Starting phenix.real_space_refine on Sat Jul 4 05:56:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7jpv_22424/07_2026/7jpv_22424.cif Found real_map, /net/cci-nas-00/data/ceres_data/7jpv_22424/07_2026/7jpv_22424.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/cci-nas-00/data/ceres_data/7jpv_22424/07_2026/7jpv_22424.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7jpv_22424/07_2026/7jpv_22424.map" model { file = "/net/cci-nas-00/data/ceres_data/7jpv_22424/07_2026/7jpv_22424.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7jpv_22424/07_2026/7jpv_22424.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7jpv_22424/07_2026/7jpv_22424.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7jpv_22424/07_2026/7jpv_22424.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= 0.000 sd= 0.004 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: 6 Type Number sf(0) Gaussians Ca 1 9.91 5 P 10 5.49 5 S 107 5.16 5 C 11930 2.51 5 N 2940 2.21 5 O 3300 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 162 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 18288 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 8987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1115, 8987 Classifications: {'peptide': 1115} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 36, 'TRANS': 1078} Chain breaks: 10 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 10 Chain: "E" Number of atoms: 1080 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1080 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 6, 'TRANS': 132} Chain breaks: 2 Chain: "F" Number of atoms: 7804 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 973, 7796 Classifications: {'peptide': 973} Link IDs: {'PCIS': 2, 'PTRANS': 43, 'TRANS': 927} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 973, 7796 Classifications: {'peptide': 973} Link IDs: {'PCIS': 2, 'PTRANS': 43, 'TRANS': 927} Chain breaks: 2 bond proxies already assigned to first conformer: 7954 Chain: "A" Number of atoms: 363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 363 Unusual residues: {' CA': 1, '3PE': 9} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 97 Unresolved non-hydrogen angles: 99 Unresolved non-hydrogen dihedrals: 93 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'3PE:plan-1': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 54 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.80, per 1000 atoms: 0.26 Number of scatterers: 18288 At special positions: 0 Unit cell: (144.82, 141.478, 158.188, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 1 19.99 S 107 16.00 P 10 15.00 O 3300 8.00 N 2940 7.00 C 11930 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A 226 " - pdb=" SG CYS A 254 " distance=2.03 Simple disulfide: pdb=" SG CYS A 245 " - pdb=" SG CYS A 261 " distance=2.03 Simple disulfide: pdb=" SG CYS A 957 " - pdb=" SG CYS A 968 " distance=2.03 Simple disulfide: pdb=" SG CYS A1338 " - pdb=" SG CYS A1352 " distance=2.03 Simple disulfide: pdb=" SG CYS F 305 " - pdb=" SG CYS F1047 " distance=2.04 Simple disulfide: pdb=" SG CYS F 356 " - pdb=" SG CYS F1062 " distance=2.03 Simple disulfide: pdb=" SG CYS F 406 " - pdb=" SG CYS F1074 " distance=2.03 Simple disulfide: pdb=" SG CYS F 670 " - pdb=" SG CYS F 700 " distance=2.03 Simple disulfide: pdb=" SG CYS F 844 " - pdb=" SG CYS F 853 " distance=2.03 Simple disulfide: pdb=" SG CYS F 907 " - pdb=" SG CYS F 977 " distance=2.03 Simple disulfide: pdb=" SG CYS F 999 " - pdb=" SG CYS F1029 " distance=2.03 Simple disulfide: pdb=" SG CYS F1002 " - pdb=" SG CYS F1027 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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=5, symmetry=0 Number of additional bonds: simple=5, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.26 Conformation dependent library (CDL) restraints added in 1.0 seconds 4388 Ramachandran restraints generated. 2194 Oldfield, 0 Emsley, 2194 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4218 Finding SS restraints... Secondary structure from input PDB file: 92 helices and 16 sheets defined 53.4% alpha, 9.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.51 Creating SS restraints... Processing helix chain 'A' and resid 56 through 65 Processing helix chain 'A' and resid 80 through 106 removed outlier: 3.599A pdb=" N LYS A 88 " --> pdb=" O LEU A 84 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N TYR A 91 " --> pdb=" O GLU A 87 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE A 92 " --> pdb=" O LYS A 88 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N ILE A 106 " --> pdb=" O ALA A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 143 removed outlier: 3.849A pdb=" N GLN A 141 " --> pdb=" O ALA A 137 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ASN A 143 " --> pdb=" O LEU A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 166 Processing helix chain 'A' and resid 167 through 171 removed outlier: 3.719A pdb=" N ARG A 171 " --> pdb=" O ARG A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 179 removed outlier: 3.670A pdb=" N VAL A 176 " --> pdb=" O PRO A 172 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL A 179 " --> pdb=" O LEU A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 193 removed outlier: 3.907A pdb=" N GLN A 183 " --> pdb=" O VAL A 179 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL A 184 " --> pdb=" O PRO A 180 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N VAL A 185 " --> pdb=" O SER A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 218 Processing helix chain 'A' and resid 277 through 290 Processing helix chain 'A' and resid 293 through 302 removed outlier: 3.687A pdb=" N VAL A 297 " --> pdb=" O GLY A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 346 removed outlier: 4.284A pdb=" N PHE A 314 " --> pdb=" O PRO A 310 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N PHE A 324 " --> pdb=" O LEU A 320 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ILE A 325 " --> pdb=" O GLY A 321 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU A 326 " --> pdb=" O SER A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 434 through 450 removed outlier: 4.296A pdb=" N ILE A 441 " --> pdb=" O LEU A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 487 removed outlier: 3.553A pdb=" N THR A 461 " --> pdb=" O PRO A 457 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ILE A 466 " --> pdb=" O HIS A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 491 removed outlier: 3.780A pdb=" N TYR A 491 " --> pdb=" O LEU A 488 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 488 through 491' Processing helix chain 'A' and resid 494 through 498 Processing helix chain 'A' and resid 499 through 515 Processing helix chain 'A' and resid 520 through 530 removed outlier: 3.569A pdb=" N ILE A 524 " --> pdb=" O THR A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 531 through 535 removed outlier: 3.823A pdb=" N LEU A 535 " --> pdb=" O LEU A 532 " (cutoff:3.500A) Processing helix chain 'A' and resid 536 through 542 removed outlier: 3.654A pdb=" N TRP A 542 " --> pdb=" O ILE A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 582 removed outlier: 5.719A pdb=" N SER A 561 " --> pdb=" O ARG A 557 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N LEU A 562 " --> pdb=" O SER A 558 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 612 Processing helix chain 'A' and resid 615 through 627 removed outlier: 3.523A pdb=" N VAL A 619 " --> pdb=" O ASP A 615 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N TYR A 621 " --> pdb=" O ASN A 617 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ASN A 622 " --> pdb=" O SER A 618 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLY A 623 " --> pdb=" O VAL A 619 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N TYR A 627 " --> pdb=" O GLY A 623 " (cutoff:3.500A) Processing helix chain 'A' and resid 631 through 636 removed outlier: 4.052A pdb=" N LEU A 636 " --> pdb=" O TYR A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 639 through 647 Processing helix chain 'A' and resid 647 through 657 removed outlier: 3.649A pdb=" N ILE A 651 " --> pdb=" O CYS A 647 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU A 652 " --> pdb=" O GLY A 648 " (cutoff:3.500A) Processing helix chain 'A' and resid 663 through 673 removed outlier: 3.639A pdb=" N ALA A 667 " --> pdb=" O ASN A 663 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLU A 668 " --> pdb=" O LEU A 664 " (cutoff:3.500A) Processing helix chain 'A' and resid 798 through 811 removed outlier: 3.639A pdb=" N LEU A 807 " --> pdb=" O ASN A 803 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ILE A 809 " --> pdb=" O ILE A 805 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LEU A 810 " --> pdb=" O LEU A 806 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LEU A 811 " --> pdb=" O LEU A 807 " (cutoff:3.500A) Processing helix chain 'A' and resid 813 through 818 removed outlier: 3.746A pdb=" N ALA A 817 " --> pdb=" O SER A 813 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ALA A 818 " --> pdb=" O ALA A 814 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 813 through 818' Processing helix chain 'A' and resid 828 through 852 removed outlier: 3.716A pdb=" N ALA A 838 " --> pdb=" O TYR A 834 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N PHE A 843 " --> pdb=" O PHE A 839 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N GLU A 846 " --> pdb=" O VAL A 842 " (cutoff:3.500A) Processing helix chain 'A' and resid 868 through 881 removed outlier: 4.176A pdb=" N SER A 879 " --> pdb=" O VAL A 875 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N LEU A 880 " --> pdb=" O VAL A 876 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ILE A 881 " --> pdb=" O ALA A 877 " (cutoff:3.500A) Processing helix chain 'A' and resid 893 through 899 removed outlier: 3.997A pdb=" N ARG A 897 " --> pdb=" O VAL A 893 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N VAL A 898 " --> pdb=" O LYS A 894 " (cutoff:3.500A) Processing helix chain 'A' and resid 907 through 912 removed outlier: 3.776A pdb=" N LYS A 912 " --> pdb=" O ILE A 908 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 928 removed outlier: 4.068A pdb=" N VAL A 917 " --> pdb=" O GLY A 913 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ARG A 926 " --> pdb=" O PHE A 922 " (cutoff:3.500A) Processing helix chain 'A' and resid 929 through 950 removed outlier: 4.044A pdb=" N VAL A 934 " --> pdb=" O ASN A 930 " (cutoff:3.500A) Processing helix chain 'A' and resid 977 through 979 No H-bonds generated for 'chain 'A' and resid 977 through 979' Processing helix chain 'A' and resid 999 through 1012 Processing helix chain 'A' and resid 1015 through 1024 removed outlier: 3.653A pdb=" N LEU A1019 " --> pdb=" O GLY A1015 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ARG A1022 " --> pdb=" O GLN A1018 " (cutoff:3.500A) Processing helix chain 'A' and resid 1043 through 1048 removed outlier: 3.548A pdb=" N TYR A1048 " --> pdb=" O PHE A1044 " (cutoff:3.500A) Processing helix chain 'A' and resid 1054 through 1072 removed outlier: 3.504A pdb=" N VAL A1064 " --> pdb=" O PHE A1060 " (cutoff:3.500A) Processing helix chain 'A' and resid 1084 through 1095 removed outlier: 3.977A pdb=" N VAL A1089 " --> pdb=" O GLN A1085 " (cutoff:3.500A) removed outlier: 5.382A pdb=" N GLN A1090 " --> pdb=" O ARG A1086 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ALA A1095 " --> pdb=" O TYR A1091 " (cutoff:3.500A) Processing helix chain 'A' and resid 1105 through 1116 removed outlier: 4.890A pdb=" N VAL A1111 " --> pdb=" O TYR A1107 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N VAL A1114 " --> pdb=" O GLN A1110 " (cutoff:3.500A) Processing helix chain 'A' and resid 1117 through 1137 removed outlier: 3.710A pdb=" N GLU A1121 " --> pdb=" O SER A1117 " (cutoff:3.500A) Processing helix chain 'A' and resid 1152 through 1171 Processing helix chain 'A' and resid 1180 through 1206 Processing helix chain 'A' and resid 1232 through 1235 Processing helix chain 'A' and resid 1236 through 1241 removed outlier: 4.112A pdb=" N VAL A1240 " --> pdb=" O ARG A1236 " (cutoff:3.500A) Processing helix chain 'A' and resid 1242 through 1249 removed outlier: 3.945A pdb=" N LYS A1245 " --> pdb=" O ARG A1242 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ARG A1249 " --> pdb=" O LEU A1246 " (cutoff:3.500A) Processing helix chain 'A' and resid 1250 through 1262 removed outlier: 3.901A pdb=" N THR A1255 " --> pdb=" O GLU A1251 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU A1256 " --> pdb=" O GLY A1252 " (cutoff:3.500A) Processing helix chain 'A' and resid 1269 through 1289 removed outlier: 3.806A pdb=" N ILE A1274 " --> pdb=" O VAL A1270 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL A1275 " --> pdb=" O ALA A1271 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL A1283 " --> pdb=" O PHE A1279 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ILE A1284 " --> pdb=" O ILE A1280 " (cutoff:3.500A) Processing helix chain 'A' and resid 1308 through 1322 Processing helix chain 'A' and resid 1324 through 1332 removed outlier: 3.557A pdb=" N ILE A1328 " --> pdb=" O ALA A1324 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU A1330 " --> pdb=" O GLN A1326 " (cutoff:3.500A) Processing helix chain 'A' and resid 1356 through 1381 removed outlier: 3.669A pdb=" N ILE A1362 " --> pdb=" O TYR A1358 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N SER A1363 " --> pdb=" O TYR A1359 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL A1379 " --> pdb=" O LEU A1375 " (cutoff:3.500A) Processing helix chain 'A' and resid 1383 through 1388 Processing helix chain 'A' and resid 1395 through 1410 removed outlier: 3.552A pdb=" N LEU A1399 " --> pdb=" O GLY A1395 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA A1407 " --> pdb=" O LYS A1403 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLU A1408 " --> pdb=" O ALA A1404 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N TYR A1409 " --> pdb=" O ILE A1405 " (cutoff:3.500A) Processing helix chain 'A' and resid 1425 through 1429 Processing helix chain 'E' and resid 6 through 29 removed outlier: 3.577A pdb=" N VAL E 18 " --> pdb=" O PHE E 14 " (cutoff:3.500A) Processing helix chain 'E' and resid 108 through 127 removed outlier: 3.867A pdb=" N CYS E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N MET E 127 " --> pdb=" O ILE E 123 " (cutoff:3.500A) Processing helix chain 'E' and resid 129 through 135 removed outlier: 3.538A pdb=" N LYS E 132 " --> pdb=" O PHE E 129 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N ASP E 134 " --> pdb=" O LYS E 131 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N TYR E 135 " --> pdb=" O LYS E 132 " (cutoff:3.500A) Processing helix chain 'E' and resid 136 through 163 removed outlier: 3.583A pdb=" N SER E 141 " --> pdb=" O LEU E 137 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N MET E 142 " --> pdb=" O ARG E 138 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N VAL E 153 " --> pdb=" O LEU E 149 " (cutoff:3.500A) Processing helix chain 'E' and resid 179 through 204 removed outlier: 3.741A pdb=" N VAL E 190 " --> pdb=" O CYS E 186 " (cutoff:3.500A) Processing helix chain 'F' and resid 29 through 51 removed outlier: 3.570A pdb=" N THR F 46 " --> pdb=" O GLU F 42 " (cutoff:3.500A) Processing helix chain 'F' and resid 53 through 64 removed outlier: 3.617A pdb=" N GLU F 62 " --> pdb=" O VAL F 58 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N TYR F 64 " --> pdb=" O ILE F 60 " (cutoff:3.500A) Processing helix chain 'F' and resid 76 through 110 removed outlier: 3.680A pdb=" N LEU F 97 " --> pdb=" O ARG F 93 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ARG F 99 " --> pdb=" O LYS F 95 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N LEU F 100 " --> pdb=" O ALA F 96 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ALA F 110 " --> pdb=" O LYS F 106 " (cutoff:3.500A) Processing helix chain 'F' and resid 178 through 188 removed outlier: 3.506A pdb=" N ASN F 183 " --> pdb=" O THR F 179 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N GLU F 184 " --> pdb=" O ILE F 180 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N THR F 188 " --> pdb=" O GLU F 184 " (cutoff:3.500A) Processing helix chain 'F' and resid 191 through 202 Processing helix chain 'F' and resid 239 through 242 Processing helix chain 'F' and resid 243 through 250 Processing helix chain 'F' and resid 263 through 267 Processing helix chain 'F' and resid 268 through 283 removed outlier: 3.629A pdb=" N LYS F 272 " --> pdb=" O GLY F 268 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N THR F 276 " --> pdb=" O LYS F 272 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLU F 283 " --> pdb=" O SER F 279 " (cutoff:3.500A) Processing helix chain 'F' and resid 313 through 325 Processing helix chain 'F' and resid 334 through 346 removed outlier: 3.710A pdb=" N GLY F 338 " --> pdb=" O ASP F 334 " (cutoff:3.500A) Processing helix chain 'F' and resid 371 through 379 removed outlier: 3.547A pdb=" N PHE F 375 " --> pdb=" O ALA F 371 " (cutoff:3.500A) Processing helix chain 'F' and resid 398 through 408 removed outlier: 3.516A pdb=" N GLN F 402 " --> pdb=" O ARG F 398 " (cutoff:3.500A) Processing helix chain 'F' and resid 418 through 422 removed outlier: 3.521A pdb=" N ILE F 421 " --> pdb=" O ILE F 418 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ARG F 422 " --> pdb=" O GLY F 419 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 418 through 422' Processing helix chain 'F' and resid 428 through 433 Processing helix chain 'F' and resid 433 through 438 Processing helix chain 'F' and resid 496 through 501 removed outlier: 3.655A pdb=" N LYS F 500 " --> pdb=" O LEU F 496 " (cutoff:3.500A) Processing helix chain 'F' and resid 542 through 546 removed outlier: 3.620A pdb=" N LYS F 545 " --> pdb=" O ASN F 542 " (cutoff:3.500A) Processing helix chain 'F' and resid 562 through 566 Processing helix chain 'F' and resid 572 through 582 removed outlier: 4.332A pdb=" N ASP F 582 " --> pdb=" O ASN F 578 " (cutoff:3.500A) Processing helix chain 'F' and resid 640 through 649 Processing helix chain 'F' and resid 650 through 651 No H-bonds generated for 'chain 'F' and resid 650 through 651' Processing helix chain 'F' and resid 652 through 654 No H-bonds generated for 'chain 'F' and resid 652 through 654' Processing helix chain 'F' and resid 655 through 660 Processing helix chain 'F' and resid 678 through 693 removed outlier: 3.545A pdb=" N ARG F 692 " --> pdb=" O GLU F 688 " (cutoff:3.500A) Processing helix chain 'F' and resid 701 through 722 removed outlier: 3.702A pdb=" N ILE F 705 " --> pdb=" O ASN F 701 " (cutoff:3.500A) Processing helix chain 'F' and resid 748 through 753 removed outlier: 3.936A pdb=" N GLU F 753 " --> pdb=" O LYS F 749 " (cutoff:3.500A) Processing helix chain 'F' and resid 764 through 773 Processing helix chain 'F' and resid 820 through 830 Processing helix chain 'F' and resid 877 through 882 removed outlier: 3.677A pdb=" N ILE F 881 " --> pdb=" O PHE F 877 " (cutoff:3.500A) Processing helix chain 'F' and resid 882 through 892 Processing helix chain 'F' and resid 1045 through 1049 removed outlier: 3.540A pdb=" N ASP F1048 " --> pdb=" O ASP F1045 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 225 through 228 removed outlier: 3.916A pdb=" N THR A 225 " --> pdb=" O ARG A 262 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ARG A 262 " --> pdb=" O THR A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 955 through 956 Processing sheet with id=AA3, first strand: chain 'A' and resid 971 through 975 Processing sheet with id=AA4, first strand: chain 'F' and resid 68 through 72 Processing sheet with id=AA5, first strand: chain 'F' and resid 144 through 146 removed outlier: 6.122A pdb=" N VAL F 124 " --> pdb=" O GLN F 145 " (cutoff:3.500A) removed outlier: 9.531A pdb=" N VAL F 168 " --> pdb=" O VAL F 125 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N TYR F 127 " --> pdb=" O VAL F 168 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'F' and resid 152 through 153 Processing sheet with id=AA7, first strand: chain 'F' and resid 217 through 220 removed outlier: 3.826A pdb=" N GLY F 488 " --> pdb=" O VAL F 468 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 217 through 220 removed outlier: 3.826A pdb=" N GLY F 488 " --> pdb=" O VAL F 468 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 300 through 302 removed outlier: 6.193A pdb=" N ILE F 360 " --> pdb=" O PHE F 387 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N PHE F 389 " --> pdb=" O ILE F 360 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N LEU F 362 " --> pdb=" O PHE F 389 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N VAL F 391 " --> pdb=" O LEU F 362 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N THR F 364 " --> pdb=" O VAL F 391 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N TYR F 411 " --> pdb=" O VAL F 386 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 523 through 525 removed outlier: 6.159A pdb=" N ALA F 516 " --> pdb=" O LEU F 524 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N PHE F 515 " --> pdb=" O ALA F 623 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU F 624 " --> pdb=" O THR F 610 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU F 626 " --> pdb=" O THR F 608 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLY F 586 " --> pdb=" O TRP F 611 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 661 through 663 removed outlier: 3.941A pdb=" N THR F 744 " --> pdb=" O PHE F 663 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N PHE F 736 " --> pdb=" O GLY F 816 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N LYS F 818 " --> pdb=" O LYS F 733 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 661 through 663 removed outlier: 3.941A pdb=" N THR F 744 " --> pdb=" O PHE F 663 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N PHE F 736 " --> pdb=" O GLY F 816 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N MET F 796 " --> pdb=" O THR F 779 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 803 through 804 Processing sheet with id=AB5, first strand: chain 'F' and resid 862 through 864 removed outlier: 6.664A pdb=" N ILE F 855 " --> pdb=" O LEU F 863 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N ILE F1005 " --> pdb=" O GLU F1022 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 895 through 897 Processing sheet with id=AB7, first strand: chain 'F' and resid 900 through 907 removed outlier: 5.655A pdb=" N TYR F 901 " --> pdb=" O GLN F 981 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N GLN F 981 " --> pdb=" O TYR F 901 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N TYR F 903 " --> pdb=" O THR F 979 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N THR F 979 " --> pdb=" O TYR F 903 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N ILE F 978 " --> pdb=" O SER F1041 " (cutoff:3.500A) 854 hydrogen bonds defined for protein. 2459 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: 3.15 Time building geometry restraints manager: 1.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.04 - 1.20: 1 1.20 - 1.36: 5702 1.36 - 1.51: 6507 1.51 - 1.67: 6312 1.67 - 1.83: 166 Bond restraints: 18688 Sorted by residual: bond pdb=" C ASN A1036 " pdb=" N ASN A1037 " ideal model delta sigma weight residual 1.334 1.044 0.290 1.27e-02 6.20e+03 5.21e+02 bond pdb=" C21 3PE A1908 " pdb=" O21 3PE A1908 " ideal model delta sigma weight residual 1.316 1.455 -0.139 2.00e-02 2.50e+03 4.80e+01 bond pdb=" C21 3PE A1902 " pdb=" O21 3PE A1902 " ideal model delta sigma weight residual 1.316 1.454 -0.138 2.00e-02 2.50e+03 4.78e+01 bond pdb=" C21 3PE A1905 " pdb=" O21 3PE A1905 " ideal model delta sigma weight residual 1.316 1.453 -0.137 2.00e-02 2.50e+03 4.73e+01 bond pdb=" C21 3PE A1906 " pdb=" O21 3PE A1906 " ideal model delta sigma weight residual 1.316 1.453 -0.137 2.00e-02 2.50e+03 4.69e+01 ... (remaining 18683 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.05: 24629 2.05 - 4.11: 510 4.11 - 6.16: 87 6.16 - 8.21: 9 8.21 - 10.27: 25 Bond angle restraints: 25260 Sorted by residual: angle pdb=" N GLY A1062 " pdb=" CA GLY A1062 " pdb=" C GLY A1062 " ideal model delta sigma weight residual 112.77 107.77 5.00 1.28e+00 6.10e-01 1.52e+01 angle pdb=" N ILE A1052 " pdb=" CA ILE A1052 " pdb=" C ILE A1052 " ideal model delta sigma weight residual 110.36 114.20 -3.84 1.05e+00 9.07e-01 1.34e+01 angle pdb=" N LEU A 937 " pdb=" CA LEU A 937 " pdb=" C LEU A 937 " ideal model delta sigma weight residual 112.45 107.54 4.91 1.39e+00 5.18e-01 1.25e+01 angle pdb=" N PHE A1060 " pdb=" CA PHE A1060 " pdb=" C PHE A1060 " ideal model delta sigma weight residual 112.23 107.80 4.43 1.26e+00 6.30e-01 1.24e+01 angle pdb=" C2 3PE A1903 " pdb=" O21 3PE A1903 " pdb=" C21 3PE A1903 " ideal model delta sigma weight residual 121.04 110.77 10.27 3.00e+00 1.11e-01 1.17e+01 ... (remaining 25255 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 9533 17.90 - 35.79: 1120 35.79 - 53.69: 381 53.69 - 71.59: 91 71.59 - 89.49: 33 Dihedral angle restraints: 11158 sinusoidal: 4628 harmonic: 6530 Sorted by residual: dihedral pdb=" CB CYS F 999 " pdb=" SG CYS F 999 " pdb=" SG CYS F1029 " pdb=" CB CYS F1029 " ideal model delta sinusoidal sigma weight residual 93.00 -178.32 -88.68 1 1.00e+01 1.00e-02 9.38e+01 dihedral pdb=" CB CYS F 670 " pdb=" SG CYS F 670 " pdb=" SG CYS F 700 " pdb=" CB CYS F 700 " ideal model delta sinusoidal sigma weight residual -86.00 -158.79 72.79 1 1.00e+01 1.00e-02 6.76e+01 dihedral pdb=" CB CYS A 226 " pdb=" SG CYS A 226 " pdb=" SG CYS A 254 " pdb=" CB CYS A 254 " ideal model delta sinusoidal sigma weight residual 93.00 161.60 -68.60 1 1.00e+01 1.00e-02 6.10e+01 ... (remaining 11155 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 1954 0.040 - 0.080: 682 0.080 - 0.121: 154 0.121 - 0.161: 24 0.161 - 0.201: 3 Chirality restraints: 2817 Sorted by residual: chirality pdb=" CA PHE A 314 " pdb=" N PHE A 314 " pdb=" C PHE A 314 " pdb=" CB PHE A 314 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.01e+00 chirality pdb=" CA VAL A1034 " pdb=" N VAL A1034 " pdb=" C VAL A1034 " pdb=" CB VAL A1034 " both_signs ideal model delta sigma weight residual False 2.44 2.64 -0.20 2.00e-01 2.50e+01 9.72e-01 chirality pdb=" CA GLU A 76 " pdb=" N GLU A 76 " pdb=" C GLU A 76 " pdb=" CB GLU A 76 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.34e-01 ... (remaining 2814 not shown) Planarity restraints: 3153 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A 51 " 0.040 5.00e-02 4.00e+02 6.11e-02 5.97e+00 pdb=" N PRO A 52 " -0.106 5.00e-02 4.00e+02 pdb=" CA PRO A 52 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 52 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU F 141 " 0.036 5.00e-02 4.00e+02 5.48e-02 4.80e+00 pdb=" N PRO F 142 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO F 142 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO F 142 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TRP A 300 " -0.010 2.00e-02 2.50e+03 2.02e-02 4.09e+00 pdb=" C TRP A 300 " 0.035 2.00e-02 2.50e+03 pdb=" O TRP A 300 " -0.013 2.00e-02 2.50e+03 pdb=" N VAL A 301 " -0.012 2.00e-02 2.50e+03 ... (remaining 3150 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 207 2.61 - 3.18: 16162 3.18 - 3.76: 26683 3.76 - 4.33: 38099 4.33 - 4.90: 63469 Nonbonded interactions: 144620 Sorted by model distance: nonbonded pdb=" O TYR A 210 " pdb=" OH TYR A 313 " model vdw 2.040 3.040 nonbonded pdb=" N 3PE A1910 " pdb=" O14 3PE A1910 " model vdw 2.079 3.120 nonbonded pdb=" N 3PE A1903 " pdb=" O14 3PE A1903 " model vdw 2.080 3.120 nonbonded pdb=" OD2 ASP F 154 " pdb=" OH TYR F 163 " model vdw 2.100 3.040 nonbonded pdb=" O TYR F 61 " pdb=" OH TYR F 68 " model vdw 2.135 3.040 ... (remaining 144615 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.50 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: 1.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 17.750 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.050 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: 0.000 Load rotamer database and sin/cos tables:1.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 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 : 0.012 0.884 18705 Z= 1.099 Angle : 0.757 10.266 25284 Z= 0.386 Chirality : 0.042 0.201 2817 Planarity : 0.004 0.061 3153 Dihedral : 18.048 89.487 6904 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 13.69 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.57 % Favored : 93.25 % Rotamer: Outliers : 7.64 % Allowed : 20.88 % Favored : 71.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.99 (0.15), residues: 2194 helix: -1.82 (0.13), residues: 1070 sheet: -2.70 (0.33), residues: 192 loop : -3.62 (0.17), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 769 TYR 0.016 0.001 TYR A1109 PHE 0.016 0.001 PHE F 157 TRP 0.023 0.001 TRP F 187 HIS 0.003 0.001 HIS F 888 Details of bonding type rmsd/Z covalent geometry : bond 0.00628 / 0.33 (18688) covalent geometry : angle 0.75573 / 0.39 (25260) SS BOND : bond 0.00374 / 0.27 ( 12) SS BOND : angle 1.44121 / 0.88 ( 24) hydrogen bonds : bond 0.16517 / 10.49 ( 831) hydrogen bonds : angle 6.67026 / 4.75 ( 2459) Misc. bond : bond 0.64095 / 32.46 ( 5) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4388 Ramachandran restraints generated. 2194 Oldfield, 0 Emsley, 2194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4388 Ramachandran restraints generated. 2194 Oldfield, 0 Emsley, 2194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 150 poor density : 282 time to evaluate : 0.702 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 92 PHE cc_start: 0.8495 (t80) cc_final: 0.8249 (t80) REVERT: A 343 LYS cc_start: 0.5271 (ptpp) cc_final: 0.5063 (pttt) REVERT: A 828 ARG cc_start: 0.4607 (ttp-170) cc_final: 0.4278 (tpp-160) REVERT: A 938 LEU cc_start: 0.8497 (OUTLIER) cc_final: 0.8109 (mp) REVERT: A 1040 GLU cc_start: 0.7960 (OUTLIER) cc_final: 0.7723 (pm20) REVERT: A 1060 PHE cc_start: 0.7847 (OUTLIER) cc_final: 0.6656 (t80) REVERT: A 1186 ASP cc_start: 0.8159 (t0) cc_final: 0.7872 (t0) REVERT: A 1205 PHE cc_start: 0.4638 (t80) cc_final: 0.4438 (t80) REVERT: A 1316 LEU cc_start: 0.9172 (OUTLIER) cc_final: 0.8752 (mp) REVERT: A 1381 MET cc_start: 0.6965 (OUTLIER) cc_final: 0.6293 (tmm) REVERT: E 189 PHE cc_start: 0.7287 (t80) cc_final: 0.6984 (t80) REVERT: F 281 MET cc_start: 0.8844 (tpp) cc_final: 0.8426 (ttm) REVERT: F 348 ASN cc_start: 0.8484 (OUTLIER) cc_final: 0.8271 (t0) REVERT: F 368 GLU cc_start: 0.7367 (pt0) cc_final: 0.7133 (pt0) REVERT: F 380 LYS cc_start: 0.8418 (ttpp) cc_final: 0.7895 (ttpt) REVERT: F 413 TYR cc_start: 0.9275 (m-80) cc_final: 0.8964 (m-80) REVERT: F 442 LYS cc_start: 0.8742 (ttpp) cc_final: 0.8386 (ttpt) REVERT: F 604 LYS cc_start: 0.8378 (mtmm) cc_final: 0.8132 (mttm) REVERT: F 858 ASP cc_start: 0.7960 (p0) cc_final: 0.7630 (p0) outliers start: 150 outliers final: 112 residues processed: 410 average time/residue: 0.1264 time to fit residues: 79.8634 Evaluate side-chains 361 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 243 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 65 CYS Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain A residue 468 ASN Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 510 GLU Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 541 TYR Chi-restraints excluded: chain A residue 547 ASN Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 647 CYS Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 792 CYS Chi-restraints excluded: chain A residue 804 PHE Chi-restraints excluded: chain A residue 819 GLU Chi-restraints excluded: chain A residue 873 LEU Chi-restraints excluded: chain A residue 892 VAL Chi-restraints excluded: chain A residue 895 ILE Chi-restraints excluded: chain A residue 899 LEU Chi-restraints excluded: chain A residue 925 ILE Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 933 LEU Chi-restraints excluded: chain A residue 934 VAL Chi-restraints excluded: chain A residue 935 THR Chi-restraints excluded: chain A residue 938 LEU Chi-restraints excluded: chain A residue 964 THR Chi-restraints excluded: chain A residue 999 ASN Chi-restraints excluded: chain A residue 1007 LEU Chi-restraints excluded: chain A residue 1011 SER Chi-restraints excluded: chain A residue 1029 GLU Chi-restraints excluded: chain A residue 1038 ARG Chi-restraints excluded: chain A residue 1039 VAL Chi-restraints excluded: chain A residue 1040 GLU Chi-restraints excluded: chain A residue 1041 MET Chi-restraints excluded: chain A residue 1047 ILE Chi-restraints excluded: chain A residue 1050 ILE Chi-restraints excluded: chain A residue 1052 ILE Chi-restraints excluded: chain A residue 1054 PHE Chi-restraints excluded: chain A residue 1059 ILE Chi-restraints excluded: chain A residue 1060 PHE Chi-restraints excluded: chain A residue 1067 THR Chi-restraints excluded: chain A residue 1069 GLN Chi-restraints excluded: chain A residue 1082 ASP Chi-restraints excluded: chain A residue 1093 LEU Chi-restraints excluded: chain A residue 1115 VAL Chi-restraints excluded: chain A residue 1141 HIS Chi-restraints excluded: chain A residue 1149 ILE Chi-restraints excluded: chain A residue 1159 ILE Chi-restraints excluded: chain A residue 1163 LEU Chi-restraints excluded: chain A residue 1198 ILE Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1255 THR Chi-restraints excluded: chain A residue 1272 LEU Chi-restraints excluded: chain A residue 1273 LEU Chi-restraints excluded: chain A residue 1289 PHE Chi-restraints excluded: chain A residue 1295 VAL Chi-restraints excluded: chain A residue 1316 LEU Chi-restraints excluded: chain A residue 1380 ILE Chi-restraints excluded: chain A residue 1381 MET Chi-restraints excluded: chain A residue 1397 HIS Chi-restraints excluded: chain E residue 27 VAL Chi-restraints excluded: chain E residue 157 VAL Chi-restraints excluded: chain E residue 179 SER Chi-restraints excluded: chain F residue 32 THR Chi-restraints excluded: chain F residue 59 ASP Chi-restraints excluded: chain F residue 94 SER Chi-restraints excluded: chain F residue 116 ASP Chi-restraints excluded: chain F residue 125 VAL Chi-restraints excluded: chain F residue 181 VAL Chi-restraints excluded: chain F residue 205 LEU Chi-restraints excluded: chain F residue 240 VAL Chi-restraints excluded: chain F residue 270 THR Chi-restraints excluded: chain F residue 303 VAL Chi-restraints excluded: chain F residue 348 ASN Chi-restraints excluded: chain F residue 360 ILE Chi-restraints excluded: chain F residue 465 THR Chi-restraints excluded: chain F residue 478 LYS Chi-restraints excluded: chain F residue 479 THR Chi-restraints excluded: chain F residue 552 ASN Chi-restraints excluded: chain F residue 594 VAL Chi-restraints excluded: chain F residue 610 THR Chi-restraints excluded: chain F residue 612 THR Chi-restraints excluded: chain F residue 652 LYS Chi-restraints excluded: chain F residue 680 THR Chi-restraints excluded: chain F residue 694 THR Chi-restraints excluded: chain F residue 729 ILE Chi-restraints excluded: chain F residue 735 ARG Chi-restraints excluded: chain F residue 739 THR Chi-restraints excluded: chain F residue 744 THR Chi-restraints excluded: chain F residue 798 SER Chi-restraints excluded: chain F residue 815 VAL Chi-restraints excluded: chain F residue 817 ILE Chi-restraints excluded: chain F residue 821 VAL Chi-restraints excluded: chain F residue 853 CYS Chi-restraints excluded: chain F residue 874 ILE Chi-restraints excluded: chain F residue 997 LEU Chi-restraints excluded: chain F residue 1002 CYS Chi-restraints excluded: chain F residue 1008 VAL Chi-restraints excluded: chain F residue 1014 THR Chi-restraints excluded: chain F residue 1019 ILE Chi-restraints excluded: chain F residue 1068 LEU Chi-restraints excluded: chain F residue 1074 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 216 optimal weight: 6.9990 chunk 98 optimal weight: 3.9990 chunk 194 optimal weight: 0.9990 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 6.9990 chunk 200 optimal weight: 6.9990 chunk 212 optimal weight: 2.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 ASN A 307 ASN ** A 453 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 547 ASN A 599 ASN A 797 ASN A 948 GLN A1058 ASN A1085 GLN A1108 GLN A1138 GLN A1154 ASN F 65 GLN F 74 ASN F 307 GLN ** F 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 484 GLN F 511 ASN F 644 GLN F 679 ASN F 685 ASN F 888 HIS F 983 GLN ** F1007 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F1065 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.145586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.110048 restraints weight = 26809.175| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 2.34 r_work: 0.3022 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2886 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2881 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2881 r_free = 0.2881 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2881 r_free = 0.2881 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2881 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.1176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 18705 Z= 0.182 Angle : 0.603 8.040 25284 Z= 0.315 Chirality : 0.043 0.161 2817 Planarity : 0.005 0.067 3153 Dihedral : 13.672 89.478 2898 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.66 % Favored : 92.29 % Rotamer: Outliers : 7.28 % Allowed : 22.91 % Favored : 69.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.50 (0.17), residues: 2194 helix: -0.37 (0.15), residues: 1084 sheet: -2.37 (0.33), residues: 208 loop : -3.12 (0.19), residues: 902 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 138 TYR 0.012 0.001 TYR A1109 PHE 0.022 0.001 PHE A1185 TRP 0.019 0.001 TRP F 187 HIS 0.003 0.001 HIS F 888 Details of bonding type rmsd/Z covalent geometry : bond 0.00431 / 0.18 (18688) covalent geometry : angle 0.60246 / 0.31 (25260) SS BOND : bond 0.00360 / 0.26 ( 12) SS BOND : angle 1.25690 / 0.83 ( 24) hydrogen bonds : bond 0.04186 / 2.70 ( 831) hydrogen bonds : angle 4.50443 / 3.18 ( 2459) Misc. bond : bond 0.00068 / 0.03 ( 5) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4388 Ramachandran restraints generated. 2194 Oldfield, 0 Emsley, 2194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4388 Ramachandran restraints generated. 2194 Oldfield, 0 Emsley, 2194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 269 time to evaluate : 0.680 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.9217 (OUTLIER) cc_final: 0.8602 (mtm) REVERT: A 92 PHE cc_start: 0.8432 (t80) cc_final: 0.8172 (t80) REVERT: A 182 LEU cc_start: 0.8365 (OUTLIER) cc_final: 0.8095 (tt) REVERT: A 305 ILE cc_start: 0.8847 (tt) cc_final: 0.8619 (tt) REVERT: A 340 GLU cc_start: 0.7036 (mm-30) cc_final: 0.6628 (mm-30) REVERT: A 483 MET cc_start: 0.3330 (tmm) cc_final: 0.3041 (tpt) REVERT: A 828 ARG cc_start: 0.4925 (ttp-170) cc_final: 0.4176 (tpp-160) REVERT: A 938 LEU cc_start: 0.8191 (OUTLIER) cc_final: 0.7936 (mp) REVERT: A 1060 PHE cc_start: 0.8146 (OUTLIER) cc_final: 0.7205 (t80) REVERT: A 1186 ASP cc_start: 0.8727 (t0) cc_final: 0.8369 (t0) REVERT: A 1205 PHE cc_start: 0.4345 (t80) cc_final: 0.4012 (t80) REVERT: A 1286 MET cc_start: 0.9058 (mtp) cc_final: 0.8762 (mtm) REVERT: A 1366 MET cc_start: 0.8782 (OUTLIER) cc_final: 0.8555 (mtp) REVERT: E 189 PHE cc_start: 0.6808 (t80) cc_final: 0.6563 (t80) REVERT: F 248 GLN cc_start: 0.9324 (OUTLIER) cc_final: 0.8872 (pp30) REVERT: F 281 MET cc_start: 0.9135 (tpp) cc_final: 0.8797 (ttm) REVERT: F 380 LYS cc_start: 0.8800 (ttpp) cc_final: 0.8267 (ttpt) REVERT: F 413 TYR cc_start: 0.9519 (m-80) cc_final: 0.9189 (m-80) REVERT: F 442 LYS cc_start: 0.9155 (ttpp) cc_final: 0.8864 (ttpt) REVERT: F 593 LEU cc_start: 0.9009 (OUTLIER) cc_final: 0.8745 (pp) REVERT: F 604 LYS cc_start: 0.8812 (mtmm) cc_final: 0.8397 (mttm) REVERT: F 669 TYR cc_start: 0.8482 (m-80) cc_final: 0.8248 (m-80) REVERT: F 858 ASP cc_start: 0.8629 (p0) cc_final: 0.8327 (p0) REVERT: F 1005 ILE cc_start: 0.8679 (mt) cc_final: 0.8410 (mt) outliers start: 143 outliers final: 101 residues processed: 389 average time/residue: 0.1129 time to fit residues: 70.1091 Evaluate side-chains 355 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 247 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 468 ASN Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain A residue 510 GLU Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 541 TYR Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 788 VAL Chi-restraints excluded: chain A residue 792 CYS Chi-restraints excluded: chain A residue 804 PHE Chi-restraints excluded: chain A residue 876 VAL Chi-restraints excluded: chain A residue 933 LEU Chi-restraints excluded: chain A residue 934 VAL Chi-restraints excluded: chain A residue 935 THR Chi-restraints excluded: chain A residue 938 LEU Chi-restraints excluded: chain A residue 964 THR Chi-restraints excluded: chain A residue 1007 LEU Chi-restraints excluded: chain A residue 1029 GLU Chi-restraints excluded: chain A residue 1039 VAL Chi-restraints excluded: chain A residue 1052 ILE Chi-restraints excluded: chain A residue 1058 ASN Chi-restraints excluded: chain A residue 1060 PHE Chi-restraints excluded: chain A residue 1069 GLN Chi-restraints excluded: chain A residue 1108 GLN Chi-restraints excluded: chain A residue 1115 VAL Chi-restraints excluded: chain A residue 1141 HIS Chi-restraints excluded: chain A residue 1149 ILE Chi-restraints excluded: chain A residue 1163 LEU Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1267 LEU Chi-restraints excluded: chain A residue 1272 LEU Chi-restraints excluded: chain A residue 1289 PHE Chi-restraints excluded: chain A residue 1343 ASP Chi-restraints excluded: chain A residue 1366 MET Chi-restraints excluded: chain A residue 1400 ASP Chi-restraints excluded: chain E residue 134 ASP Chi-restraints excluded: chain E residue 162 VAL Chi-restraints excluded: chain F residue 32 THR Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 61 TYR Chi-restraints excluded: chain F residue 74 ASN Chi-restraints excluded: chain F residue 116 ASP Chi-restraints excluded: chain F residue 124 VAL Chi-restraints excluded: chain F residue 125 VAL Chi-restraints excluded: chain F residue 181 VAL Chi-restraints excluded: chain F residue 200 GLU Chi-restraints excluded: chain F residue 205 LEU Chi-restraints excluded: chain F residue 240 VAL Chi-restraints excluded: chain F residue 248 GLN Chi-restraints excluded: chain F residue 270 THR Chi-restraints excluded: chain F residue 303 VAL Chi-restraints excluded: chain F residue 348 ASN Chi-restraints excluded: chain F residue 360 ILE Chi-restraints excluded: chain F residue 401 ILE Chi-restraints excluded: chain F residue 421 ILE Chi-restraints excluded: chain F residue 423 ILE Chi-restraints excluded: chain F residue 476 GLU Chi-restraints excluded: chain F residue 479 THR Chi-restraints excluded: chain F residue 523 VAL Chi-restraints excluded: chain F residue 543 LEU Chi-restraints excluded: chain F residue 593 LEU Chi-restraints excluded: chain F residue 594 VAL Chi-restraints excluded: chain F residue 608 THR Chi-restraints excluded: chain F residue 610 THR Chi-restraints excluded: chain F residue 612 THR Chi-restraints excluded: chain F residue 617 THR Chi-restraints excluded: chain F residue 652 LYS Chi-restraints excluded: chain F residue 677 ASP Chi-restraints excluded: chain F residue 680 THR Chi-restraints excluded: chain F residue 694 THR Chi-restraints excluded: chain F residue 735 ARG Chi-restraints excluded: chain F residue 739 THR Chi-restraints excluded: chain F residue 744 THR Chi-restraints excluded: chain F residue 815 VAL Chi-restraints excluded: chain F residue 817 ILE Chi-restraints excluded: chain F residue 821 VAL Chi-restraints excluded: chain F residue 850 VAL Chi-restraints excluded: chain F residue 853 CYS Chi-restraints excluded: chain F residue 982 THR Chi-restraints excluded: chain F residue 997 LEU Chi-restraints excluded: chain F residue 1002 CYS Chi-restraints excluded: chain F residue 1008 VAL Chi-restraints excluded: chain F residue 1014 THR Chi-restraints excluded: chain F residue 1019 ILE Chi-restraints excluded: chain F residue 1027 CYS Chi-restraints excluded: chain F residue 1038 GLU Chi-restraints excluded: chain F residue 1062 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 48 optimal weight: 0.9990 chunk 209 optimal weight: 8.9990 chunk 189 optimal weight: 4.9990 chunk 18 optimal weight: 0.9980 chunk 10 optimal weight: 8.9990 chunk 160 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 79 optimal weight: 0.9990 chunk 71 optimal weight: 5.9990 chunk 186 optimal weight: 6.9990 chunk 123 optimal weight: 6.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 ASN A 307 ASN A 327 ASN A 453 HIS A 547 ASN A1108 GLN F 74 ASN ** F 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 981 GLN ** F1007 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F1065 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.147026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.111217 restraints weight = 26920.509| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 2.37 r_work: 0.3041 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2907 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2910 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2910 r_free = 0.2910 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2910 r_free = 0.2910 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2910 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.1501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 18705 Z= 0.142 Angle : 0.554 7.230 25284 Z= 0.289 Chirality : 0.042 0.244 2817 Planarity : 0.004 0.059 3153 Dihedral : 12.249 78.759 2801 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.34 % Favored : 93.62 % Rotamer: Outliers : 6.98 % Allowed : 23.17 % Favored : 69.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.83 (0.18), residues: 2194 helix: 0.21 (0.16), residues: 1089 sheet: -2.07 (0.32), residues: 221 loop : -2.86 (0.19), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 138 TYR 0.012 0.001 TYR A1109 PHE 0.020 0.001 PHE A1185 TRP 0.019 0.001 TRP F 187 HIS 0.002 0.001 HIS F 888 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.14 (18688) covalent geometry : angle 0.55351 / 0.29 (25260) SS BOND : bond 0.00324 / 0.24 ( 12) SS BOND : angle 1.09764 / 0.72 ( 24) hydrogen bonds : bond 0.03681 / 2.39 ( 831) hydrogen bonds : angle 4.20586 / 2.96 ( 2459) Misc. bond : bond 0.00052 / 0.03 ( 5) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4388 Ramachandran restraints generated. 2194 Oldfield, 0 Emsley, 2194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4388 Ramachandran restraints generated. 2194 Oldfield, 0 Emsley, 2194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 265 time to evaluate : 0.673 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.9193 (OUTLIER) cc_final: 0.8566 (mtm) REVERT: A 182 LEU cc_start: 0.8319 (OUTLIER) cc_final: 0.8030 (tt) REVERT: A 183 GLN cc_start: 0.8284 (OUTLIER) cc_final: 0.7545 (mt0) REVERT: A 305 ILE cc_start: 0.8847 (tt) cc_final: 0.8606 (tt) REVERT: A 464 GLN cc_start: 0.7660 (OUTLIER) cc_final: 0.7016 (mt0) REVERT: A 483 MET cc_start: 0.3156 (tmm) cc_final: 0.2795 (tpt) REVERT: A 652 LEU cc_start: 0.9165 (tt) cc_final: 0.8952 (tt) REVERT: A 828 ARG cc_start: 0.4814 (ttp-170) cc_final: 0.4090 (tpp-160) REVERT: A 938 LEU cc_start: 0.8259 (OUTLIER) cc_final: 0.8014 (mp) REVERT: A 1018 GLN cc_start: 0.8873 (OUTLIER) cc_final: 0.8356 (mt0) REVERT: A 1029 GLU cc_start: 0.7844 (OUTLIER) cc_final: 0.7390 (tp30) REVERT: A 1060 PHE cc_start: 0.8008 (OUTLIER) cc_final: 0.7048 (t80) REVERT: A 1101 TYR cc_start: 0.7220 (m-80) cc_final: 0.6552 (m-80) REVERT: A 1168 LYS cc_start: 0.7753 (mtpp) cc_final: 0.7544 (mtmt) REVERT: A 1186 ASP cc_start: 0.8666 (t0) cc_final: 0.8176 (t0) REVERT: A 1205 PHE cc_start: 0.4199 (t80) cc_final: 0.3869 (t80) REVERT: E 110 ILE cc_start: 0.8382 (OUTLIER) cc_final: 0.7929 (mt) REVERT: F 114 ARG cc_start: 0.8391 (mtp85) cc_final: 0.7983 (mtt180) REVERT: F 281 MET cc_start: 0.9127 (tpp) cc_final: 0.8787 (ttm) REVERT: F 380 LYS cc_start: 0.8801 (ttpp) cc_final: 0.8251 (ttpt) REVERT: F 593 LEU cc_start: 0.8931 (OUTLIER) cc_final: 0.8614 (pp) REVERT: F 604 LYS cc_start: 0.8773 (mtmm) cc_final: 0.8355 (mttm) REVERT: F 728 ASN cc_start: 0.8493 (m-40) cc_final: 0.7694 (t0) REVERT: F 858 ASP cc_start: 0.8612 (p0) cc_final: 0.8251 (p0) REVERT: F 1005 ILE cc_start: 0.8716 (mt) cc_final: 0.8432 (mt) outliers start: 137 outliers final: 95 residues processed: 375 average time/residue: 0.1241 time to fit residues: 73.8166 Evaluate side-chains 356 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 251 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 183 GLN Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 453 HIS Chi-restraints excluded: chain A residue 464 GLN Chi-restraints excluded: chain A residue 468 ASN Chi-restraints excluded: chain A residue 476 THR Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain A residue 510 GLU Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 788 VAL Chi-restraints excluded: chain A residue 792 CYS Chi-restraints excluded: chain A residue 876 VAL Chi-restraints excluded: chain A residue 934 VAL Chi-restraints excluded: chain A residue 938 LEU Chi-restraints excluded: chain A residue 964 THR Chi-restraints excluded: chain A residue 1007 LEU Chi-restraints excluded: chain A residue 1018 GLN Chi-restraints excluded: chain A residue 1029 GLU Chi-restraints excluded: chain A residue 1039 VAL Chi-restraints excluded: chain A residue 1052 ILE Chi-restraints excluded: chain A residue 1060 PHE Chi-restraints excluded: chain A residue 1069 GLN Chi-restraints excluded: chain A residue 1108 GLN Chi-restraints excluded: chain A residue 1141 HIS Chi-restraints excluded: chain A residue 1149 ILE Chi-restraints excluded: chain A residue 1163 LEU Chi-restraints excluded: chain A residue 1240 VAL Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1267 LEU Chi-restraints excluded: chain A residue 1272 LEU Chi-restraints excluded: chain A residue 1273 LEU Chi-restraints excluded: chain A residue 1289 PHE Chi-restraints excluded: chain A residue 1343 ASP Chi-restraints excluded: chain A residue 1380 ILE Chi-restraints excluded: chain A residue 1388 THR Chi-restraints excluded: chain A residue 1400 ASP Chi-restraints excluded: chain E residue 24 MET Chi-restraints excluded: chain E residue 110 ILE Chi-restraints excluded: chain E residue 134 ASP Chi-restraints excluded: chain E residue 162 VAL Chi-restraints excluded: chain F residue 32 THR Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 61 TYR Chi-restraints excluded: chain F residue 74 ASN Chi-restraints excluded: chain F residue 116 ASP Chi-restraints excluded: chain F residue 125 VAL Chi-restraints excluded: chain F residue 160 GLN Chi-restraints excluded: chain F residue 181 VAL Chi-restraints excluded: chain F residue 194 VAL Chi-restraints excluded: chain F residue 200 GLU Chi-restraints excluded: chain F residue 205 LEU Chi-restraints excluded: chain F residue 240 VAL Chi-restraints excluded: chain F residue 270 THR Chi-restraints excluded: chain F residue 303 VAL Chi-restraints excluded: chain F residue 351 VAL Chi-restraints excluded: chain F residue 360 ILE Chi-restraints excluded: chain F residue 401 ILE Chi-restraints excluded: chain F residue 423 ILE Chi-restraints excluded: chain F residue 523 VAL Chi-restraints excluded: chain F residue 524 LEU Chi-restraints excluded: chain F residue 543 LEU Chi-restraints excluded: chain F residue 593 LEU Chi-restraints excluded: chain F residue 610 THR Chi-restraints excluded: chain F residue 612 THR Chi-restraints excluded: chain F residue 617 THR Chi-restraints excluded: chain F residue 652 LYS Chi-restraints excluded: chain F residue 677 ASP Chi-restraints excluded: chain F residue 680 THR Chi-restraints excluded: chain F residue 694 THR Chi-restraints excluded: chain F residue 735 ARG Chi-restraints excluded: chain F residue 739 THR Chi-restraints excluded: chain F residue 744 THR Chi-restraints excluded: chain F residue 815 VAL Chi-restraints excluded: chain F residue 817 ILE Chi-restraints excluded: chain F residue 821 VAL Chi-restraints excluded: chain F residue 850 VAL Chi-restraints excluded: chain F residue 982 THR Chi-restraints excluded: chain F residue 997 LEU Chi-restraints excluded: chain F residue 1002 CYS Chi-restraints excluded: chain F residue 1008 VAL Chi-restraints excluded: chain F residue 1014 THR Chi-restraints excluded: chain F residue 1019 ILE Chi-restraints excluded: chain F residue 1026 THR Chi-restraints excluded: chain F residue 1027 CYS Chi-restraints excluded: chain F residue 1062 CYS Chi-restraints excluded: chain F residue 1068 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 143 optimal weight: 0.9990 chunk 66 optimal weight: 0.9990 chunk 207 optimal weight: 0.1980 chunk 131 optimal weight: 0.7980 chunk 153 optimal weight: 0.9980 chunk 99 optimal weight: 0.9990 chunk 157 optimal weight: 1.9990 chunk 37 optimal weight: 0.0570 chunk 118 optimal weight: 3.9990 chunk 127 optimal weight: 6.9990 chunk 86 optimal weight: 3.9990 overall best weight: 0.6100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 ASN A 302 ASN A 307 ASN A 547 ASN A1108 GLN F 74 ASN ** F 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1007 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F1039 GLN F1065 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.149510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.114021 restraints weight = 26945.195| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 2.37 r_work: 0.3082 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2945 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2943 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2943 r_free = 0.2943 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2943 r_free = 0.2943 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2943 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.1825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 18705 Z= 0.105 Angle : 0.525 9.450 25284 Z= 0.273 Chirality : 0.040 0.155 2817 Planarity : 0.004 0.060 3153 Dihedral : 11.418 59.880 2787 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.61 % Favored : 94.35 % Rotamer: Outliers : 5.50 % Allowed : 24.59 % Favored : 69.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.35 (0.18), residues: 2194 helix: 0.57 (0.16), residues: 1092 sheet: -1.90 (0.32), residues: 219 loop : -2.57 (0.20), residues: 883 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1099 TYR 0.013 0.001 TYR E 176 PHE 0.020 0.001 PHE E 182 TRP 0.019 0.001 TRP F 187 HIS 0.018 0.001 HIS A 453 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.11 (18688) covalent geometry : angle 0.52121 / 0.27 (25260) SS BOND : bond 0.00371 / 0.26 ( 12) SS BOND : angle 2.18552 / 1.11 ( 24) hydrogen bonds : bond 0.03196 / 2.09 ( 831) hydrogen bonds : angle 3.97399 / 2.80 ( 2459) Misc. bond : bond 0.00158 / 0.08 ( 5) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4388 Ramachandran restraints generated. 2194 Oldfield, 0 Emsley, 2194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4388 Ramachandran restraints generated. 2194 Oldfield, 0 Emsley, 2194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 273 time to evaluate : 0.625 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 182 LEU cc_start: 0.8232 (OUTLIER) cc_final: 0.7931 (tt) REVERT: A 183 GLN cc_start: 0.8230 (OUTLIER) cc_final: 0.7483 (mt0) REVERT: A 305 ILE cc_start: 0.8809 (tt) cc_final: 0.8575 (tt) REVERT: A 483 MET cc_start: 0.3326 (tmm) cc_final: 0.2820 (tpt) REVERT: A 652 LEU cc_start: 0.9128 (tt) cc_final: 0.8844 (tt) REVERT: A 828 ARG cc_start: 0.4625 (ttp-170) cc_final: 0.4064 (tpp-160) REVERT: A 916 HIS cc_start: 0.4145 (t-90) cc_final: 0.2334 (m90) REVERT: A 1060 PHE cc_start: 0.8019 (OUTLIER) cc_final: 0.7020 (t80) REVERT: A 1186 ASP cc_start: 0.8522 (t0) cc_final: 0.8023 (t0) REVERT: A 1205 PHE cc_start: 0.4176 (t80) cc_final: 0.3899 (t80) REVERT: F 114 ARG cc_start: 0.8278 (mtp85) cc_final: 0.7840 (mtt180) REVERT: F 281 MET cc_start: 0.9102 (tpp) cc_final: 0.8797 (ttm) REVERT: F 380 LYS cc_start: 0.8875 (ttpp) cc_final: 0.8331 (ttpt) REVERT: F 442 LYS cc_start: 0.9033 (ttpp) cc_final: 0.8795 (ttpt) REVERT: F 593 LEU cc_start: 0.8865 (OUTLIER) cc_final: 0.8536 (pp) REVERT: F 669 TYR cc_start: 0.8030 (m-80) cc_final: 0.7821 (m-80) REVERT: F 727 LYS cc_start: 0.8771 (mmtm) cc_final: 0.8548 (mmtm) REVERT: F 728 ASN cc_start: 0.8489 (m-40) cc_final: 0.7693 (t0) REVERT: F 858 ASP cc_start: 0.8606 (p0) cc_final: 0.8241 (p0) REVERT: F 1005 ILE cc_start: 0.8674 (mt) cc_final: 0.8405 (mt) outliers start: 108 outliers final: 80 residues processed: 355 average time/residue: 0.1163 time to fit residues: 65.9653 Evaluate side-chains 344 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 260 time to evaluate : 0.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 183 GLN Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain A residue 479 MET Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 647 CYS Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 792 CYS Chi-restraints excluded: chain A residue 876 VAL Chi-restraints excluded: chain A residue 925 ILE Chi-restraints excluded: chain A residue 933 LEU Chi-restraints excluded: chain A residue 934 VAL Chi-restraints excluded: chain A residue 1007 LEU Chi-restraints excluded: chain A residue 1039 VAL Chi-restraints excluded: chain A residue 1060 PHE Chi-restraints excluded: chain A residue 1069 GLN Chi-restraints excluded: chain A residue 1108 GLN Chi-restraints excluded: chain A residue 1111 VAL Chi-restraints excluded: chain A residue 1141 HIS Chi-restraints excluded: chain A residue 1149 ILE Chi-restraints excluded: chain A residue 1240 VAL Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1267 LEU Chi-restraints excluded: chain A residue 1272 LEU Chi-restraints excluded: chain A residue 1289 PHE Chi-restraints excluded: chain A residue 1343 ASP Chi-restraints excluded: chain A residue 1388 THR Chi-restraints excluded: chain A residue 1397 HIS Chi-restraints excluded: chain A residue 1400 ASP Chi-restraints excluded: chain E residue 24 MET Chi-restraints excluded: chain F residue 32 THR Chi-restraints excluded: chain F residue 61 TYR Chi-restraints excluded: chain F residue 116 ASP Chi-restraints excluded: chain F residue 125 VAL Chi-restraints excluded: chain F residue 194 VAL Chi-restraints excluded: chain F residue 205 LEU Chi-restraints excluded: chain F residue 270 THR Chi-restraints excluded: chain F residue 303 VAL Chi-restraints excluded: chain F residue 351 VAL Chi-restraints excluded: chain F residue 360 ILE Chi-restraints excluded: chain F residue 401 ILE Chi-restraints excluded: chain F residue 524 LEU Chi-restraints excluded: chain F residue 543 LEU Chi-restraints excluded: chain F residue 593 LEU Chi-restraints excluded: chain F residue 610 THR Chi-restraints excluded: chain F residue 612 THR Chi-restraints excluded: chain F residue 617 THR Chi-restraints excluded: chain F residue 652 LYS Chi-restraints excluded: chain F residue 677 ASP Chi-restraints excluded: chain F residue 680 THR Chi-restraints excluded: chain F residue 694 THR Chi-restraints excluded: chain F residue 735 ARG Chi-restraints excluded: chain F residue 739 THR Chi-restraints excluded: chain F residue 744 THR Chi-restraints excluded: chain F residue 817 ILE Chi-restraints excluded: chain F residue 821 VAL Chi-restraints excluded: chain F residue 850 VAL Chi-restraints excluded: chain F residue 853 CYS Chi-restraints excluded: chain F residue 982 THR Chi-restraints excluded: chain F residue 1002 CYS Chi-restraints excluded: chain F residue 1008 VAL Chi-restraints excluded: chain F residue 1014 THR Chi-restraints excluded: chain F residue 1019 ILE Chi-restraints excluded: chain F residue 1026 THR Chi-restraints excluded: chain F residue 1027 CYS Chi-restraints excluded: chain F residue 1038 GLU Chi-restraints excluded: chain F residue 1062 CYS Chi-restraints excluded: chain F residue 1068 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 23 optimal weight: 0.9980 chunk 165 optimal weight: 3.9990 chunk 209 optimal weight: 7.9990 chunk 116 optimal weight: 0.7980 chunk 163 optimal weight: 2.9990 chunk 169 optimal weight: 0.4980 chunk 109 optimal weight: 8.9990 chunk 73 optimal weight: 1.9990 chunk 18 optimal weight: 4.9990 chunk 206 optimal weight: 6.9990 chunk 129 optimal weight: 0.5980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 ASN A 453 HIS A 930 ASN A1058 ASN A1108 GLN A1398 HIS ** F 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1007 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F1065 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.149255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.113574 restraints weight = 26727.157| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 2.38 r_work: 0.3075 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2940 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2943 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2943 r_free = 0.2943 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2943 r_free = 0.2943 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2943 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.2022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 18705 Z= 0.116 Angle : 0.522 7.537 25284 Z= 0.271 Chirality : 0.041 0.159 2817 Planarity : 0.004 0.057 3153 Dihedral : 10.806 59.440 2765 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.79 % Favored : 94.16 % Rotamer: Outliers : 6.36 % Allowed : 24.03 % Favored : 69.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.02 (0.18), residues: 2194 helix: 0.81 (0.16), residues: 1084 sheet: -1.75 (0.33), residues: 210 loop : -2.33 (0.20), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1099 TYR 0.010 0.001 TYR E 176 PHE 0.025 0.001 PHE E 182 TRP 0.017 0.001 TRP F 187 HIS 0.002 0.000 HIS F 888 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 (18688) covalent geometry : angle 0.51960 / 0.27 (25260) SS BOND : bond 0.00258 / 0.19 ( 12) SS BOND : angle 1.78373 / 0.94 ( 24) hydrogen bonds : bond 0.03139 / 2.05 ( 831) hydrogen bonds : angle 3.90327 / 2.74 ( 2459) Misc. bond : bond 0.00061 / 0.03 ( 5) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4388 Ramachandran restraints generated. 2194 Oldfield, 0 Emsley, 2194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4388 Ramachandran restraints generated. 2194 Oldfield, 0 Emsley, 2194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 280 time to evaluate : 0.707 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.9169 (OUTLIER) cc_final: 0.8496 (mtm) REVERT: A 182 LEU cc_start: 0.8273 (OUTLIER) cc_final: 0.7980 (tt) REVERT: A 183 GLN cc_start: 0.8242 (OUTLIER) cc_final: 0.7473 (mt0) REVERT: A 243 SER cc_start: 0.9348 (p) cc_final: 0.9123 (t) REVERT: A 464 GLN cc_start: 0.7575 (OUTLIER) cc_final: 0.7030 (mt0) REVERT: A 483 MET cc_start: 0.3318 (tmm) cc_final: 0.2815 (tpt) REVERT: A 828 ARG cc_start: 0.4638 (ttp-170) cc_final: 0.4033 (tpp-160) REVERT: A 1018 GLN cc_start: 0.8856 (OUTLIER) cc_final: 0.8307 (mt0) REVERT: A 1060 PHE cc_start: 0.8032 (OUTLIER) cc_final: 0.7068 (t80) REVERT: A 1186 ASP cc_start: 0.8528 (t0) cc_final: 0.8118 (t0) REVERT: A 1239 ARG cc_start: 0.8213 (OUTLIER) cc_final: 0.7703 (ptp-170) REVERT: A 1286 MET cc_start: 0.8898 (mtp) cc_final: 0.8597 (mtm) REVERT: E 206 ARG cc_start: 0.5656 (OUTLIER) cc_final: 0.4961 (mmp-170) REVERT: F 281 MET cc_start: 0.9121 (tpp) cc_final: 0.8768 (ttm) REVERT: F 380 LYS cc_start: 0.8879 (ttpp) cc_final: 0.8379 (ttpt) REVERT: F 442 LYS cc_start: 0.8984 (ttpp) cc_final: 0.8719 (ttpt) REVERT: F 593 LEU cc_start: 0.8887 (OUTLIER) cc_final: 0.8553 (pp) REVERT: F 727 LYS cc_start: 0.8803 (mmtm) cc_final: 0.8584 (mmtm) REVERT: F 728 ASN cc_start: 0.8425 (m-40) cc_final: 0.7746 (t0) REVERT: F 858 ASP cc_start: 0.8559 (p0) cc_final: 0.8230 (p0) REVERT: F 1005 ILE cc_start: 0.8690 (mt) cc_final: 0.8398 (mt) outliers start: 125 outliers final: 88 residues processed: 381 average time/residue: 0.1110 time to fit residues: 67.9064 Evaluate side-chains 353 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 256 time to evaluate : 0.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 183 GLN Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 291 MET Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 464 GLN Chi-restraints excluded: chain A residue 468 ASN Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain A residue 479 MET Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 647 CYS Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 788 VAL Chi-restraints excluded: chain A residue 876 VAL Chi-restraints excluded: chain A residue 925 ILE Chi-restraints excluded: chain A residue 933 LEU Chi-restraints excluded: chain A residue 934 VAL Chi-restraints excluded: chain A residue 983 MET Chi-restraints excluded: chain A residue 1007 LEU Chi-restraints excluded: chain A residue 1018 GLN Chi-restraints excluded: chain A residue 1039 VAL Chi-restraints excluded: chain A residue 1060 PHE Chi-restraints excluded: chain A residue 1108 GLN Chi-restraints excluded: chain A residue 1111 VAL Chi-restraints excluded: chain A residue 1141 HIS Chi-restraints excluded: chain A residue 1149 ILE Chi-restraints excluded: chain A residue 1239 ARG Chi-restraints excluded: chain A residue 1240 VAL Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1267 LEU Chi-restraints excluded: chain A residue 1272 LEU Chi-restraints excluded: chain A residue 1273 LEU Chi-restraints excluded: chain A residue 1289 PHE Chi-restraints excluded: chain A residue 1295 VAL Chi-restraints excluded: chain A residue 1343 ASP Chi-restraints excluded: chain A residue 1380 ILE Chi-restraints excluded: chain A residue 1388 THR Chi-restraints excluded: chain A residue 1397 HIS Chi-restraints excluded: chain A residue 1400 ASP Chi-restraints excluded: chain A residue 1429 ILE Chi-restraints excluded: chain E residue 24 MET Chi-restraints excluded: chain E residue 179 SER Chi-restraints excluded: chain E residue 206 ARG Chi-restraints excluded: chain F residue 32 THR Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 61 TYR Chi-restraints excluded: chain F residue 116 ASP Chi-restraints excluded: chain F residue 125 VAL Chi-restraints excluded: chain F residue 205 LEU Chi-restraints excluded: chain F residue 240 VAL Chi-restraints excluded: chain F residue 270 THR Chi-restraints excluded: chain F residue 303 VAL Chi-restraints excluded: chain F residue 351 VAL Chi-restraints excluded: chain F residue 360 ILE Chi-restraints excluded: chain F residue 401 ILE Chi-restraints excluded: chain F residue 476 GLU Chi-restraints excluded: chain F residue 593 LEU Chi-restraints excluded: chain F residue 610 THR Chi-restraints excluded: chain F residue 612 THR Chi-restraints excluded: chain F residue 617 THR Chi-restraints excluded: chain F residue 652 LYS Chi-restraints excluded: chain F residue 680 THR Chi-restraints excluded: chain F residue 694 THR Chi-restraints excluded: chain F residue 735 ARG Chi-restraints excluded: chain F residue 739 THR Chi-restraints excluded: chain F residue 744 THR Chi-restraints excluded: chain F residue 817 ILE Chi-restraints excluded: chain F residue 821 VAL Chi-restraints excluded: chain F residue 850 VAL Chi-restraints excluded: chain F residue 853 CYS Chi-restraints excluded: chain F residue 982 THR Chi-restraints excluded: chain F residue 1002 CYS Chi-restraints excluded: chain F residue 1008 VAL Chi-restraints excluded: chain F residue 1014 THR Chi-restraints excluded: chain F residue 1019 ILE Chi-restraints excluded: chain F residue 1026 THR Chi-restraints excluded: chain F residue 1027 CYS Chi-restraints excluded: chain F residue 1038 GLU Chi-restraints excluded: chain F residue 1062 CYS Chi-restraints excluded: chain F residue 1068 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 128 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 86 optimal weight: 4.9990 chunk 37 optimal weight: 0.2980 chunk 178 optimal weight: 2.9990 chunk 133 optimal weight: 0.0970 chunk 21 optimal weight: 5.9990 chunk 42 optimal weight: 3.9990 chunk 105 optimal weight: 3.9990 chunk 172 optimal weight: 0.8980 chunk 10 optimal weight: 0.0970 overall best weight: 0.8778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 ASN A1108 GLN ** A1397 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1007 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F1065 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.149532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.114307 restraints weight = 26495.135| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 2.34 r_work: 0.3084 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2950 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2952 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2952 r_free = 0.2952 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2952 r_free = 0.2952 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2952 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.2185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 18705 Z= 0.113 Angle : 0.526 9.869 25284 Z= 0.272 Chirality : 0.041 0.155 2817 Planarity : 0.004 0.058 3153 Dihedral : 10.425 59.204 2761 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.93 % Favored : 94.03 % Rotamer: Outliers : 5.86 % Allowed : 24.90 % Favored : 69.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.83 (0.18), residues: 2194 helix: 0.93 (0.16), residues: 1094 sheet: -1.68 (0.32), residues: 210 loop : -2.20 (0.20), residues: 890 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 846 TYR 0.018 0.001 TYR A1101 PHE 0.030 0.001 PHE A 92 TRP 0.017 0.001 TRP F 187 HIS 0.002 0.000 HIS A1398 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.11 (18688) covalent geometry : angle 0.52394 / 0.27 (25260) SS BOND : bond 0.00293 / 0.20 ( 12) SS BOND : angle 1.57262 / 0.84 ( 24) hydrogen bonds : bond 0.03088 / 2.01 ( 831) hydrogen bonds : angle 3.85180 / 2.70 ( 2459) Misc. bond : bond 0.00039 / 0.02 ( 5) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4388 Ramachandran restraints generated. 2194 Oldfield, 0 Emsley, 2194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4388 Ramachandran restraints generated. 2194 Oldfield, 0 Emsley, 2194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 267 time to evaluate : 0.687 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.9160 (OUTLIER) cc_final: 0.8503 (mtm) REVERT: A 182 LEU cc_start: 0.8263 (OUTLIER) cc_final: 0.7993 (tt) REVERT: A 183 GLN cc_start: 0.8274 (OUTLIER) cc_final: 0.7470 (mt0) REVERT: A 243 SER cc_start: 0.9294 (p) cc_final: 0.9080 (t) REVERT: A 326 LEU cc_start: 0.8783 (OUTLIER) cc_final: 0.8401 (mp) REVERT: A 464 GLN cc_start: 0.7650 (OUTLIER) cc_final: 0.7186 (mt0) REVERT: A 483 MET cc_start: 0.3180 (tmm) cc_final: 0.2711 (tpt) REVERT: A 500 ASP cc_start: 0.7365 (OUTLIER) cc_final: 0.6888 (p0) REVERT: A 828 ARG cc_start: 0.4617 (ttp-170) cc_final: 0.4018 (tpp-160) REVERT: A 916 HIS cc_start: 0.3602 (t70) cc_final: 0.1539 (m90) REVERT: A 1018 GLN cc_start: 0.8843 (OUTLIER) cc_final: 0.8293 (mt0) REVERT: A 1060 PHE cc_start: 0.7987 (OUTLIER) cc_final: 0.7037 (t80) REVERT: A 1108 GLN cc_start: 0.5973 (OUTLIER) cc_final: 0.5709 (pp30) REVERT: A 1182 TRP cc_start: 0.8979 (m100) cc_final: 0.8620 (m100) REVERT: A 1186 ASP cc_start: 0.8522 (t0) cc_final: 0.8081 (t0) REVERT: A 1239 ARG cc_start: 0.8216 (OUTLIER) cc_final: 0.7724 (ptp-170) REVERT: E 30 ASP cc_start: 0.6128 (m-30) cc_final: 0.5890 (m-30) REVERT: E 206 ARG cc_start: 0.5693 (OUTLIER) cc_final: 0.4941 (mmp-170) REVERT: F 248 GLN cc_start: 0.9316 (OUTLIER) cc_final: 0.8827 (pp30) REVERT: F 281 MET cc_start: 0.9112 (tpp) cc_final: 0.8756 (ttm) REVERT: F 380 LYS cc_start: 0.8876 (ttpp) cc_final: 0.8333 (ttpt) REVERT: F 404 MET cc_start: 0.9063 (mtp) cc_final: 0.8837 (mtp) REVERT: F 593 LEU cc_start: 0.8881 (OUTLIER) cc_final: 0.8523 (pp) REVERT: F 646 ARG cc_start: 0.8036 (ttp80) cc_final: 0.7773 (ttp-110) REVERT: F 727 LYS cc_start: 0.8801 (mmtm) cc_final: 0.8568 (mmtm) REVERT: F 728 ASN cc_start: 0.8413 (m-40) cc_final: 0.7868 (t0) REVERT: F 858 ASP cc_start: 0.8581 (p0) cc_final: 0.8235 (p0) outliers start: 115 outliers final: 88 residues processed: 358 average time/residue: 0.1131 time to fit residues: 64.0888 Evaluate side-chains 357 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 256 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 183 GLN Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 291 MET Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 464 GLN Chi-restraints excluded: chain A residue 468 ASN Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain A residue 479 MET Chi-restraints excluded: chain A residue 500 ASP Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 647 CYS Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 788 VAL Chi-restraints excluded: chain A residue 876 VAL Chi-restraints excluded: chain A residue 925 ILE Chi-restraints excluded: chain A residue 933 LEU Chi-restraints excluded: chain A residue 934 VAL Chi-restraints excluded: chain A residue 1007 LEU Chi-restraints excluded: chain A residue 1018 GLN Chi-restraints excluded: chain A residue 1039 VAL Chi-restraints excluded: chain A residue 1060 PHE Chi-restraints excluded: chain A residue 1108 GLN Chi-restraints excluded: chain A residue 1111 VAL Chi-restraints excluded: chain A residue 1115 VAL Chi-restraints excluded: chain A residue 1117 SER Chi-restraints excluded: chain A residue 1141 HIS Chi-restraints excluded: chain A residue 1149 ILE Chi-restraints excluded: chain A residue 1205 PHE Chi-restraints excluded: chain A residue 1239 ARG Chi-restraints excluded: chain A residue 1240 VAL Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1267 LEU Chi-restraints excluded: chain A residue 1272 LEU Chi-restraints excluded: chain A residue 1273 LEU Chi-restraints excluded: chain A residue 1289 PHE Chi-restraints excluded: chain A residue 1295 VAL Chi-restraints excluded: chain A residue 1343 ASP Chi-restraints excluded: chain A residue 1381 MET Chi-restraints excluded: chain A residue 1388 THR Chi-restraints excluded: chain A residue 1397 HIS Chi-restraints excluded: chain A residue 1400 ASP Chi-restraints excluded: chain A residue 1429 ILE Chi-restraints excluded: chain E residue 24 MET Chi-restraints excluded: chain E residue 153 VAL Chi-restraints excluded: chain E residue 179 SER Chi-restraints excluded: chain E residue 206 ARG Chi-restraints excluded: chain F residue 32 THR Chi-restraints excluded: chain F residue 61 TYR Chi-restraints excluded: chain F residue 116 ASP Chi-restraints excluded: chain F residue 125 VAL Chi-restraints excluded: chain F residue 194 VAL Chi-restraints excluded: chain F residue 240 VAL Chi-restraints excluded: chain F residue 248 GLN Chi-restraints excluded: chain F residue 270 THR Chi-restraints excluded: chain F residue 303 VAL Chi-restraints excluded: chain F residue 351 VAL Chi-restraints excluded: chain F residue 360 ILE Chi-restraints excluded: chain F residue 401 ILE Chi-restraints excluded: chain F residue 423 ILE Chi-restraints excluded: chain F residue 476 GLU Chi-restraints excluded: chain F residue 543 LEU Chi-restraints excluded: chain F residue 593 LEU Chi-restraints excluded: chain F residue 610 THR Chi-restraints excluded: chain F residue 612 THR Chi-restraints excluded: chain F residue 617 THR Chi-restraints excluded: chain F residue 652 LYS Chi-restraints excluded: chain F residue 680 THR Chi-restraints excluded: chain F residue 694 THR Chi-restraints excluded: chain F residue 735 ARG Chi-restraints excluded: chain F residue 739 THR Chi-restraints excluded: chain F residue 744 THR Chi-restraints excluded: chain F residue 817 ILE Chi-restraints excluded: chain F residue 821 VAL Chi-restraints excluded: chain F residue 850 VAL Chi-restraints excluded: chain F residue 853 CYS Chi-restraints excluded: chain F residue 982 THR Chi-restraints excluded: chain F residue 1002 CYS Chi-restraints excluded: chain F residue 1008 VAL Chi-restraints excluded: chain F residue 1014 THR Chi-restraints excluded: chain F residue 1019 ILE Chi-restraints excluded: chain F residue 1026 THR Chi-restraints excluded: chain F residue 1027 CYS Chi-restraints excluded: chain F residue 1038 GLU Chi-restraints excluded: chain F residue 1062 CYS Chi-restraints excluded: chain F residue 1068 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 206 optimal weight: 3.9990 chunk 113 optimal weight: 9.9990 chunk 105 optimal weight: 7.9990 chunk 209 optimal weight: 8.9990 chunk 7 optimal weight: 10.0000 chunk 101 optimal weight: 2.9990 chunk 68 optimal weight: 5.9990 chunk 121 optimal weight: 10.0000 chunk 127 optimal weight: 0.9980 chunk 106 optimal weight: 5.9990 chunk 200 optimal weight: 0.7980 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 ASN A 663 ASN A 916 HIS A 930 ASN ** F 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1007 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F1065 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.145178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.109718 restraints weight = 26764.856| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 2.30 r_work: 0.3011 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2875 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2878 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2878 r_free = 0.2878 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2878 r_free = 0.2878 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2878 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.2029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 18705 Z= 0.242 Angle : 0.625 8.373 25284 Z= 0.323 Chirality : 0.045 0.171 2817 Planarity : 0.005 0.070 3153 Dihedral : 10.765 59.883 2756 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.11 % Favored : 92.84 % Rotamer: Outliers : 6.26 % Allowed : 24.54 % Favored : 69.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.06 (0.18), residues: 2194 helix: 0.71 (0.16), residues: 1094 sheet: -1.77 (0.32), residues: 210 loop : -2.28 (0.20), residues: 890 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG A1099 TYR 0.015 0.002 TYR A1109 PHE 0.023 0.002 PHE A 92 TRP 0.014 0.001 TRP A1016 HIS 0.003 0.001 HIS A1139 Details of bonding type rmsd/Z covalent geometry : bond 0.00584 / 0.24 (18688) covalent geometry : angle 0.62285 / 0.32 (25260) SS BOND : bond 0.00429 / 0.30 ( 12) SS BOND : angle 1.92995 / 1.08 ( 24) hydrogen bonds : bond 0.03939 / 2.54 ( 831) hydrogen bonds : angle 4.14681 / 2.89 ( 2459) Misc. bond : bond 0.00085 / 0.04 ( 5) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4388 Ramachandran restraints generated. 2194 Oldfield, 0 Emsley, 2194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4388 Ramachandran restraints generated. 2194 Oldfield, 0 Emsley, 2194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 249 time to evaluate : 0.707 Fit side-chains revert: symmetry clash REVERT: A 74 MET cc_start: 0.9156 (OUTLIER) cc_final: 0.8747 (mtm) REVERT: A 182 LEU cc_start: 0.8409 (OUTLIER) cc_final: 0.8161 (tt) REVERT: A 183 GLN cc_start: 0.8269 (OUTLIER) cc_final: 0.7512 (mt0) REVERT: A 464 GLN cc_start: 0.7599 (OUTLIER) cc_final: 0.6972 (mt0) REVERT: A 480 LEU cc_start: 0.3669 (OUTLIER) cc_final: 0.3326 (mp) REVERT: A 483 MET cc_start: 0.3295 (tmm) cc_final: 0.2705 (tpt) REVERT: A 500 ASP cc_start: 0.7394 (OUTLIER) cc_final: 0.6928 (p0) REVERT: A 819 GLU cc_start: 0.7809 (OUTLIER) cc_final: 0.7523 (mm-30) REVERT: A 828 ARG cc_start: 0.4552 (ttp-170) cc_final: 0.3933 (tpp-160) REVERT: A 916 HIS cc_start: 0.3566 (t-170) cc_final: 0.1696 (m90) REVERT: A 1018 GLN cc_start: 0.8936 (OUTLIER) cc_final: 0.8397 (mt0) REVERT: A 1060 PHE cc_start: 0.8019 (OUTLIER) cc_final: 0.7145 (t80) REVERT: A 1186 ASP cc_start: 0.8630 (t0) cc_final: 0.8138 (t0) REVERT: F 114 ARG cc_start: 0.8422 (mtp85) cc_final: 0.8209 (mtt90) REVERT: F 248 GLN cc_start: 0.9340 (OUTLIER) cc_final: 0.8865 (pp30) REVERT: F 281 MET cc_start: 0.9174 (tpp) cc_final: 0.8342 (tpp) REVERT: F 380 LYS cc_start: 0.8827 (ttpp) cc_final: 0.8260 (ttpt) REVERT: F 727 LYS cc_start: 0.8844 (mmtm) cc_final: 0.8598 (mmtm) REVERT: F 728 ASN cc_start: 0.8399 (m-40) cc_final: 0.7755 (t0) REVERT: F 858 ASP cc_start: 0.8693 (p0) cc_final: 0.8354 (p0) outliers start: 123 outliers final: 91 residues processed: 346 average time/residue: 0.1219 time to fit residues: 66.5993 Evaluate side-chains 345 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 244 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 183 GLN Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 291 MET Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 324 PHE Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 464 GLN Chi-restraints excluded: chain A residue 468 ASN Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain A residue 479 MET Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 500 ASP Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 647 CYS Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 788 VAL Chi-restraints excluded: chain A residue 819 GLU Chi-restraints excluded: chain A residue 873 LEU Chi-restraints excluded: chain A residue 876 VAL Chi-restraints excluded: chain A residue 933 LEU Chi-restraints excluded: chain A residue 934 VAL Chi-restraints excluded: chain A residue 1007 LEU Chi-restraints excluded: chain A residue 1018 GLN Chi-restraints excluded: chain A residue 1039 VAL Chi-restraints excluded: chain A residue 1060 PHE Chi-restraints excluded: chain A residue 1111 VAL Chi-restraints excluded: chain A residue 1115 VAL Chi-restraints excluded: chain A residue 1117 SER Chi-restraints excluded: chain A residue 1141 HIS Chi-restraints excluded: chain A residue 1149 ILE Chi-restraints excluded: chain A residue 1163 LEU Chi-restraints excluded: chain A residue 1198 ILE Chi-restraints excluded: chain A residue 1205 PHE Chi-restraints excluded: chain A residue 1240 VAL Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1267 LEU Chi-restraints excluded: chain A residue 1272 LEU Chi-restraints excluded: chain A residue 1273 LEU Chi-restraints excluded: chain A residue 1289 PHE Chi-restraints excluded: chain A residue 1295 VAL Chi-restraints excluded: chain A residue 1343 ASP Chi-restraints excluded: chain A residue 1380 ILE Chi-restraints excluded: chain A residue 1388 THR Chi-restraints excluded: chain A residue 1397 HIS Chi-restraints excluded: chain A residue 1400 ASP Chi-restraints excluded: chain A residue 1429 ILE Chi-restraints excluded: chain E residue 24 MET Chi-restraints excluded: chain E residue 27 VAL Chi-restraints excluded: chain E residue 153 VAL Chi-restraints excluded: chain E residue 179 SER Chi-restraints excluded: chain F residue 32 THR Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 61 TYR Chi-restraints excluded: chain F residue 116 ASP Chi-restraints excluded: chain F residue 125 VAL Chi-restraints excluded: chain F residue 194 VAL Chi-restraints excluded: chain F residue 240 VAL Chi-restraints excluded: chain F residue 248 GLN Chi-restraints excluded: chain F residue 270 THR Chi-restraints excluded: chain F residue 303 VAL Chi-restraints excluded: chain F residue 351 VAL Chi-restraints excluded: chain F residue 360 ILE Chi-restraints excluded: chain F residue 401 ILE Chi-restraints excluded: chain F residue 423 ILE Chi-restraints excluded: chain F residue 543 LEU Chi-restraints excluded: chain F residue 610 THR Chi-restraints excluded: chain F residue 612 THR Chi-restraints excluded: chain F residue 617 THR Chi-restraints excluded: chain F residue 652 LYS Chi-restraints excluded: chain F residue 680 THR Chi-restraints excluded: chain F residue 694 THR Chi-restraints excluded: chain F residue 735 ARG Chi-restraints excluded: chain F residue 739 THR Chi-restraints excluded: chain F residue 744 THR Chi-restraints excluded: chain F residue 817 ILE Chi-restraints excluded: chain F residue 821 VAL Chi-restraints excluded: chain F residue 850 VAL Chi-restraints excluded: chain F residue 853 CYS Chi-restraints excluded: chain F residue 982 THR Chi-restraints excluded: chain F residue 1002 CYS Chi-restraints excluded: chain F residue 1008 VAL Chi-restraints excluded: chain F residue 1014 THR Chi-restraints excluded: chain F residue 1019 ILE Chi-restraints excluded: chain F residue 1026 THR Chi-restraints excluded: chain F residue 1027 CYS Chi-restraints excluded: chain F residue 1062 CYS Chi-restraints excluded: chain F residue 1068 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 107 optimal weight: 0.4980 chunk 67 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 163 optimal weight: 0.4980 chunk 217 optimal weight: 0.0770 chunk 86 optimal weight: 3.9990 chunk 104 optimal weight: 2.9990 chunk 28 optimal weight: 0.6980 chunk 196 optimal weight: 8.9990 chunk 110 optimal weight: 2.9990 chunk 174 optimal weight: 0.6980 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 ASN A1108 GLN ** A1397 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1007 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F1065 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.150279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.115001 restraints weight = 26504.221| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 2.33 r_work: 0.3099 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2963 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2966 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2966 r_free = 0.2966 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2966 r_free = 0.2966 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2966 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.2373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 18705 Z= 0.103 Angle : 0.528 7.705 25284 Z= 0.272 Chirality : 0.041 0.152 2817 Planarity : 0.004 0.057 3153 Dihedral : 9.977 59.808 2756 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.75 % Favored : 94.21 % Rotamer: Outliers : 5.40 % Allowed : 25.31 % Favored : 69.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.71 (0.18), residues: 2194 helix: 1.00 (0.16), residues: 1105 sheet: -1.65 (0.32), residues: 212 loop : -2.13 (0.21), residues: 877 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A1099 TYR 0.013 0.001 TYR E 176 PHE 0.025 0.001 PHE A 92 TRP 0.020 0.001 TRP F 187 HIS 0.002 0.000 HIS A 996 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.10 (18688) covalent geometry : angle 0.52622 / 0.27 (25260) SS BOND : bond 0.00200 / 0.15 ( 12) SS BOND : angle 1.37390 / 0.75 ( 24) hydrogen bonds : bond 0.02972 / 1.94 ( 831) hydrogen bonds : angle 3.83556 / 2.69 ( 2459) Misc. bond : bond 0.00059 / 0.03 ( 5) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4388 Ramachandran restraints generated. 2194 Oldfield, 0 Emsley, 2194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4388 Ramachandran restraints generated. 2194 Oldfield, 0 Emsley, 2194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 282 time to evaluate : 0.484 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 182 LEU cc_start: 0.8274 (OUTLIER) cc_final: 0.8009 (tt) REVERT: A 183 GLN cc_start: 0.8223 (OUTLIER) cc_final: 0.7458 (mt0) REVERT: A 243 SER cc_start: 0.9290 (p) cc_final: 0.9051 (t) REVERT: A 326 LEU cc_start: 0.8726 (OUTLIER) cc_final: 0.8371 (mp) REVERT: A 460 LEU cc_start: 0.8713 (OUTLIER) cc_final: 0.8385 (tp) REVERT: A 464 GLN cc_start: 0.7622 (OUTLIER) cc_final: 0.7189 (mt0) REVERT: A 480 LEU cc_start: 0.3393 (OUTLIER) cc_final: 0.3109 (mp) REVERT: A 483 MET cc_start: 0.3224 (tmm) cc_final: 0.2723 (tpt) REVERT: A 500 ASP cc_start: 0.7293 (OUTLIER) cc_final: 0.6813 (p0) REVERT: A 828 ARG cc_start: 0.4669 (ttp-170) cc_final: 0.4058 (tpp-160) REVERT: A 916 HIS cc_start: 0.3329 (t-170) cc_final: 0.1507 (m90) REVERT: A 1018 GLN cc_start: 0.8849 (OUTLIER) cc_final: 0.8287 (mt0) REVERT: A 1060 PHE cc_start: 0.8065 (OUTLIER) cc_final: 0.7290 (t80) REVERT: A 1182 TRP cc_start: 0.8958 (m100) cc_final: 0.8674 (m100) REVERT: A 1186 ASP cc_start: 0.8435 (t0) cc_final: 0.7968 (t0) REVERT: A 1286 MET cc_start: 0.8906 (mtp) cc_final: 0.8630 (mtm) REVERT: E 30 ASP cc_start: 0.6077 (m-30) cc_final: 0.5768 (m-30) REVERT: F 248 GLN cc_start: 0.9296 (OUTLIER) cc_final: 0.8799 (pp30) REVERT: F 281 MET cc_start: 0.9074 (tpp) cc_final: 0.8734 (ttm) REVERT: F 311 GLN cc_start: 0.9161 (OUTLIER) cc_final: 0.8777 (tp40) REVERT: F 380 LYS cc_start: 0.8868 (ttpp) cc_final: 0.8374 (ttpt) REVERT: F 646 ARG cc_start: 0.8034 (ttp80) cc_final: 0.7766 (ttp-110) REVERT: F 727 LYS cc_start: 0.8751 (mmtm) cc_final: 0.8513 (mmtm) REVERT: F 728 ASN cc_start: 0.8446 (m-40) cc_final: 0.7878 (t0) REVERT: F 858 ASP cc_start: 0.8580 (p0) cc_final: 0.8221 (p0) REVERT: F 1049 MET cc_start: 0.8204 (ttm) cc_final: 0.7959 (mtp) outliers start: 106 outliers final: 81 residues processed: 364 average time/residue: 0.1135 time to fit residues: 65.8310 Evaluate side-chains 352 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 260 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 183 GLN Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 291 MET Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 464 GLN Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain A residue 479 MET Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 500 ASP Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 647 CYS Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 788 VAL Chi-restraints excluded: chain A residue 876 VAL Chi-restraints excluded: chain A residue 896 LEU Chi-restraints excluded: chain A residue 1007 LEU Chi-restraints excluded: chain A residue 1018 GLN Chi-restraints excluded: chain A residue 1060 PHE Chi-restraints excluded: chain A residue 1108 GLN Chi-restraints excluded: chain A residue 1111 VAL Chi-restraints excluded: chain A residue 1115 VAL Chi-restraints excluded: chain A residue 1141 HIS Chi-restraints excluded: chain A residue 1149 ILE Chi-restraints excluded: chain A residue 1240 VAL Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1267 LEU Chi-restraints excluded: chain A residue 1272 LEU Chi-restraints excluded: chain A residue 1273 LEU Chi-restraints excluded: chain A residue 1289 PHE Chi-restraints excluded: chain A residue 1295 VAL Chi-restraints excluded: chain A residue 1343 ASP Chi-restraints excluded: chain A residue 1388 THR Chi-restraints excluded: chain A residue 1397 HIS Chi-restraints excluded: chain A residue 1400 ASP Chi-restraints excluded: chain A residue 1429 ILE Chi-restraints excluded: chain E residue 153 VAL Chi-restraints excluded: chain E residue 179 SER Chi-restraints excluded: chain F residue 32 THR Chi-restraints excluded: chain F residue 61 TYR Chi-restraints excluded: chain F residue 116 ASP Chi-restraints excluded: chain F residue 125 VAL Chi-restraints excluded: chain F residue 200 GLU Chi-restraints excluded: chain F residue 205 LEU Chi-restraints excluded: chain F residue 240 VAL Chi-restraints excluded: chain F residue 248 GLN Chi-restraints excluded: chain F residue 270 THR Chi-restraints excluded: chain F residue 303 VAL Chi-restraints excluded: chain F residue 311 GLN Chi-restraints excluded: chain F residue 360 ILE Chi-restraints excluded: chain F residue 401 ILE Chi-restraints excluded: chain F residue 423 ILE Chi-restraints excluded: chain F residue 476 GLU Chi-restraints excluded: chain F residue 543 LEU Chi-restraints excluded: chain F residue 610 THR Chi-restraints excluded: chain F residue 612 THR Chi-restraints excluded: chain F residue 617 THR Chi-restraints excluded: chain F residue 652 LYS Chi-restraints excluded: chain F residue 680 THR Chi-restraints excluded: chain F residue 694 THR Chi-restraints excluded: chain F residue 735 ARG Chi-restraints excluded: chain F residue 739 THR Chi-restraints excluded: chain F residue 744 THR Chi-restraints excluded: chain F residue 817 ILE Chi-restraints excluded: chain F residue 821 VAL Chi-restraints excluded: chain F residue 850 VAL Chi-restraints excluded: chain F residue 853 CYS Chi-restraints excluded: chain F residue 982 THR Chi-restraints excluded: chain F residue 1002 CYS Chi-restraints excluded: chain F residue 1008 VAL Chi-restraints excluded: chain F residue 1014 THR Chi-restraints excluded: chain F residue 1019 ILE Chi-restraints excluded: chain F residue 1026 THR Chi-restraints excluded: chain F residue 1027 CYS Chi-restraints excluded: chain F residue 1062 CYS Chi-restraints excluded: chain F residue 1065 ASN Chi-restraints excluded: chain F residue 1068 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 36 optimal weight: 0.8980 chunk 133 optimal weight: 0.2980 chunk 4 optimal weight: 0.0040 chunk 75 optimal weight: 4.9990 chunk 176 optimal weight: 9.9990 chunk 109 optimal weight: 10.0000 chunk 5 optimal weight: 0.8980 chunk 149 optimal weight: 3.9990 chunk 97 optimal weight: 7.9990 chunk 80 optimal weight: 0.7980 chunk 70 optimal weight: 0.9980 overall best weight: 0.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 ASN A1108 GLN ** A1397 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1007 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F1065 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.150170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.114745 restraints weight = 26489.546| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 2.36 r_work: 0.3098 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2962 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2959 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2959 r_free = 0.2959 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2959 r_free = 0.2959 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2959 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.2534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 18705 Z= 0.105 Angle : 0.535 9.971 25284 Z= 0.276 Chirality : 0.041 0.151 2817 Planarity : 0.004 0.058 3153 Dihedral : 9.710 59.733 2754 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.56 % Favored : 94.39 % Rotamer: Outliers : 4.79 % Allowed : 26.58 % Favored : 68.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.58 (0.18), residues: 2194 helix: 1.05 (0.16), residues: 1113 sheet: -1.62 (0.32), residues: 212 loop : -1.99 (0.21), residues: 869 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A1099 TYR 0.023 0.001 TYR F 632 PHE 0.024 0.001 PHE A 92 TRP 0.018 0.001 TRP F 187 HIS 0.002 0.000 HIS A1398 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.11 (18688) covalent geometry : angle 0.53333 / 0.28 (25260) SS BOND : bond 0.00215 / 0.16 ( 12) SS BOND : angle 1.36350 / 0.75 ( 24) hydrogen bonds : bond 0.02943 / 1.92 ( 831) hydrogen bonds : angle 3.75871 / 2.63 ( 2459) Misc. bond : bond 0.00041 / 0.02 ( 5) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4388 Ramachandran restraints generated. 2194 Oldfield, 0 Emsley, 2194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4388 Ramachandran restraints generated. 2194 Oldfield, 0 Emsley, 2194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 266 time to evaluate : 0.609 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 182 LEU cc_start: 0.8254 (OUTLIER) cc_final: 0.7985 (tt) REVERT: A 183 GLN cc_start: 0.8263 (OUTLIER) cc_final: 0.7463 (mt0) REVERT: A 243 SER cc_start: 0.9282 (p) cc_final: 0.9070 (t) REVERT: A 326 LEU cc_start: 0.8735 (OUTLIER) cc_final: 0.8390 (mp) REVERT: A 460 LEU cc_start: 0.8720 (OUTLIER) cc_final: 0.8414 (tp) REVERT: A 464 GLN cc_start: 0.7564 (OUTLIER) cc_final: 0.7176 (mt0) REVERT: A 480 LEU cc_start: 0.3414 (OUTLIER) cc_final: 0.3116 (mp) REVERT: A 483 MET cc_start: 0.3232 (tmm) cc_final: 0.2780 (tpt) REVERT: A 500 ASP cc_start: 0.7298 (OUTLIER) cc_final: 0.6796 (p0) REVERT: A 828 ARG cc_start: 0.4555 (ttp-170) cc_final: 0.4008 (tpp-160) REVERT: A 1018 GLN cc_start: 0.8860 (OUTLIER) cc_final: 0.8285 (mt0) REVERT: A 1060 PHE cc_start: 0.8072 (OUTLIER) cc_final: 0.7341 (t80) REVERT: A 1182 TRP cc_start: 0.8933 (m100) cc_final: 0.8662 (m100) REVERT: A 1186 ASP cc_start: 0.8321 (t0) cc_final: 0.7899 (t0) REVERT: A 1286 MET cc_start: 0.8904 (mtp) cc_final: 0.8593 (mtm) REVERT: E 24 MET cc_start: 0.7244 (tpp) cc_final: 0.7024 (tpp) REVERT: E 30 ASP cc_start: 0.6158 (m-30) cc_final: 0.5835 (m-30) REVERT: F 281 MET cc_start: 0.9069 (tpp) cc_final: 0.8720 (ttm) REVERT: F 311 GLN cc_start: 0.9142 (OUTLIER) cc_final: 0.8836 (tp40) REVERT: F 646 ARG cc_start: 0.8030 (ttp80) cc_final: 0.7760 (ttp-110) REVERT: F 727 LYS cc_start: 0.8754 (mmtm) cc_final: 0.8515 (mmtm) REVERT: F 728 ASN cc_start: 0.8487 (m-40) cc_final: 0.7955 (t0) REVERT: F 858 ASP cc_start: 0.8605 (p0) cc_final: 0.8244 (p0) REVERT: F 1049 MET cc_start: 0.8210 (ttm) cc_final: 0.7872 (mtp) outliers start: 94 outliers final: 79 residues processed: 342 average time/residue: 0.1277 time to fit residues: 69.1491 Evaluate side-chains 343 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 254 time to evaluate : 0.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 183 GLN Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 291 MET Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 464 GLN Chi-restraints excluded: chain A residue 479 MET Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 500 ASP Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 541 TYR Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 647 CYS Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 788 VAL Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 876 VAL Chi-restraints excluded: chain A residue 896 LEU Chi-restraints excluded: chain A residue 1007 LEU Chi-restraints excluded: chain A residue 1018 GLN Chi-restraints excluded: chain A residue 1060 PHE Chi-restraints excluded: chain A residue 1108 GLN Chi-restraints excluded: chain A residue 1117 SER Chi-restraints excluded: chain A residue 1141 HIS Chi-restraints excluded: chain A residue 1149 ILE Chi-restraints excluded: chain A residue 1240 VAL Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1267 LEU Chi-restraints excluded: chain A residue 1272 LEU Chi-restraints excluded: chain A residue 1273 LEU Chi-restraints excluded: chain A residue 1289 PHE Chi-restraints excluded: chain A residue 1295 VAL Chi-restraints excluded: chain A residue 1343 ASP Chi-restraints excluded: chain A residue 1388 THR Chi-restraints excluded: chain A residue 1397 HIS Chi-restraints excluded: chain A residue 1400 ASP Chi-restraints excluded: chain A residue 1429 ILE Chi-restraints excluded: chain E residue 153 VAL Chi-restraints excluded: chain E residue 179 SER Chi-restraints excluded: chain F residue 32 THR Chi-restraints excluded: chain F residue 36 TRP Chi-restraints excluded: chain F residue 61 TYR Chi-restraints excluded: chain F residue 116 ASP Chi-restraints excluded: chain F residue 125 VAL Chi-restraints excluded: chain F residue 200 GLU Chi-restraints excluded: chain F residue 205 LEU Chi-restraints excluded: chain F residue 240 VAL Chi-restraints excluded: chain F residue 270 THR Chi-restraints excluded: chain F residue 303 VAL Chi-restraints excluded: chain F residue 311 GLN Chi-restraints excluded: chain F residue 360 ILE Chi-restraints excluded: chain F residue 401 ILE Chi-restraints excluded: chain F residue 423 ILE Chi-restraints excluded: chain F residue 476 GLU Chi-restraints excluded: chain F residue 543 LEU Chi-restraints excluded: chain F residue 610 THR Chi-restraints excluded: chain F residue 612 THR Chi-restraints excluded: chain F residue 652 LYS Chi-restraints excluded: chain F residue 680 THR Chi-restraints excluded: chain F residue 694 THR Chi-restraints excluded: chain F residue 735 ARG Chi-restraints excluded: chain F residue 739 THR Chi-restraints excluded: chain F residue 744 THR Chi-restraints excluded: chain F residue 817 ILE Chi-restraints excluded: chain F residue 821 VAL Chi-restraints excluded: chain F residue 850 VAL Chi-restraints excluded: chain F residue 853 CYS Chi-restraints excluded: chain F residue 982 THR Chi-restraints excluded: chain F residue 1002 CYS Chi-restraints excluded: chain F residue 1008 VAL Chi-restraints excluded: chain F residue 1014 THR Chi-restraints excluded: chain F residue 1019 ILE Chi-restraints excluded: chain F residue 1026 THR Chi-restraints excluded: chain F residue 1027 CYS Chi-restraints excluded: chain F residue 1065 ASN Chi-restraints excluded: chain F residue 1068 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 145 optimal weight: 0.2980 chunk 67 optimal weight: 3.9990 chunk 168 optimal weight: 5.9990 chunk 140 optimal weight: 2.9990 chunk 78 optimal weight: 9.9990 chunk 176 optimal weight: 10.0000 chunk 10 optimal weight: 2.9990 chunk 31 optimal weight: 0.0980 chunk 101 optimal weight: 0.9990 chunk 163 optimal weight: 1.9990 chunk 74 optimal weight: 0.8980 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 ASN A1108 GLN ** A1397 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 297 ASN ** F 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1007 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F1065 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.149904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.114372 restraints weight = 26463.716| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 2.29 r_work: 0.3098 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2963 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2967 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2967 r_free = 0.2967 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2967 r_free = 0.2967 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2967 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.2566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 18705 Z= 0.114 Angle : 0.537 9.678 25284 Z= 0.277 Chirality : 0.041 0.154 2817 Planarity : 0.004 0.058 3153 Dihedral : 9.601 59.297 2752 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.61 % Favored : 94.35 % Rotamer: Outliers : 4.84 % Allowed : 26.73 % Favored : 68.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.53 (0.18), residues: 2194 helix: 1.11 (0.16), residues: 1104 sheet: -1.53 (0.32), residues: 210 loop : -1.98 (0.21), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG F 846 TYR 0.022 0.001 TYR F 632 PHE 0.024 0.001 PHE A 92 TRP 0.017 0.001 TRP F 187 HIS 0.002 0.000 HIS A1398 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.11 (18688) covalent geometry : angle 0.53600 / 0.28 (25260) SS BOND : bond 0.00230 / 0.17 ( 12) SS BOND : angle 1.36533 / 0.75 ( 24) hydrogen bonds : bond 0.02987 / 1.95 ( 831) hydrogen bonds : angle 3.75617 / 2.62 ( 2459) Misc. bond : bond 0.00042 / 0.02 ( 5) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4388 Ramachandran restraints generated. 2194 Oldfield, 0 Emsley, 2194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4388 Ramachandran restraints generated. 2194 Oldfield, 0 Emsley, 2194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 258 time to evaluate : 0.761 Fit side-chains revert: symmetry clash REVERT: A 182 LEU cc_start: 0.8261 (OUTLIER) cc_final: 0.7998 (tt) REVERT: A 183 GLN cc_start: 0.8322 (OUTLIER) cc_final: 0.7516 (mt0) REVERT: A 243 SER cc_start: 0.9281 (p) cc_final: 0.9074 (t) REVERT: A 326 LEU cc_start: 0.8734 (OUTLIER) cc_final: 0.8366 (mp) REVERT: A 460 LEU cc_start: 0.8730 (OUTLIER) cc_final: 0.8413 (tp) REVERT: A 464 GLN cc_start: 0.7559 (OUTLIER) cc_final: 0.7181 (mt0) REVERT: A 480 LEU cc_start: 0.3483 (OUTLIER) cc_final: 0.3145 (mp) REVERT: A 483 MET cc_start: 0.3054 (tmm) cc_final: 0.2594 (tpt) REVERT: A 500 ASP cc_start: 0.7285 (OUTLIER) cc_final: 0.6769 (p0) REVERT: A 828 ARG cc_start: 0.4554 (ttp-170) cc_final: 0.3961 (tpp-160) REVERT: A 916 HIS cc_start: 0.3848 (t-90) cc_final: 0.1776 (m90) REVERT: A 1018 GLN cc_start: 0.8839 (OUTLIER) cc_final: 0.8258 (mt0) REVERT: A 1060 PHE cc_start: 0.8069 (OUTLIER) cc_final: 0.7368 (t80) REVERT: A 1182 TRP cc_start: 0.8924 (m100) cc_final: 0.8677 (m100) REVERT: A 1186 ASP cc_start: 0.8335 (t0) cc_final: 0.7922 (t0) REVERT: A 1286 MET cc_start: 0.8869 (mtp) cc_final: 0.8559 (mtm) REVERT: E 24 MET cc_start: 0.7237 (tpp) cc_final: 0.7021 (tpp) REVERT: E 30 ASP cc_start: 0.6153 (m-30) cc_final: 0.5832 (m-30) REVERT: E 176 TYR cc_start: 0.5481 (p90) cc_final: 0.5246 (m-10) REVERT: F 114 ARG cc_start: 0.8244 (mtp85) cc_final: 0.8022 (mtt90) REVERT: F 281 MET cc_start: 0.9085 (tpp) cc_final: 0.8714 (ttm) REVERT: F 311 GLN cc_start: 0.9137 (OUTLIER) cc_final: 0.8829 (tp40) REVERT: F 727 LYS cc_start: 0.8776 (mmtm) cc_final: 0.8524 (mmtm) REVERT: F 728 ASN cc_start: 0.8450 (m-40) cc_final: 0.7967 (t0) REVERT: F 858 ASP cc_start: 0.8598 (p0) cc_final: 0.8232 (p0) REVERT: F 1049 MET cc_start: 0.8197 (ttm) cc_final: 0.7868 (mtp) REVERT: F 1068 LEU cc_start: 0.8584 (pt) cc_final: 0.8359 (tt) outliers start: 95 outliers final: 77 residues processed: 335 average time/residue: 0.1127 time to fit residues: 60.0226 Evaluate side-chains 341 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 254 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 183 GLN Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 291 MET Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 464 GLN Chi-restraints excluded: chain A residue 468 ASN Chi-restraints excluded: chain A residue 479 MET Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 500 ASP Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 647 CYS Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 788 VAL Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 876 VAL Chi-restraints excluded: chain A residue 896 LEU Chi-restraints excluded: chain A residue 1007 LEU Chi-restraints excluded: chain A residue 1018 GLN Chi-restraints excluded: chain A residue 1060 PHE Chi-restraints excluded: chain A residue 1108 GLN Chi-restraints excluded: chain A residue 1117 SER Chi-restraints excluded: chain A residue 1141 HIS Chi-restraints excluded: chain A residue 1149 ILE Chi-restraints excluded: chain A residue 1240 VAL Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1267 LEU Chi-restraints excluded: chain A residue 1272 LEU Chi-restraints excluded: chain A residue 1273 LEU Chi-restraints excluded: chain A residue 1289 PHE Chi-restraints excluded: chain A residue 1295 VAL Chi-restraints excluded: chain A residue 1343 ASP Chi-restraints excluded: chain A residue 1381 MET Chi-restraints excluded: chain A residue 1388 THR Chi-restraints excluded: chain A residue 1397 HIS Chi-restraints excluded: chain A residue 1400 ASP Chi-restraints excluded: chain A residue 1429 ILE Chi-restraints excluded: chain E residue 153 VAL Chi-restraints excluded: chain E residue 179 SER Chi-restraints excluded: chain F residue 36 TRP Chi-restraints excluded: chain F residue 61 TYR Chi-restraints excluded: chain F residue 116 ASP Chi-restraints excluded: chain F residue 125 VAL Chi-restraints excluded: chain F residue 200 GLU Chi-restraints excluded: chain F residue 205 LEU Chi-restraints excluded: chain F residue 240 VAL Chi-restraints excluded: chain F residue 270 THR Chi-restraints excluded: chain F residue 297 ASN Chi-restraints excluded: chain F residue 303 VAL Chi-restraints excluded: chain F residue 311 GLN Chi-restraints excluded: chain F residue 360 ILE Chi-restraints excluded: chain F residue 401 ILE Chi-restraints excluded: chain F residue 423 ILE Chi-restraints excluded: chain F residue 476 GLU Chi-restraints excluded: chain F residue 543 LEU Chi-restraints excluded: chain F residue 610 THR Chi-restraints excluded: chain F residue 612 THR Chi-restraints excluded: chain F residue 652 LYS Chi-restraints excluded: chain F residue 680 THR Chi-restraints excluded: chain F residue 694 THR Chi-restraints excluded: chain F residue 735 ARG Chi-restraints excluded: chain F residue 739 THR Chi-restraints excluded: chain F residue 744 THR Chi-restraints excluded: chain F residue 821 VAL Chi-restraints excluded: chain F residue 850 VAL Chi-restraints excluded: chain F residue 853 CYS Chi-restraints excluded: chain F residue 982 THR Chi-restraints excluded: chain F residue 1002 CYS Chi-restraints excluded: chain F residue 1008 VAL Chi-restraints excluded: chain F residue 1014 THR Chi-restraints excluded: chain F residue 1019 ILE Chi-restraints excluded: chain F residue 1026 THR Chi-restraints excluded: chain F residue 1027 CYS Chi-restraints excluded: chain F residue 1065 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 3 optimal weight: 0.8980 chunk 93 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 110 optimal weight: 6.9990 chunk 92 optimal weight: 0.0170 chunk 70 optimal weight: 0.7980 chunk 105 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 132 optimal weight: 2.9990 chunk 201 optimal weight: 4.9990 overall best weight: 0.9220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 ASN ** A1397 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 297 ASN ** F 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1007 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.150616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.114580 restraints weight = 26690.991| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 2.33 r_work: 0.3097 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2963 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2967 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2967 r_free = 0.2967 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2967 r_free = 0.2967 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2967 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.2591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.158 18705 Z= 0.191 Angle : 0.931 59.200 25284 Z= 0.554 Chirality : 0.055 1.828 2817 Planarity : 0.005 0.150 3153 Dihedral : 9.534 59.307 2748 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.52 % Favored : 94.39 % Rotamer: Outliers : 4.63 % Allowed : 26.93 % Favored : 68.43 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 2.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.53 (0.18), residues: 2194 helix: 1.11 (0.16), residues: 1104 sheet: -1.53 (0.32), residues: 210 loop : -1.98 (0.21), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG F 846 TYR 0.020 0.001 TYR F 632 PHE 0.030 0.001 PHE A1125 TRP 0.017 0.001 TRP F 187 HIS 0.002 0.000 HIS A1398 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.19 (18688) covalent geometry : angle 0.93080 / 0.55 (25260) SS BOND : bond 0.00226 / 0.17 ( 12) SS BOND : angle 1.31033 / 0.73 ( 24) hydrogen bonds : bond 0.02992 / 1.95 ( 831) hydrogen bonds : angle 3.76477 / 2.63 ( 2459) Misc. bond : bond 0.00037 / 0.02 ( 5) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5268.63 seconds wall clock time: 90 minutes 33.17 seconds (5433.17 seconds total)