 0.8277 (mtm) outliers start: 73 outliers final: 57 residues processed: 527 average time/residue: 0.3787 time to fit residues: 309.4012 Evaluate side-chains 538 residues out of total 2798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 476 time to evaluate : 2.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 ASN Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 563 GLN Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 721 SER Chi-restraints excluded: chain B residue 974 SER Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 451 TYR Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 610 VAL Chi-restraints excluded: chain C residue 651 ILE Chi-restraints excluded: chain C residue 654 GLU Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 819 GLU Chi-restraints excluded: chain C residue 895 GLN Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 1051 SER Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 306 PHE Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 973 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 279 optimal weight: 2.9990 chunk 294 optimal weight: 1.9990 chunk 268 optimal weight: 1.9990 chunk 286 optimal weight: 0.0970 chunk 172 optimal weight: 0.9990 chunk 124 optimal weight: 3.9990 chunk 224 optimal weight: 0.7980 chunk 87 optimal weight: 1.9990 chunk 258 optimal weight: 3.9990 chunk 270 optimal weight: 0.9980 chunk 285 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 969 ASN ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 928 ASN A 655 HIS A 969 ASN A1002 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7407 moved from start: 0.3868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 25662 Z= 0.194 Angle : 0.586 12.503 34902 Z= 0.296 Chirality : 0.045 0.196 3936 Planarity : 0.004 0.079 4529 Dihedral : 3.993 21.272 3440 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 2.36 % Allowed : 20.30 % Favored : 77.34 % 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: -1.33 (0.14), residues: 3164 helix: 0.77 (0.22), residues: 626 sheet: -0.35 (0.19), residues: 645 loop : -1.73 (0.13), residues: 1893 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 353 HIS 0.004 0.001 HIS B1083 PHE 0.041 0.001 PHE B 374 TYR 0.026 0.001 TYR C1138 ARG 0.008 0.001 ARG C 190 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6328 Ramachandran restraints generated. 3164 Oldfield, 0 Emsley, 3164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6328 Ramachandran restraints generated. 3164 Oldfield, 0 Emsley, 3164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 543 residues out of total 2798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 477 time to evaluate : 2.854 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 159 VAL cc_start: 0.7592 (OUTLIER) cc_final: 0.7326 (m) REVERT: B 177 MET cc_start: -0.4000 (mmp) cc_final: -0.4724 (mmt) REVERT: B 277 LEU cc_start: 0.8526 (mm) cc_final: 0.8243 (mp) REVERT: B 353 TRP cc_start: 0.6098 (p90) cc_final: 0.5628 (p90) REVERT: B 355 ARG cc_start: 0.7810 (mpp-170) cc_final: 0.7293 (ttp80) REVERT: B 400 PHE cc_start: 0.8152 (p90) cc_final: 0.7816 (p90) REVERT: B 432 CYS cc_start: 0.2404 (OUTLIER) cc_final: 0.0632 (m) REVERT: B 563 GLN cc_start: 0.5148 (OUTLIER) cc_final: 0.4898 (tp40) REVERT: B 1127 ASP cc_start: 0.7130 (t0) cc_final: 0.6737 (t0) REVERT: C 99 ASN cc_start: 0.8145 (m-40) cc_final: 0.7931 (p0) REVERT: C 120 VAL cc_start: 0.8675 (m) cc_final: 0.8355 (p) REVERT: C 238 PHE cc_start: 0.6918 (p90) cc_final: 0.6510 (p90) REVERT: C 294 ASP cc_start: 0.6839 (p0) cc_final: 0.6166 (p0) REVERT: C 441 LEU cc_start: 0.6486 (mt) cc_final: 0.5789 (tt) REVERT: C 497 PHE cc_start: 0.3492 (m-80) cc_final: 0.3197 (m-80) REVERT: C 657 ASN cc_start: 0.8222 (t0) cc_final: 0.8015 (t0) REVERT: C 779 GLN cc_start: 0.8265 (tt0) cc_final: 0.7982 (tm-30) REVERT: C 1005 GLN cc_start: 0.7951 (mm-40) cc_final: 0.7667 (mt0) REVERT: C 1073 LYS cc_start: 0.8237 (tmtt) cc_final: 0.8031 (mtpt) REVERT: C 1139 ASP cc_start: 0.7791 (t0) cc_final: 0.7526 (t0) REVERT: A 104 TRP cc_start: 0.7566 (m-90) cc_final: 0.7150 (m-90) REVERT: A 133 PHE cc_start: 0.6545 (m-80) cc_final: 0.5414 (m-80) REVERT: A 190 ARG cc_start: 0.6714 (mtt180) cc_final: 0.6302 (mtt-85) REVERT: A 195 LYS cc_start: 0.7155 (mmmt) cc_final: 0.6278 (mmmt) REVERT: A 201 PHE cc_start: 0.6521 (t80) cc_final: 0.5835 (t80) REVERT: A 281 GLU cc_start: 0.7377 (pm20) cc_final: 0.6937 (pp20) REVERT: A 390 LEU cc_start: 0.8318 (OUTLIER) cc_final: 0.8026 (pp) REVERT: A 400 PHE cc_start: 0.6956 (p90) cc_final: 0.6565 (p90) REVERT: A 495 TYR cc_start: 0.7061 (OUTLIER) cc_final: 0.6482 (t80) REVERT: A 580 GLN cc_start: 0.6509 (tp40) cc_final: 0.6271 (tp40) REVERT: A 607 GLN cc_start: 0.7983 (mp10) cc_final: 0.7419 (mp10) outliers start: 66 outliers final: 59 residues processed: 513 average time/residue: 0.3824 time to fit residues: 304.6103 Evaluate side-chains 540 residues out of total 2798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 476 time to evaluate : 2.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 ASN Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 563 GLN Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 721 SER Chi-restraints excluded: chain B residue 974 SER Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 451 TYR Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 610 VAL Chi-restraints excluded: chain C residue 651 ILE Chi-restraints excluded: chain C residue 654 GLU Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 819 GLU Chi-restraints excluded: chain C residue 895 GLN Chi-restraints excluded: chain C residue 1051 SER Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 306 PHE Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1083 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 188 optimal weight: 1.9990 chunk 302 optimal weight: 0.0060 chunk 184 optimal weight: 1.9990 chunk 143 optimal weight: 5.9990 chunk 210 optimal weight: 3.9990 chunk 317 optimal weight: 0.3980 chunk 292 optimal weight: 0.9980 chunk 253 optimal weight: 0.3980 chunk 26 optimal weight: 3.9990 chunk 195 optimal weight: 2.9990 chunk 155 optimal weight: 4.9990 overall best weight: 0.7598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 14 GLN B 969 ASN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1088 HIS A 498 GLN A 655 HIS A 779 GLN A 787 GLN A 969 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7407 moved from start: 0.3980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 25662 Z= 0.197 Angle : 0.600 12.457 34902 Z= 0.304 Chirality : 0.045 0.194 3936 Planarity : 0.005 0.147 4529 Dihedral : 4.076 23.480 3440 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 2.29 % Allowed : 20.59 % Favored : 77.13 % 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: -1.31 (0.14), residues: 3164 helix: 0.79 (0.22), residues: 632 sheet: -0.29 (0.20), residues: 643 loop : -1.75 (0.13), residues: 1889 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 353 HIS 0.003 0.001 HIS B1083 PHE 0.050 0.001 PHE B 374 TYR 0.026 0.001 TYR C1138 ARG 0.013 0.001 ARG C 357 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6328 Ramachandran restraints generated. 3164 Oldfield, 0 Emsley, 3164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6328 Ramachandran restraints generated. 3164 Oldfield, 0 Emsley, 3164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 551 residues out of total 2798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 487 time to evaluate : 2.720 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 159 VAL cc_start: 0.7588 (OUTLIER) cc_final: 0.7329 (m) REVERT: B 177 MET cc_start: -0.4224 (mmp) cc_final: -0.4904 (mmt) REVERT: B 277 LEU cc_start: 0.8553 (mm) cc_final: 0.8265 (mp) REVERT: B 324 GLU cc_start: 0.7817 (mm-30) cc_final: 0.7586 (mm-30) REVERT: B 353 TRP cc_start: 0.6083 (p90) cc_final: 0.5609 (p90) REVERT: B 355 ARG cc_start: 0.7815 (mpp-170) cc_final: 0.7274 (ttp80) REVERT: B 400 PHE cc_start: 0.8184 (p90) cc_final: 0.7849 (p90) REVERT: B 432 CYS cc_start: 0.2284 (OUTLIER) cc_final: 0.0441 (m) REVERT: B 563 GLN cc_start: 0.5163 (OUTLIER) cc_final: 0.4948 (tp40) REVERT: B 1127 ASP cc_start: 0.7133 (t0) cc_final: 0.6787 (t0) REVERT: C 99 ASN cc_start: 0.8156 (m-40) cc_final: 0.7930 (p0) REVERT: C 120 VAL cc_start: 0.8694 (m) cc_final: 0.8368 (p) REVERT: C 238 PHE cc_start: 0.6883 (p90) cc_final: 0.6542 (p90) REVERT: C 441 LEU cc_start: 0.6552 (mt) cc_final: 0.5834 (tt) REVERT: C 497 PHE cc_start: 0.3500 (m-80) cc_final: 0.3213 (m-80) REVERT: C 779 GLN cc_start: 0.8265 (tt0) cc_final: 0.8035 (tm-30) REVERT: C 1005 GLN cc_start: 0.7942 (mm-40) cc_final: 0.7662 (mt0) REVERT: C 1139 ASP cc_start: 0.7775 (t0) cc_final: 0.7523 (t0) REVERT: A 39 PRO cc_start: 0.8734 (Cg_endo) cc_final: 0.8485 (Cg_exo) REVERT: A 41 LYS cc_start: 0.8927 (mmtt) cc_final: 0.8638 (mmtp) REVERT: A 104 TRP cc_start: 0.7556 (m-90) cc_final: 0.7124 (m-90) REVERT: A 133 PHE cc_start: 0.6636 (m-80) cc_final: 0.5417 (m-80) REVERT: A 190 ARG cc_start: 0.6790 (mtt180) cc_final: 0.6251 (mtt-85) REVERT: A 195 LYS cc_start: 0.7099 (mmmt) cc_final: 0.6166 (mmmt) REVERT: A 201 PHE cc_start: 0.6520 (t80) cc_final: 0.5801 (t80) REVERT: A 281 GLU cc_start: 0.7415 (pm20) cc_final: 0.6951 (pp20) REVERT: A 400 PHE cc_start: 0.6970 (p90) cc_final: 0.6571 (p90) REVERT: A 495 TYR cc_start: 0.7069 (OUTLIER) cc_final: 0.6586 (t80) REVERT: A 607 GLN cc_start: 0.7998 (mp10) cc_final: 0.7416 (mp10) REVERT: A 779 GLN cc_start: 0.8539 (tp40) cc_final: 0.8287 (tp-100) outliers start: 64 outliers final: 57 residues processed: 523 average time/residue: 0.3756 time to fit residues: 303.2338 Evaluate side-chains 534 residues out of total 2798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 473 time to evaluate : 2.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 ASN Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 563 GLN Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 721 SER Chi-restraints excluded: chain B residue 974 SER Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 451 TYR Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 610 VAL Chi-restraints excluded: chain C residue 651 ILE Chi-restraints excluded: chain C residue 654 GLU Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 819 GLU Chi-restraints excluded: chain C residue 895 GLN Chi-restraints excluded: chain C residue 1051 SER Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 306 PHE Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1083 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 201 optimal weight: 0.9990 chunk 269 optimal weight: 0.3980 chunk 77 optimal weight: 3.9990 chunk 233 optimal weight: 4.9990 chunk 37 optimal weight: 8.9990 chunk 70 optimal weight: 2.9990 chunk 253 optimal weight: 1.9990 chunk 106 optimal weight: 10.0000 chunk 260 optimal weight: 3.9990 chunk 32 optimal weight: 0.9980 chunk 46 optimal weight: 3.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 536 ASN B 787 GLN B 957 GLN C 49 HIS ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 448 ASN C 657 ASN C 764 ASN A 655 HIS ** A 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 914 ASN A 969 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.150162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.117183 restraints weight = 52229.296| |-----------------------------------------------------------------------------| r_work (start): 0.3618 rms_B_bonded: 3.65 r_work: 0.3506 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.4193 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: