Starting phenix.real_space_refine on Mon Feb 19 15:12:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w94_32360/02_2024/7w94_32360.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w94_32360/02_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_32360/02_2024/7w94_32360.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w94_32360/02_2024/7w94_32360.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w94_32360/02_2024/7w94_32360.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w94_32360/02_2024/7w94_32360.pdb" } 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-5238/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: 12.93, per 1000 atoms: 0.52 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: 8.88 Conformation dependent library (CDL) restraints added in 4.6 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: 3.24 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: 10.62 Time building geometry restraints manager: 9.30 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 2.440 nonbonded pdb=" OG1 THR B 20 " pdb=" O LYS B 77 " model vdw 2.292 2.440 nonbonded pdb=" O GLN B 607 " pdb=" OH TYR B 674 " model vdw 2.309 2.440 nonbonded pdb=" OG1 THR B 33 " pdb=" O GLY B 219 " model vdw 2.313 2.440 nonbonded pdb=" OG SER B 349 " pdb=" O ARG B 452 " model vdw 2.320 2.440 ... (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 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: 4.870 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: 0.050 Extract box with map and model: 18.760 Check model and map are aligned: 0.000 Set scattering table: 0.520 Process input model: 65.950 Find NCS groups from input model: 1.810 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 95.070 ------------------------------------------------------------------------------- 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 : 2.953 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: 0.3966 time to fit residues: 394.7789 Evaluate side-chains 523 residues out of total 2798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 522 time to evaluate : 2.589 ------------------------------------------------------------------------------- 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: 2.9990 chunk 241 optimal weight: 0.3980 chunk 134 optimal weight: 0.4980 chunk 82 optimal weight: 2.9990 chunk 163 optimal weight: 0.1980 chunk 129 optimal weight: 4.9990 chunk 250 optimal weight: 0.8980 chunk 96 optimal weight: 3.9990 chunk 152 optimal weight: 3.9990 chunk 186 optimal weight: 2.9990 chunk 289 optimal weight: 4.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 GLN B 360 ASN B 370 ASN ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 481 ASN B 519 HIS ** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 655 HIS B 690 GLN B 709 ASN B 774 GLN B 969 ASN ** B1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1135 ASN C 99 ASN C 121 ASN C 137 ASN C 165 ASN C 218 GLN C 343 ASN C 544 ASN C 563 GLN C 655 HIS C 657 ASN C 804 GLN C 965 GLN A 149 ASN A 370 ASN A 422 ASN ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 655 HIS ** A 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1002 GLN A1074 ASN A1083 HIS A1106 GLN Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7352 moved from start: 0.2220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 25662 Z= 0.235 Angle : 0.600 11.327 34902 Z= 0.307 Chirality : 0.045 0.359 3936 Planarity : 0.004 0.063 4529 Dihedral : 4.123 24.120 3441 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 2.39 % Allowed : 13.12 % Favored : 84.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.14 (0.12), residues: 3164 helix: -2.84 (0.14), residues: 612 sheet: -0.91 (0.19), residues: 657 loop : -2.33 (0.12), residues: 1895 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 104 HIS 0.007 0.001 HIS A 49 PHE 0.026 0.002 PHE C 55 TYR 0.021 0.001 TYR B 91 ARG 0.008 0.001 ARG A 357 *********************** 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 601 residues out of total 2798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 534 time to evaluate : 2.462 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: 0.8462 (tm-30) cc_final: 0.8238 (tm-30) REVERT: B 91 TYR cc_start: 0.8303 (t80) cc_final: 0.8075 (t80) REVERT: B 177 MET cc_start: -0.4509 (mmp) cc_final: -0.4888 (mmp) REVERT: B 227 VAL cc_start: 0.7395 (m) cc_final: 0.7161 (p) REVERT: B 244 LEU cc_start: 0.2968 (OUTLIER) cc_final: 0.2352 (pt) REVERT: B 277 LEU cc_start: 0.8443 (mm) cc_final: 0.8164 (mp) REVERT: B 353 TRP cc_start: 0.6039 (p90) cc_final: 0.5747 (p90) REVERT: B 355 ARG cc_start: 0.7401 (mpp-170) cc_final: 0.7145 (ttp80) REVERT: B 432 CYS cc_start: 0.2562 (OUTLIER) cc_final: 0.1398 (m) REVERT: B 498 GLN cc_start: 0.6807 (mm110) cc_final: 0.6192 (tp40) REVERT: B 773 GLU cc_start: 0.7476 (tt0) cc_final: 0.6885 (tt0) REVERT: B 820 ASP cc_start: 0.8140 (t0) cc_final: 0.7812 (t0) REVERT: B 902 MET cc_start: 0.7415 (OUTLIER) cc_final: 0.7165 (mmm) REVERT: B 1127 ASP cc_start: 0.7155 (t0) cc_final: 0.6744 (t0) REVERT: C 99 ASN cc_start: 0.8105 (m110) cc_final: 0.7834 (p0) REVERT: C 140 PHE cc_start: 0.6901 (m-80) cc_final: 0.6615 (m-80) REVERT: C 238 PHE cc_start: 0.6856 (p90) cc_final: 0.6573 (p90) REVERT: C 239 GLN cc_start: 0.6748 (mm-40) cc_final: 0.6447 (mm-40) REVERT: C 353 TRP cc_start: 0.4833 (p-90) cc_final: 0.4575 (p-90) REVERT: C 355 ARG cc_start: 0.6150 (tpp-160) cc_final: 0.5616 (tpp-160) REVERT: C 441 LEU cc_start: 0.6700 (mt) cc_final: 0.6009 (tt) REVERT: C 559 PHE cc_start: 0.7110 (m-80) cc_final: 0.6697 (m-80) REVERT: C 745 ASP cc_start: 0.6640 (t0) cc_final: 0.6266 (t0) REVERT: C 776 LYS cc_start: 0.8642 (ttmt) cc_final: 0.8309 (ttmt) REVERT: C 804 GLN cc_start: 0.8355 (mm110) cc_final: 0.8150 (mm110) REVERT: C 960 ASN cc_start: 0.8104 (t0) cc_final: 0.7801 (t0) REVERT: C 1017 GLU cc_start: 0.8023 (tm-30) cc_final: 0.7805 (tm-30) REVERT: C 1073 LYS cc_start: 0.8235 (tmtt) cc_final: 0.7994 (mtpt) REVERT: A 40 ASP cc_start: 0.7557 (t70) cc_final: 0.7310 (t70) REVERT: A 44 ARG cc_start: 0.7956 (mtt90) cc_final: 0.7531 (mpp80) REVERT: A 53 ASP cc_start: 0.7379 (t0) cc_final: 0.6902 (t0) REVERT: A 55 PHE cc_start: 0.7265 (m-80) cc_final: 0.6955 (m-80) REVERT: A 86 PHE cc_start: 0.7819 (t80) cc_final: 0.7587 (t80) REVERT: A 133 PHE cc_start: 0.6253 (m-80) cc_final: 0.5421 (m-80) REVERT: A 177 MET cc_start: -0.3269 (mtp) cc_final: -0.4102 (mtt) REVERT: A 189 LEU cc_start: 0.8737 (tp) cc_final: 0.8524 (tp) REVERT: A 190 ARG cc_start: 0.6628 (mtt180) cc_final: 0.5482 (mtt180) REVERT: A 201 PHE cc_start: 0.6780 (t80) cc_final: 0.5885 (t80) REVERT: A 207 HIS cc_start: 0.6746 (m-70) cc_final: 0.6045 (m90) REVERT: A 390 LEU cc_start: 0.8215 (pp) cc_final: 0.7843 (pp) REVERT: A 400 PHE cc_start: 0.6974 (p90) cc_final: 0.6627 (p90) REVERT: A 556 ASN cc_start: 0.7595 (t0) cc_final: 0.7350 (t0) REVERT: A 606 ASN cc_start: 0.8546 (m-40) cc_final: 0.8328 (m-40) REVERT: A 607 GLN cc_start: 0.8041 (mp10) cc_final: 0.7448 (mp10) REVERT: A 643 PHE cc_start: 0.8276 (t80) cc_final: 0.8055 (t80) REVERT: A 675 GLN cc_start: 0.7279 (tm-30) cc_final: 0.7054 (tm-30) REVERT: A 779 GLN cc_start: 0.8035 (OUTLIER) cc_final: 0.7468 (mp10) REVERT: A 869 MET cc_start: 0.8241 (mtt) cc_final: 0.7994 (mtt) REVERT: A 900 MET cc_start: 0.8389 (mtm) cc_final: 0.8140 (mtm) REVERT: A 918 GLU cc_start: 0.7947 (OUTLIER) cc_final: 0.7679 (mp0) REVERT: A 973 ILE cc_start: 0.9154 (tt) cc_final: 0.8890 (pt) REVERT: A 1030 SER cc_start: 0.8852 (m) cc_final: 0.8620 (t) REVERT: A 1111 GLU cc_start: 0.7584 (pm20) cc_final: 0.7293 (pt0) outliers start: 67 outliers final: 38 residues processed: 563 average time/residue: 0.4287 time to fit residues: 363.3085 Evaluate side-chains 541 residues out of total 2798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 498 time to evaluate : 3.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 228 ASP 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 731 MET Chi-restraints excluded: chain B residue 816 SER Chi-restraints excluded: chain B residue 867 ASP Chi-restraints excluded: chain B residue 902 MET 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 87 ASN Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 451 TYR Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 867 ASP Chi-restraints excluded: chain C residue 895 GLN Chi-restraints excluded: chain C residue 933 LYS Chi-restraints excluded: chain C residue 936 ASP Chi-restraints excluded: chain C residue 969 ASN Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain C residue 1117 THR Chi-restraints excluded: chain C residue 1125 ASN Chi-restraints excluded: chain A residue 30 ASN 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 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 745 ASP Chi-restraints excluded: chain A residue 779 GLN Chi-restraints excluded: chain A residue 918 GLU Chi-restraints excluded: chain A residue 1083 HIS Chi-restraints excluded: chain A residue 1118 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 160 optimal weight: 0.6980 chunk 89 optimal weight: 2.9990 chunk 241 optimal weight: 0.6980 chunk 197 optimal weight: 0.7980 chunk 79 optimal weight: 1.9990 chunk 290 optimal weight: 0.6980 chunk 313 optimal weight: 0.0980 chunk 258 optimal weight: 0.0010 chunk 287 optimal weight: 0.0980 chunk 98 optimal weight: 1.9990 chunk 232 optimal weight: 1.9990 overall best weight: 0.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 196 ASN B 394 ASN B 422 ASN B 544 ASN B 563 GLN ** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 969 ASN C 657 ASN C 762 GLN C 928 ASN C 955 ASN ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 448 ASN A 450 ASN A1106 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7320 moved from start: 0.2558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 25662 Z= 0.140 Angle : 0.533 12.479 34902 Z= 0.267 Chirality : 0.044 0.313 3936 Planarity : 0.004 0.053 4529 Dihedral : 3.890 19.899 3440 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.47 % Allowed : 15.94 % Favored : 81.59 % 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: -2.39 (0.13), residues: 3164 helix: -1.18 (0.20), residues: 619 sheet: -0.75 (0.19), residues: 664 loop : -2.13 (0.12), residues: 1881 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 104 HIS 0.008 0.001 HIS A1083 PHE 0.021 0.001 PHE B 374 TYR 0.024 0.001 TYR A 421 ARG 0.009 0.000 ARG B 328 *********************** 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 579 residues out of total 2798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 510 time to evaluate : 2.873 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: 0.8477 (tm-30) cc_final: 0.8269 (tm-30) REVERT: B 177 MET cc_start: -0.4542 (mmp) cc_final: -0.4914 (mmp) REVERT: B 244 LEU cc_start: 0.3147 (OUTLIER) cc_final: 0.2649 (pt) REVERT: B 353 TRP cc_start: 0.5852 (p90) cc_final: 0.5593 (p90) REVERT: B 355 ARG cc_start: 0.7444 (mpp-170) cc_final: 0.7141 (ttp80) REVERT: B 432 CYS cc_start: 0.2317 (OUTLIER) cc_final: 0.1120 (m) REVERT: B 498 GLN cc_start: 0.6752 (mm110) cc_final: 0.6256 (tp-100) REVERT: B 560 LEU cc_start: 0.8118 (tp) cc_final: 0.7715 (tp) REVERT: B 820 ASP cc_start: 0.8115 (t0) cc_final: 0.7813 (t0) REVERT: B 902 MET cc_start: 0.7359 (OUTLIER) cc_final: 0.7141 (mmm) REVERT: B 1127 ASP cc_start: 0.7009 (t0) cc_final: 0.6584 (t0) REVERT: C 99 ASN cc_start: 0.8082 (m110) cc_final: 0.7813 (p0) REVERT: C 140 PHE cc_start: 0.6921 (m-80) cc_final: 0.6611 (m-80) REVERT: C 238 PHE cc_start: 0.6963 (p90) cc_final: 0.6690 (p90) REVERT: C 239 GLN cc_start: 0.6839 (mm-40) cc_final: 0.6593 (mm-40) REVERT: C 441 LEU cc_start: 0.6653 (mt) cc_final: 0.6015 (tt) REVERT: C 497 PHE cc_start: 0.2940 (m-80) cc_final: 0.2474 (m-80) REVERT: C 745 ASP cc_start: 0.6613 (t0) cc_final: 0.6255 (t0) REVERT: C 776 LYS cc_start: 0.8593 (ttmt) cc_final: 0.8325 (ttpp) REVERT: C 779 GLN cc_start: 0.8112 (tt0) cc_final: 0.7878 (tm-30) REVERT: C 784 GLN cc_start: 0.7679 (tt0) cc_final: 0.7338 (tt0) REVERT: C 896 ILE cc_start: 0.8201 (mt) cc_final: 0.7916 (tt) REVERT: C 960 ASN cc_start: 0.8147 (t0) cc_final: 0.7929 (t0) REVERT: C 1005 GLN cc_start: 0.7889 (mm-40) cc_final: 0.7523 (mt0) REVERT: C 1073 LYS cc_start: 0.8237 (tmtt) cc_final: 0.8003 (mtpt) REVERT: A 40 ASP cc_start: 0.7539 (t70) cc_final: 0.7285 (t0) REVERT: A 53 ASP cc_start: 0.7411 (t0) cc_final: 0.6815 (t0) REVERT: A 55 PHE cc_start: 0.7220 (m-80) cc_final: 0.6716 (m-80) REVERT: A 86 PHE cc_start: 0.7871 (t80) cc_final: 0.7613 (t80) REVERT: A 133 PHE cc_start: 0.6172 (m-80) cc_final: 0.5346 (m-80) REVERT: A 177 MET cc_start: -0.3286 (mtp) cc_final: -0.4479 (mtp) REVERT: A 189 LEU cc_start: 0.8695 (tp) cc_final: 0.8493 (tp) REVERT: A 190 ARG cc_start: 0.6638 (mtt180) cc_final: 0.5667 (mtt180) REVERT: A 195 LYS cc_start: 0.7493 (mmmt) cc_final: 0.7160 (mmmt) REVERT: A 196 ASN cc_start: 0.7872 (p0) cc_final: 0.7641 (p0) REVERT: A 201 PHE cc_start: 0.6762 (t80) cc_final: 0.5954 (t80) REVERT: A 390 LEU cc_start: 0.8235 (OUTLIER) cc_final: 0.7945 (pp) REVERT: A 400 PHE cc_start: 0.6820 (p90) cc_final: 0.6512 (p90) REVERT: A 513 LEU cc_start: 0.7744 (mt) cc_final: 0.7478 (mp) REVERT: A 556 ASN cc_start: 0.7591 (t0) cc_final: 0.7331 (t0) REVERT: A 580 GLN cc_start: 0.6026 (tp40) cc_final: 0.5603 (tp40) REVERT: A 643 PHE cc_start: 0.8158 (t80) cc_final: 0.7891 (t80) REVERT: A 646 ARG cc_start: 0.7533 (mpp80) cc_final: 0.7074 (mpp80) REVERT: A 651 ILE cc_start: 0.8829 (tt) cc_final: 0.8569 (pt) REVERT: A 869 MET cc_start: 0.8160 (mtt) cc_final: 0.7906 (mtt) REVERT: A 900 MET cc_start: 0.8398 (mtm) cc_final: 0.8171 (mtm) REVERT: A 918 GLU cc_start: 0.7939 (mp0) cc_final: 0.7705 (mp0) REVERT: A 1091 ARG cc_start: 0.7426 (tpp80) cc_final: 0.7192 (tpp80) outliers start: 69 outliers final: 43 residues processed: 543 average time/residue: 0.4016 time to fit residues: 332.5810 Evaluate side-chains 529 residues out of total 2798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 482 time to evaluate : 2.940 ------------------------------------------------------------------------------- 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 138 ASP Chi-restraints excluded: chain B residue 196 ASN Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 305 SER 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 779 GLN Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 1010 GLN 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 80 ASP Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 451 TYR Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 867 ASP Chi-restraints excluded: chain C residue 895 GLN Chi-restraints excluded: chain C residue 933 LYS Chi-restraints excluded: chain C residue 936 ASP Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 969 ASN Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain A residue 30 ASN Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 306 PHE Chi-restraints excluded: chain A residue 317 ASN 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 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 745 ASP Chi-restraints excluded: chain A residue 1002 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 286 optimal weight: 0.0870 chunk 218 optimal weight: 0.3980 chunk 150 optimal weight: 9.9990 chunk 32 optimal weight: 4.9990 chunk 138 optimal weight: 8.9990 chunk 194 optimal weight: 2.9990 chunk 291 optimal weight: 1.9990 chunk 308 optimal weight: 2.9990 chunk 152 optimal weight: 6.9990 chunk 276 optimal weight: 0.7980 chunk 83 optimal weight: 0.6980 overall best weight: 0.7960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 196 ASN ** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 641 ASN B 787 GLN B 969 ASN C 239 GLN C 655 HIS C 928 ASN ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1083 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7366 moved from start: 0.2874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 25662 Z= 0.190 Angle : 0.527 9.243 34902 Z= 0.268 Chirality : 0.044 0.269 3936 Planarity : 0.004 0.048 4529 Dihedral : 3.924 19.206 3440 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 3.00 % Allowed : 17.58 % Favored : 79.41 % 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: -2.05 (0.14), residues: 3164 helix: -0.47 (0.21), residues: 619 sheet: -0.65 (0.19), residues: 683 loop : -2.03 (0.13), residues: 1862 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 104 HIS 0.005 0.001 HIS B1083 PHE 0.017 0.001 PHE B 168 TYR 0.026 0.001 TYR C1138 ARG 0.007 0.001 ARG A 995 *********************** 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 569 residues out of total 2798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 485 time to evaluate : 2.698 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: 0.8485 (tm-30) cc_final: 0.8270 (tm-30) REVERT: B 177 MET cc_start: -0.4475 (mmp) cc_final: -0.4950 (mmp) REVERT: B 244 LEU cc_start: 0.3120 (OUTLIER) cc_final: 0.2645 (pt) REVERT: B 277 LEU cc_start: 0.8468 (mm) cc_final: 0.8172 (mp) REVERT: B 353 TRP cc_start: 0.5954 (p90) cc_final: 0.5638 (p90) REVERT: B 355 ARG cc_start: 0.7613 (mpp-170) cc_final: 0.7088 (ttp80) REVERT: B 432 CYS cc_start: 0.2154 (OUTLIER) cc_final: 0.0953 (m) REVERT: B 498 GLN cc_start: 0.6751 (mm110) cc_final: 0.6196 (tp-100) REVERT: B 819 GLU cc_start: 0.7134 (mt-10) cc_final: 0.6871 (mt-10) REVERT: B 820 ASP cc_start: 0.8131 (t0) cc_final: 0.7855 (t0) REVERT: B 1127 ASP cc_start: 0.7111 (t0) cc_final: 0.6663 (t0) REVERT: C 99 ASN cc_start: 0.8108 (m110) cc_final: 0.7872 (p0) REVERT: C 120 VAL cc_start: 0.8615 (m) cc_final: 0.8397 (p) REVERT: C 140 PHE cc_start: 0.6967 (m-80) cc_final: 0.6697 (m-80) REVERT: C 238 PHE cc_start: 0.6945 (p90) cc_final: 0.6645 (p90) REVERT: C 239 GLN cc_start: 0.6741 (OUTLIER) cc_final: 0.6470 (mm-40) REVERT: C 353 TRP cc_start: 0.4897 (p-90) cc_final: 0.4543 (p-90) REVERT: C 355 ARG cc_start: 0.6153 (tpp-160) cc_final: 0.5410 (tpp-160) REVERT: C 441 LEU cc_start: 0.6520 (mt) cc_final: 0.5926 (tt) REVERT: C 497 PHE cc_start: 0.3172 (m-80) cc_final: 0.2912 (m-80) REVERT: C 745 ASP cc_start: 0.6852 (t0) cc_final: 0.6477 (t0) REVERT: C 776 LYS cc_start: 0.8594 (ttmt) cc_final: 0.8303 (ttpp) REVERT: C 779 GLN cc_start: 0.8168 (tt0) cc_final: 0.7935 (tm-30) REVERT: C 896 ILE cc_start: 0.8271 (mt) cc_final: 0.7970 (tt) REVERT: C 960 ASN cc_start: 0.8181 (t0) cc_final: 0.7976 (t0) REVERT: C 1005 GLN cc_start: 0.7931 (mm-40) cc_final: 0.7635 (mt0) REVERT: C 1073 LYS cc_start: 0.8239 (tmtt) cc_final: 0.7998 (mtpt) REVERT: A 53 ASP cc_start: 0.7381 (t0) cc_final: 0.6790 (t0) REVERT: A 55 PHE cc_start: 0.7273 (m-80) cc_final: 0.6815 (m-80) REVERT: A 86 PHE cc_start: 0.7911 (t80) cc_final: 0.7620 (t80) REVERT: A 133 PHE cc_start: 0.6295 (m-80) cc_final: 0.5463 (m-80) REVERT: A 189 LEU cc_start: 0.8668 (tp) cc_final: 0.8448 (tp) REVERT: A 195 LYS cc_start: 0.7468 (mmmt) cc_final: 0.7234 (mmmt) REVERT: A 196 ASN cc_start: 0.7843 (p0) cc_final: 0.7573 (p0) REVERT: A 201 PHE cc_start: 0.6592 (t80) cc_final: 0.5890 (t80) REVERT: A 390 LEU cc_start: 0.8274 (OUTLIER) cc_final: 0.7998 (pp) REVERT: A 400 PHE cc_start: 0.6848 (p90) cc_final: 0.6519 (p90) REVERT: A 495 TYR cc_start: 0.7285 (OUTLIER) cc_final: 0.6257 (t80) REVERT: A 513 LEU cc_start: 0.7743 (mt) cc_final: 0.7441 (mp) REVERT: A 556 ASN cc_start: 0.7662 (t0) cc_final: 0.7416 (t0) REVERT: A 580 GLN cc_start: 0.6192 (tp40) cc_final: 0.5724 (tp40) REVERT: A 607 GLN cc_start: 0.8020 (mp10) cc_final: 0.7411 (mp10) REVERT: A 651 ILE cc_start: 0.8941 (tt) cc_final: 0.8658 (pt) REVERT: A 814 LYS cc_start: 0.8244 (mmtt) cc_final: 0.7776 (mmmt) REVERT: A 869 MET cc_start: 0.8220 (mtt) cc_final: 0.7916 (mtt) REVERT: A 900 MET cc_start: 0.8464 (mtm) cc_final: 0.8178 (mtm) REVERT: A 1029 MET cc_start: 0.8551 (tpp) cc_final: 0.8331 (tpp) outliers start: 84 outliers final: 58 residues processed: 527 average time/residue: 0.3866 time to fit residues: 311.9150 Evaluate side-chains 543 residues out of total 2798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 480 time to evaluate : 2.658 ------------------------------------------------------------------------------- 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 87 ASN 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 138 ASP Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 228 ASP 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 721 SER Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 1101 HIS 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 80 ASP Chi-restraints excluded: chain C residue 87 ASN 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 341 VAL Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 451 TYR Chi-restraints excluded: chain C residue 540 ASN 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 816 SER Chi-restraints excluded: chain C residue 867 ASP Chi-restraints excluded: chain C residue 895 GLN Chi-restraints excluded: chain C residue 933 LYS Chi-restraints excluded: chain C residue 936 ASP Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 969 ASN Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain A residue 30 ASN Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 306 PHE Chi-restraints excluded: chain A residue 317 ASN 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 569 ILE Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain A residue 1118 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 256 optimal weight: 5.9990 chunk 175 optimal weight: 2.9990 chunk 4 optimal weight: 0.6980 chunk 229 optimal weight: 0.0980 chunk 127 optimal weight: 5.9990 chunk 263 optimal weight: 2.9990 chunk 213 optimal weight: 0.0060 chunk 0 optimal weight: 9.9990 chunk 157 optimal weight: 0.8980 chunk 276 optimal weight: 0.9990 chunk 77 optimal weight: 3.9990 overall best weight: 0.5398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 196 ASN ** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 787 GLN B 969 ASN ** C 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 928 ASN ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7357 moved from start: 0.3059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 25662 Z= 0.157 Angle : 0.519 12.568 34902 Z= 0.261 Chirality : 0.043 0.243 3936 Planarity : 0.003 0.048 4529 Dihedral : 3.840 18.789 3440 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.97 % Allowed : 18.83 % Favored : 78.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.79 (0.14), residues: 3164 helix: -0.03 (0.22), residues: 620 sheet: -0.53 (0.19), residues: 671 loop : -1.92 (0.13), residues: 1873 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 104 HIS 0.004 0.001 HIS B1083 PHE 0.020 0.001 PHE A 643 TYR 0.026 0.001 TYR C1138 ARG 0.009 0.000 ARG A1091 *********************** 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 573 residues out of total 2798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 490 time to evaluate : 2.558 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: 0.8474 (tm-30) cc_final: 0.8267 (tm-30) REVERT: B 177 MET cc_start: -0.4401 (mmp) cc_final: -0.4906 (mmp) REVERT: B 277 LEU cc_start: 0.8486 (mm) cc_final: 0.8184 (mp) REVERT: B 353 TRP cc_start: 0.5876 (p90) cc_final: 0.5617 (p90) REVERT: B 355 ARG cc_start: 0.7653 (mpp-170) cc_final: 0.7114 (ttp80) REVERT: B 432 CYS cc_start: 0.2105 (OUTLIER) cc_final: 0.0761 (m) REVERT: B 498 GLN cc_start: 0.6919 (mm110) cc_final: 0.6437 (tp-100) REVERT: B 551 VAL cc_start: 0.7676 (m) cc_final: 0.7409 (m) REVERT: B 760 CYS cc_start: 0.5596 (m) cc_final: 0.5245 (m) REVERT: B 773 GLU cc_start: 0.7719 (tp30) cc_final: 0.7095 (tp30) REVERT: B 776 LYS cc_start: 0.8201 (ttpp) cc_final: 0.7504 (ttpp) REVERT: B 819 GLU cc_start: 0.7168 (mt-10) cc_final: 0.6909 (mt-10) REVERT: B 820 ASP cc_start: 0.8159 (t0) cc_final: 0.7889 (t0) REVERT: B 1127 ASP cc_start: 0.7145 (t0) cc_final: 0.6682 (t0) REVERT: C 99 ASN cc_start: 0.8087 (m110) cc_final: 0.7851 (p0) REVERT: C 120 VAL cc_start: 0.8687 (m) cc_final: 0.8345 (p) REVERT: C 140 PHE cc_start: 0.7003 (m-80) cc_final: 0.6697 (m-80) REVERT: C 238 PHE cc_start: 0.6984 (p90) cc_final: 0.6639 (p90) REVERT: C 353 TRP cc_start: 0.4948 (p-90) cc_final: 0.4600 (p-90) REVERT: C 441 LEU cc_start: 0.6436 (mt) cc_final: 0.5870 (tt) REVERT: C 745 ASP cc_start: 0.6916 (t0) cc_final: 0.6551 (t0) REVERT: C 776 LYS cc_start: 0.8594 (ttmt) cc_final: 0.8326 (ttpp) REVERT: C 779 GLN cc_start: 0.8206 (tt0) cc_final: 0.7947 (tm-30) REVERT: C 896 ILE cc_start: 0.8284 (mt) cc_final: 0.7988 (tt) REVERT: C 960 ASN cc_start: 0.8196 (t0) cc_final: 0.7979 (t0) REVERT: C 1005 GLN cc_start: 0.7897 (mm-40) cc_final: 0.7621 (mt0) REVERT: C 1073 LYS cc_start: 0.8249 (tmtt) cc_final: 0.8006 (mtpt) REVERT: A 53 ASP cc_start: 0.7315 (t0) cc_final: 0.6695 (t70) REVERT: A 55 PHE cc_start: 0.7271 (m-80) cc_final: 0.6689 (m-80) REVERT: A 86 PHE cc_start: 0.7863 (t80) cc_final: 0.7611 (t80) REVERT: A 104 TRP cc_start: 0.7529 (m-90) cc_final: 0.7300 (m-90) REVERT: A 133 PHE cc_start: 0.6303 (m-80) cc_final: 0.5498 (m-80) REVERT: A 177 MET cc_start: -0.4189 (mtt) cc_final: -0.5717 (mtt) REVERT: A 189 LEU cc_start: 0.8669 (tp) cc_final: 0.8453 (tp) REVERT: A 196 ASN cc_start: 0.7822 (p0) cc_final: 0.7509 (p0) REVERT: A 201 PHE cc_start: 0.6514 (t80) cc_final: 0.5819 (t80) REVERT: A 390 LEU cc_start: 0.8302 (OUTLIER) cc_final: 0.8041 (pp) REVERT: A 400 PHE cc_start: 0.6720 (p90) cc_final: 0.6378 (p90) REVERT: A 495 TYR cc_start: 0.7143 (OUTLIER) cc_final: 0.6301 (t80) REVERT: A 513 LEU cc_start: 0.7705 (mt) cc_final: 0.7442 (mp) REVERT: A 556 ASN cc_start: 0.7687 (t0) cc_final: 0.7440 (t0) REVERT: A 651 ILE cc_start: 0.8984 (tt) cc_final: 0.8694 (pt) REVERT: A 814 LYS cc_start: 0.8271 (mmtt) cc_final: 0.7782 (mmmt) REVERT: A 869 MET cc_start: 0.8206 (mtt) cc_final: 0.7875 (mtt) REVERT: A 900 MET cc_start: 0.8471 (mtm) cc_final: 0.8173 (mtm) outliers start: 83 outliers final: 65 residues processed: 535 average time/residue: 0.3866 time to fit residues: 317.1579 Evaluate side-chains 546 residues out of total 2798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 478 time to evaluate : 2.653 ------------------------------------------------------------------------------- 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 87 ASN 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 138 ASP Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 196 ASN Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 315 THR 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 731 MET Chi-restraints excluded: chain B residue 867 ASP Chi-restraints excluded: chain B residue 981 LEU 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 80 ASP Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 227 VAL 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 389 ASP Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 451 TYR 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 867 ASP Chi-restraints excluded: chain C residue 895 GLN Chi-restraints excluded: chain C residue 933 LYS Chi-restraints excluded: chain C residue 936 ASP Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 969 ASN Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain A residue 30 ASN 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 294 ASP Chi-restraints excluded: chain A residue 306 PHE Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 317 ASN 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 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 745 ASP 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: 0.0980 chunk 277 optimal weight: 2.9990 chunk 60 optimal weight: 0.8980 chunk 181 optimal weight: 0.0970 chunk 76 optimal weight: 0.0870 chunk 308 optimal weight: 0.5980 chunk 256 optimal weight: 7.9990 chunk 142 optimal weight: 10.0000 chunk 25 optimal weight: 4.9990 chunk 102 optimal weight: 1.9990 chunk 162 optimal weight: 2.9990 overall best weight: 0.3556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 196 ASN B 564 GLN B 969 ASN C 784 GLN C 928 ASN ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 914 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7339 moved from start: 0.3211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 25662 Z= 0.140 Angle : 0.517 8.216 34902 Z= 0.260 Chirality : 0.043 0.224 3936 Planarity : 0.003 0.047 4529 Dihedral : 3.789 21.781 3440 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 3.29 % Allowed : 19.12 % Favored : 77.59 % 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: -1.59 (0.14), residues: 3164 helix: 0.34 (0.22), residues: 619 sheet: -0.42 (0.20), residues: 658 loop : -1.86 (0.13), residues: 1887 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 104 HIS 0.006 0.001 HIS A 655 PHE 0.032 0.001 PHE C 306 TYR 0.025 0.001 TYR C1138 ARG 0.007 0.000 ARG A 995 *********************** 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 570 residues out of total 2798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 478 time to evaluate : 3.031 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 177 MET cc_start: -0.4340 (mmp) cc_final: -0.4875 (mmt) REVERT: B 277 LEU cc_start: 0.8485 (mm) cc_final: 0.8179 (mp) REVERT: B 353 TRP cc_start: 0.5822 (p90) cc_final: 0.5585 (p90) REVERT: B 355 ARG cc_start: 0.7684 (mpp-170) cc_final: 0.7134 (ttp80) REVERT: B 432 CYS cc_start: 0.2176 (OUTLIER) cc_final: 0.0760 (m) REVERT: B 498 GLN cc_start: 0.6920 (mm110) cc_final: 0.6447 (tp-100) REVERT: B 760 CYS cc_start: 0.5420 (m) cc_final: 0.5059 (m) REVERT: B 773 GLU cc_start: 0.7724 (tp30) cc_final: 0.7169 (tp30) REVERT: B 776 LYS cc_start: 0.8480 (ttpp) cc_final: 0.7638 (ttpp) REVERT: B 819 GLU cc_start: 0.7175 (mt-10) cc_final: 0.6921 (mt-10) REVERT: B 820 ASP cc_start: 0.8170 (t0) cc_final: 0.7899 (t0) REVERT: B 1127 ASP cc_start: 0.7104 (t0) cc_final: 0.6656 (t0) REVERT: C 99 ASN cc_start: 0.8088 (m110) cc_final: 0.7824 (p0) REVERT: C 120 VAL cc_start: 0.8636 (m) cc_final: 0.8291 (p) REVERT: C 140 PHE cc_start: 0.7026 (m-80) cc_final: 0.6683 (m-80) REVERT: C 238 PHE cc_start: 0.6936 (p90) cc_final: 0.6660 (p90) REVERT: C 324 GLU cc_start: 0.5821 (tp30) cc_final: 0.5573 (tp30) REVERT: C 441 LEU cc_start: 0.6337 (mt) cc_final: 0.5768 (tt) REVERT: C 525 CYS cc_start: 0.2244 (OUTLIER) cc_final: 0.1828 (m) REVERT: C 779 GLN cc_start: 0.8183 (tt0) cc_final: 0.7934 (tm-30) REVERT: C 896 ILE cc_start: 0.8297 (mt) cc_final: 0.7990 (tt) REVERT: C 1073 LYS cc_start: 0.8243 (tmtt) cc_final: 0.8003 (mtpt) REVERT: C 1092 GLU cc_start: 0.7230 (pm20) cc_final: 0.6966 (pm20) REVERT: A 53 ASP cc_start: 0.7330 (t0) cc_final: 0.6694 (t70) REVERT: A 55 PHE cc_start: 0.7253 (m-80) cc_final: 0.6640 (m-80) REVERT: A 129 LYS cc_start: 0.7876 (mmtt) cc_final: 0.7432 (mmtm) REVERT: A 189 LEU cc_start: 0.8630 (tp) cc_final: 0.8430 (tp) REVERT: A 195 LYS cc_start: 0.7359 (mmmt) cc_final: 0.6721 (mmmt) REVERT: A 196 ASN cc_start: 0.7716 (p0) cc_final: 0.7492 (p0) REVERT: A 201 PHE cc_start: 0.6554 (t80) cc_final: 0.5848 (t80) REVERT: A 390 LEU cc_start: 0.8294 (OUTLIER) cc_final: 0.8041 (pp) REVERT: A 420 ASP cc_start: 0.6831 (t0) cc_final: 0.6547 (t0) REVERT: A 495 TYR cc_start: 0.7079 (OUTLIER) cc_final: 0.6413 (t80) REVERT: A 814 LYS cc_start: 0.8290 (mmtt) cc_final: 0.7770 (mmmt) REVERT: A 869 MET cc_start: 0.8170 (mtt) cc_final: 0.7854 (mtt) REVERT: A 900 MET cc_start: 0.8465 (mtm) cc_final: 0.8173 (mtm) outliers start: 92 outliers final: 70 residues processed: 536 average time/residue: 0.3827 time to fit residues: 318.6880 Evaluate side-chains 549 residues out of total 2798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 475 time to evaluate : 2.859 ------------------------------------------------------------------------------- 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 138 ASP Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 560 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 867 ASP Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1125 ASN Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 227 VAL 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 389 ASP Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 451 TYR Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 525 CYS 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 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 867 ASP Chi-restraints excluded: chain C residue 895 GLN Chi-restraints excluded: chain C residue 936 ASP Chi-restraints excluded: chain C residue 969 ASN Chi-restraints excluded: chain C residue 1051 SER Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain A residue 30 ASN 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 294 ASP Chi-restraints excluded: chain A residue 306 PHE Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 317 ASN 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 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 745 ASP 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: 0.9980 chunk 225 optimal weight: 1.9990 chunk 174 optimal weight: 0.8980 chunk 259 optimal weight: 5.9990 chunk 172 optimal weight: 1.9990 chunk 307 optimal weight: 2.9990 chunk 192 optimal weight: 4.9990 chunk 187 optimal weight: 2.9990 chunk 141 optimal weight: 3.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 787 GLN B 969 ASN C 49 HIS C 764 ASN C 928 ASN C 955 ASN C1088 HIS ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 99 ASN ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7479 moved from start: 0.3675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 25662 Z= 0.367 Angle : 0.645 13.242 34902 Z= 0.333 Chirality : 0.047 0.210 3936 Planarity : 0.004 0.055 4529 Dihedral : 4.409 22.755 3440 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 13.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 3.57 % Allowed : 19.84 % Favored : 76.59 % 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: -1.80 (0.14), residues: 3164 helix: 0.27 (0.22), residues: 606 sheet: -0.57 (0.19), residues: 651 loop : -2.02 (0.13), residues: 1907 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 104 HIS 0.019 0.002 HIS C 207 PHE 0.035 0.002 PHE C 497 TYR 0.030 0.002 TYR C1138 ARG 0.012 0.001 ARG A 457 *********************** 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 598 residues out of total 2798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 498 time to evaluate : 2.769 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: 0.7902 (OUTLIER) cc_final: 0.7655 (m) REVERT: B 177 MET cc_start: -0.4009 (mmp) cc_final: -0.4635 (mmt) REVERT: B 277 LEU cc_start: 0.8562 (mm) cc_final: 0.8273 (mp) REVERT: B 353 TRP cc_start: 0.6222 (p90) cc_final: 0.5736 (p90) REVERT: B 432 CYS cc_start: 0.2415 (OUTLIER) cc_final: 0.0765 (m) REVERT: B 773 GLU cc_start: 0.7801 (tp30) cc_final: 0.7258 (tp30) REVERT: B 776 LYS cc_start: 0.8536 (ttpp) cc_final: 0.7738 (ttpp) REVERT: B 819 GLU cc_start: 0.7281 (mt-10) cc_final: 0.6992 (mt-10) REVERT: B 820 ASP cc_start: 0.8250 (t0) cc_final: 0.8047 (t0) REVERT: B 1127 ASP cc_start: 0.7262 (t0) cc_final: 0.6848 (t0) REVERT: C 99 ASN cc_start: 0.8192 (m110) cc_final: 0.7957 (p0) REVERT: C 102 ARG cc_start: 0.7249 (mmm160) cc_final: 0.6816 (mmm160) REVERT: C 120 VAL cc_start: 0.8634 (m) cc_final: 0.8252 (p) REVERT: C 238 PHE cc_start: 0.7037 (p90) cc_final: 0.6718 (p90) REVERT: C 441 LEU cc_start: 0.6414 (mt) cc_final: 0.5750 (tt) REVERT: C 524 VAL cc_start: 0.6691 (OUTLIER) cc_final: 0.5590 (p) REVERT: C 779 GLN cc_start: 0.8270 (tt0) cc_final: 0.7990 (tm-30) REVERT: C 1017 GLU cc_start: 0.8123 (tm-30) cc_final: 0.7905 (tm-30) REVERT: C 1073 LYS cc_start: 0.8276 (tmtt) cc_final: 0.7965 (mtpt) REVERT: C 1092 GLU cc_start: 0.7471 (pm20) cc_final: 0.7254 (pm20) REVERT: C 1139 ASP cc_start: 0.7787 (t0) cc_final: 0.7545 (t0) REVERT: A 39 PRO cc_start: 0.8852 (Cg_endo) cc_final: 0.8584 (Cg_exo) REVERT: A 133 PHE cc_start: 0.6684 (m-80) cc_final: 0.5516 (m-80) REVERT: A 190 ARG cc_start: 0.8129 (mtt180) cc_final: 0.7823 (mtt-85) REVERT: A 400 PHE cc_start: 0.7109 (p90) cc_final: 0.6759 (p90) REVERT: A 495 TYR cc_start: 0.7321 (OUTLIER) cc_final: 0.6523 (t80) REVERT: A 532 ASN cc_start: 0.7920 (t0) cc_final: 0.7706 (t0) REVERT: A 607 GLN cc_start: 0.8176 (mp10) cc_final: 0.7559 (mp10) REVERT: A 896 ILE cc_start: 0.8113 (mt) cc_final: 0.7885 (tt) REVERT: A 900 MET cc_start: 0.8623 (mtm) cc_final: 0.8376 (mtm) REVERT: A 935 GLN cc_start: 0.8104 (tp-100) cc_final: 0.7862 (tp-100) REVERT: A 995 ARG cc_start: 0.8284 (mmm-85) cc_final: 0.7795 (mmm-85) outliers start: 100 outliers final: 76 residues processed: 555 average time/residue: 0.3830 time to fit residues: 326.9167 Evaluate side-chains 566 residues out of total 2798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 486 time to evaluate : 2.900 ------------------------------------------------------------------------------- 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 227 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 563 GLN Chi-restraints excluded: chain B residue 721 SER Chi-restraints excluded: chain B residue 779 GLN Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1125 ASN Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 190 ARG Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 334 ASN Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 451 TYR Chi-restraints excluded: chain C residue 524 VAL 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 791 THR Chi-restraints excluded: chain C residue 816 SER Chi-restraints excluded: chain C residue 867 ASP Chi-restraints excluded: chain C residue 895 GLN Chi-restraints excluded: chain C residue 933 LYS Chi-restraints excluded: chain C residue 936 ASP Chi-restraints excluded: chain C residue 969 ASN Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1051 SER Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain A residue 30 ASN 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 306 PHE Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 317 ASN 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 409 GLN Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 436 TRP 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 549 THR 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 745 ASP 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 1118 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 190 optimal weight: 0.6980 chunk 122 optimal weight: 0.0670 chunk 183 optimal weight: 0.8980 chunk 92 optimal weight: 0.9990 chunk 60 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 195 optimal weight: 2.9990 chunk 209 optimal weight: 0.9980 chunk 152 optimal weight: 6.9990 chunk 28 optimal weight: 0.7980 chunk 241 optimal weight: 0.6980 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 969 ASN ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 196 ASN A 779 GLN A 907 ASN A 913 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7416 moved from start: 0.3762 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= 0.175 Angle : 0.570 12.129 34902 Z= 0.289 Chirality : 0.044 0.196 3936 Planarity : 0.004 0.070 4529 Dihedral : 4.131 21.977 3440 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 3.11 % Allowed : 21.09 % Favored : 75.80 % 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: -1.56 (0.14), residues: 3164 helix: 0.63 (0.22), residues: 612 sheet: -0.42 (0.20), residues: 640 loop : -1.92 (0.13), residues: 1912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 353 HIS 0.005 0.001 HIS A 655 PHE 0.039 0.001 PHE C 306 TYR 0.025 0.001 TYR C1138 ARG 0.005 0.000 ARG B 328 *********************** 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 576 residues out of total 2798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 489 time to evaluate : 2.709 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: 0.7785 (OUTLIER) cc_final: 0.7537 (m) REVERT: B 177 MET cc_start: -0.4013 (mmp) cc_final: -0.4677 (mmt) REVERT: B 277 LEU cc_start: 0.8523 (mm) cc_final: 0.8234 (mp) REVERT: B 353 TRP cc_start: 0.5847 (p90) cc_final: 0.5555 (p90) REVERT: B 400 PHE cc_start: 0.8276 (p90) cc_final: 0.7802 (p90) REVERT: B 432 CYS cc_start: 0.2453 (OUTLIER) cc_final: 0.0796 (m) REVERT: B 498 GLN cc_start: 0.6413 (mm-40) cc_final: 0.6165 (tp-100) REVERT: B 773 GLU cc_start: 0.7725 (tp30) cc_final: 0.7205 (tp30) REVERT: B 776 LYS cc_start: 0.8511 (ttpp) cc_final: 0.7718 (ttpp) REVERT: B 819 GLU cc_start: 0.7215 (mt-10) cc_final: 0.6965 (mt-10) REVERT: B 1127 ASP cc_start: 0.7141 (t0) cc_final: 0.6752 (t0) REVERT: C 99 ASN cc_start: 0.8113 (m110) cc_final: 0.7874 (p0) REVERT: C 102 ARG cc_start: 0.7247 (mmm160) cc_final: 0.6807 (mmm160) REVERT: C 120 VAL cc_start: 0.8603 (m) cc_final: 0.8233 (p) REVERT: C 238 PHE cc_start: 0.7010 (p90) cc_final: 0.6792 (p90) REVERT: C 277 LEU cc_start: 0.8154 (mm) cc_final: 0.7841 (mp) REVERT: C 441 LEU cc_start: 0.6286 (mt) cc_final: 0.5631 (tt) REVERT: C 657 ASN cc_start: 0.8204 (t0) cc_final: 0.7992 (t0) REVERT: C 779 GLN cc_start: 0.8261 (tt0) cc_final: 0.8044 (tm-30) REVERT: C 896 ILE cc_start: 0.8431 (mt) cc_final: 0.8099 (tt) REVERT: C 1073 LYS cc_start: 0.8230 (tmtt) cc_final: 0.7995 (mtpt) REVERT: C 1092 GLU cc_start: 0.7309 (pm20) cc_final: 0.7101 (pm20) REVERT: C 1139 ASP cc_start: 0.7728 (t0) cc_final: 0.7513 (t0) REVERT: A 39 PRO cc_start: 0.8838 (Cg_endo) cc_final: 0.8567 (Cg_exo) REVERT: A 41 LYS cc_start: 0.8974 (OUTLIER) cc_final: 0.8715 (mmtt) REVERT: A 55 PHE cc_start: 0.7455 (m-80) cc_final: 0.7136 (m-80) REVERT: A 104 TRP cc_start: 0.7604 (m-90) cc_final: 0.7202 (m-90) REVERT: A 133 PHE cc_start: 0.6624 (m-80) cc_final: 0.5478 (m-80) REVERT: A 190 ARG cc_start: 0.8040 (mtt180) cc_final: 0.7732 (mtt180) REVERT: A 400 PHE cc_start: 0.6983 (p90) cc_final: 0.6612 (p90) REVERT: A 495 TYR cc_start: 0.7251 (OUTLIER) cc_final: 0.6611 (t80) REVERT: A 532 ASN cc_start: 0.7833 (t0) cc_final: 0.7604 (t0) REVERT: A 580 GLN cc_start: 0.6620 (tp40) cc_final: 0.6208 (tp40) REVERT: A 607 GLN cc_start: 0.8061 (mp10) cc_final: 0.7498 (mp10) REVERT: A 896 ILE cc_start: 0.8058 (mt) cc_final: 0.7853 (tt) REVERT: A 935 GLN cc_start: 0.8109 (tp-100) cc_final: 0.7862 (tp-100) REVERT: A 995 ARG cc_start: 0.8202 (mmm-85) cc_final: 0.7737 (mmm-85) outliers start: 87 outliers final: 68 residues processed: 538 average time/residue: 0.3824 time to fit residues: 316.2228 Evaluate side-chains 554 residues out of total 2798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 482 time to evaluate : 2.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 ASN 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 227 VAL Chi-restraints excluded: chain B residue 315 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 563 GLN Chi-restraints excluded: chain B residue 721 SER Chi-restraints excluded: chain B residue 974 SER Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1125 ASN Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 190 ARG Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 334 ASN Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 451 TYR Chi-restraints excluded: chain C residue 495 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 867 ASP Chi-restraints excluded: chain C residue 895 GLN Chi-restraints excluded: chain C residue 936 ASP Chi-restraints excluded: chain C residue 969 ASN Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1051 SER Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain A residue 30 ASN Chi-restraints excluded: chain A residue 41 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 177 MET 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 317 ASN 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 409 GLN Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 436 TRP 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 745 ASP 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 1018 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: 0.8980 chunk 268 optimal weight: 1.9990 chunk 286 optimal weight: 0.3980 chunk 172 optimal weight: 0.0470 chunk 124 optimal weight: 6.9990 chunk 224 optimal weight: 0.5980 chunk 87 optimal weight: 1.9990 chunk 258 optimal weight: 2.9990 chunk 270 optimal weight: 2.9990 chunk 285 optimal weight: 0.2980 overall best weight: 0.4478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 969 ASN C 955 ASN C1002 GLN ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 196 ASN ** A 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 616 ASN A 655 HIS A 779 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7388 moved from start: 0.3855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 25662 Z= 0.155 Angle : 0.562 11.650 34902 Z= 0.284 Chirality : 0.044 0.196 3936 Planarity : 0.004 0.060 4529 Dihedral : 4.017 20.678 3440 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 2.86 % Allowed : 21.59 % Favored : 75.55 % 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: -1.39 (0.14), residues: 3164 helix: 0.92 (0.23), residues: 612 sheet: -0.30 (0.20), residues: 645 loop : -1.87 (0.13), residues: 1907 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP A 353 HIS 0.004 0.001 HIS B1083 PHE 0.036 0.001 PHE C 306 TYR 0.022 0.001 TYR C1138 ARG 0.004 0.000 ARG A 995 *********************** 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 559 residues out of total 2798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 479 time to evaluate : 2.937 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: 0.7680 (OUTLIER) cc_final: 0.7422 (m) REVERT: B 177 MET cc_start: -0.4119 (mmp) cc_final: -0.4763 (mmt) REVERT: B 277 LEU cc_start: 0.8524 (mm) cc_final: 0.8156 (mp) REVERT: B 353 TRP cc_start: 0.5858 (p90) cc_final: 0.5490 (p90) REVERT: B 400 PHE cc_start: 0.8186 (p90) cc_final: 0.7724 (p90) REVERT: B 432 CYS cc_start: 0.2321 (OUTLIER) cc_final: 0.0548 (m) REVERT: B 537 LYS cc_start: 0.8239 (mmtt) cc_final: 0.8008 (mmtm) REVERT: B 819 GLU cc_start: 0.7217 (mt-10) cc_final: 0.6981 (mt-10) REVERT: B 955 ASN cc_start: 0.8385 (t0) cc_final: 0.8107 (t0) REVERT: B 1127 ASP cc_start: 0.7111 (t0) cc_final: 0.6751 (t0) REVERT: B 1137 VAL cc_start: 0.9122 (t) cc_final: 0.8915 (m) REVERT: C 99 ASN cc_start: 0.8089 (m110) cc_final: 0.7880 (p0) REVERT: C 102 ARG cc_start: 0.7249 (mmm160) cc_final: 0.6800 (mmm160) REVERT: C 120 VAL cc_start: 0.8621 (m) cc_final: 0.8297 (p) REVERT: C 238 PHE cc_start: 0.7010 (p90) cc_final: 0.6718 (p90) REVERT: C 277 LEU cc_start: 0.8134 (mm) cc_final: 0.7845 (mp) REVERT: C 441 LEU cc_start: 0.6205 (mt) cc_final: 0.5547 (tt) REVERT: C 657 ASN cc_start: 0.8205 (t0) cc_final: 0.8002 (t0) REVERT: C 779 GLN cc_start: 0.8261 (tt0) cc_final: 0.8055 (tm-30) REVERT: C 896 ILE cc_start: 0.8407 (mt) cc_final: 0.8060 (tt) REVERT: C 1073 LYS cc_start: 0.8225 (tmtt) cc_final: 0.7992 (mtpt) REVERT: C 1092 GLU cc_start: 0.7261 (pm20) cc_final: 0.7001 (pm20) REVERT: C 1139 ASP cc_start: 0.7732 (t0) cc_final: 0.7517 (t0) REVERT: A 39 PRO cc_start: 0.8722 (Cg_endo) cc_final: 0.8443 (Cg_exo) REVERT: A 41 LYS cc_start: 0.8948 (OUTLIER) cc_final: 0.8696 (mmtt) REVERT: A 104 TRP cc_start: 0.7588 (m-90) cc_final: 0.7208 (m-90) REVERT: A 133 PHE cc_start: 0.6596 (m-80) cc_final: 0.5423 (m-80) REVERT: A 190 ARG cc_start: 0.7959 (mtt180) cc_final: 0.7603 (mtt180) REVERT: A 195 LYS cc_start: 0.6902 (mmmt) cc_final: 0.6299 (mmmt) REVERT: A 201 PHE cc_start: 0.6724 (t80) cc_final: 0.5883 (t80) REVERT: A 289 VAL cc_start: 0.8835 (t) cc_final: 0.8618 (m) REVERT: A 315 THR cc_start: 0.8527 (OUTLIER) cc_final: 0.8230 (t) REVERT: A 400 PHE cc_start: 0.6951 (p90) cc_final: 0.6574 (p90) REVERT: A 409 GLN cc_start: 0.6998 (OUTLIER) cc_final: 0.6741 (pt0) REVERT: A 495 TYR cc_start: 0.7309 (OUTLIER) cc_final: 0.6828 (t80) REVERT: A 580 GLN cc_start: 0.6618 (tp40) cc_final: 0.6356 (mm110) REVERT: A 995 ARG cc_start: 0.8117 (mmm-85) cc_final: 0.7696 (mmm-85) outliers start: 80 outliers final: 66 residues processed: 522 average time/residue: 0.3882 time to fit residues: 311.6017 Evaluate side-chains 542 residues out of total 2798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 470 time to evaluate : 2.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 30 ASN 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 226 LEU Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 563 GLN Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 721 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 87 ASN Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 334 ASN Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 451 TYR Chi-restraints excluded: chain C residue 495 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 816 SER Chi-restraints excluded: chain C residue 867 ASP Chi-restraints excluded: chain C residue 895 GLN Chi-restraints excluded: chain C residue 936 ASP Chi-restraints excluded: chain C residue 969 ASN Chi-restraints excluded: chain C residue 1002 GLN Chi-restraints excluded: chain C residue 1051 SER Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain A residue 30 ASN Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 117 LEU 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 317 ASN 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 409 GLN Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 436 TRP 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 533 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 745 ASP 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 188 optimal weight: 0.9990 chunk 302 optimal weight: 0.0020 chunk 184 optimal weight: 0.2980 chunk 143 optimal weight: 7.9990 chunk 210 optimal weight: 3.9990 chunk 317 optimal weight: 4.9990 chunk 292 optimal weight: 0.9980 chunk 253 optimal weight: 5.9990 chunk 26 optimal weight: 1.9990 chunk 195 optimal weight: 0.1980 chunk 155 optimal weight: 9.9990 overall best weight: 0.4990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 969 ASN C 901 GLN ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 196 ASN ** A 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 779 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7385 moved from start: 0.3927 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= 0.161 Angle : 0.572 11.693 34902 Z= 0.288 Chirality : 0.044 0.195 3936 Planarity : 0.004 0.053 4529 Dihedral : 3.983 24.944 3440 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 2.75 % Allowed : 21.94 % Favored : 75.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.15), residues: 3164 helix: 1.03 (0.23), residues: 612 sheet: -0.31 (0.20), residues: 653 loop : -1.83 (0.13), residues: 1899 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP A 353 HIS 0.004 0.001 HIS B1083 PHE 0.052 0.001 PHE B 374 TYR 0.022 0.001 TYR C1138 ARG 0.007 0.000 ARG A 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: 77 poor density : 474 time to evaluate : 2.532 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: 0.7636 (OUTLIER) cc_final: 0.7378 (m) REVERT: B 177 MET cc_start: -0.4169 (mmp) cc_final: -0.4819 (mmt) REVERT: B 277 LEU cc_start: 0.8531 (mm) cc_final: 0.8218 (mp) REVERT: B 353 TRP cc_start: 0.5837 (p90) cc_final: 0.5475 (p90) REVERT: B 400 PHE cc_start: 0.8260 (p90) cc_final: 0.7786 (p90) REVERT: B 432 CYS cc_start: 0.2059 (OUTLIER) cc_final: 0.0237 (m) REVERT: B 819 GLU cc_start: 0.7245 (mt-10) cc_final: 0.7006 (mt-10) REVERT: B 955 ASN cc_start: 0.8372 (t0) cc_final: 0.8097 (t0) REVERT: B 1127 ASP cc_start: 0.7098 (t0) cc_final: 0.6793 (t0) REVERT: C 99 ASN cc_start: 0.8097 (m110) cc_final: 0.7897 (p0) REVERT: C 102 ARG cc_start: 0.7257 (mmm160) cc_final: 0.6803 (mmm160) REVERT: C 119 ILE cc_start: 0.8613 (tt) cc_final: 0.8265 (tp) REVERT: C 120 VAL cc_start: 0.8671 (m) cc_final: 0.8241 (p) REVERT: C 238 PHE cc_start: 0.6957 (p90) cc_final: 0.6750 (p90) REVERT: C 239 GLN cc_start: 0.6825 (mm-40) cc_final: 0.6537 (mm-40) REVERT: C 277 LEU cc_start: 0.8141 (mm) cc_final: 0.7835 (mp) REVERT: C 441 LEU cc_start: 0.6183 (mt) cc_final: 0.5524 (tt) REVERT: C 657 ASN cc_start: 0.8217 (t0) cc_final: 0.8007 (t0) REVERT: C 896 ILE cc_start: 0.8403 (mt) cc_final: 0.8069 (tt) REVERT: C 1073 LYS cc_start: 0.8225 (tmtt) cc_final: 0.7989 (mtpt) REVERT: C 1092 GLU cc_start: 0.7251 (pm20) cc_final: 0.6980 (pm20) REVERT: C 1139 ASP cc_start: 0.7738 (t0) cc_final: 0.7525 (t0) REVERT: A 39 PRO cc_start: 0.8741 (Cg_endo) cc_final: 0.8481 (Cg_exo) REVERT: A 41 LYS cc_start: 0.8968 (OUTLIER) cc_final: 0.8716 (mmtt) REVERT: A 104 TRP cc_start: 0.7557 (m-90) cc_final: 0.7200 (m-90) REVERT: A 133 PHE cc_start: 0.6534 (m-80) cc_final: 0.5426 (m-80) REVERT: A 195 LYS cc_start: 0.6881 (mmmt) cc_final: 0.6069 (mmmt) REVERT: A 201 PHE cc_start: 0.6675 (t80) cc_final: 0.5695 (t80) REVERT: A 289 VAL cc_start: 0.8864 (t) cc_final: 0.8661 (m) REVERT: A 315 THR cc_start: 0.8520 (OUTLIER) cc_final: 0.8237 (t) REVERT: A 353 TRP cc_start: 0.6446 (p90) cc_final: 0.5813 (p90) REVERT: A 400 PHE cc_start: 0.6958 (p90) cc_final: 0.6570 (p90) REVERT: A 409 GLN cc_start: 0.6953 (OUTLIER) cc_final: 0.6690 (pt0) REVERT: A 495 TYR cc_start: 0.7345 (OUTLIER) cc_final: 0.6914 (t80) REVERT: A 580 GLN cc_start: 0.6622 (tp40) cc_final: 0.6407 (mm110) REVERT: A 607 GLN cc_start: 0.7991 (mp10) cc_final: 0.7350 (mp10) REVERT: A 935 GLN cc_start: 0.8180 (tp-100) cc_final: 0.7900 (tp40) REVERT: A 995 ARG cc_start: 0.8091 (mmm-85) cc_final: 0.7691 (mmm-85) outliers start: 77 outliers final: 64 residues processed: 514 average time/residue: 0.4119 time to fit residues: 326.8631 Evaluate side-chains 536 residues out of total 2798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 466 time to evaluate : 3.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 30 ASN 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 226 LEU Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 563 GLN Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 721 SER Chi-restraints excluded: chain B residue 780 GLU 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 87 ASN Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 334 ASN Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 451 TYR Chi-restraints excluded: chain C residue 495 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 705 VAL Chi-restraints excluded: chain C residue 707 TYR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 816 SER Chi-restraints excluded: chain C residue 867 ASP Chi-restraints excluded: chain C residue 895 GLN Chi-restraints excluded: chain C residue 936 ASP Chi-restraints excluded: chain C residue 969 ASN Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1051 SER Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain A residue 30 ASN Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 306 PHE Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 317 ASN 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 409 GLN Chi-restraints excluded: chain A residue 436 TRP 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 533 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 745 ASP 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 201 optimal weight: 1.9990 chunk 269 optimal weight: 2.9990 chunk 77 optimal weight: 0.9980 chunk 233 optimal weight: 9.9990 chunk 37 optimal weight: 5.9990 chunk 70 optimal weight: 2.9990 chunk 253 optimal weight: 6.9990 chunk 106 optimal weight: 10.0000 chunk 260 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 46 optimal weight: 8.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 14 GLN B 787 GLN B 969 ASN C 764 ASN ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 616 ASN A 655 HIS A 914 ASN A 992 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.147718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.115130 restraints weight = 52531.444| |-----------------------------------------------------------------------------| r_work (start): 0.3591 rms_B_bonded: 3.63 r_work: 0.3477 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.4297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.051 25662 Z= 0.428 Angle : 0.703 12.258 34902 Z= 0.366 Chirality : 0.049 0.206 3936 Planarity : 0.005 0.134 4529 Dihedral : 4.698 25.519 3440 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 15.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.08 % Favored : 92.92 % Rotamer: Outliers : 3.07 % Allowed : 21.91 % Favored : 75.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.71 (0.14), residues: 3164 helix: 0.58 (0.22), residues: 601 sheet: -0.52 (0.20), residues: 650 loop : -2.04 (0.13), residues: 1913 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 353 HIS 0.008 0.002 HIS A 655 PHE 0.054 0.002 PHE B 374 TYR 0.030 0.002 TYR C1138 ARG 0.020 0.001 ARG A 457 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6752.78 seconds wall clock time: 122 minutes 38.53 seconds (7358.53 seconds total)