Starting phenix.real_space_refine on Sat Aug 23 14:38:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6j8h_9781/08_2025/6j8h_9781_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6j8h_9781/08_2025/6j8h_9781.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6j8h_9781/08_2025/6j8h_9781.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6j8h_9781/08_2025/6j8h_9781.map" model { file = "/net/cci-nas-00/data/ceres_data/6j8h_9781/08_2025/6j8h_9781_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6j8h_9781/08_2025/6j8h_9781_neut.cif" } resolution = 3.2 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= 0.001 sd= 0.012 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 966 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 97 5.16 5 C 7724 2.51 5 N 1861 2.21 5 O 2081 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 35 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11763 Number of models: 1 Model: "" Number of chains: 8 Chain: "C" Number of atoms: 980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 980 Classifications: {'peptide': 120} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 113} Chain: "A" Number of atoms: 9192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1140, 9192 Classifications: {'peptide': 1140} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 29, 'TRANS': 1107} Chain breaks: 3 Chain: "B" Number of atoms: 1416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1416 Classifications: {'peptide': 173} Link IDs: {'TRANS': 172} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 49 Unusual residues: {'9SL': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 2.88, per 1000 atoms: 0.24 Number of scatterers: 11763 At special positions: 0 Unit cell: (133.102, 141.83, 112.373, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 97 16.00 O 2081 8.00 N 1861 7.00 C 7724 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS C 50 " - pdb=" SG CYS C 127 " distance=2.57 Simple disulfide: pdb=" SG CYS C 55 " - pdb=" SG CYS A 895 " distance=2.45 Simple disulfide: pdb=" SG CYS C 72 " - pdb=" SG CYS C 75 " distance=2.04 Simple disulfide: pdb=" SG CYS A 275 " - pdb=" SG CYS A 324 " distance=1.90 Simple disulfide: pdb=" SG CYS A 897 " - pdb=" SG CYS A 903 " distance=2.68 Simple disulfide: pdb=" SG CYS A 935 " - pdb=" SG CYS A 944 " distance=2.00 Simple disulfide: pdb=" SG CYS A1350 " - pdb=" SG CYS A1370 " distance=1.95 Simple disulfide: pdb=" SG CYS A1715 " - pdb=" SG CYS A1730 " distance=2.12 Simple disulfide: pdb=" SG CYS B 21 " - pdb=" SG CYS B 43 " distance=1.88 Simple disulfide: pdb=" SG CYS B 40 " - pdb=" SG CYS B 121 " distance=2.00 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 Atom "HETATM11600 O5 NAG D 1 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " NAG-ASN " NAG A2005 " - " ASN A1375 " " NAG A2006 " - " ASN A 283 " " NAG B 301 " - " ASN B 93 " " NAG B 302 " - " ASN B 110 " " NAG B 303 " - " ASN B 114 " " NAG B 304 " - " ASN B 135 " " NAG C 301 " - " ASN C 66 " " NAG D 1 " - " ASN A1352 " " NAG E 1 " - " ASN A1366 " Time building additional restraints: 0.87 Conformation dependent library (CDL) restraints added in 612.3 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2714 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 7 sheets defined 68.9% alpha, 8.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'C' and resid 92 through 96 Processing helix chain 'C' and resid 104 through 108 Processing helix chain 'C' and resid 118 through 122 Processing helix chain 'A' and resid 115 through 124 Processing helix chain 'A' and resid 125 through 144 removed outlier: 3.805A pdb=" N SER A 129 " --> pdb=" O HIS A 125 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N MET A 130 " --> pdb=" O SER A 126 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE A 141 " --> pdb=" O LEU A 137 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N PHE A 142 " --> pdb=" O THR A 138 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N THR A 144 " --> pdb=" O CYS A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 176 removed outlier: 4.229A pdb=" N VAL A 155 " --> pdb=" O TRP A 151 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LYS A 170 " --> pdb=" O GLU A 166 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N PHE A 176 " --> pdb=" O LEU A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 186 removed outlier: 4.516A pdb=" N ASP A 186 " --> pdb=" O THR A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 204 removed outlier: 4.007A pdb=" N TRP A 190 " --> pdb=" O ASP A 186 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N LEU A 191 " --> pdb=" O PRO A 187 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ASP A 192 " --> pdb=" O TRP A 188 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLU A 203 " --> pdb=" O ALA A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 215 Processing helix chain 'A' and resid 218 through 228 removed outlier: 3.837A pdb=" N LEU A 222 " --> pdb=" O VAL A 218 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N THR A 224 " --> pdb=" O ARG A 220 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N ILE A 225 " --> pdb=" O ALA A 221 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N SER A 226 " --> pdb=" O LEU A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 245 removed outlier: 3.750A pdb=" N LYS A 244 " --> pdb=" O GLN A 240 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU A 245 " --> pdb=" O SER A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 268 Processing helix chain 'A' and resid 269 through 271 No H-bonds generated for 'chain 'A' and resid 269 through 271' Processing helix chain 'A' and resid 280 through 284 removed outlier: 4.209A pdb=" N ASN A 283 " --> pdb=" O LEU A 280 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU A 284 " --> pdb=" O GLU A 281 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 280 through 284' Processing helix chain 'A' and resid 285 through 293 removed outlier: 3.849A pdb=" N ASN A 291 " --> pdb=" O GLU A 287 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N THR A 292 " --> pdb=" O SER A 288 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU A 293 " --> pdb=" O ILE A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 303 removed outlier: 3.540A pdb=" N LYS A 301 " --> pdb=" O GLU A 297 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N TYR A 302 " --> pdb=" O ASP A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 359 Processing helix chain 'A' and resid 362 through 375 removed outlier: 4.039A pdb=" N LEU A 366 " --> pdb=" O TYR A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 390 removed outlier: 3.895A pdb=" N PHE A 382 " --> pdb=" O TYR A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 417 removed outlier: 3.533A pdb=" N GLU A 407 " --> pdb=" O MET A 403 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLU A 415 " --> pdb=" O ALA A 411 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ALA A 416 " --> pdb=" O ASN A 412 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LYS A 417 " --> pdb=" O ILE A 413 " (cutoff:3.500A) Processing helix chain 'A' and resid 727 through 740 removed outlier: 3.663A pdb=" N ILE A 731 " --> pdb=" O SER A 727 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LYS A 732 " --> pdb=" O PRO A 728 " (cutoff:3.500A) Processing helix chain 'A' and resid 745 through 762 removed outlier: 3.762A pdb=" N THR A 751 " --> pdb=" O ASP A 747 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ILE A 752 " --> pdb=" O LEU A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 769 through 799 removed outlier: 3.704A pdb=" N ALA A 797 " --> pdb=" O LEU A 793 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N MET A 798 " --> pdb=" O LYS A 794 " (cutoff:3.500A) Processing helix chain 'A' and resid 799 through 806 removed outlier: 4.478A pdb=" N VAL A 806 " --> pdb=" O GLU A 802 " (cutoff:3.500A) Processing helix chain 'A' and resid 806 through 823 removed outlier: 3.782A pdb=" N ILE A 815 " --> pdb=" O PHE A 811 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N LEU A 823 " --> pdb=" O SER A 819 " (cutoff:3.500A) Processing helix chain 'A' and resid 832 through 837 removed outlier: 3.670A pdb=" N SER A 836 " --> pdb=" O SER A 832 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N PHE A 837 " --> pdb=" O VAL A 833 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 832 through 837' Processing helix chain 'A' and resid 838 through 847 removed outlier: 3.558A pdb=" N LEU A 845 " --> pdb=" O VAL A 842 " (cutoff:3.500A) Processing helix chain 'A' and resid 849 through 864 removed outlier: 3.621A pdb=" N SER A 862 " --> pdb=" O ILE A 858 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N VAL A 863 " --> pdb=" O ILE A 859 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 896 removed outlier: 5.243A pdb=" N LYS A 890 " --> pdb=" O GLN A 886 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N SER A 891 " --> pdb=" O LEU A 887 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LYS A 893 " --> pdb=" O GLY A 889 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 925 removed outlier: 3.704A pdb=" N CYS A 925 " --> pdb=" O PHE A 921 " (cutoff:3.500A) Processing helix chain 'A' and resid 927 through 940 removed outlier: 4.418A pdb=" N THR A 931 " --> pdb=" O GLU A 927 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ASP A 934 " --> pdb=" O GLU A 930 " (cutoff:3.500A) Processing helix chain 'A' and resid 940 through 972 Processing helix chain 'A' and resid 1176 through 1191 removed outlier: 4.206A pdb=" N ASN A1180 " --> pdb=" O LYS A1176 " (cutoff:3.500A) Processing helix chain 'A' and resid 1191 through 1212 removed outlier: 3.984A pdb=" N LEU A1209 " --> pdb=" O SER A1205 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ALA A1210 " --> pdb=" O SER A1206 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N PHE A1211 " --> pdb=" O GLY A1207 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N GLU A1212 " --> pdb=" O ALA A1208 " (cutoff:3.500A) Processing helix chain 'A' and resid 1213 through 1218 removed outlier: 4.142A pdb=" N GLU A1217 " --> pdb=" O ILE A1214 " (cutoff:3.500A) Processing helix chain 'A' and resid 1219 through 1255 removed outlier: 3.534A pdb=" N LYS A1223 " --> pdb=" O LYS A1219 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LYS A1231 " --> pdb=" O GLU A1227 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ILE A1232 " --> pdb=" O TYR A1228 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N TYR A1250 " --> pdb=" O ILE A1246 " (cutoff:3.500A) removed outlier: 9.241A pdb=" N LYS A1251 " --> pdb=" O ALA A1247 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N THR A1252 " --> pdb=" O TYR A1248 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N THR A1255 " --> pdb=" O LYS A1251 " (cutoff:3.500A) Processing helix chain 'A' and resid 1256 through 1279 Processing helix chain 'A' and resid 1286 through 1291 removed outlier: 3.911A pdb=" N THR A1291 " --> pdb=" O LYS A1287 " (cutoff:3.500A) Processing helix chain 'A' and resid 1292 through 1298 Proline residue: A1297 - end of helix Processing helix chain 'A' and resid 1299 through 1304 removed outlier: 4.203A pdb=" N ARG A1303 " --> pdb=" O ARG A1299 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N PHE A1304 " --> pdb=" O ALA A1300 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1299 through 1304' Processing helix chain 'A' and resid 1304 through 1344 removed outlier: 3.611A pdb=" N VAL A1310 " --> pdb=" O GLY A1306 " (cutoff:3.500A) Proline residue: A1319 - end of helix removed outlier: 3.503A pdb=" N VAL A1324 " --> pdb=" O SER A1320 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ILE A1334 " --> pdb=" O ILE A1330 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N PHE A1335 " --> pdb=" O PHE A1331 " (cutoff:3.500A) Processing helix chain 'A' and resid 1366 through 1377 removed outlier: 3.640A pdb=" N ALA A1372 " --> pdb=" O SER A1368 " (cutoff:3.500A) Processing helix chain 'A' and resid 1391 through 1405 removed outlier: 3.515A pdb=" N LEU A1397 " --> pdb=" O GLY A1393 " (cutoff:3.500A) Processing helix chain 'A' and resid 1407 through 1418 removed outlier: 3.926A pdb=" N ILE A1411 " --> pdb=" O GLY A1407 " (cutoff:3.500A) Processing helix chain 'A' and resid 1433 through 1445 removed outlier: 3.726A pdb=" N PHE A1437 " --> pdb=" O MET A1433 " (cutoff:3.500A) Processing helix chain 'A' and resid 1445 through 1467 Processing helix chain 'A' and resid 1475 through 1488 removed outlier: 3.763A pdb=" N LEU A1488 " --> pdb=" O ALA A1484 " (cutoff:3.500A) Processing helix chain 'A' and resid 1502 through 1514 removed outlier: 3.660A pdb=" N ILE A1508 " --> pdb=" O ILE A1504 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ASN A1514 " --> pdb=" O ASP A1510 " (cutoff:3.500A) Processing helix chain 'A' and resid 1514 through 1534 removed outlier: 3.566A pdb=" N ASP A1518 " --> pdb=" O ASN A1514 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N MET A1532 " --> pdb=" O ASN A1528 " (cutoff:3.500A) Processing helix chain 'A' and resid 1540 through 1570 Processing helix chain 'A' and resid 1570 through 1576 removed outlier: 4.127A pdb=" N PHE A1574 " --> pdb=" O ARG A1570 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N THR A1575 " --> pdb=" O HIS A1571 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N VAL A1576 " --> pdb=" O TYR A1572 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1570 through 1576' Processing helix chain 'A' and resid 1576 through 1603 Processing helix chain 'A' and resid 1605 through 1614 removed outlier: 4.225A pdb=" N PHE A1609 " --> pdb=" O SER A1605 " (cutoff:3.500A) Processing helix chain 'A' and resid 1616 through 1621 removed outlier: 4.146A pdb=" N ILE A1620 " --> pdb=" O ARG A1616 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU A1621 " --> pdb=" O ILE A1617 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1616 through 1621' Processing helix chain 'A' and resid 1622 through 1627 removed outlier: 4.069A pdb=" N GLY A1626 " --> pdb=" O ARG A1622 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA A1627 " --> pdb=" O LEU A1623 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1622 through 1627' Processing helix chain 'A' and resid 1627 through 1640 removed outlier: 3.505A pdb=" N THR A1632 " --> pdb=" O LYS A1628 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LEU A1633 " --> pdb=" O GLY A1629 " (cutoff:3.500A) Processing helix chain 'A' and resid 1640 through 1667 removed outlier: 3.584A pdb=" N ALA A1667 " --> pdb=" O MET A1663 " (cutoff:3.500A) Processing helix chain 'A' and resid 1683 through 1696 removed outlier: 4.331A pdb=" N THR A1696 " --> pdb=" O PHE A1692 " (cutoff:3.500A) Processing helix chain 'A' and resid 1699 through 1709 Proline residue: A1706 - end of helix removed outlier: 3.739A pdb=" N ASN A1709 " --> pdb=" O ALA A1705 " (cutoff:3.500A) Processing helix chain 'A' and resid 1732 through 1768 Processing helix chain 'B' and resid 83 through 87 Processing helix chain 'B' and resid 153 through 192 removed outlier: 3.501A pdb=" N TYR B 180 " --> pdb=" O ALA B 176 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LYS B 183 " --> pdb=" O ILE B 179 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N THR B 189 " --> pdb=" O ILE B 185 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLU B 190 " --> pdb=" O ALA B 186 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA B 192 " --> pdb=" O ALA B 188 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 31 through 33 Processing sheet with id=AA2, first strand: chain 'C' and resid 37 through 40 removed outlier: 6.303A pdb=" N LEU C 38 " --> pdb=" O GLN C 145 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU C 81 " --> pdb=" O TRP C 67 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N TYR C 69 " --> pdb=" O MET C 79 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N MET C 79 " --> pdb=" O TYR C 69 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 46 through 48 Processing sheet with id=AA4, first strand: chain 'A' and resid 273 through 277 Processing sheet with id=AA5, first strand: chain 'A' and resid 1357 through 1358 Processing sheet with id=AA6, first strand: chain 'B' and resid 29 through 31 removed outlier: 5.934A pdb=" N ALA B 30 " --> pdb=" O VAL B 147 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL B 138 " --> pdb=" O VAL B 123 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N ASN B 50 " --> pdb=" O PHE B 128 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N THR B 55 " --> pdb=" O ARG B 72 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N ARG B 72 " --> pdb=" O THR B 55 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N TRP B 57 " --> pdb=" O ILE B 70 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 36 through 41 718 hydrogen bonds defined for protein. 2067 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: 2.33 Time building geometry restraints manager: 1.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.34: 3525 1.34 - 1.50: 3627 1.50 - 1.67: 4730 1.67 - 1.84: 154 1.84 - 2.01: 2 Bond restraints: 12038 Sorted by residual: bond pdb=" C12 9SL A2007 " pdb=" N11 9SL A2007 " ideal model delta sigma weight residual 1.284 1.505 -0.221 2.00e-02 2.50e+03 1.22e+02 bond pdb=" C1 NAG A2005 " pdb=" C2 NAG A2005 " ideal model delta sigma weight residual 1.532 1.663 -0.131 2.00e-02 2.50e+03 4.27e+01 bond pdb=" CB CYS C 127 " pdb=" SG CYS C 127 " ideal model delta sigma weight residual 1.808 2.008 -0.200 3.30e-02 9.18e+02 3.68e+01 bond pdb=" C12 9SL A2007 " pdb=" N13 9SL A2007 " ideal model delta sigma weight residual 1.370 1.486 -0.116 2.00e-02 2.50e+03 3.34e+01 bond pdb=" C CYS A 324 " pdb=" N PRO A 325 " ideal model delta sigma weight residual 1.332 1.398 -0.067 1.26e-02 6.30e+03 2.81e+01 ... (remaining 12033 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.42: 15641 3.42 - 6.83: 574 6.83 - 10.25: 59 10.25 - 13.67: 27 13.67 - 17.09: 9 Bond angle restraints: 16310 Sorted by residual: angle pdb=" N TYR A 302 " pdb=" CA TYR A 302 " pdb=" C TYR A 302 " ideal model delta sigma weight residual 111.36 124.73 -13.37 1.09e+00 8.42e-01 1.50e+02 angle pdb=" N CYS A 925 " pdb=" CA CYS A 925 " pdb=" C CYS A 925 " ideal model delta sigma weight residual 110.55 94.36 16.19 1.35e+00 5.49e-01 1.44e+02 angle pdb=" N TYR A 304 " pdb=" CA TYR A 304 " pdb=" C TYR A 304 " ideal model delta sigma weight residual 110.97 123.84 -12.87 1.09e+00 8.42e-01 1.39e+02 angle pdb=" N GLN A1378 " pdb=" CA GLN A1378 " pdb=" C GLN A1378 " ideal model delta sigma weight residual 111.36 124.09 -12.73 1.09e+00 8.42e-01 1.36e+02 angle pdb=" N LEU B 101 " pdb=" CA LEU B 101 " pdb=" C LEU B 101 " ideal model delta sigma weight residual 111.07 122.02 -10.95 1.07e+00 8.73e-01 1.05e+02 ... (remaining 16305 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.78: 5829 17.78 - 35.56: 838 35.56 - 53.35: 438 53.35 - 71.13: 146 71.13 - 88.91: 20 Dihedral angle restraints: 7271 sinusoidal: 3069 harmonic: 4202 Sorted by residual: dihedral pdb=" CB CYS B 40 " pdb=" SG CYS B 40 " pdb=" SG CYS B 121 " pdb=" CB CYS B 121 " ideal model delta sinusoidal sigma weight residual -86.00 -23.93 -62.07 1 1.00e+01 1.00e-02 5.10e+01 dihedral pdb=" CB CYS A 935 " pdb=" SG CYS A 935 " pdb=" SG CYS A 944 " pdb=" CB CYS A 944 " ideal model delta sinusoidal sigma weight residual 93.00 152.13 -59.13 1 1.00e+01 1.00e-02 4.67e+01 dihedral pdb=" CB CYS A1715 " pdb=" SG CYS A1715 " pdb=" SG CYS A1730 " pdb=" CB CYS A1730 " ideal model delta sinusoidal sigma weight residual 93.00 33.93 59.07 1 1.00e+01 1.00e-02 4.67e+01 ... (remaining 7268 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.152: 1670 0.152 - 0.303: 203 0.303 - 0.455: 19 0.455 - 0.607: 8 0.607 - 0.758: 1 Chirality restraints: 1901 Sorted by residual: chirality pdb=" C1 NAG E 2 " pdb=" O4 NAG E 1 " pdb=" C2 NAG E 2 " pdb=" O5 NAG E 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.64 -0.76 2.00e-02 2.50e+03 1.44e+03 chirality pdb=" C1 NAG D 2 " pdb=" O4 NAG D 1 " pdb=" C2 NAG D 2 " pdb=" O5 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.51 0.11 2.00e-02 2.50e+03 2.98e+01 chirality pdb=" C1 NAG B 302 " pdb=" ND2 ASN B 110 " pdb=" C2 NAG B 302 " pdb=" O5 NAG B 302 " both_signs ideal model delta sigma weight residual False -2.40 -1.80 -0.60 2.00e-01 2.50e+01 8.89e+00 ... (remaining 1898 not shown) Planarity restraints: 1995 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 301 " 0.359 2.00e-02 2.50e+03 3.08e-01 1.19e+03 pdb=" C7 NAG B 301 " -0.086 2.00e-02 2.50e+03 pdb=" C8 NAG B 301 " 0.129 2.00e-02 2.50e+03 pdb=" N2 NAG B 301 " -0.549 2.00e-02 2.50e+03 pdb=" O7 NAG B 301 " 0.147 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 110 " 0.198 2.00e-02 2.50e+03 2.52e-01 7.94e+02 pdb=" CG ASN B 110 " -0.080 2.00e-02 2.50e+03 pdb=" OD1 ASN B 110 " 0.018 2.00e-02 2.50e+03 pdb=" ND2 ASN B 110 " -0.430 2.00e-02 2.50e+03 pdb=" C1 NAG B 302 " 0.294 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 135 " -0.091 2.00e-02 2.50e+03 2.17e-01 5.87e+02 pdb=" CG ASN B 135 " 0.064 2.00e-02 2.50e+03 pdb=" OD1 ASN B 135 " -0.121 2.00e-02 2.50e+03 pdb=" ND2 ASN B 135 " 0.388 2.00e-02 2.50e+03 pdb=" C1 NAG B 304 " -0.239 2.00e-02 2.50e+03 ... (remaining 1992 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.49: 142 2.49 - 3.09: 9476 3.09 - 3.69: 17136 3.69 - 4.30: 25526 4.30 - 4.90: 41671 Nonbonded interactions: 93951 Sorted by model distance: nonbonded pdb=" N GLN A1541 " pdb=" OE1 GLN A1541 " model vdw 1.886 3.120 nonbonded pdb=" O3 NAG E 2 " pdb=" O7 NAG E 2 " model vdw 1.980 3.040 nonbonded pdb=" OD1 ASN A1375 " pdb=" O5 NAG A2005 " model vdw 2.032 3.040 nonbonded pdb=" O SER A1430 " pdb=" N TYR A1432 " model vdw 2.036 3.120 nonbonded pdb=" NE2 GLN A 360 " pdb=" OG SER A 390 " model vdw 2.047 3.120 ... (remaining 93946 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'D' selection = chain 'E' } 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=0.41 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: 1.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 11.740 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 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:1.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 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 : 0.014 0.654 12059 Z= 0.851 Angle : 1.903 55.340 16363 Z= 1.161 Chirality : 0.104 0.758 1901 Planarity : 0.010 0.308 1986 Dihedral : 21.716 88.910 4527 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 58.60 Ramachandran Plot: Outliers : 1.34 % Allowed : 2.04 % Favored : 96.62 % Rotamer: Outliers : 27.17 % Allowed : 18.94 % Favored : 53.88 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.14 % 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 aren not related in a simple way. whole: 2.87 (0.21), residues: 1421 helix: 3.08 (0.16), residues: 810 sheet: 1.54 (0.44), residues: 132 loop : -0.14 (0.28), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 356 TYR 0.025 0.002 TYR A1429 PHE 0.022 0.002 PHE B 54 TRP 0.015 0.002 TRP A1700 HIS 0.009 0.001 HIS A 766 Details of bonding type rmsd covalent geometry : bond 0.01049 (12038) covalent geometry : angle 1.53981 (16310) SS BOND : bond 0.30865 ( 10) SS BOND : angle 26.51575 ( 20) hydrogen bonds : bond 0.28481 ( 718) hydrogen bonds : angle 7.51551 ( 2067) link_BETA1-4 : bond 0.00200 ( 2) link_BETA1-4 : angle 5.53209 ( 6) link_NAG-ASN : bond 0.05791 ( 9) link_NAG-ASN : angle 15.29840 ( 27) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 580 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 350 poor density : 230 time to evaluate : 0.442 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 130 MET cc_start: 0.5859 (OUTLIER) cc_final: 0.5432 (mpp) REVERT: A 143 MET cc_start: 0.8372 (OUTLIER) cc_final: 0.8157 (mtt) REVERT: A 181 PHE cc_start: 0.2690 (OUTLIER) cc_final: 0.2174 (m-80) REVERT: A 206 ASN cc_start: 0.3090 (OUTLIER) cc_final: 0.2354 (t0) REVERT: A 209 ASN cc_start: 0.3988 (OUTLIER) cc_final: 0.3122 (t0) REVERT: A 298 ASP cc_start: 0.8609 (OUTLIER) cc_final: 0.8227 (t0) REVERT: A 371 LEU cc_start: 0.9015 (OUTLIER) cc_final: 0.8463 (mp) REVERT: A 379 MET cc_start: 0.8636 (OUTLIER) cc_final: 0.8316 (ttt) REVERT: A 387 PHE cc_start: 0.8075 (OUTLIER) cc_final: 0.7470 (m-10) REVERT: A 410 GLN cc_start: 0.7362 (OUTLIER) cc_final: 0.6552 (tm-30) REVERT: A 761 MET cc_start: 0.7465 (mtm) cc_final: 0.7018 (mtm) REVERT: A 764 GLU cc_start: 0.7794 (OUTLIER) cc_final: 0.7529 (mt-10) REVERT: A 769 THR cc_start: 0.8154 (OUTLIER) cc_final: 0.7562 (p) REVERT: A 774 ASN cc_start: 0.7075 (OUTLIER) cc_final: 0.6784 (t0) REVERT: A 780 ASN cc_start: 0.7203 (OUTLIER) cc_final: 0.6931 (t0) REVERT: A 796 ILE cc_start: 0.7488 (OUTLIER) cc_final: 0.7216 (mp) REVERT: A 831 LEU cc_start: 0.4648 (OUTLIER) cc_final: 0.4354 (tp) REVERT: A 848 SER cc_start: 0.8063 (OUTLIER) cc_final: 0.7797 (m) REVERT: A 893 LYS cc_start: 0.8318 (tptm) cc_final: 0.8004 (tttm) REVERT: A 1226 LEU cc_start: 0.8529 (OUTLIER) cc_final: 0.8298 (mt) REVERT: A 1251 LYS cc_start: 0.8495 (OUTLIER) cc_final: 0.8271 (ttpt) REVERT: A 1296 ARG cc_start: 0.8481 (OUTLIER) cc_final: 0.8223 (mtt180) REVERT: A 1323 ASN cc_start: 0.7912 (OUTLIER) cc_final: 0.7572 (m-40) REVERT: A 1358 ARG cc_start: 0.7862 (OUTLIER) cc_final: 0.6064 (mtm-85) REVERT: A 1385 LEU cc_start: 0.7834 (OUTLIER) cc_final: 0.7634 (mp) REVERT: A 1399 LEU cc_start: 0.9000 (OUTLIER) cc_final: 0.8291 (mp) REVERT: A 1465 LYS cc_start: 0.8293 (OUTLIER) cc_final: 0.7867 (tttm) REVERT: A 1474 MET cc_start: 0.9108 (OUTLIER) cc_final: 0.8820 (mtp) REVERT: A 1478 GLN cc_start: 0.7918 (OUTLIER) cc_final: 0.7294 (mt0) REVERT: A 1497 ILE cc_start: 0.4665 (OUTLIER) cc_final: 0.4414 (mt) REVERT: A 1503 LYS cc_start: 0.3753 (OUTLIER) cc_final: 0.2863 (tptm) REVERT: A 1515 GLN cc_start: 0.6839 (OUTLIER) cc_final: 0.6612 (pp30) REVERT: A 1533 MET cc_start: 0.8601 (OUTLIER) cc_final: 0.8370 (mtt) REVERT: A 1537 GLU cc_start: 0.8165 (OUTLIER) cc_final: 0.7514 (tm-30) REVERT: A 1566 LEU cc_start: 0.8145 (OUTLIER) cc_final: 0.7648 (mp) REVERT: A 1570 ARG cc_start: 0.7001 (OUTLIER) cc_final: 0.6400 (mtm180) REVERT: A 1582 ASP cc_start: 0.7685 (t0) cc_final: 0.7362 (t0) REVERT: A 1621 LEU cc_start: 0.8624 (OUTLIER) cc_final: 0.8396 (mt) REVERT: A 1634 LEU cc_start: 0.8948 (OUTLIER) cc_final: 0.8688 (mp) REVERT: A 1735 VAL cc_start: 0.9035 (p) cc_final: 0.8811 (p) REVERT: A 1755 TYR cc_start: 0.6859 (OUTLIER) cc_final: 0.6200 (t80) REVERT: B 46 ARG cc_start: 0.8702 (OUTLIER) cc_final: 0.7868 (mtp-110) REVERT: B 101 LEU cc_start: 0.8340 (OUTLIER) cc_final: 0.8068 (mt) REVERT: B 131 ASN cc_start: 0.7401 (OUTLIER) cc_final: 0.7200 (t0) REVERT: B 162 MET cc_start: 0.7124 (tpt) cc_final: 0.6450 (ttp) REVERT: B 178 MET cc_start: 0.7140 (OUTLIER) cc_final: 0.5057 (ttt) outliers start: 350 outliers final: 134 residues processed: 497 average time/residue: 0.0972 time to fit residues: 66.8018 Evaluate side-chains 352 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 175 poor density : 177 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 30 MET Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 52 PHE Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 130 MET Chi-restraints excluded: chain C residue 148 MET Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 134 CYS Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 143 MET Chi-restraints excluded: chain A residue 146 ASN Chi-restraints excluded: chain A residue 153 LYS Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 181 PHE Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 206 ASN Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 209 ASN Chi-restraints excluded: chain A residue 217 ARG Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 255 CYS Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 298 ASP Chi-restraints excluded: chain A residue 300 ARG Chi-restraints excluded: chain A residue 311 ASP Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 318 SER Chi-restraints excluded: chain A residue 349 TRP Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 358 MET Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 379 MET Chi-restraints excluded: chain A residue 387 PHE Chi-restraints excluded: chain A residue 406 LYS Chi-restraints excluded: chain A residue 410 GLN Chi-restraints excluded: chain A residue 412 ASN Chi-restraints excluded: chain A residue 726 CYS Chi-restraints excluded: chain A residue 733 PHE Chi-restraints excluded: chain A residue 748 LEU Chi-restraints excluded: chain A residue 750 ILE Chi-restraints excluded: chain A residue 751 THR Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain A residue 763 MET Chi-restraints excluded: chain A residue 764 GLU Chi-restraints excluded: chain A residue 765 HIS Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 773 LYS Chi-restraints excluded: chain A residue 774 ASN Chi-restraints excluded: chain A residue 776 LEU Chi-restraints excluded: chain A residue 780 ASN Chi-restraints excluded: chain A residue 790 GLU Chi-restraints excluded: chain A residue 794 LYS Chi-restraints excluded: chain A residue 795 LEU Chi-restraints excluded: chain A residue 796 ILE Chi-restraints excluded: chain A residue 808 TRP Chi-restraints excluded: chain A residue 821 VAL Chi-restraints excluded: chain A residue 825 LEU Chi-restraints excluded: chain A residue 831 LEU Chi-restraints excluded: chain A residue 834 LEU Chi-restraints excluded: chain A residue 835 ARG Chi-restraints excluded: chain A residue 837 PHE Chi-restraints excluded: chain A residue 838 ARG Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 848 SER Chi-restraints excluded: chain A residue 854 MET Chi-restraints excluded: chain A residue 870 THR Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 873 LEU Chi-restraints excluded: chain A residue 887 LEU Chi-restraints excluded: chain A residue 898 LYS Chi-restraints excluded: chain A residue 910 MET Chi-restraints excluded: chain A residue 916 SER Chi-restraints excluded: chain A residue 918 LEU Chi-restraints excluded: chain A residue 952 MET Chi-restraints excluded: chain A residue 967 LEU Chi-restraints excluded: chain A residue 968 LEU Chi-restraints excluded: chain A residue 1206 SER Chi-restraints excluded: chain A residue 1209 LEU Chi-restraints excluded: chain A residue 1226 LEU Chi-restraints excluded: chain A residue 1232 ILE Chi-restraints excluded: chain A residue 1251 LYS Chi-restraints excluded: chain A residue 1264 LEU Chi-restraints excluded: chain A residue 1274 VAL Chi-restraints excluded: chain A residue 1278 LEU Chi-restraints excluded: chain A residue 1283 LEU Chi-restraints excluded: chain A residue 1286 ILE Chi-restraints excluded: chain A residue 1289 LEU Chi-restraints excluded: chain A residue 1293 ARG Chi-restraints excluded: chain A residue 1295 LEU Chi-restraints excluded: chain A residue 1296 ARG Chi-restraints excluded: chain A residue 1299 ARG Chi-restraints excluded: chain A residue 1307 MET Chi-restraints excluded: chain A residue 1309 VAL Chi-restraints excluded: chain A residue 1323 ASN Chi-restraints excluded: chain A residue 1325 LEU Chi-restraints excluded: chain A residue 1326 LEU Chi-restraints excluded: chain A residue 1350 CYS Chi-restraints excluded: chain A residue 1354 THR Chi-restraints excluded: chain A residue 1358 ARG Chi-restraints excluded: chain A residue 1385 LEU Chi-restraints excluded: chain A residue 1399 LEU Chi-restraints excluded: chain A residue 1416 VAL Chi-restraints excluded: chain A residue 1419 VAL Chi-restraints excluded: chain A residue 1449 LEU Chi-restraints excluded: chain A residue 1465 LYS Chi-restraints excluded: chain A residue 1467 LEU Chi-restraints excluded: chain A residue 1474 MET Chi-restraints excluded: chain A residue 1478 GLN Chi-restraints excluded: chain A residue 1479 LYS Chi-restraints excluded: chain A residue 1486 LYS Chi-restraints excluded: chain A residue 1497 ILE Chi-restraints excluded: chain A residue 1503 LYS Chi-restraints excluded: chain A residue 1504 ILE Chi-restraints excluded: chain A residue 1511 LEU Chi-restraints excluded: chain A residue 1515 GLN Chi-restraints excluded: chain A residue 1519 ILE Chi-restraints excluded: chain A residue 1528 ASN Chi-restraints excluded: chain A residue 1533 MET Chi-restraints excluded: chain A residue 1537 GLU Chi-restraints excluded: chain A residue 1557 LEU Chi-restraints excluded: chain A residue 1561 GLU Chi-restraints excluded: chain A residue 1566 LEU Chi-restraints excluded: chain A residue 1570 ARG Chi-restraints excluded: chain A residue 1571 HIS Chi-restraints excluded: chain A residue 1598 LEU Chi-restraints excluded: chain A residue 1601 THR Chi-restraints excluded: chain A residue 1602 TYR Chi-restraints excluded: chain A residue 1605 SER Chi-restraints excluded: chain A residue 1608 LEU Chi-restraints excluded: chain A residue 1621 LEU Chi-restraints excluded: chain A residue 1628 LYS Chi-restraints excluded: chain A residue 1634 LEU Chi-restraints excluded: chain A residue 1637 LEU Chi-restraints excluded: chain A residue 1644 LEU Chi-restraints excluded: chain A residue 1649 LEU Chi-restraints excluded: chain A residue 1673 ASP Chi-restraints excluded: chain A residue 1687 SER Chi-restraints excluded: chain A residue 1707 ILE Chi-restraints excluded: chain A residue 1711 LYS Chi-restraints excluded: chain A residue 1719 LYS Chi-restraints excluded: chain A residue 1725 SER Chi-restraints excluded: chain A residue 1749 LEU Chi-restraints excluded: chain A residue 1754 MET Chi-restraints excluded: chain A residue 1755 TYR Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 48 GLU Chi-restraints excluded: chain B residue 66 GLU Chi-restraints excluded: chain B residue 67 PHE Chi-restraints excluded: chain B residue 76 GLU Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 84 GLU Chi-restraints excluded: chain B residue 95 SER Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 102 GLN Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 121 CYS Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 131 ASN Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 178 MET Chi-restraints excluded: chain B residue 180 TYR Chi-restraints excluded: chain B residue 191 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 98 optimal weight: 8.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.5980 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 0.8980 chunk 55 optimal weight: 2.9990 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 59 ASN C 82 GLN C 89 ASN C 118 GLN A 125 HIS A 146 ASN ** A 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 270 ASN A 278 ASN A 360 GLN A 410 GLN A 766 HIS A 774 ASN A 909 HIS A 911 ASN A1276 ASN A1478 GLN A1551 ASN A1571 HIS A1709 ASN A1721 HIS A1732 ASN A1762 ASN B 61 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.162067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.123582 restraints weight = 15642.304| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 1.94 r_work: 0.3198 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3080 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2991 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2991 r_free = 0.2991 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2991 r_free = 0.2991 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2991 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.3045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 12059 Z= 0.205 Angle : 0.866 13.299 16363 Z= 0.429 Chirality : 0.051 0.705 1901 Planarity : 0.005 0.056 1986 Dihedral : 16.242 102.612 2200 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.42 % Allowed : 2.81 % Favored : 96.76 % Rotamer: Outliers : 12.42 % Allowed : 22.83 % Favored : 64.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.14 % 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 aren not related in a simple way. whole: 1.81 (0.22), residues: 1421 helix: 2.23 (0.17), residues: 836 sheet: 0.86 (0.45), residues: 126 loop : -0.65 (0.29), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 94 TYR 0.027 0.002 TYR B 180 PHE 0.026 0.002 PHE B 54 TRP 0.019 0.002 TRP A 151 HIS 0.008 0.002 HIS A 766 Details of bonding type rmsd covalent geometry : bond 0.00441 (12038) covalent geometry : angle 0.83826 (16310) SS BOND : bond 0.00749 ( 10) SS BOND : angle 1.68595 ( 20) hydrogen bonds : bond 0.06467 ( 718) hydrogen bonds : angle 5.40537 ( 2067) link_BETA1-4 : bond 0.01350 ( 2) link_BETA1-4 : angle 5.09648 ( 6) link_NAG-ASN : bond 0.00836 ( 9) link_NAG-ASN : angle 4.75039 ( 27) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 160 poor density : 234 time to evaluate : 0.319 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 113 MET cc_start: 0.5594 (tpp) cc_final: 0.5043 (mtp) REVERT: C 129 ILE cc_start: 0.5421 (OUTLIER) cc_final: 0.4958 (mt) REVERT: C 130 MET cc_start: 0.5645 (OUTLIER) cc_final: 0.4085 (mpp) REVERT: A 133 MET cc_start: 0.8463 (tmm) cc_final: 0.8203 (tmm) REVERT: A 164 THR cc_start: 0.8042 (p) cc_final: 0.7756 (m) REVERT: A 181 PHE cc_start: 0.2158 (OUTLIER) cc_final: 0.0381 (t80) REVERT: A 190 TRP cc_start: 0.7728 (m-10) cc_final: 0.7359 (m-10) REVERT: A 209 ASN cc_start: 0.4122 (OUTLIER) cc_final: 0.3761 (t0) REVERT: A 214 ARG cc_start: 0.8301 (mmp80) cc_final: 0.7793 (mmp80) REVERT: A 217 ARG cc_start: 0.8302 (ptm160) cc_final: 0.8058 (ptm-80) REVERT: A 298 ASP cc_start: 0.8788 (OUTLIER) cc_final: 0.8449 (t0) REVERT: A 300 ARG cc_start: 0.8506 (OUTLIER) cc_final: 0.8227 (mtt180) REVERT: A 371 LEU cc_start: 0.9314 (OUTLIER) cc_final: 0.8760 (mp) REVERT: A 379 MET cc_start: 0.8980 (ttp) cc_final: 0.8761 (ttt) REVERT: A 387 PHE cc_start: 0.8434 (OUTLIER) cc_final: 0.7745 (m-10) REVERT: A 755 VAL cc_start: 0.8230 (OUTLIER) cc_final: 0.7984 (t) REVERT: A 764 GLU cc_start: 0.8362 (OUTLIER) cc_final: 0.7953 (mt-10) REVERT: A 780 ASN cc_start: 0.7513 (OUTLIER) cc_final: 0.7173 (t0) REVERT: A 839 LEU cc_start: 0.8804 (OUTLIER) cc_final: 0.8522 (pp) REVERT: A 857 LYS cc_start: 0.7297 (ttpt) cc_final: 0.6609 (tttp) REVERT: A 893 LYS cc_start: 0.8598 (tptm) cc_final: 0.8146 (tttt) REVERT: A 918 LEU cc_start: 0.9125 (OUTLIER) cc_final: 0.8805 (mt) REVERT: A 971 PHE cc_start: 0.6936 (t80) cc_final: 0.6340 (t80) REVERT: A 1251 LYS cc_start: 0.8681 (OUTLIER) cc_final: 0.8338 (ttpt) REVERT: A 1269 SER cc_start: 0.8598 (OUTLIER) cc_final: 0.8327 (m) REVERT: A 1295 LEU cc_start: 0.9369 (OUTLIER) cc_final: 0.9008 (mt) REVERT: A 1305 GLU cc_start: 0.7467 (mp0) cc_final: 0.7056 (mt-10) REVERT: A 1323 ASN cc_start: 0.7930 (OUTLIER) cc_final: 0.7686 (m-40) REVERT: A 1328 CYS cc_start: 0.8792 (m) cc_final: 0.8543 (m) REVERT: A 1386 LYS cc_start: 0.8538 (OUTLIER) cc_final: 0.8268 (ttpt) REVERT: A 1399 LEU cc_start: 0.9104 (OUTLIER) cc_final: 0.8305 (mp) REVERT: A 1449 LEU cc_start: 0.8815 (OUTLIER) cc_final: 0.8521 (tp) REVERT: A 1461 ASN cc_start: 0.8012 (m-40) cc_final: 0.7789 (m-40) REVERT: A 1465 LYS cc_start: 0.8399 (tppt) cc_final: 0.8031 (tttm) REVERT: A 1474 MET cc_start: 0.9232 (mtt) cc_final: 0.8946 (mtp) REVERT: A 1479 LYS cc_start: 0.8350 (OUTLIER) cc_final: 0.7985 (mtpt) REVERT: A 1503 LYS cc_start: 0.3986 (OUTLIER) cc_final: 0.3312 (tptm) REVERT: A 1515 GLN cc_start: 0.6262 (OUTLIER) cc_final: 0.5887 (pp30) REVERT: A 1537 GLU cc_start: 0.8542 (OUTLIER) cc_final: 0.7877 (tm-30) REVERT: A 1570 ARG cc_start: 0.7371 (OUTLIER) cc_final: 0.7075 (mtm180) REVERT: A 1582 ASP cc_start: 0.8290 (t0) cc_final: 0.7903 (m-30) REVERT: A 1602 TYR cc_start: 0.5100 (OUTLIER) cc_final: 0.3490 (t80) REVERT: A 1711 LYS cc_start: 0.7713 (OUTLIER) cc_final: 0.7322 (pttt) REVERT: A 1749 LEU cc_start: 0.8769 (OUTLIER) cc_final: 0.8451 (mp) REVERT: A 1755 TYR cc_start: 0.7227 (OUTLIER) cc_final: 0.6589 (t80) REVERT: B 79 GLN cc_start: 0.8082 (mt0) cc_final: 0.7854 (mt0) REVERT: B 81 GLU cc_start: 0.7625 (tp30) cc_final: 0.7367 (tp30) REVERT: B 101 LEU cc_start: 0.8428 (OUTLIER) cc_final: 0.8086 (mt) REVERT: B 131 ASN cc_start: 0.8047 (OUTLIER) cc_final: 0.7683 (t0) REVERT: B 162 MET cc_start: 0.7058 (tpt) cc_final: 0.6691 (ttp) REVERT: B 178 MET cc_start: 0.7876 (mmm) cc_final: 0.5744 (ttt) outliers start: 160 outliers final: 65 residues processed: 348 average time/residue: 0.0808 time to fit residues: 41.0643 Evaluate side-chains 284 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 188 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 130 MET Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 134 CYS Chi-restraints excluded: chain A residue 146 ASN Chi-restraints excluded: chain A residue 181 PHE Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 209 ASN Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 298 ASP Chi-restraints excluded: chain A residue 300 ARG Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 311 ASP Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 318 SER Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 387 PHE Chi-restraints excluded: chain A residue 412 ASN Chi-restraints excluded: chain A residue 733 PHE Chi-restraints excluded: chain A residue 748 LEU Chi-restraints excluded: chain A residue 750 ILE Chi-restraints excluded: chain A residue 752 ILE Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain A residue 763 MET Chi-restraints excluded: chain A residue 764 GLU Chi-restraints excluded: chain A residue 765 HIS Chi-restraints excluded: chain A residue 776 LEU Chi-restraints excluded: chain A residue 780 ASN Chi-restraints excluded: chain A residue 808 TRP Chi-restraints excluded: chain A residue 834 LEU Chi-restraints excluded: chain A residue 837 PHE Chi-restraints excluded: chain A residue 839 LEU Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 848 SER Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 876 ILE Chi-restraints excluded: chain A residue 916 SER Chi-restraints excluded: chain A residue 918 LEU Chi-restraints excluded: chain A residue 952 MET Chi-restraints excluded: chain A residue 968 LEU Chi-restraints excluded: chain A residue 1184 THR Chi-restraints excluded: chain A residue 1209 LEU Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1251 LYS Chi-restraints excluded: chain A residue 1269 SER Chi-restraints excluded: chain A residue 1289 LEU Chi-restraints excluded: chain A residue 1295 LEU Chi-restraints excluded: chain A residue 1299 ARG Chi-restraints excluded: chain A residue 1323 ASN Chi-restraints excluded: chain A residue 1326 LEU Chi-restraints excluded: chain A residue 1354 THR Chi-restraints excluded: chain A residue 1386 LYS Chi-restraints excluded: chain A residue 1399 LEU Chi-restraints excluded: chain A residue 1419 VAL Chi-restraints excluded: chain A residue 1449 LEU Chi-restraints excluded: chain A residue 1467 LEU Chi-restraints excluded: chain A residue 1479 LYS Chi-restraints excluded: chain A residue 1503 LYS Chi-restraints excluded: chain A residue 1504 ILE Chi-restraints excluded: chain A residue 1515 GLN Chi-restraints excluded: chain A residue 1519 ILE Chi-restraints excluded: chain A residue 1537 GLU Chi-restraints excluded: chain A residue 1557 LEU Chi-restraints excluded: chain A residue 1570 ARG Chi-restraints excluded: chain A residue 1580 ILE Chi-restraints excluded: chain A residue 1594 PHE Chi-restraints excluded: chain A residue 1601 THR Chi-restraints excluded: chain A residue 1602 TYR Chi-restraints excluded: chain A residue 1608 LEU Chi-restraints excluded: chain A residue 1649 LEU Chi-restraints excluded: chain A residue 1711 LYS Chi-restraints excluded: chain A residue 1749 LEU Chi-restraints excluded: chain A residue 1754 MET Chi-restraints excluded: chain A residue 1755 TYR Chi-restraints excluded: chain B residue 48 GLU Chi-restraints excluded: chain B residue 66 GLU Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 110 ASN Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 131 ASN Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 141 LYS Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 180 TYR Chi-restraints excluded: chain B residue 191 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 58 optimal weight: 0.7980 chunk 36 optimal weight: 3.9990 chunk 97 optimal weight: 6.9990 chunk 44 optimal weight: 6.9990 chunk 82 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 130 optimal weight: 0.4980 chunk 15 optimal weight: 3.9990 chunk 93 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 105 optimal weight: 0.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 74 ASN C 136 HIS ** A 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1378 GLN A1528 ASN B 102 GLN B 115 HIS B 122 HIS B 143 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.161675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.123036 restraints weight = 15703.287| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 1.99 r_work: 0.3176 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3060 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.3707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 12059 Z= 0.161 Angle : 0.718 12.461 16363 Z= 0.355 Chirality : 0.045 0.473 1901 Planarity : 0.004 0.044 1986 Dihedral : 12.880 71.649 1977 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.28 % Allowed : 3.45 % Favored : 96.27 % Rotamer: Outliers : 9.47 % Allowed : 24.22 % Favored : 66.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.14 % 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 aren not related in a simple way. whole: 1.51 (0.22), residues: 1421 helix: 2.08 (0.17), residues: 843 sheet: 0.58 (0.44), residues: 133 loop : -1.00 (0.29), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 214 TYR 0.024 0.002 TYR A1755 PHE 0.017 0.001 PHE B 54 TRP 0.020 0.001 TRP A1408 HIS 0.005 0.001 HIS C 136 Details of bonding type rmsd covalent geometry : bond 0.00346 (12038) covalent geometry : angle 0.68869 (16310) SS BOND : bond 0.00526 ( 10) SS BOND : angle 1.76810 ( 20) hydrogen bonds : bond 0.05330 ( 718) hydrogen bonds : angle 4.94954 ( 2067) link_BETA1-4 : bond 0.01722 ( 2) link_BETA1-4 : angle 4.54213 ( 6) link_NAG-ASN : bond 0.00700 ( 9) link_NAG-ASN : angle 4.34370 ( 27) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 206 time to evaluate : 0.269 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 113 MET cc_start: 0.5409 (tpp) cc_final: 0.4983 (mtm) REVERT: C 130 MET cc_start: 0.5808 (OUTLIER) cc_final: 0.4974 (tmm) REVERT: A 181 PHE cc_start: 0.2062 (OUTLIER) cc_final: 0.0312 (t80) REVERT: A 207 LEU cc_start: 0.3602 (OUTLIER) cc_final: 0.0503 (mp) REVERT: A 209 ASN cc_start: 0.4000 (OUTLIER) cc_final: 0.3469 (t0) REVERT: A 217 ARG cc_start: 0.8440 (ptm160) cc_final: 0.8047 (ptm-80) REVERT: A 300 ARG cc_start: 0.8632 (OUTLIER) cc_final: 0.8382 (mtt180) REVERT: A 371 LEU cc_start: 0.9267 (OUTLIER) cc_final: 0.8736 (mp) REVERT: A 379 MET cc_start: 0.8944 (ttp) cc_final: 0.8712 (ttt) REVERT: A 387 PHE cc_start: 0.8417 (OUTLIER) cc_final: 0.7742 (m-10) REVERT: A 755 VAL cc_start: 0.8485 (OUTLIER) cc_final: 0.8270 (t) REVERT: A 764 GLU cc_start: 0.8445 (OUTLIER) cc_final: 0.8087 (mt-10) REVERT: A 771 GLU cc_start: 0.7672 (OUTLIER) cc_final: 0.7320 (pt0) REVERT: A 794 LYS cc_start: 0.5749 (OUTLIER) cc_final: 0.5482 (ttmm) REVERT: A 818 LEU cc_start: 0.7898 (mp) cc_final: 0.7653 (mt) REVERT: A 893 LYS cc_start: 0.8709 (tptm) cc_final: 0.8158 (tmtt) REVERT: A 918 LEU cc_start: 0.9212 (OUTLIER) cc_final: 0.8936 (mt) REVERT: A 971 PHE cc_start: 0.7079 (t80) cc_final: 0.6460 (t80) REVERT: A 1251 LYS cc_start: 0.8697 (tmmt) cc_final: 0.8372 (ttmt) REVERT: A 1295 LEU cc_start: 0.9264 (OUTLIER) cc_final: 0.9007 (mt) REVERT: A 1299 ARG cc_start: 0.8777 (OUTLIER) cc_final: 0.7892 (ptp-110) REVERT: A 1305 GLU cc_start: 0.7330 (mp0) cc_final: 0.7044 (mt-10) REVERT: A 1323 ASN cc_start: 0.8089 (OUTLIER) cc_final: 0.7723 (m-40) REVERT: A 1328 CYS cc_start: 0.8754 (m) cc_final: 0.8405 (m) REVERT: A 1358 ARG cc_start: 0.8379 (OUTLIER) cc_final: 0.8090 (ttm170) REVERT: A 1399 LEU cc_start: 0.9056 (OUTLIER) cc_final: 0.8477 (mp) REVERT: A 1449 LEU cc_start: 0.8827 (OUTLIER) cc_final: 0.8572 (tp) REVERT: A 1464 LYS cc_start: 0.7940 (OUTLIER) cc_final: 0.7468 (tttp) REVERT: A 1465 LYS cc_start: 0.8364 (OUTLIER) cc_final: 0.8017 (tttm) REVERT: A 1474 MET cc_start: 0.9206 (mtt) cc_final: 0.8947 (mtp) REVERT: A 1503 LYS cc_start: 0.4124 (OUTLIER) cc_final: 0.3297 (tptm) REVERT: A 1515 GLN cc_start: 0.6357 (OUTLIER) cc_final: 0.6023 (pp30) REVERT: A 1537 GLU cc_start: 0.8544 (OUTLIER) cc_final: 0.7923 (tm-30) REVERT: A 1582 ASP cc_start: 0.8274 (t0) cc_final: 0.7907 (m-30) REVERT: A 1602 TYR cc_start: 0.5039 (OUTLIER) cc_final: 0.3705 (t80) REVERT: A 1639 MET cc_start: 0.8163 (mmp) cc_final: 0.7939 (mmp) REVERT: A 1711 LYS cc_start: 0.7914 (OUTLIER) cc_final: 0.7528 (pttt) REVERT: B 32 TYR cc_start: 0.8874 (t80) cc_final: 0.8509 (t80) REVERT: B 101 LEU cc_start: 0.8318 (OUTLIER) cc_final: 0.7976 (mt) REVERT: B 131 ASN cc_start: 0.8143 (OUTLIER) cc_final: 0.7805 (t0) REVERT: B 151 ASN cc_start: 0.7620 (t0) cc_final: 0.7340 (m-40) REVERT: B 178 MET cc_start: 0.7806 (mmm) cc_final: 0.6004 (ttt) outliers start: 122 outliers final: 61 residues processed: 300 average time/residue: 0.0742 time to fit residues: 32.7346 Evaluate side-chains 278 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 190 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 66 ASN Chi-restraints excluded: chain C residue 130 MET Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 134 CYS Chi-restraints excluded: chain A residue 146 ASN Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 181 PHE Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 209 ASN Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 268 MET Chi-restraints excluded: chain A residue 300 ARG Chi-restraints excluded: chain A residue 311 ASP Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 318 SER Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 387 PHE Chi-restraints excluded: chain A residue 403 MET Chi-restraints excluded: chain A residue 406 LYS Chi-restraints excluded: chain A residue 412 ASN Chi-restraints excluded: chain A residue 733 PHE Chi-restraints excluded: chain A residue 741 VAL Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain A residue 764 GLU Chi-restraints excluded: chain A residue 765 HIS Chi-restraints excluded: chain A residue 771 GLU Chi-restraints excluded: chain A residue 780 ASN Chi-restraints excluded: chain A residue 794 LYS Chi-restraints excluded: chain A residue 808 TRP Chi-restraints excluded: chain A residue 825 LEU Chi-restraints excluded: chain A residue 837 PHE Chi-restraints excluded: chain A residue 842 VAL Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 876 ILE Chi-restraints excluded: chain A residue 918 LEU Chi-restraints excluded: chain A residue 935 CYS Chi-restraints excluded: chain A residue 952 MET Chi-restraints excluded: chain A residue 968 LEU Chi-restraints excluded: chain A residue 1184 THR Chi-restraints excluded: chain A residue 1277 THR Chi-restraints excluded: chain A residue 1295 LEU Chi-restraints excluded: chain A residue 1299 ARG Chi-restraints excluded: chain A residue 1323 ASN Chi-restraints excluded: chain A residue 1353 THR Chi-restraints excluded: chain A residue 1358 ARG Chi-restraints excluded: chain A residue 1385 LEU Chi-restraints excluded: chain A residue 1399 LEU Chi-restraints excluded: chain A residue 1419 VAL Chi-restraints excluded: chain A residue 1449 LEU Chi-restraints excluded: chain A residue 1464 LYS Chi-restraints excluded: chain A residue 1465 LYS Chi-restraints excluded: chain A residue 1467 LEU Chi-restraints excluded: chain A residue 1499 ARG Chi-restraints excluded: chain A residue 1503 LYS Chi-restraints excluded: chain A residue 1504 ILE Chi-restraints excluded: chain A residue 1515 GLN Chi-restraints excluded: chain A residue 1524 LEU Chi-restraints excluded: chain A residue 1537 GLU Chi-restraints excluded: chain A residue 1556 ILE Chi-restraints excluded: chain A residue 1557 LEU Chi-restraints excluded: chain A residue 1563 VAL Chi-restraints excluded: chain A residue 1580 ILE Chi-restraints excluded: chain A residue 1594 PHE Chi-restraints excluded: chain A residue 1602 TYR Chi-restraints excluded: chain A residue 1608 LEU Chi-restraints excluded: chain A residue 1614 LEU Chi-restraints excluded: chain A residue 1637 LEU Chi-restraints excluded: chain A residue 1694 ILE Chi-restraints excluded: chain A residue 1711 LYS Chi-restraints excluded: chain B residue 48 GLU Chi-restraints excluded: chain B residue 66 GLU Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 131 ASN Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 179 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 97 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 13 optimal weight: 6.9990 chunk 45 optimal weight: 4.9990 chunk 70 optimal weight: 0.0020 chunk 108 optimal weight: 4.9990 chunk 37 optimal weight: 3.9990 chunk 9 optimal weight: 20.0000 chunk 85 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 overall best weight: 1.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.159823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.121542 restraints weight = 15633.866| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 2.12 r_work: 0.3148 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3030 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.4027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 12059 Z= 0.179 Angle : 0.707 11.647 16363 Z= 0.346 Chirality : 0.045 0.453 1901 Planarity : 0.004 0.040 1986 Dihedral : 11.500 71.339 1923 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.59 % Favored : 96.20 % Rotamer: Outliers : 9.78 % Allowed : 24.53 % Favored : 65.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.14 % 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 aren not related in a simple way. whole: 1.25 (0.22), residues: 1421 helix: 1.91 (0.17), residues: 843 sheet: 0.43 (0.44), residues: 133 loop : -1.19 (0.28), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 214 TYR 0.023 0.002 TYR A1755 PHE 0.019 0.001 PHE B 54 TRP 0.015 0.001 TRP A1408 HIS 0.005 0.001 HIS B 122 Details of bonding type rmsd covalent geometry : bond 0.00413 (12038) covalent geometry : angle 0.68165 (16310) SS BOND : bond 0.00424 ( 10) SS BOND : angle 1.61761 ( 20) hydrogen bonds : bond 0.05031 ( 718) hydrogen bonds : angle 4.82127 ( 2067) link_BETA1-4 : bond 0.01526 ( 2) link_BETA1-4 : angle 4.40221 ( 6) link_NAG-ASN : bond 0.00605 ( 9) link_NAG-ASN : angle 3.98596 ( 27) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 202 time to evaluate : 0.291 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 113 MET cc_start: 0.5088 (tpp) cc_final: 0.4837 (mtp) REVERT: C 130 MET cc_start: 0.5690 (OUTLIER) cc_final: 0.5250 (ttm) REVERT: A 181 PHE cc_start: 0.2036 (OUTLIER) cc_final: 0.1231 (m-80) REVERT: A 217 ARG cc_start: 0.8462 (ptm160) cc_final: 0.8048 (ptm-80) REVERT: A 300 ARG cc_start: 0.8664 (OUTLIER) cc_final: 0.8402 (mtt180) REVERT: A 311 ASP cc_start: 0.9518 (OUTLIER) cc_final: 0.9265 (p0) REVERT: A 371 LEU cc_start: 0.9231 (OUTLIER) cc_final: 0.8696 (mp) REVERT: A 387 PHE cc_start: 0.8394 (OUTLIER) cc_final: 0.7670 (m-10) REVERT: A 764 GLU cc_start: 0.8683 (OUTLIER) cc_final: 0.8402 (mt-10) REVERT: A 771 GLU cc_start: 0.7504 (OUTLIER) cc_final: 0.6945 (pt0) REVERT: A 780 ASN cc_start: 0.7663 (OUTLIER) cc_final: 0.7254 (t0) REVERT: A 794 LYS cc_start: 0.5742 (OUTLIER) cc_final: 0.5490 (ttmm) REVERT: A 839 LEU cc_start: 0.8848 (OUTLIER) cc_final: 0.8509 (pp) REVERT: A 893 LYS cc_start: 0.8599 (tptm) cc_final: 0.8054 (tttt) REVERT: A 918 LEU cc_start: 0.9187 (OUTLIER) cc_final: 0.8957 (mt) REVERT: A 971 PHE cc_start: 0.6830 (t80) cc_final: 0.6229 (t80) REVERT: A 1251 LYS cc_start: 0.8744 (tmmt) cc_final: 0.8328 (ttmt) REVERT: A 1299 ARG cc_start: 0.8818 (OUTLIER) cc_final: 0.7927 (ptp-110) REVERT: A 1305 GLU cc_start: 0.7271 (mp0) cc_final: 0.6991 (mt-10) REVERT: A 1322 MET cc_start: 0.8445 (mmm) cc_final: 0.8042 (mmm) REVERT: A 1323 ASN cc_start: 0.8065 (OUTLIER) cc_final: 0.7667 (m-40) REVERT: A 1328 CYS cc_start: 0.8771 (m) cc_final: 0.8424 (m) REVERT: A 1399 LEU cc_start: 0.9014 (OUTLIER) cc_final: 0.8514 (mp) REVERT: A 1449 LEU cc_start: 0.8832 (OUTLIER) cc_final: 0.8591 (tp) REVERT: A 1465 LYS cc_start: 0.8377 (OUTLIER) cc_final: 0.8038 (tttm) REVERT: A 1474 MET cc_start: 0.9189 (mtt) cc_final: 0.8977 (mtp) REVERT: A 1485 MET cc_start: 0.7366 (mtm) cc_final: 0.7107 (ttm) REVERT: A 1503 LYS cc_start: 0.4235 (OUTLIER) cc_final: 0.3342 (tptm) REVERT: A 1515 GLN cc_start: 0.6133 (OUTLIER) cc_final: 0.5717 (pp30) REVERT: A 1537 GLU cc_start: 0.8554 (OUTLIER) cc_final: 0.7904 (tm-30) REVERT: A 1543 MET cc_start: 0.8561 (tpp) cc_final: 0.8233 (tpp) REVERT: A 1582 ASP cc_start: 0.8127 (t0) cc_final: 0.7822 (m-30) REVERT: A 1602 TYR cc_start: 0.4902 (OUTLIER) cc_final: 0.3521 (t80) REVERT: A 1711 LYS cc_start: 0.8048 (OUTLIER) cc_final: 0.7543 (pttm) REVERT: B 100 ASP cc_start: 0.8739 (p0) cc_final: 0.8504 (p0) REVERT: B 131 ASN cc_start: 0.8152 (OUTLIER) cc_final: 0.7870 (t0) REVERT: B 151 ASN cc_start: 0.7610 (t0) cc_final: 0.7349 (m-40) REVERT: B 162 MET cc_start: 0.7177 (mmt) cc_final: 0.6355 (ptm) REVERT: B 178 MET cc_start: 0.7737 (mmm) cc_final: 0.6157 (ttp) outliers start: 126 outliers final: 62 residues processed: 294 average time/residue: 0.0795 time to fit residues: 34.4962 Evaluate side-chains 277 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 192 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 66 ASN Chi-restraints excluded: chain C residue 130 MET Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 134 CYS Chi-restraints excluded: chain A residue 146 ASN Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 181 PHE Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 268 MET Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 300 ARG Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 311 ASP Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 318 SER Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 387 PHE Chi-restraints excluded: chain A residue 403 MET Chi-restraints excluded: chain A residue 412 ASN Chi-restraints excluded: chain A residue 733 PHE Chi-restraints excluded: chain A residue 752 ILE Chi-restraints excluded: chain A residue 764 GLU Chi-restraints excluded: chain A residue 765 HIS Chi-restraints excluded: chain A residue 771 GLU Chi-restraints excluded: chain A residue 780 ASN Chi-restraints excluded: chain A residue 794 LYS Chi-restraints excluded: chain A residue 808 TRP Chi-restraints excluded: chain A residue 825 LEU Chi-restraints excluded: chain A residue 833 VAL Chi-restraints excluded: chain A residue 837 PHE Chi-restraints excluded: chain A residue 839 LEU Chi-restraints excluded: chain A residue 842 VAL Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 876 ILE Chi-restraints excluded: chain A residue 918 LEU Chi-restraints excluded: chain A residue 952 MET Chi-restraints excluded: chain A residue 968 LEU Chi-restraints excluded: chain A residue 1184 THR Chi-restraints excluded: chain A residue 1264 LEU Chi-restraints excluded: chain A residue 1277 THR Chi-restraints excluded: chain A residue 1299 ARG Chi-restraints excluded: chain A residue 1323 ASN Chi-restraints excluded: chain A residue 1353 THR Chi-restraints excluded: chain A residue 1385 LEU Chi-restraints excluded: chain A residue 1399 LEU Chi-restraints excluded: chain A residue 1419 VAL Chi-restraints excluded: chain A residue 1449 LEU Chi-restraints excluded: chain A residue 1465 LYS Chi-restraints excluded: chain A residue 1467 LEU Chi-restraints excluded: chain A residue 1503 LYS Chi-restraints excluded: chain A residue 1504 ILE Chi-restraints excluded: chain A residue 1515 GLN Chi-restraints excluded: chain A residue 1524 LEU Chi-restraints excluded: chain A residue 1537 GLU Chi-restraints excluded: chain A residue 1556 ILE Chi-restraints excluded: chain A residue 1557 LEU Chi-restraints excluded: chain A residue 1580 ILE Chi-restraints excluded: chain A residue 1594 PHE Chi-restraints excluded: chain A residue 1602 TYR Chi-restraints excluded: chain A residue 1614 LEU Chi-restraints excluded: chain A residue 1637 LEU Chi-restraints excluded: chain A residue 1711 LYS Chi-restraints excluded: chain A residue 1719 LYS Chi-restraints excluded: chain A residue 1754 MET Chi-restraints excluded: chain B residue 66 GLU Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 131 ASN Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 179 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 36 optimal weight: 3.9990 chunk 106 optimal weight: 4.9990 chunk 29 optimal weight: 0.0970 chunk 46 optimal weight: 0.2980 chunk 117 optimal weight: 4.9990 chunk 90 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 97 optimal weight: 0.8980 chunk 86 optimal weight: 0.9990 chunk 78 optimal weight: 0.0870 chunk 135 optimal weight: 3.9990 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1551 ASN A1732 ASN A1762 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.163430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.125450 restraints weight = 15545.946| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 2.14 r_work: 0.3206 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3086 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.4401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 12059 Z= 0.124 Angle : 0.639 11.212 16363 Z= 0.312 Chirality : 0.042 0.354 1901 Planarity : 0.003 0.036 1986 Dihedral : 10.859 71.174 1906 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.94 % Favored : 95.85 % Rotamer: Outliers : 6.99 % Allowed : 26.24 % Favored : 66.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.14 % 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 aren not related in a simple way. whole: 1.48 (0.22), residues: 1421 helix: 2.09 (0.18), residues: 843 sheet: 0.33 (0.43), residues: 134 loop : -1.02 (0.29), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 214 TYR 0.019 0.001 TYR A1739 PHE 0.016 0.001 PHE B 54 TRP 0.010 0.001 TRP A1408 HIS 0.003 0.001 HIS C 139 Details of bonding type rmsd covalent geometry : bond 0.00247 (12038) covalent geometry : angle 0.61423 (16310) SS BOND : bond 0.00374 ( 10) SS BOND : angle 0.99625 ( 20) hydrogen bonds : bond 0.04188 ( 718) hydrogen bonds : angle 4.55341 ( 2067) link_BETA1-4 : bond 0.01416 ( 2) link_BETA1-4 : angle 3.85617 ( 6) link_NAG-ASN : bond 0.00829 ( 9) link_NAG-ASN : angle 3.89614 ( 27) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 211 time to evaluate : 0.376 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 130 MET cc_start: 0.5905 (tmm) cc_final: 0.5322 (ttm) REVERT: A 181 PHE cc_start: 0.1769 (OUTLIER) cc_final: 0.1158 (m-80) REVERT: A 217 ARG cc_start: 0.8472 (ptm160) cc_final: 0.8047 (ptm-80) REVERT: A 300 ARG cc_start: 0.8625 (OUTLIER) cc_final: 0.8389 (mtt180) REVERT: A 311 ASP cc_start: 0.9488 (OUTLIER) cc_final: 0.9166 (p0) REVERT: A 371 LEU cc_start: 0.9222 (OUTLIER) cc_final: 0.8723 (mp) REVERT: A 387 PHE cc_start: 0.8396 (OUTLIER) cc_final: 0.7570 (m-10) REVERT: A 764 GLU cc_start: 0.8648 (OUTLIER) cc_final: 0.8305 (mt-10) REVERT: A 771 GLU cc_start: 0.7429 (OUTLIER) cc_final: 0.6798 (pt0) REVERT: A 780 ASN cc_start: 0.7631 (OUTLIER) cc_final: 0.7215 (t0) REVERT: A 794 LYS cc_start: 0.5749 (OUTLIER) cc_final: 0.5528 (ttmm) REVERT: A 839 LEU cc_start: 0.8817 (OUTLIER) cc_final: 0.8550 (pp) REVERT: A 893 LYS cc_start: 0.8694 (tptm) cc_final: 0.8129 (tttt) REVERT: A 894 GLU cc_start: 0.8109 (mt-10) cc_final: 0.7749 (mm-30) REVERT: A 1224 ILE cc_start: 0.8652 (tp) cc_final: 0.8147 (tp) REVERT: A 1251 LYS cc_start: 0.8735 (tmmt) cc_final: 0.8343 (ttmt) REVERT: A 1270 LEU cc_start: 0.8820 (tt) cc_final: 0.8524 (tp) REVERT: A 1322 MET cc_start: 0.8312 (mmm) cc_final: 0.7878 (mmm) REVERT: A 1323 ASN cc_start: 0.8049 (OUTLIER) cc_final: 0.7642 (m-40) REVERT: A 1328 CYS cc_start: 0.8691 (m) cc_final: 0.8323 (m) REVERT: A 1367 ARG cc_start: 0.7953 (ttt90) cc_final: 0.7499 (ttt-90) REVERT: A 1399 LEU cc_start: 0.8952 (OUTLIER) cc_final: 0.8526 (mp) REVERT: A 1449 LEU cc_start: 0.8805 (OUTLIER) cc_final: 0.8597 (tp) REVERT: A 1457 ILE cc_start: 0.7419 (OUTLIER) cc_final: 0.7098 (mm) REVERT: A 1465 LYS cc_start: 0.8424 (tppt) cc_final: 0.8090 (tttm) REVERT: A 1503 LYS cc_start: 0.4506 (OUTLIER) cc_final: 0.3656 (tptm) REVERT: A 1515 GLN cc_start: 0.6168 (OUTLIER) cc_final: 0.5662 (pp30) REVERT: A 1537 GLU cc_start: 0.8473 (OUTLIER) cc_final: 0.7851 (tm-30) REVERT: A 1541 GLN cc_start: 0.7119 (OUTLIER) cc_final: 0.6590 (tm-30) REVERT: A 1602 TYR cc_start: 0.4841 (OUTLIER) cc_final: 0.3332 (t80) REVERT: A 1754 MET cc_start: 0.7997 (OUTLIER) cc_final: 0.7690 (tmm) REVERT: B 100 ASP cc_start: 0.8749 (p0) cc_final: 0.8467 (p0) REVERT: B 131 ASN cc_start: 0.8065 (OUTLIER) cc_final: 0.7845 (t0) REVERT: B 162 MET cc_start: 0.7166 (mmt) cc_final: 0.6350 (ptm) REVERT: B 178 MET cc_start: 0.7562 (mmm) cc_final: 0.6189 (tmm) outliers start: 90 outliers final: 46 residues processed: 279 average time/residue: 0.0802 time to fit residues: 32.9689 Evaluate side-chains 264 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 197 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 66 ASN Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 146 ASN Chi-restraints excluded: chain A residue 181 PHE Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 268 MET Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 300 ARG Chi-restraints excluded: chain A residue 311 ASP Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 362 TYR Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 387 PHE Chi-restraints excluded: chain A residue 403 MET Chi-restraints excluded: chain A residue 412 ASN Chi-restraints excluded: chain A residue 733 PHE Chi-restraints excluded: chain A residue 752 ILE Chi-restraints excluded: chain A residue 764 GLU Chi-restraints excluded: chain A residue 765 HIS Chi-restraints excluded: chain A residue 771 GLU Chi-restraints excluded: chain A residue 780 ASN Chi-restraints excluded: chain A residue 794 LYS Chi-restraints excluded: chain A residue 808 TRP Chi-restraints excluded: chain A residue 825 LEU Chi-restraints excluded: chain A residue 837 PHE Chi-restraints excluded: chain A residue 839 LEU Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 935 CYS Chi-restraints excluded: chain A residue 968 LEU Chi-restraints excluded: chain A residue 1184 THR Chi-restraints excluded: chain A residue 1264 LEU Chi-restraints excluded: chain A residue 1323 ASN Chi-restraints excluded: chain A residue 1326 LEU Chi-restraints excluded: chain A residue 1399 LEU Chi-restraints excluded: chain A residue 1419 VAL Chi-restraints excluded: chain A residue 1449 LEU Chi-restraints excluded: chain A residue 1457 ILE Chi-restraints excluded: chain A residue 1467 LEU Chi-restraints excluded: chain A residue 1503 LYS Chi-restraints excluded: chain A residue 1504 ILE Chi-restraints excluded: chain A residue 1515 GLN Chi-restraints excluded: chain A residue 1519 ILE Chi-restraints excluded: chain A residue 1534 VAL Chi-restraints excluded: chain A residue 1537 GLU Chi-restraints excluded: chain A residue 1541 GLN Chi-restraints excluded: chain A residue 1556 ILE Chi-restraints excluded: chain A residue 1557 LEU Chi-restraints excluded: chain A residue 1580 ILE Chi-restraints excluded: chain A residue 1594 PHE Chi-restraints excluded: chain A residue 1602 TYR Chi-restraints excluded: chain A residue 1614 LEU Chi-restraints excluded: chain A residue 1694 ILE Chi-restraints excluded: chain A residue 1720 VAL Chi-restraints excluded: chain A residue 1754 MET Chi-restraints excluded: chain B residue 66 GLU Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 131 ASN Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 179 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 46 optimal weight: 6.9990 chunk 17 optimal weight: 4.9990 chunk 88 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 73 optimal weight: 2.9990 chunk 51 optimal weight: 9.9990 chunk 126 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 chunk 14 optimal weight: 6.9990 chunk 64 optimal weight: 0.9990 chunk 100 optimal weight: 6.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 ASN A1551 ASN A1732 ASN B 102 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.160230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.121882 restraints weight = 15669.891| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 2.11 r_work: 0.3159 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3043 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.4539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 12059 Z= 0.165 Angle : 0.670 10.232 16363 Z= 0.328 Chirality : 0.043 0.402 1901 Planarity : 0.004 0.038 1986 Dihedral : 10.140 68.685 1885 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.73 % Favored : 96.06 % Rotamer: Outliers : 6.91 % Allowed : 26.48 % Favored : 66.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.14 % 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 aren not related in a simple way. whole: 1.29 (0.22), residues: 1421 helix: 1.90 (0.17), residues: 851 sheet: 0.39 (0.45), residues: 134 loop : -1.12 (0.29), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 214 TYR 0.027 0.002 TYR B 32 PHE 0.018 0.001 PHE B 54 TRP 0.010 0.001 TRP B 57 HIS 0.005 0.001 HIS B 122 Details of bonding type rmsd covalent geometry : bond 0.00382 (12038) covalent geometry : angle 0.64699 (16310) SS BOND : bond 0.00393 ( 10) SS BOND : angle 1.31106 ( 20) hydrogen bonds : bond 0.04568 ( 718) hydrogen bonds : angle 4.59621 ( 2067) link_BETA1-4 : bond 0.01159 ( 2) link_BETA1-4 : angle 4.12476 ( 6) link_NAG-ASN : bond 0.00573 ( 9) link_NAG-ASN : angle 3.79636 ( 27) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 194 time to evaluate : 0.417 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 130 MET cc_start: 0.5940 (tmm) cc_final: 0.5391 (ttm) REVERT: A 181 PHE cc_start: 0.1738 (OUTLIER) cc_final: 0.1098 (m-80) REVERT: A 371 LEU cc_start: 0.9201 (OUTLIER) cc_final: 0.8660 (mp) REVERT: A 387 PHE cc_start: 0.8439 (OUTLIER) cc_final: 0.7622 (m-10) REVERT: A 403 MET cc_start: 0.8310 (OUTLIER) cc_final: 0.8076 (mtm) REVERT: A 764 GLU cc_start: 0.8620 (OUTLIER) cc_final: 0.8349 (mt-10) REVERT: A 771 GLU cc_start: 0.7465 (OUTLIER) cc_final: 0.7040 (pt0) REVERT: A 794 LYS cc_start: 0.5795 (OUTLIER) cc_final: 0.5576 (ttmm) REVERT: A 818 LEU cc_start: 0.7822 (mp) cc_final: 0.7619 (mt) REVERT: A 839 LEU cc_start: 0.8856 (OUTLIER) cc_final: 0.8570 (pp) REVERT: A 893 LYS cc_start: 0.8650 (tptm) cc_final: 0.8040 (tttt) REVERT: A 894 GLU cc_start: 0.8141 (mt-10) cc_final: 0.7716 (mm-30) REVERT: A 971 PHE cc_start: 0.6859 (t80) cc_final: 0.6232 (t80) REVERT: A 1251 LYS cc_start: 0.8769 (tmmt) cc_final: 0.8350 (ttmt) REVERT: A 1270 LEU cc_start: 0.8872 (tt) cc_final: 0.8631 (tp) REVERT: A 1322 MET cc_start: 0.8324 (mmm) cc_final: 0.7885 (mmm) REVERT: A 1323 ASN cc_start: 0.8019 (OUTLIER) cc_final: 0.7598 (m-40) REVERT: A 1328 CYS cc_start: 0.8704 (m) cc_final: 0.8375 (m) REVERT: A 1367 ARG cc_start: 0.8149 (ttt90) cc_final: 0.7648 (ttt-90) REVERT: A 1399 LEU cc_start: 0.8997 (OUTLIER) cc_final: 0.8600 (mp) REVERT: A 1449 LEU cc_start: 0.8830 (OUTLIER) cc_final: 0.8620 (tp) REVERT: A 1465 LYS cc_start: 0.8467 (tppt) cc_final: 0.8124 (tttm) REVERT: A 1485 MET cc_start: 0.7390 (ttm) cc_final: 0.7174 (ttm) REVERT: A 1503 LYS cc_start: 0.4300 (OUTLIER) cc_final: 0.3250 (tptm) REVERT: A 1515 GLN cc_start: 0.5913 (OUTLIER) cc_final: 0.5457 (pp30) REVERT: A 1537 GLU cc_start: 0.8530 (OUTLIER) cc_final: 0.7844 (tm-30) REVERT: A 1541 GLN cc_start: 0.7162 (OUTLIER) cc_final: 0.6476 (tm-30) REVERT: A 1602 TYR cc_start: 0.5006 (OUTLIER) cc_final: 0.3286 (t80) REVERT: A 1711 LYS cc_start: 0.8077 (ptpp) cc_final: 0.7870 (ptmm) REVERT: A 1732 ASN cc_start: 0.8266 (t0) cc_final: 0.8047 (t0) REVERT: B 100 ASP cc_start: 0.8680 (p0) cc_final: 0.8341 (p0) REVERT: B 162 MET cc_start: 0.7282 (mmt) cc_final: 0.6428 (ptm) REVERT: B 178 MET cc_start: 0.7663 (mmm) cc_final: 0.6266 (tmm) outliers start: 89 outliers final: 59 residues processed: 259 average time/residue: 0.0792 time to fit residues: 30.6143 Evaluate side-chains 265 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 190 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 66 ASN Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 134 CYS Chi-restraints excluded: chain A residue 146 ASN Chi-restraints excluded: chain A residue 181 PHE Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 268 MET Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 311 ASP Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 387 PHE Chi-restraints excluded: chain A residue 403 MET Chi-restraints excluded: chain A residue 412 ASN Chi-restraints excluded: chain A residue 733 PHE Chi-restraints excluded: chain A residue 752 ILE Chi-restraints excluded: chain A residue 764 GLU Chi-restraints excluded: chain A residue 765 HIS Chi-restraints excluded: chain A residue 768 MET Chi-restraints excluded: chain A residue 771 GLU Chi-restraints excluded: chain A residue 780 ASN Chi-restraints excluded: chain A residue 794 LYS Chi-restraints excluded: chain A residue 808 TRP Chi-restraints excluded: chain A residue 825 LEU Chi-restraints excluded: chain A residue 833 VAL Chi-restraints excluded: chain A residue 837 PHE Chi-restraints excluded: chain A residue 839 LEU Chi-restraints excluded: chain A residue 842 VAL Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 968 LEU Chi-restraints excluded: chain A residue 1184 THR Chi-restraints excluded: chain A residue 1264 LEU Chi-restraints excluded: chain A residue 1277 THR Chi-restraints excluded: chain A residue 1323 ASN Chi-restraints excluded: chain A residue 1326 LEU Chi-restraints excluded: chain A residue 1376 VAL Chi-restraints excluded: chain A residue 1385 LEU Chi-restraints excluded: chain A residue 1399 LEU Chi-restraints excluded: chain A residue 1419 VAL Chi-restraints excluded: chain A residue 1449 LEU Chi-restraints excluded: chain A residue 1467 LEU Chi-restraints excluded: chain A residue 1503 LYS Chi-restraints excluded: chain A residue 1504 ILE Chi-restraints excluded: chain A residue 1515 GLN Chi-restraints excluded: chain A residue 1519 ILE Chi-restraints excluded: chain A residue 1524 LEU Chi-restraints excluded: chain A residue 1534 VAL Chi-restraints excluded: chain A residue 1537 GLU Chi-restraints excluded: chain A residue 1541 GLN Chi-restraints excluded: chain A residue 1556 ILE Chi-restraints excluded: chain A residue 1557 LEU Chi-restraints excluded: chain A residue 1580 ILE Chi-restraints excluded: chain A residue 1594 PHE Chi-restraints excluded: chain A residue 1602 TYR Chi-restraints excluded: chain A residue 1614 LEU Chi-restraints excluded: chain A residue 1637 LEU Chi-restraints excluded: chain A residue 1694 ILE Chi-restraints excluded: chain A residue 1719 LYS Chi-restraints excluded: chain A residue 1720 VAL Chi-restraints excluded: chain A residue 1754 MET Chi-restraints excluded: chain B residue 60 ARG Chi-restraints excluded: chain B residue 66 GLU Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 179 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 125 optimal weight: 0.8980 chunk 47 optimal weight: 7.9990 chunk 78 optimal weight: 0.8980 chunk 139 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 126 optimal weight: 0.6980 chunk 132 optimal weight: 0.5980 chunk 137 optimal weight: 0.9990 chunk 85 optimal weight: 3.9990 chunk 111 optimal weight: 0.4980 chunk 12 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 89 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.162798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.124807 restraints weight = 15610.381| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 2.03 r_work: 0.3207 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3087 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.4771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 12059 Z= 0.120 Angle : 0.621 15.761 16363 Z= 0.302 Chirality : 0.041 0.368 1901 Planarity : 0.003 0.037 1986 Dihedral : 9.690 67.281 1877 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.28 % Allowed : 3.87 % Favored : 95.85 % Rotamer: Outliers : 6.13 % Allowed : 27.41 % Favored : 66.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.14 % 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 aren not related in a simple way. whole: 1.50 (0.22), residues: 1421 helix: 2.08 (0.18), residues: 853 sheet: 0.41 (0.44), residues: 134 loop : -1.05 (0.29), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 214 TYR 0.028 0.001 TYR B 32 PHE 0.016 0.001 PHE B 54 TRP 0.009 0.001 TRP A1408 HIS 0.003 0.001 HIS C 139 Details of bonding type rmsd covalent geometry : bond 0.00252 (12038) covalent geometry : angle 0.60002 (16310) SS BOND : bond 0.00331 ( 10) SS BOND : angle 1.03084 ( 20) hydrogen bonds : bond 0.04003 ( 718) hydrogen bonds : angle 4.42727 ( 2067) link_BETA1-4 : bond 0.01290 ( 2) link_BETA1-4 : angle 3.80316 ( 6) link_NAG-ASN : bond 0.00625 ( 9) link_NAG-ASN : angle 3.52068 ( 27) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 204 time to evaluate : 0.275 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 130 MET cc_start: 0.5930 (tmm) cc_final: 0.5368 (ttm) REVERT: A 181 PHE cc_start: 0.1799 (OUTLIER) cc_final: 0.1471 (m-80) REVERT: A 371 LEU cc_start: 0.9199 (OUTLIER) cc_final: 0.8726 (mp) REVERT: A 387 PHE cc_start: 0.8411 (OUTLIER) cc_final: 0.7580 (m-10) REVERT: A 403 MET cc_start: 0.8305 (OUTLIER) cc_final: 0.8047 (mtm) REVERT: A 764 GLU cc_start: 0.8642 (OUTLIER) cc_final: 0.8330 (mt-10) REVERT: A 771 GLU cc_start: 0.7397 (OUTLIER) cc_final: 0.6794 (pt0) REVERT: A 778 ILE cc_start: 0.7823 (tt) cc_final: 0.7394 (pt) REVERT: A 780 ASN cc_start: 0.7524 (OUTLIER) cc_final: 0.7080 (t0) REVERT: A 794 LYS cc_start: 0.5785 (OUTLIER) cc_final: 0.5544 (ttmm) REVERT: A 839 LEU cc_start: 0.8782 (OUTLIER) cc_final: 0.8539 (pp) REVERT: A 893 LYS cc_start: 0.8631 (tptm) cc_final: 0.8054 (tttt) REVERT: A 894 GLU cc_start: 0.8060 (mt-10) cc_final: 0.7705 (mm-30) REVERT: A 971 PHE cc_start: 0.6839 (t80) cc_final: 0.6198 (t80) REVERT: A 1183 LYS cc_start: 0.8290 (mttt) cc_final: 0.8052 (mtpt) REVERT: A 1251 LYS cc_start: 0.8758 (tmmt) cc_final: 0.8371 (ttpt) REVERT: A 1270 LEU cc_start: 0.8875 (tt) cc_final: 0.8666 (tp) REVERT: A 1322 MET cc_start: 0.8224 (mmm) cc_final: 0.7780 (mmm) REVERT: A 1323 ASN cc_start: 0.8040 (OUTLIER) cc_final: 0.7586 (m-40) REVERT: A 1328 CYS cc_start: 0.8640 (m) cc_final: 0.8297 (m) REVERT: A 1367 ARG cc_start: 0.8065 (ttt90) cc_final: 0.7585 (ttt-90) REVERT: A 1399 LEU cc_start: 0.8987 (OUTLIER) cc_final: 0.8608 (mp) REVERT: A 1465 LYS cc_start: 0.8463 (tppt) cc_final: 0.8116 (tttm) REVERT: A 1503 LYS cc_start: 0.4595 (OUTLIER) cc_final: 0.3591 (tptm) REVERT: A 1515 GLN cc_start: 0.5551 (OUTLIER) cc_final: 0.5042 (pp30) REVERT: A 1537 GLU cc_start: 0.8459 (OUTLIER) cc_final: 0.7794 (tm-30) REVERT: A 1541 GLN cc_start: 0.7113 (OUTLIER) cc_final: 0.6444 (tm-30) REVERT: A 1602 TYR cc_start: 0.5213 (OUTLIER) cc_final: 0.3542 (t80) REVERT: A 1754 MET cc_start: 0.7994 (OUTLIER) cc_final: 0.7677 (tmm) REVERT: B 100 ASP cc_start: 0.8708 (p0) cc_final: 0.8369 (p0) REVERT: B 162 MET cc_start: 0.7307 (mmt) cc_final: 0.6435 (ptm) REVERT: B 178 MET cc_start: 0.7588 (mmm) cc_final: 0.6286 (tmm) outliers start: 79 outliers final: 51 residues processed: 261 average time/residue: 0.0849 time to fit residues: 32.5010 Evaluate side-chains 262 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 194 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 66 ASN Chi-restraints excluded: chain A residue 134 CYS Chi-restraints excluded: chain A residue 146 ASN Chi-restraints excluded: chain A residue 181 PHE Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 268 MET Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 311 ASP Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 387 PHE Chi-restraints excluded: chain A residue 403 MET Chi-restraints excluded: chain A residue 412 ASN Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 733 PHE Chi-restraints excluded: chain A residue 752 ILE Chi-restraints excluded: chain A residue 764 GLU Chi-restraints excluded: chain A residue 765 HIS Chi-restraints excluded: chain A residue 768 MET Chi-restraints excluded: chain A residue 771 GLU Chi-restraints excluded: chain A residue 780 ASN Chi-restraints excluded: chain A residue 794 LYS Chi-restraints excluded: chain A residue 808 TRP Chi-restraints excluded: chain A residue 825 LEU Chi-restraints excluded: chain A residue 837 PHE Chi-restraints excluded: chain A residue 839 LEU Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 919 ILE Chi-restraints excluded: chain A residue 929 ILE Chi-restraints excluded: chain A residue 935 CYS Chi-restraints excluded: chain A residue 968 LEU Chi-restraints excluded: chain A residue 1184 THR Chi-restraints excluded: chain A residue 1264 LEU Chi-restraints excluded: chain A residue 1292 LEU Chi-restraints excluded: chain A residue 1323 ASN Chi-restraints excluded: chain A residue 1326 LEU Chi-restraints excluded: chain A residue 1376 VAL Chi-restraints excluded: chain A residue 1385 LEU Chi-restraints excluded: chain A residue 1399 LEU Chi-restraints excluded: chain A residue 1419 VAL Chi-restraints excluded: chain A residue 1467 LEU Chi-restraints excluded: chain A residue 1503 LYS Chi-restraints excluded: chain A residue 1504 ILE Chi-restraints excluded: chain A residue 1515 GLN Chi-restraints excluded: chain A residue 1519 ILE Chi-restraints excluded: chain A residue 1537 GLU Chi-restraints excluded: chain A residue 1541 GLN Chi-restraints excluded: chain A residue 1556 ILE Chi-restraints excluded: chain A residue 1557 LEU Chi-restraints excluded: chain A residue 1580 ILE Chi-restraints excluded: chain A residue 1594 PHE Chi-restraints excluded: chain A residue 1602 TYR Chi-restraints excluded: chain A residue 1614 LEU Chi-restraints excluded: chain A residue 1637 LEU Chi-restraints excluded: chain A residue 1694 ILE Chi-restraints excluded: chain A residue 1719 LYS Chi-restraints excluded: chain A residue 1720 VAL Chi-restraints excluded: chain A residue 1754 MET Chi-restraints excluded: chain B residue 60 ARG Chi-restraints excluded: chain B residue 66 GLU Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 179 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 6 optimal weight: 20.0000 chunk 28 optimal weight: 0.9980 chunk 95 optimal weight: 0.8980 chunk 17 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 48 optimal weight: 4.9990 chunk 12 optimal weight: 5.9990 chunk 131 optimal weight: 0.9990 chunk 11 optimal weight: 6.9990 chunk 132 optimal weight: 3.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 89 ASN B 102 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.161641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.123564 restraints weight = 15611.541| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 2.03 r_work: 0.3170 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3049 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.4844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12059 Z= 0.137 Angle : 0.641 14.712 16363 Z= 0.310 Chirality : 0.042 0.367 1901 Planarity : 0.003 0.041 1986 Dihedral : 9.460 64.315 1871 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.28 % Allowed : 3.66 % Favored : 96.06 % Rotamer: Outliers : 5.98 % Allowed : 27.48 % Favored : 66.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.14 % 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 aren not related in a simple way. whole: 1.45 (0.22), residues: 1421 helix: 2.04 (0.18), residues: 854 sheet: 0.41 (0.44), residues: 134 loop : -1.09 (0.29), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 214 TYR 0.028 0.001 TYR B 32 PHE 0.016 0.001 PHE B 54 TRP 0.010 0.001 TRP A1408 HIS 0.004 0.001 HIS B 122 Details of bonding type rmsd covalent geometry : bond 0.00305 (12038) covalent geometry : angle 0.62003 (16310) SS BOND : bond 0.00347 ( 10) SS BOND : angle 1.12029 ( 20) hydrogen bonds : bond 0.04137 ( 718) hydrogen bonds : angle 4.44821 ( 2067) link_BETA1-4 : bond 0.01268 ( 2) link_BETA1-4 : angle 3.95432 ( 6) link_NAG-ASN : bond 0.00591 ( 9) link_NAG-ASN : angle 3.47032 ( 27) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 195 time to evaluate : 0.300 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 85 MET cc_start: 0.5405 (tpt) cc_final: 0.4679 (mtt) REVERT: C 130 MET cc_start: 0.5936 (tmm) cc_final: 0.5353 (ttm) REVERT: A 181 PHE cc_start: 0.1465 (OUTLIER) cc_final: -0.0056 (t80) REVERT: A 371 LEU cc_start: 0.9167 (OUTLIER) cc_final: 0.8644 (mp) REVERT: A 387 PHE cc_start: 0.8391 (OUTLIER) cc_final: 0.7633 (m-10) REVERT: A 403 MET cc_start: 0.8284 (OUTLIER) cc_final: 0.8014 (mtm) REVERT: A 771 GLU cc_start: 0.7379 (OUTLIER) cc_final: 0.6783 (pt0) REVERT: A 778 ILE cc_start: 0.7837 (tt) cc_final: 0.7409 (pt) REVERT: A 794 LYS cc_start: 0.5671 (OUTLIER) cc_final: 0.5446 (ttmm) REVERT: A 839 LEU cc_start: 0.8841 (OUTLIER) cc_final: 0.8599 (pp) REVERT: A 893 LYS cc_start: 0.8653 (tptm) cc_final: 0.8062 (tttt) REVERT: A 894 GLU cc_start: 0.8076 (mt-10) cc_final: 0.7725 (mm-30) REVERT: A 1183 LYS cc_start: 0.8343 (mttt) cc_final: 0.8128 (mtpt) REVERT: A 1251 LYS cc_start: 0.8757 (tmmt) cc_final: 0.8347 (ttmt) REVERT: A 1323 ASN cc_start: 0.8027 (OUTLIER) cc_final: 0.7561 (m-40) REVERT: A 1328 CYS cc_start: 0.8651 (m) cc_final: 0.8335 (m) REVERT: A 1367 ARG cc_start: 0.8198 (ttt90) cc_final: 0.7698 (ttt-90) REVERT: A 1399 LEU cc_start: 0.9005 (OUTLIER) cc_final: 0.8646 (mp) REVERT: A 1465 LYS cc_start: 0.8465 (tppt) cc_final: 0.8109 (tttm) REVERT: A 1503 LYS cc_start: 0.4410 (OUTLIER) cc_final: 0.3388 (tptm) REVERT: A 1515 GLN cc_start: 0.5710 (OUTLIER) cc_final: 0.5278 (pp30) REVERT: A 1537 GLU cc_start: 0.8487 (OUTLIER) cc_final: 0.7811 (tm-30) REVERT: A 1541 GLN cc_start: 0.7120 (OUTLIER) cc_final: 0.6441 (tm-30) REVERT: A 1602 TYR cc_start: 0.5223 (OUTLIER) cc_final: 0.3536 (t80) REVERT: A 1754 MET cc_start: 0.8020 (OUTLIER) cc_final: 0.7706 (tmm) REVERT: B 100 ASP cc_start: 0.8699 (p0) cc_final: 0.8348 (p0) REVERT: B 162 MET cc_start: 0.7286 (mmt) cc_final: 0.6411 (ptm) REVERT: B 178 MET cc_start: 0.7532 (mmm) cc_final: 0.6246 (tmm) outliers start: 77 outliers final: 57 residues processed: 251 average time/residue: 0.0782 time to fit residues: 29.3739 Evaluate side-chains 266 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 194 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 66 ASN Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 134 CYS Chi-restraints excluded: chain A residue 146 ASN Chi-restraints excluded: chain A residue 181 PHE Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 268 MET Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 311 ASP Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 387 PHE Chi-restraints excluded: chain A residue 403 MET Chi-restraints excluded: chain A residue 412 ASN Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 733 PHE Chi-restraints excluded: chain A residue 752 ILE Chi-restraints excluded: chain A residue 765 HIS Chi-restraints excluded: chain A residue 768 MET Chi-restraints excluded: chain A residue 771 GLU Chi-restraints excluded: chain A residue 780 ASN Chi-restraints excluded: chain A residue 794 LYS Chi-restraints excluded: chain A residue 808 TRP Chi-restraints excluded: chain A residue 825 LEU Chi-restraints excluded: chain A residue 837 PHE Chi-restraints excluded: chain A residue 839 LEU Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 919 ILE Chi-restraints excluded: chain A residue 929 ILE Chi-restraints excluded: chain A residue 935 CYS Chi-restraints excluded: chain A residue 968 LEU Chi-restraints excluded: chain A residue 1184 THR Chi-restraints excluded: chain A residue 1264 LEU Chi-restraints excluded: chain A residue 1283 LEU Chi-restraints excluded: chain A residue 1292 LEU Chi-restraints excluded: chain A residue 1323 ASN Chi-restraints excluded: chain A residue 1326 LEU Chi-restraints excluded: chain A residue 1353 THR Chi-restraints excluded: chain A residue 1376 VAL Chi-restraints excluded: chain A residue 1385 LEU Chi-restraints excluded: chain A residue 1399 LEU Chi-restraints excluded: chain A residue 1419 VAL Chi-restraints excluded: chain A residue 1467 LEU Chi-restraints excluded: chain A residue 1503 LYS Chi-restraints excluded: chain A residue 1504 ILE Chi-restraints excluded: chain A residue 1515 GLN Chi-restraints excluded: chain A residue 1519 ILE Chi-restraints excluded: chain A residue 1534 VAL Chi-restraints excluded: chain A residue 1537 GLU Chi-restraints excluded: chain A residue 1541 GLN Chi-restraints excluded: chain A residue 1556 ILE Chi-restraints excluded: chain A residue 1557 LEU Chi-restraints excluded: chain A residue 1580 ILE Chi-restraints excluded: chain A residue 1594 PHE Chi-restraints excluded: chain A residue 1602 TYR Chi-restraints excluded: chain A residue 1614 LEU Chi-restraints excluded: chain A residue 1637 LEU Chi-restraints excluded: chain A residue 1694 ILE Chi-restraints excluded: chain A residue 1719 LYS Chi-restraints excluded: chain A residue 1720 VAL Chi-restraints excluded: chain A residue 1754 MET Chi-restraints excluded: chain B residue 66 GLU Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 179 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 129 optimal weight: 0.9990 chunk 63 optimal weight: 0.7980 chunk 134 optimal weight: 0.9990 chunk 105 optimal weight: 5.9990 chunk 46 optimal weight: 8.9990 chunk 42 optimal weight: 7.9990 chunk 132 optimal weight: 6.9990 chunk 126 optimal weight: 1.9990 chunk 139 optimal weight: 5.9990 chunk 23 optimal weight: 0.5980 chunk 86 optimal weight: 2.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 89 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.161574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.122966 restraints weight = 15505.581| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 2.04 r_work: 0.3162 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3041 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.4931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12059 Z= 0.132 Angle : 0.630 14.244 16363 Z= 0.306 Chirality : 0.041 0.361 1901 Planarity : 0.003 0.038 1986 Dihedral : 9.261 62.139 1868 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.28 % Allowed : 3.87 % Favored : 95.85 % Rotamer: Outliers : 6.21 % Allowed : 27.02 % Favored : 66.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.14 % 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 aren not related in a simple way. whole: 1.47 (0.22), residues: 1421 helix: 2.01 (0.17), residues: 860 sheet: 0.44 (0.45), residues: 134 loop : -1.04 (0.29), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 214 TYR 0.027 0.001 TYR B 32 PHE 0.016 0.001 PHE B 54 TRP 0.010 0.001 TRP A1408 HIS 0.004 0.001 HIS B 122 Details of bonding type rmsd covalent geometry : bond 0.00295 (12038) covalent geometry : angle 0.61006 (16310) SS BOND : bond 0.00332 ( 10) SS BOND : angle 1.06892 ( 20) hydrogen bonds : bond 0.04060 ( 718) hydrogen bonds : angle 4.41887 ( 2067) link_BETA1-4 : bond 0.01295 ( 2) link_BETA1-4 : angle 3.89348 ( 6) link_NAG-ASN : bond 0.00591 ( 9) link_NAG-ASN : angle 3.39662 ( 27) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 193 time to evaluate : 0.307 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 85 MET cc_start: 0.5348 (tpt) cc_final: 0.4673 (mtt) REVERT: C 130 MET cc_start: 0.5961 (tmm) cc_final: 0.5362 (ttm) REVERT: A 181 PHE cc_start: 0.1394 (OUTLIER) cc_final: -0.0084 (t80) REVERT: A 371 LEU cc_start: 0.9158 (OUTLIER) cc_final: 0.8652 (mp) REVERT: A 387 PHE cc_start: 0.8404 (OUTLIER) cc_final: 0.7733 (m-10) REVERT: A 403 MET cc_start: 0.8306 (OUTLIER) cc_final: 0.8027 (mtm) REVERT: A 771 GLU cc_start: 0.7361 (OUTLIER) cc_final: 0.6770 (pt0) REVERT: A 778 ILE cc_start: 0.7889 (tt) cc_final: 0.7450 (pt) REVERT: A 794 LYS cc_start: 0.5776 (OUTLIER) cc_final: 0.5561 (ttmm) REVERT: A 808 TRP cc_start: 0.6845 (OUTLIER) cc_final: 0.5756 (t-100) REVERT: A 893 LYS cc_start: 0.8651 (tptm) cc_final: 0.8066 (tttt) REVERT: A 894 GLU cc_start: 0.8079 (mt-10) cc_final: 0.7727 (mm-30) REVERT: A 1183 LYS cc_start: 0.8311 (mttt) cc_final: 0.8099 (mttt) REVERT: A 1251 LYS cc_start: 0.8744 (tmmt) cc_final: 0.8338 (ttmt) REVERT: A 1323 ASN cc_start: 0.8018 (OUTLIER) cc_final: 0.7565 (m-40) REVERT: A 1328 CYS cc_start: 0.8664 (m) cc_final: 0.8326 (m) REVERT: A 1367 ARG cc_start: 0.8216 (ttt90) cc_final: 0.7713 (ttt-90) REVERT: A 1399 LEU cc_start: 0.8995 (OUTLIER) cc_final: 0.8645 (mp) REVERT: A 1465 LYS cc_start: 0.8493 (tppt) cc_final: 0.8121 (tttm) REVERT: A 1503 LYS cc_start: 0.4179 (OUTLIER) cc_final: 0.3250 (tptm) REVERT: A 1515 GLN cc_start: 0.5716 (OUTLIER) cc_final: 0.5310 (pp30) REVERT: A 1537 GLU cc_start: 0.8480 (OUTLIER) cc_final: 0.7800 (tm-30) REVERT: A 1541 GLN cc_start: 0.7121 (OUTLIER) cc_final: 0.6439 (tm-30) REVERT: A 1602 TYR cc_start: 0.5157 (OUTLIER) cc_final: 0.3508 (t80) REVERT: A 1754 MET cc_start: 0.8030 (OUTLIER) cc_final: 0.7728 (tmm) REVERT: B 100 ASP cc_start: 0.8718 (p0) cc_final: 0.8361 (p0) REVERT: B 162 MET cc_start: 0.7280 (mmt) cc_final: 0.6395 (ptm) REVERT: B 178 MET cc_start: 0.7528 (mmm) cc_final: 0.6258 (tmm) outliers start: 80 outliers final: 60 residues processed: 252 average time/residue: 0.0783 time to fit residues: 29.3133 Evaluate side-chains 265 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 190 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 66 ASN Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 134 CYS Chi-restraints excluded: chain A residue 146 ASN Chi-restraints excluded: chain A residue 181 PHE Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 268 MET Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 311 ASP Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 387 PHE Chi-restraints excluded: chain A residue 403 MET Chi-restraints excluded: chain A residue 412 ASN Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 733 PHE Chi-restraints excluded: chain A residue 752 ILE Chi-restraints excluded: chain A residue 765 HIS Chi-restraints excluded: chain A residue 768 MET Chi-restraints excluded: chain A residue 771 GLU Chi-restraints excluded: chain A residue 780 ASN Chi-restraints excluded: chain A residue 794 LYS Chi-restraints excluded: chain A residue 808 TRP Chi-restraints excluded: chain A residue 825 LEU Chi-restraints excluded: chain A residue 837 PHE Chi-restraints excluded: chain A residue 839 LEU Chi-restraints excluded: chain A residue 842 VAL Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 919 ILE Chi-restraints excluded: chain A residue 929 ILE Chi-restraints excluded: chain A residue 935 CYS Chi-restraints excluded: chain A residue 968 LEU Chi-restraints excluded: chain A residue 1184 THR Chi-restraints excluded: chain A residue 1264 LEU Chi-restraints excluded: chain A residue 1277 THR Chi-restraints excluded: chain A residue 1283 LEU Chi-restraints excluded: chain A residue 1292 LEU Chi-restraints excluded: chain A residue 1323 ASN Chi-restraints excluded: chain A residue 1326 LEU Chi-restraints excluded: chain A residue 1353 THR Chi-restraints excluded: chain A residue 1376 VAL Chi-restraints excluded: chain A residue 1385 LEU Chi-restraints excluded: chain A residue 1399 LEU Chi-restraints excluded: chain A residue 1419 VAL Chi-restraints excluded: chain A residue 1467 LEU Chi-restraints excluded: chain A residue 1503 LYS Chi-restraints excluded: chain A residue 1504 ILE Chi-restraints excluded: chain A residue 1515 GLN Chi-restraints excluded: chain A residue 1534 VAL Chi-restraints excluded: chain A residue 1537 GLU Chi-restraints excluded: chain A residue 1541 GLN Chi-restraints excluded: chain A residue 1556 ILE Chi-restraints excluded: chain A residue 1557 LEU Chi-restraints excluded: chain A residue 1580 ILE Chi-restraints excluded: chain A residue 1594 PHE Chi-restraints excluded: chain A residue 1602 TYR Chi-restraints excluded: chain A residue 1614 LEU Chi-restraints excluded: chain A residue 1637 LEU Chi-restraints excluded: chain A residue 1694 ILE Chi-restraints excluded: chain A residue 1719 LYS Chi-restraints excluded: chain A residue 1720 VAL Chi-restraints excluded: chain A residue 1754 MET Chi-restraints excluded: chain B residue 66 GLU Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 99 LYS Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 179 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 118 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 36 optimal weight: 0.7980 chunk 116 optimal weight: 0.8980 chunk 23 optimal weight: 0.9980 chunk 19 optimal weight: 9.9990 chunk 89 optimal weight: 4.9990 chunk 122 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 chunk 12 optimal weight: 6.9990 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 89 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.160940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.122705 restraints weight = 15549.722| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 1.91 r_work: 0.3180 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3060 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.4978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12059 Z= 0.147 Angle : 0.655 13.846 16363 Z= 0.318 Chirality : 0.042 0.355 1901 Planarity : 0.003 0.038 1986 Dihedral : 9.248 59.689 1868 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.28 % Allowed : 3.94 % Favored : 95.78 % Rotamer: Outliers : 5.67 % Allowed : 27.95 % Favored : 66.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.14 % 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 aren not related in a simple way. whole: 1.38 (0.22), residues: 1421 helix: 1.96 (0.17), residues: 860 sheet: 0.43 (0.45), residues: 134 loop : -1.11 (0.29), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 214 TYR 0.027 0.001 TYR B 32 PHE 0.017 0.001 PHE B 54 TRP 0.010 0.001 TRP A1408 HIS 0.004 0.001 HIS B 122 Details of bonding type rmsd covalent geometry : bond 0.00335 (12038) covalent geometry : angle 0.62955 (16310) SS BOND : bond 0.00340 ( 10) SS BOND : angle 1.16716 ( 20) hydrogen bonds : bond 0.04163 ( 718) hydrogen bonds : angle 4.45776 ( 2067) link_BETA1-4 : bond 0.01277 ( 2) link_BETA1-4 : angle 3.96515 ( 6) link_NAG-ASN : bond 0.00452 ( 9) link_NAG-ASN : angle 3.98831 ( 27) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 193 time to evaluate : 0.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 84 ARG cc_start: 0.6703 (ttp80) cc_final: 0.6490 (ttp-110) REVERT: C 85 MET cc_start: 0.5408 (tpt) cc_final: 0.4757 (mtt) REVERT: C 130 MET cc_start: 0.6049 (tmm) cc_final: 0.5429 (ttm) REVERT: A 181 PHE cc_start: 0.1676 (OUTLIER) cc_final: 0.1323 (m-80) REVERT: A 371 LEU cc_start: 0.9191 (OUTLIER) cc_final: 0.8668 (mp) REVERT: A 403 MET cc_start: 0.8267 (OUTLIER) cc_final: 0.7979 (mtm) REVERT: A 771 GLU cc_start: 0.7357 (OUTLIER) cc_final: 0.7036 (pt0) REVERT: A 794 LYS cc_start: 0.5985 (OUTLIER) cc_final: 0.5751 (ttmm) REVERT: A 808 TRP cc_start: 0.6836 (OUTLIER) cc_final: 0.5839 (t-100) REVERT: A 893 LYS cc_start: 0.8678 (tptm) cc_final: 0.8116 (tttt) REVERT: A 894 GLU cc_start: 0.8074 (mt-10) cc_final: 0.7743 (mm-30) REVERT: A 1183 LYS cc_start: 0.8343 (mttt) cc_final: 0.8128 (mttt) REVERT: A 1201 MET cc_start: 0.8980 (mmp) cc_final: 0.8722 (mmp) REVERT: A 1251 LYS cc_start: 0.8745 (tmmt) cc_final: 0.8350 (ttmt) REVERT: A 1323 ASN cc_start: 0.8053 (OUTLIER) cc_final: 0.7600 (m-40) REVERT: A 1328 CYS cc_start: 0.8711 (m) cc_final: 0.8413 (m) REVERT: A 1367 ARG cc_start: 0.8216 (ttt90) cc_final: 0.7768 (ttt-90) REVERT: A 1399 LEU cc_start: 0.9048 (OUTLIER) cc_final: 0.8721 (mp) REVERT: A 1465 LYS cc_start: 0.8459 (tppt) cc_final: 0.8073 (tttm) REVERT: A 1503 LYS cc_start: 0.4270 (OUTLIER) cc_final: 0.3251 (tptm) REVERT: A 1515 GLN cc_start: 0.5852 (OUTLIER) cc_final: 0.5472 (pp30) REVERT: A 1537 GLU cc_start: 0.8494 (OUTLIER) cc_final: 0.7790 (tm-30) REVERT: A 1541 GLN cc_start: 0.7184 (OUTLIER) cc_final: 0.6502 (tm-30) REVERT: A 1602 TYR cc_start: 0.5174 (OUTLIER) cc_final: 0.3569 (t80) REVERT: A 1732 ASN cc_start: 0.8189 (t0) cc_final: 0.7923 (t0) REVERT: B 100 ASP cc_start: 0.8663 (p0) cc_final: 0.8310 (p0) REVERT: B 162 MET cc_start: 0.7379 (mmt) cc_final: 0.6467 (ptm) REVERT: B 178 MET cc_start: 0.7582 (mmm) cc_final: 0.6316 (tmm) outliers start: 73 outliers final: 56 residues processed: 248 average time/residue: 0.0803 time to fit residues: 29.8575 Evaluate side-chains 258 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 189 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 66 ASN Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 134 CYS Chi-restraints excluded: chain A residue 146 ASN Chi-restraints excluded: chain A residue 181 PHE Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 268 MET Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 311 ASP Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 403 MET Chi-restraints excluded: chain A residue 412 ASN Chi-restraints excluded: chain A residue 733 PHE Chi-restraints excluded: chain A residue 752 ILE Chi-restraints excluded: chain A residue 765 HIS Chi-restraints excluded: chain A residue 768 MET Chi-restraints excluded: chain A residue 771 GLU Chi-restraints excluded: chain A residue 780 ASN Chi-restraints excluded: chain A residue 794 LYS Chi-restraints excluded: chain A residue 808 TRP Chi-restraints excluded: chain A residue 825 LEU Chi-restraints excluded: chain A residue 837 PHE Chi-restraints excluded: chain A residue 839 LEU Chi-restraints excluded: chain A residue 842 VAL Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 919 ILE Chi-restraints excluded: chain A residue 929 ILE Chi-restraints excluded: chain A residue 935 CYS Chi-restraints excluded: chain A residue 968 LEU Chi-restraints excluded: chain A residue 1184 THR Chi-restraints excluded: chain A residue 1264 LEU Chi-restraints excluded: chain A residue 1277 THR Chi-restraints excluded: chain A residue 1283 LEU Chi-restraints excluded: chain A residue 1292 LEU Chi-restraints excluded: chain A residue 1323 ASN Chi-restraints excluded: chain A residue 1326 LEU Chi-restraints excluded: chain A residue 1353 THR Chi-restraints excluded: chain A residue 1385 LEU Chi-restraints excluded: chain A residue 1399 LEU Chi-restraints excluded: chain A residue 1419 VAL Chi-restraints excluded: chain A residue 1467 LEU Chi-restraints excluded: chain A residue 1503 LYS Chi-restraints excluded: chain A residue 1504 ILE Chi-restraints excluded: chain A residue 1515 GLN Chi-restraints excluded: chain A residue 1534 VAL Chi-restraints excluded: chain A residue 1537 GLU Chi-restraints excluded: chain A residue 1541 GLN Chi-restraints excluded: chain A residue 1556 ILE Chi-restraints excluded: chain A residue 1557 LEU Chi-restraints excluded: chain A residue 1580 ILE Chi-restraints excluded: chain A residue 1594 PHE Chi-restraints excluded: chain A residue 1602 TYR Chi-restraints excluded: chain A residue 1614 LEU Chi-restraints excluded: chain A residue 1637 LEU Chi-restraints excluded: chain A residue 1694 ILE Chi-restraints excluded: chain A residue 1719 LYS Chi-restraints excluded: chain A residue 1720 VAL Chi-restraints excluded: chain B residue 66 GLU Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 179 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 68.2548 > 50: distance: 25 - 118: 34.451 distance: 28 - 115: 34.659 distance: 40 - 101: 28.067 distance: 66 - 70: 7.369 distance: 70 - 71: 10.555 distance: 71 - 72: 4.206 distance: 71 - 74: 7.409 distance: 72 - 73: 5.464 distance: 72 - 79: 19.811 distance: 74 - 75: 6.367 distance: 75 - 76: 7.101 distance: 79 - 80: 16.973 distance: 80 - 81: 34.590 distance: 80 - 83: 20.793 distance: 81 - 82: 43.322 distance: 81 - 87: 38.190 distance: 83 - 84: 16.566 distance: 84 - 85: 18.293 distance: 85 - 86: 14.880 distance: 87 - 88: 19.581 distance: 88 - 89: 10.686 distance: 88 - 91: 31.156 distance: 89 - 90: 31.399 distance: 89 - 98: 20.959 distance: 91 - 92: 21.552 distance: 92 - 93: 27.214 distance: 92 - 94: 19.155 distance: 93 - 95: 31.219 distance: 94 - 96: 10.671 distance: 95 - 97: 17.423 distance: 96 - 97: 13.038 distance: 98 - 99: 26.846 distance: 99 - 100: 40.788 distance: 99 - 102: 44.107 distance: 100 - 101: 47.358 distance: 100 - 106: 50.365 distance: 102 - 103: 23.839 distance: 103 - 104: 24.136 distance: 103 - 105: 27.598 distance: 106 - 107: 23.344 distance: 106 - 165: 24.176 distance: 107 - 108: 18.117 distance: 107 - 110: 43.577 distance: 108 - 109: 31.946 distance: 108 - 115: 19.064 distance: 109 - 162: 21.378 distance: 110 - 111: 18.354 distance: 111 - 112: 17.223 distance: 112 - 113: 15.589 distance: 112 - 114: 8.065 distance: 115 - 116: 26.014 distance: 116 - 117: 31.818 distance: 116 - 119: 24.705 distance: 117 - 118: 52.376 distance: 117 - 126: 34.677 distance: 119 - 120: 37.448 distance: 120 - 121: 20.279 distance: 120 - 122: 29.978 distance: 121 - 123: 29.087 distance: 122 - 124: 23.739 distance: 123 - 125: 14.811 distance: 124 - 125: 6.760 distance: 126 - 127: 7.173 distance: 127 - 128: 21.592 distance: 127 - 130: 10.577 distance: 128 - 129: 22.484 distance: 128 - 137: 16.158 distance: 130 - 131: 29.314 distance: 131 - 132: 7.300 distance: 132 - 133: 13.046 distance: 133 - 134: 4.201 distance: 134 - 135: 4.656 distance: 137 - 138: 16.686 distance: 138 - 139: 42.391 distance: 138 - 141: 17.060 distance: 139 - 140: 40.766 distance: 139 - 145: 50.089 distance: 141 - 142: 9.755 distance: 142 - 143: 14.352 distance: 143 - 144: 8.805 distance: 145 - 146: 18.847 distance: 146 - 147: 27.107 distance: 146 - 149: 26.801 distance: 147 - 148: 42.646 distance: 147 - 154: 45.361 distance: 149 - 150: 17.301 distance: 150 - 151: 18.192 distance: 151 - 152: 16.798 distance: 152 - 153: 20.747 distance: 154 - 155: 18.551 distance: 155 - 156: 31.703 distance: 155 - 158: 8.477 distance: 156 - 157: 5.579 distance: 156 - 162: 28.051 distance: 158 - 159: 21.810 distance: 158 - 160: 10.077 distance: 159 - 161: 28.081