Starting phenix.real_space_refine on Sun Jun 7 05:23:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9rst_54224/06_2026/9rst_54224.cif Found real_map, /net/cci-nas-00/data/ceres_data/9rst_54224/06_2026/9rst_54224.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9rst_54224/06_2026/9rst_54224.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9rst_54224/06_2026/9rst_54224.map" model { file = "/net/cci-nas-00/data/ceres_data/9rst_54224/06_2026/9rst_54224.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9rst_54224/06_2026/9rst_54224.cif" } resolution = 2.93 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= 0.002 sd= 0.031 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 6 5.49 5 S 172 5.16 5 C 21462 2.51 5 N 5722 2.21 5 O 6184 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 33546 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 18215 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2272, 18215 Classifications: {'peptide': 2272} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 94, 'TRANS': 2177} Chain breaks: 11 Chain: "B" Number of atoms: 2386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2386 Classifications: {'peptide': 302} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 292} Chain: "C" Number of atoms: 8633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1059, 8633 Classifications: {'peptide': 1059} Link IDs: {'PTRANS': 25, 'TRANS': 1033} Chain breaks: 4 Chain: "D" Number of atoms: 1518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1518 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 6, 'TRANS': 182} Chain breaks: 1 Chain: "E" Number of atoms: 1749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1749 Classifications: {'peptide': 211} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 205} Chain breaks: 4 Chain: "G" Number of atoms: 696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 696 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 7, 'TRANS': 80} Chain breaks: 2 Chain: "H" Number of atoms: 313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 313 Classifications: {'peptide': 39} Link IDs: {'PTRANS': 1, 'TRANS': 37} Chain: "A" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'IHP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.49, per 1000 atoms: 0.22 Number of scatterers: 33546 At special positions: 0 Unit cell: (202.484, 189.772, 160.716, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 172 16.00 P 6 15.00 O 6184 8.00 N 5722 7.00 C 21462 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.82 Conformation dependent library (CDL) restraints added in 1.3 seconds 8204 Ramachandran restraints generated. 4102 Oldfield, 0 Emsley, 4102 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7982 Finding SS restraints... Secondary structure from input PDB file: 240 helices and 12 sheets defined 73.0% alpha, 4.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.57 Creating SS restraints... Processing helix chain 'A' and resid 75 through 94 Processing helix chain 'A' and resid 97 through 119 Processing helix chain 'A' and resid 120 through 141 Processing helix chain 'A' and resid 143 through 164 removed outlier: 3.567A pdb=" N LYS A 147 " --> pdb=" O THR A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 181 removed outlier: 3.759A pdb=" N GLN A 170 " --> pdb=" O GLU A 166 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N SER A 172 " --> pdb=" O PRO A 168 " (cutoff:3.500A) removed outlier: 5.646A pdb=" N ARG A 173 " --> pdb=" O ASN A 169 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N VAL A 180 " --> pdb=" O ASN A 176 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N LEU A 181 " --> pdb=" O TYR A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 200 Processing helix chain 'A' and resid 207 through 224 Processing helix chain 'A' and resid 232 through 254 Processing helix chain 'A' and resid 254 through 259 Processing helix chain 'A' and resid 261 through 268 removed outlier: 3.551A pdb=" N ASN A 268 " --> pdb=" O SER A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 274 Processing helix chain 'A' and resid 277 through 299 Processing helix chain 'A' and resid 299 through 319 removed outlier: 4.124A pdb=" N SER A 319 " --> pdb=" O THR A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 340 Processing helix chain 'A' and resid 341 through 346 removed outlier: 3.516A pdb=" N ARG A 345 " --> pdb=" O PRO A 342 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ASP A 346 " --> pdb=" O TYR A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 358 removed outlier: 3.870A pdb=" N TYR A 358 " --> pdb=" O SER A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 381 removed outlier: 3.639A pdb=" N ARG A 367 " --> pdb=" O PHE A 363 " (cutoff:3.500A) Proline residue: A 375 - end of helix removed outlier: 4.052A pdb=" N ASP A 381 " --> pdb=" O LEU A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 389 Processing helix chain 'A' and resid 389 through 402 Processing helix chain 'A' and resid 407 through 412 removed outlier: 3.874A pdb=" N ASN A 411 " --> pdb=" O ALA A 408 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N SER A 412 " --> pdb=" O ALA A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 428 Processing helix chain 'A' and resid 429 through 431 No H-bonds generated for 'chain 'A' and resid 429 through 431' Processing helix chain 'A' and resid 432 through 448 removed outlier: 4.373A pdb=" N THR A 437 " --> pdb=" O SER A 433 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N LEU A 438 " --> pdb=" O PRO A 434 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ASP A 441 " --> pdb=" O THR A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 454 through 456 No H-bonds generated for 'chain 'A' and resid 454 through 456' Processing helix chain 'A' and resid 457 through 473 removed outlier: 3.560A pdb=" N LEU A 461 " --> pdb=" O PHE A 457 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N PHE A 462 " --> pdb=" O GLU A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 483 Processing helix chain 'A' and resid 483 through 490 removed outlier: 3.524A pdb=" N ASN A 490 " --> pdb=" O ASN A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 508 Processing helix chain 'A' and resid 511 through 529 Processing helix chain 'A' and resid 545 through 561 Processing helix chain 'A' and resid 566 through 582 Processing helix chain 'A' and resid 590 through 597 Processing helix chain 'A' and resid 598 through 604 removed outlier: 3.946A pdb=" N GLU A 603 " --> pdb=" O SER A 600 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N HIS A 604 " --> pdb=" O TYR A 601 " (cutoff:3.500A) Processing helix chain 'A' and resid 606 through 623 removed outlier: 4.003A pdb=" N LYS A 623 " --> pdb=" O ASP A 619 " (cutoff:3.500A) Processing helix chain 'A' and resid 624 through 628 removed outlier: 4.042A pdb=" N CYS A 627 " --> pdb=" O ASP A 624 " (cutoff:3.500A) Processing helix chain 'A' and resid 631 through 651 Processing helix chain 'A' and resid 654 through 664 Processing helix chain 'A' and resid 665 through 668 removed outlier: 6.582A pdb=" N ASN A 668 " --> pdb=" O LEU A 665 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 665 through 668' Processing helix chain 'A' and resid 669 through 674 Processing helix chain 'A' and resid 675 through 687 Processing helix chain 'A' and resid 690 through 705 Processing helix chain 'A' and resid 711 through 729 removed outlier: 3.747A pdb=" N SER A 715 " --> pdb=" O TYR A 711 " (cutoff:3.500A) Processing helix chain 'A' and resid 732 through 750 Processing helix chain 'A' and resid 757 through 766 Processing helix chain 'A' and resid 767 through 771 Processing helix chain 'A' and resid 773 through 792 Processing helix chain 'A' and resid 793 through 797 removed outlier: 3.526A pdb=" N THR A 796 " --> pdb=" O LYS A 793 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N ARG A 797 " --> pdb=" O GLU A 794 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 793 through 797' Processing helix chain 'A' and resid 798 through 812 Proline residue: A 804 - end of helix Processing helix chain 'A' and resid 816 through 833 removed outlier: 3.920A pdb=" N ALA A 821 " --> pdb=" O PHE A 817 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ALA A 822 " --> pdb=" O LYS A 818 " (cutoff:3.500A) Processing helix chain 'A' and resid 837 through 843 Processing helix chain 'A' and resid 845 through 857 Processing helix chain 'A' and resid 859 through 874 Processing helix chain 'A' and resid 900 through 908 Processing helix chain 'A' and resid 916 through 932 removed outlier: 3.785A pdb=" N THR A 920 " --> pdb=" O GLU A 916 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASP A 932 " --> pdb=" O LYS A 928 " (cutoff:3.500A) Processing helix chain 'A' and resid 935 through 937 No H-bonds generated for 'chain 'A' and resid 935 through 937' Processing helix chain 'A' and resid 938 through 954 Processing helix chain 'A' and resid 955 through 959 removed outlier: 3.637A pdb=" N VAL A 958 " --> pdb=" O LEU A 955 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N SER A 959 " --> pdb=" O ARG A 956 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 955 through 959' Processing helix chain 'A' and resid 960 through 973 Proline residue: A 966 - end of helix Processing helix chain 'A' and resid 979 through 994 Processing helix chain 'A' and resid 995 through 1000 removed outlier: 3.996A pdb=" N ILE A 998 " --> pdb=" O LYS A 995 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ARG A 999 " --> pdb=" O GLN A 996 " (cutoff:3.500A) Proline residue: A1000 - end of helix No H-bonds generated for 'chain 'A' and resid 995 through 1000' Processing helix chain 'A' and resid 1001 through 1013 Processing helix chain 'A' and resid 1021 through 1033 Processing helix chain 'A' and resid 1035 through 1039 removed outlier: 3.974A pdb=" N LYS A1038 " --> pdb=" O GLY A1035 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ARG A1039 " --> pdb=" O GLU A1036 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1035 through 1039' Processing helix chain 'A' and resid 1040 through 1051 removed outlier: 3.543A pdb=" N ILE A1051 " --> pdb=" O PHE A1047 " (cutoff:3.500A) Processing helix chain 'A' and resid 1061 through 1073 removed outlier: 3.666A pdb=" N VAL A1071 " --> pdb=" O LEU A1067 " (cutoff:3.500A) Processing helix chain 'A' and resid 1074 through 1079 removed outlier: 3.587A pdb=" N GLU A1078 " --> pdb=" O PRO A1075 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ASP A1079 " --> pdb=" O ASN A1076 " (cutoff:3.500A) Processing helix chain 'A' and resid 1084 through 1095 removed outlier: 4.338A pdb=" N GLU A1093 " --> pdb=" O VAL A1089 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N SER A1095 " --> pdb=" O MET A1091 " (cutoff:3.500A) Processing helix chain 'A' and resid 1097 through 1111 removed outlier: 4.418A pdb=" N LYS A1101 " --> pdb=" O GLY A1097 " (cutoff:3.500A) Processing helix chain 'A' and resid 1119 through 1133 removed outlier: 3.591A pdb=" N ASN A1133 " --> pdb=" O ARG A1129 " (cutoff:3.500A) Processing helix chain 'A' and resid 1135 through 1154 removed outlier: 4.254A pdb=" N LYS A1140 " --> pdb=" O ARG A1136 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N ALA A1141 " --> pdb=" O GLU A1137 " (cutoff:3.500A) Processing helix chain 'A' and resid 1155 through 1159 removed outlier: 3.916A pdb=" N VAL A1159 " --> pdb=" O ASP A1156 " (cutoff:3.500A) Processing helix chain 'A' and resid 1160 through 1171 Processing helix chain 'A' and resid 1175 through 1187 Processing helix chain 'A' and resid 1221 through 1229 removed outlier: 3.726A pdb=" N LEU A1225 " --> pdb=" O ASN A1221 " (cutoff:3.500A) Processing helix chain 'A' and resid 1236 through 1254 Processing helix chain 'A' and resid 1257 through 1262 Processing helix chain 'A' and resid 1263 through 1268 removed outlier: 3.594A pdb=" N SER A1268 " --> pdb=" O SER A1264 " (cutoff:3.500A) Processing helix chain 'A' and resid 1271 through 1289 removed outlier: 5.543A pdb=" N ASN A1279 " --> pdb=" O ARG A1275 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N ALA A1280 " --> pdb=" O GLU A1276 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N VAL A1287 " --> pdb=" O SER A1283 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N GLU A1288 " --> pdb=" O SER A1284 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU A1289 " --> pdb=" O CYS A1285 " (cutoff:3.500A) Processing helix chain 'A' and resid 1290 through 1307 Processing helix chain 'A' and resid 1311 through 1328 removed outlier: 3.518A pdb=" N ASP A1328 " --> pdb=" O PHE A1324 " (cutoff:3.500A) Processing helix chain 'A' and resid 1335 through 1346 Processing helix chain 'A' and resid 1348 through 1363 Processing helix chain 'A' and resid 1365 through 1379 Processing helix chain 'A' and resid 1381 through 1396 Processing helix chain 'A' and resid 1403 through 1408 Processing helix chain 'A' and resid 1410 through 1423 Processing helix chain 'A' and resid 1428 through 1443 Processing helix chain 'A' and resid 1444 through 1455 Processing helix chain 'A' and resid 1460 through 1478 Proline residue: A1469 - end of helix Processing helix chain 'A' and resid 1480 through 1488 Processing helix chain 'A' and resid 1495 through 1509 Processing helix chain 'A' and resid 1511 through 1533 removed outlier: 3.915A pdb=" N ALA A1532 " --> pdb=" O THR A1528 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N LEU A1533 " --> pdb=" O GLU A1529 " (cutoff:3.500A) Processing helix chain 'A' and resid 1537 through 1540 Processing helix chain 'A' and resid 1541 through 1562 removed outlier: 3.714A pdb=" N LYS A1562 " --> pdb=" O ILE A1558 " (cutoff:3.500A) Processing helix chain 'A' and resid 1568 through 1583 removed outlier: 3.674A pdb=" N THR A1572 " --> pdb=" O ASP A1568 " (cutoff:3.500A) Processing helix chain 'A' and resid 1587 through 1599 Processing helix chain 'A' and resid 1603 through 1606 Processing helix chain 'A' and resid 1607 through 1621 Processing helix chain 'A' and resid 1623 through 1633 Processing helix chain 'A' and resid 1650 through 1665 removed outlier: 3.693A pdb=" N GLY A1665 " --> pdb=" O LEU A1661 " (cutoff:3.500A) Processing helix chain 'A' and resid 1666 through 1685 Processing helix chain 'A' and resid 1707 through 1730 Processing helix chain 'A' and resid 1738 through 1752 Processing helix chain 'A' and resid 1755 through 1774 removed outlier: 3.653A pdb=" N TRP A1759 " --> pdb=" O TRP A1755 " (cutoff:3.500A) Processing helix chain 'A' and resid 1813 through 1834 removed outlier: 4.441A pdb=" N ARG A1819 " --> pdb=" O ASN A1815 " (cutoff:3.500A) removed outlier: 5.368A pdb=" N ILE A1822 " --> pdb=" O HIS A1818 " (cutoff:3.500A) Proline residue: A1823 - end of helix Processing helix chain 'A' and resid 1839 through 1854 Processing helix chain 'A' and resid 1856 through 1867 Processing helix chain 'A' and resid 1871 through 1877 removed outlier: 3.558A pdb=" N TRP A1875 " --> pdb=" O ILE A1872 " (cutoff:3.500A) Processing helix chain 'A' and resid 1878 through 1885 removed outlier: 3.556A pdb=" N ARG A1885 " --> pdb=" O GLN A1881 " (cutoff:3.500A) Processing helix chain 'A' and resid 1890 through 1908 Processing helix chain 'A' and resid 1908 through 1921 removed outlier: 3.732A pdb=" N LEU A1912 " --> pdb=" O HIS A1908 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N TYR A1914 " --> pdb=" O GLN A1910 " (cutoff:3.500A) Proline residue: A1915 - end of helix removed outlier: 3.643A pdb=" N LYS A1921 " --> pdb=" O MET A1917 " (cutoff:3.500A) Processing helix chain 'A' and resid 1924 through 1939 Processing helix chain 'A' and resid 1942 through 1961 removed outlier: 3.694A pdb=" N VAL A1961 " --> pdb=" O ILE A1957 " (cutoff:3.500A) Processing helix chain 'A' and resid 1962 through 1980 removed outlier: 3.853A pdb=" N GLN A1977 " --> pdb=" O ASP A1973 " (cutoff:3.500A) Processing helix chain 'A' and resid 1984 through 1999 Proline residue: A1993 - end of helix removed outlier: 3.575A pdb=" N MET A1997 " --> pdb=" O PRO A1993 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU A1998 " --> pdb=" O LEU A1994 " (cutoff:3.500A) Processing helix chain 'A' and resid 2004 through 2031 removed outlier: 5.227A pdb=" N ARG A2016 " --> pdb=" O ASN A2012 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N ASP A2017 " --> pdb=" O SER A2013 " (cutoff:3.500A) Processing helix chain 'A' and resid 2033 through 2055 removed outlier: 3.909A pdb=" N LEU A2037 " --> pdb=" O ASP A2033 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ILE A2043 " --> pdb=" O GLN A2039 " (cutoff:3.500A) Processing helix chain 'A' and resid 2056 through 2058 No H-bonds generated for 'chain 'A' and resid 2056 through 2058' Processing helix chain 'A' and resid 2063 through 2067 Processing helix chain 'A' and resid 2067 through 2073 removed outlier: 3.599A pdb=" N LEU A2071 " --> pdb=" O SER A2067 " (cutoff:3.500A) Processing helix chain 'A' and resid 2133 through 2153 removed outlier: 3.622A pdb=" N ASP A2153 " --> pdb=" O LEU A2149 " (cutoff:3.500A) Processing helix chain 'A' and resid 2153 through 2159 removed outlier: 3.543A pdb=" N ARG A2159 " --> pdb=" O GLU A2155 " (cutoff:3.500A) Processing helix chain 'A' and resid 2187 through 2198 Processing helix chain 'A' and resid 2203 through 2213 Processing helix chain 'A' and resid 2215 through 2219 removed outlier: 3.617A pdb=" N LEU A2219 " --> pdb=" O TYR A2216 " (cutoff:3.500A) Processing helix chain 'A' and resid 2220 through 2234 Processing helix chain 'A' and resid 2238 through 2247 Processing helix chain 'A' and resid 2250 through 2276 Processing helix chain 'A' and resid 2321 through 2328 removed outlier: 3.566A pdb=" N MET A2328 " --> pdb=" O LEU A2324 " (cutoff:3.500A) Processing helix chain 'A' and resid 2331 through 2334 removed outlier: 4.034A pdb=" N GLU A2334 " --> pdb=" O SER A2331 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2331 through 2334' Processing helix chain 'A' and resid 2335 through 2351 removed outlier: 3.774A pdb=" N ILE A2339 " --> pdb=" O GLY A2335 " (cutoff:3.500A) Processing helix chain 'A' and resid 2351 through 2364 removed outlier: 3.732A pdb=" N LEU A2355 " --> pdb=" O ASN A2351 " (cutoff:3.500A) Processing helix chain 'A' and resid 2413 through 2435 removed outlier: 3.546A pdb=" N ARG A2428 " --> pdb=" O LEU A2424 " (cutoff:3.500A) Processing helix chain 'A' and resid 2445 through 2458 Processing helix chain 'A' and resid 2459 through 2464 Processing helix chain 'A' and resid 2465 through 2466 No H-bonds generated for 'chain 'A' and resid 2465 through 2466' Processing helix chain 'A' and resid 2467 through 2471 Processing helix chain 'C' and resid 300 through 315 removed outlier: 3.643A pdb=" N GLN C 315 " --> pdb=" O MET C 311 " (cutoff:3.500A) Processing helix chain 'C' and resid 320 through 338 Processing helix chain 'C' and resid 339 through 343 removed outlier: 3.582A pdb=" N ARG C 342 " --> pdb=" O SER C 339 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LYS C 343 " --> pdb=" O GLU C 340 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 339 through 343' Processing helix chain 'C' and resid 349 through 359 Processing helix chain 'C' and resid 362 through 376 Processing helix chain 'C' and resid 379 through 389 Processing helix chain 'C' and resid 390 through 400 Processing helix chain 'C' and resid 402 through 404 No H-bonds generated for 'chain 'C' and resid 402 through 404' Processing helix chain 'C' and resid 405 through 422 removed outlier: 3.673A pdb=" N GLN C 411 " --> pdb=" O ILE C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 427 through 440 Processing helix chain 'C' and resid 445 through 460 removed outlier: 3.558A pdb=" N PHE C 458 " --> pdb=" O LEU C 454 " (cutoff:3.500A) Processing helix chain 'C' and resid 460 through 467 removed outlier: 3.648A pdb=" N VAL C 464 " --> pdb=" O ALA C 460 " (cutoff:3.500A) Processing helix chain 'C' and resid 468 through 475 removed outlier: 4.375A pdb=" N VAL C 472 " --> pdb=" O ARG C 468 " (cutoff:3.500A) Processing helix chain 'C' and resid 476 through 478 No H-bonds generated for 'chain 'C' and resid 476 through 478' Processing helix chain 'C' and resid 482 through 497 removed outlier: 3.571A pdb=" N ALA C 486 " --> pdb=" O SER C 482 " (cutoff:3.500A) Processing helix chain 'C' and resid 499 through 504 Processing helix chain 'C' and resid 511 through 516 removed outlier: 3.551A pdb=" N VAL C 514 " --> pdb=" O ASN C 511 " (cutoff:3.500A) Processing helix chain 'C' and resid 529 through 544 removed outlier: 3.625A pdb=" N ASN C 535 " --> pdb=" O GLU C 531 " (cutoff:3.500A) Processing helix chain 'C' and resid 546 through 554 Processing helix chain 'C' and resid 554 through 566 Proline residue: C 560 - end of helix Processing helix chain 'C' and resid 567 through 569 No H-bonds generated for 'chain 'C' and resid 567 through 569' Processing helix chain 'C' and resid 570 through 585 removed outlier: 3.994A pdb=" N TYR C 576 " --> pdb=" O ILE C 572 " (cutoff:3.500A) Processing helix chain 'C' and resid 608 through 612 Processing helix chain 'C' and resid 613 through 630 Processing helix chain 'C' and resid 632 through 641 Processing helix chain 'C' and resid 646 through 668 Processing helix chain 'C' and resid 685 through 701 Processing helix chain 'C' and resid 713 through 733 removed outlier: 4.058A pdb=" N GLU C 733 " --> pdb=" O THR C 729 " (cutoff:3.500A) Processing helix chain 'C' and resid 735 through 746 removed outlier: 3.604A pdb=" N SER C 746 " --> pdb=" O MET C 742 " (cutoff:3.500A) Processing helix chain 'C' and resid 753 through 757 Processing helix chain 'C' and resid 758 through 768 Processing helix chain 'C' and resid 769 through 771 No H-bonds generated for 'chain 'C' and resid 769 through 771' Processing helix chain 'C' and resid 772 through 783 Processing helix chain 'C' and resid 784 through 793 Processing helix chain 'C' and resid 809 through 827 removed outlier: 3.592A pdb=" N VAL C 814 " --> pdb=" O SER C 810 " (cutoff:3.500A) Processing helix chain 'C' and resid 827 through 837 Processing helix chain 'C' and resid 840 through 854 Processing helix chain 'C' and resid 872 through 882 removed outlier: 3.700A pdb=" N LYS C 876 " --> pdb=" O PHE C 872 " (cutoff:3.500A) Processing helix chain 'C' and resid 884 through 894 Processing helix chain 'C' and resid 896 through 903 removed outlier: 3.579A pdb=" N ILE C 900 " --> pdb=" O PHE C 896 " (cutoff:3.500A) Processing helix chain 'C' and resid 908 through 919 Processing helix chain 'C' and resid 920 through 922 No H-bonds generated for 'chain 'C' and resid 920 through 922' Processing helix chain 'C' and resid 927 through 940 removed outlier: 3.712A pdb=" N ARG C 931 " --> pdb=" O SER C 927 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VAL C 932 " --> pdb=" O SER C 928 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 962 Processing helix chain 'C' and resid 968 through 987 removed outlier: 4.119A pdb=" N ALA C 972 " --> pdb=" O LEU C 968 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ASN C 973 " --> pdb=" O LYS C 969 " (cutoff:3.500A) Processing helix chain 'C' and resid 988 through 991 Processing helix chain 'C' and resid 993 through 1009 Processing helix chain 'C' and resid 1018 through 1022 Processing helix chain 'C' and resid 1024 through 1031 Processing helix chain 'C' and resid 1034 through 1041 Processing helix chain 'C' and resid 1042 through 1052 removed outlier: 3.613A pdb=" N ILE C1052 " --> pdb=" O LEU C1048 " (cutoff:3.500A) Processing helix chain 'C' and resid 1053 through 1065 removed outlier: 3.968A pdb=" N GLU C1057 " --> pdb=" O ASN C1053 " (cutoff:3.500A) Processing helix chain 'C' and resid 1065 through 1081 removed outlier: 3.937A pdb=" N VAL C1071 " --> pdb=" O ASN C1067 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N HIS C1072 " --> pdb=" O ILE C1068 " (cutoff:3.500A) Processing helix chain 'C' and resid 1100 through 1106 Processing helix chain 'C' and resid 1108 through 1119 Processing helix chain 'C' and resid 1119 through 1133 Processing helix chain 'C' and resid 1134 through 1138 removed outlier: 4.440A pdb=" N MET C1137 " --> pdb=" O GLY C1134 " (cutoff:3.500A) Processing helix chain 'C' and resid 1142 through 1160 Processing helix chain 'C' and resid 1165 through 1173 removed outlier: 3.810A pdb=" N LEU C1169 " --> pdb=" O GLY C1165 " (cutoff:3.500A) Processing helix chain 'C' and resid 1173 through 1185 removed outlier: 3.824A pdb=" N ASP C1177 " --> pdb=" O SER C1173 " (cutoff:3.500A) Processing helix chain 'C' and resid 1187 through 1202 Processing helix chain 'C' and resid 1204 through 1214 Processing helix chain 'C' and resid 1234 through 1240 removed outlier: 3.576A pdb=" N SER C1240 " --> pdb=" O ASP C1236 " (cutoff:3.500A) Processing helix chain 'C' and resid 1276 through 1288 Processing helix chain 'C' and resid 1339 through 1350 Processing helix chain 'C' and resid 1355 through 1371 removed outlier: 3.635A pdb=" N LYS C1361 " --> pdb=" O ASN C1357 " (cutoff:3.500A) Processing helix chain 'C' and resid 1371 through 1376 removed outlier: 3.688A pdb=" N PHE C1375 " --> pdb=" O GLY C1371 " (cutoff:3.500A) Processing helix chain 'C' and resid 1377 through 1392 Processing helix chain 'C' and resid 1394 through 1405 Processing helix chain 'C' and resid 1407 through 1421 removed outlier: 3.684A pdb=" N ARG C1421 " --> pdb=" O HIS C1417 " (cutoff:3.500A) Processing helix chain 'D' and resid 4 through 16 Processing helix chain 'D' and resid 17 through 28 Processing helix chain 'D' and resid 29 through 32 removed outlier: 3.836A pdb=" N LEU D 32 " --> pdb=" O PRO D 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 29 through 32' Processing helix chain 'D' and resid 42 through 50 Processing helix chain 'D' and resid 52 through 63 Processing helix chain 'D' and resid 77 through 86 removed outlier: 3.596A pdb=" N MET D 84 " --> pdb=" O HIS D 80 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N LYS D 85 " --> pdb=" O LEU D 81 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 98 Processing helix chain 'D' and resid 99 through 102 removed outlier: 3.822A pdb=" N ILE D 102 " --> pdb=" O PRO D 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 99 through 102' Processing helix chain 'D' and resid 106 through 110 Processing helix chain 'D' and resid 111 through 120 Processing helix chain 'D' and resid 121 through 132 Processing helix chain 'D' and resid 144 through 153 Processing helix chain 'D' and resid 154 through 162 removed outlier: 3.819A pdb=" N MET D 160 " --> pdb=" O SER D 156 " (cutoff:3.500A) Processing helix chain 'D' and resid 187 through 198 Processing helix chain 'E' and resid 289 through 299 Processing helix chain 'E' and resid 299 through 306 Processing helix chain 'E' and resid 307 through 310 removed outlier: 3.520A pdb=" N PHE E 310 " --> pdb=" O TYR E 307 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 307 through 310' Processing helix chain 'E' and resid 311 through 335 removed outlier: 3.518A pdb=" N GLU E 332 " --> pdb=" O SER E 328 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N LEU E 333 " --> pdb=" O ASN E 329 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N PHE E 334 " --> pdb=" O VAL E 330 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ARG E 335 " --> pdb=" O ALA E 331 " (cutoff:3.500A) Processing helix chain 'E' and resid 338 through 342 removed outlier: 3.967A pdb=" N LEU E 342 " --> pdb=" O ILE E 339 " (cutoff:3.500A) Processing helix chain 'E' and resid 345 through 362 removed outlier: 3.527A pdb=" N ASP E 362 " --> pdb=" O ILE E 358 " (cutoff:3.500A) Processing helix chain 'E' and resid 369 through 393 removed outlier: 3.600A pdb=" N ILE E 373 " --> pdb=" O GLY E 369 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ILE E 392 " --> pdb=" O LEU E 388 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N VAL E 393 " --> pdb=" O GLU E 389 " (cutoff:3.500A) Processing helix chain 'E' and resid 405 through 428 removed outlier: 4.825A pdb=" N TYR E 421 " --> pdb=" O TYR E 417 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N TYR E 422 " --> pdb=" O GLN E 418 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ASP E 423 " --> pdb=" O GLU E 419 " (cutoff:3.500A) Processing helix chain 'E' and resid 428 through 436 Processing helix chain 'E' and resid 459 through 478 removed outlier: 4.831A pdb=" N LEU E 474 " --> pdb=" O ASP E 470 " (cutoff:3.500A) Proline residue: E 475 - end of helix Processing helix chain 'E' and resid 488 through 498 Processing helix chain 'E' and resid 507 through 520 Processing helix chain 'E' and resid 526 through 543 Processing helix chain 'G' and resid 2 through 18 Processing helix chain 'G' and resid 20 through 28 Processing helix chain 'G' and resid 44 through 51 Processing helix chain 'G' and resid 628 through 632 Processing helix chain 'G' and resid 638 through 644 Processing helix chain 'H' and resid 1276 through 1288 Processing sheet with id=AA1, first strand: chain 'A' and resid 1646 through 1649 Processing sheet with id=AA2, first strand: chain 'A' and resid 2060 through 2062 removed outlier: 7.190A pdb=" N VAL A2100 " --> pdb=" O CYS A2114 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N CYS A2114 " --> pdb=" O VAL A2100 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 2060 through 2062 removed outlier: 7.190A pdb=" N VAL A2100 " --> pdb=" O CYS A2114 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N CYS A2114 " --> pdb=" O VAL A2100 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N SER A2175 " --> pdb=" O LEU A2171 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 2184 through 2186 Processing sheet with id=AA5, first strand: chain 'B' and resid 24 through 29 removed outlier: 4.061A pdb=" N ARG B 26 " --> pdb=" O PHE B 16 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LEU B 5 " --> pdb=" O TRP B 17 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 38 through 40 Processing sheet with id=AA7, first strand: chain 'B' and resid 78 through 83 removed outlier: 6.542A pdb=" N SER B 93 " --> pdb=" O THR B 79 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N VAL B 81 " --> pdb=" O VAL B 91 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N VAL B 91 " --> pdb=" O VAL B 81 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 119 through 124 removed outlier: 6.121A pdb=" N ILE B 140 " --> pdb=" O GLN B 153 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N GLN B 153 " --> pdb=" O ILE B 140 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N ILE B 142 " --> pdb=" O THR B 151 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 164 through 167 removed outlier: 3.533A pdb=" N SER B 164 " --> pdb=" O ALA B 177 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU B 174 " --> pdb=" O TRP B 186 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N THR B 201 " --> pdb=" O VAL B 185 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N GLU B 187 " --> pdb=" O PRO B 199 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 210 through 215 removed outlier: 4.475A pdb=" N THR B 230 " --> pdb=" O SER B 226 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N ALA B 231 " --> pdb=" O THR B 245 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N THR B 245 " --> pdb=" O ALA B 231 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N VAL B 233 " --> pdb=" O GLU B 243 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 253 through 258 removed outlier: 6.534A pdb=" N ALA B 268 " --> pdb=" O TRP B 254 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N CYS B 256 " --> pdb=" O VAL B 266 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N VAL B 266 " --> pdb=" O CYS B 256 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N PHE B 258 " --> pdb=" O TYR B 264 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N TYR B 264 " --> pdb=" O PHE B 258 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N TYR B 273 " --> pdb=" O SER B 269 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ARG B 286 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ASP B 278 " --> pdb=" O ILE B 284 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N ILE B 284 " --> pdb=" O ASP B 278 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 1216 through 1220 removed outlier: 5.059A pdb=" N ILE C1229 " --> pdb=" O CYS C1219 " (cutoff:3.500A) 2049 hydrogen bonds defined for protein. 6033 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: 7.81 Time building geometry restraints manager: 3.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 10836 1.34 - 1.46: 6002 1.46 - 1.58: 17079 1.58 - 1.70: 6 1.70 - 1.81: 277 Bond restraints: 34200 Sorted by residual: bond pdb=" N ILE A 139 " pdb=" CA ILE A 139 " ideal model delta sigma weight residual 1.461 1.495 -0.034 1.17e-02 7.31e+03 8.27e+00 bond pdb=" C ARG A 999 " pdb=" N PRO A1000 " ideal model delta sigma weight residual 1.337 1.362 -0.026 9.80e-03 1.04e+04 6.91e+00 bond pdb=" N PHE A 142 " pdb=" CA PHE A 142 " ideal model delta sigma weight residual 1.459 1.491 -0.031 1.21e-02 6.83e+03 6.77e+00 bond pdb=" N HIS A 140 " pdb=" CA HIS A 140 " ideal model delta sigma weight residual 1.458 1.488 -0.030 1.33e-02 5.65e+03 5.19e+00 bond pdb=" N SER A 144 " pdb=" CA SER A 144 " ideal model delta sigma weight residual 1.459 1.487 -0.028 1.28e-02 6.10e+03 4.78e+00 ... (remaining 34195 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.03: 45655 2.03 - 4.07: 488 4.07 - 6.10: 81 6.10 - 8.13: 27 8.13 - 10.17: 7 Bond angle restraints: 46258 Sorted by residual: angle pdb=" C ASP A2445 " pdb=" N VAL A2446 " pdb=" CA VAL A2446 " ideal model delta sigma weight residual 120.33 123.28 -2.95 8.00e-01 1.56e+00 1.36e+01 angle pdb=" C VAL C 319 " pdb=" N ASN C 320 " pdb=" CA ASN C 320 " ideal model delta sigma weight residual 120.69 130.86 -10.17 2.95e+00 1.15e-01 1.19e+01 angle pdb=" CA ARG C1392 " pdb=" CB ARG C1392 " pdb=" CG ARG C1392 " ideal model delta sigma weight residual 114.10 120.90 -6.80 2.00e+00 2.50e-01 1.15e+01 angle pdb=" C3 IHP A2501 " pdb=" C4 IHP A2501 " pdb=" C5 IHP A2501 " ideal model delta sigma weight residual 107.91 118.01 -10.10 3.00e+00 1.11e-01 1.13e+01 angle pdb=" C ALA D 185 " pdb=" N GLN D 186 " pdb=" CA GLN D 186 " ideal model delta sigma weight residual 121.54 127.95 -6.41 1.91e+00 2.74e-01 1.13e+01 ... (remaining 46253 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.74: 19970 26.74 - 53.47: 762 53.47 - 80.21: 74 80.21 - 106.94: 7 106.94 - 133.68: 5 Dihedral angle restraints: 20818 sinusoidal: 8570 harmonic: 12248 Sorted by residual: dihedral pdb=" C4 IHP A2501 " pdb=" C2 IHP A2501 " pdb=" C3 IHP A2501 " pdb=" O12 IHP A2501 " ideal model delta sinusoidal sigma weight residual 60.90 -165.42 -133.68 1 3.00e+01 1.11e-03 1.80e+01 dihedral pdb=" C3 IHP A2501 " pdb=" C1 IHP A2501 " pdb=" C2 IHP A2501 " pdb=" O11 IHP A2501 " ideal model delta sinusoidal sigma weight residual -175.40 -58.61 -116.79 1 3.00e+01 1.11e-03 1.55e+01 dihedral pdb=" C6 IHP A2501 " pdb=" C1 IHP A2501 " pdb=" C2 IHP A2501 " pdb=" O12 IHP A2501 " ideal model delta sinusoidal sigma weight residual 61.05 176.32 -115.27 1 3.00e+01 1.11e-03 1.52e+01 ... (remaining 20815 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.992: 5289 0.992 - 1.985: 0 1.985 - 2.977: 0 2.977 - 3.969: 0 3.969 - 4.962: 4 Chirality restraints: 5293 Sorted by residual: chirality pdb=" C2 IHP A2501 " pdb=" C1 IHP A2501 " pdb=" C3 IHP A2501 " pdb=" O12 IHP A2501 " both_signs ideal model delta sigma weight residual False -2.52 2.44 -4.96 2.00e-01 2.50e+01 6.15e+02 chirality pdb=" C1 IHP A2501 " pdb=" C2 IHP A2501 " pdb=" C6 IHP A2501 " pdb=" O11 IHP A2501 " both_signs ideal model delta sigma weight residual False 2.32 -2.53 4.84 2.00e-01 2.50e+01 5.86e+02 chirality pdb=" C5 IHP A2501 " pdb=" C4 IHP A2501 " pdb=" C6 IHP A2501 " pdb=" O15 IHP A2501 " both_signs ideal model delta sigma weight residual False -2.42 2.35 -4.77 2.00e-01 2.50e+01 5.68e+02 ... (remaining 5290 not shown) Planarity restraints: 5844 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A1229 " 0.022 2.00e-02 2.50e+03 2.33e-02 1.35e+01 pdb=" CG TRP A1229 " -0.063 2.00e-02 2.50e+03 pdb=" CD1 TRP A1229 " 0.029 2.00e-02 2.50e+03 pdb=" CD2 TRP A1229 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A1229 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A1229 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A1229 " 0.011 2.00e-02 2.50e+03 pdb=" CZ2 TRP A1229 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A1229 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP A1229 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A1963 " 0.017 2.00e-02 2.50e+03 1.51e-02 5.73e+00 pdb=" CG TRP A1963 " -0.041 2.00e-02 2.50e+03 pdb=" CD1 TRP A1963 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 TRP A1963 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A1963 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A1963 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A1963 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A1963 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A1963 " 0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP A1963 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER A2172 " -0.038 5.00e-02 4.00e+02 5.80e-02 5.39e+00 pdb=" N PRO A2173 " 0.100 5.00e-02 4.00e+02 pdb=" CA PRO A2173 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO A2173 " -0.032 5.00e-02 4.00e+02 ... (remaining 5841 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 7099 2.78 - 3.31: 30908 3.31 - 3.84: 56220 3.84 - 4.37: 65223 4.37 - 4.90: 112147 Nonbonded interactions: 271597 Sorted by model distance: nonbonded pdb=" OD1 ASN A 565 " pdb=" OG1 THR A 569 " model vdw 2.252 3.040 nonbonded pdb=" O PRO A2081 " pdb=" OH TYR A2125 " model vdw 2.274 3.040 nonbonded pdb=" O VAL A1089 " pdb=" OG1 THR A1092 " model vdw 2.286 3.040 nonbonded pdb=" OG SER A 430 " pdb=" O GLY D 177 " model vdw 2.293 3.040 nonbonded pdb=" O ILE C 605 " pdb=" OH TYR C 655 " model vdw 2.296 3.040 ... (remaining 271592 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 8.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.580 Check model and map are aligned: 0.110 Set scattering table: 0.100 Process input model: 31.620 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.070 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:6.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7422 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 34200 Z= 0.136 Angle : 0.570 10.169 46258 Z= 0.303 Chirality : 0.138 4.962 5293 Planarity : 0.004 0.058 5844 Dihedral : 13.929 133.678 12836 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 0.00 % Allowed : 0.05 % Favored : 99.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.13), residues: 4102 helix: 0.71 (0.09), residues: 2787 sheet: -0.47 (0.39), residues: 178 loop : -0.81 (0.18), residues: 1137 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1623 TYR 0.020 0.001 TYR C 370 PHE 0.030 0.001 PHE A 457 TRP 0.063 0.001 TRP A1229 HIS 0.006 0.001 HIS A 396 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.14 (34200) covalent geometry : angle 0.56954 / 0.30 (46258) hydrogen bonds : bond 0.14224 / 9.91 ( 2045) hydrogen bonds : angle 5.19080 / 3.71 ( 6033) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8204 Ramachandran restraints generated. 4102 Oldfield, 0 Emsley, 4102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8204 Ramachandran restraints generated. 4102 Oldfield, 0 Emsley, 4102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1077 residues out of total 3758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1077 time to evaluate : 1.277 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 376 LEU cc_start: 0.8884 (mt) cc_final: 0.8516 (tp) REVERT: A 394 MET cc_start: 0.7830 (mmp) cc_final: 0.7622 (tmm) REVERT: A 395 VAL cc_start: 0.8834 (t) cc_final: 0.8453 (m) REVERT: A 423 ASP cc_start: 0.7589 (m-30) cc_final: 0.7346 (m-30) REVERT: A 432 ILE cc_start: 0.8303 (tp) cc_final: 0.7135 (mp) REVERT: A 436 MET cc_start: 0.7122 (mmm) cc_final: 0.6634 (mmm) REVERT: A 504 LEU cc_start: 0.7793 (mt) cc_final: 0.7471 (mm) REVERT: A 508 ILE cc_start: 0.7992 (mt) cc_final: 0.7652 (tt) REVERT: A 527 LEU cc_start: 0.8175 (mt) cc_final: 0.7530 (mp) REVERT: A 565 ASN cc_start: 0.5497 (t0) cc_final: 0.5250 (t0) REVERT: A 596 LEU cc_start: 0.8669 (mt) cc_final: 0.8451 (mm) REVERT: A 625 ASP cc_start: 0.8081 (m-30) cc_final: 0.7798 (p0) REVERT: A 640 GLU cc_start: 0.7849 (tt0) cc_final: 0.7492 (tm-30) REVERT: A 656 GLU cc_start: 0.7688 (tt0) cc_final: 0.7414 (tp30) REVERT: A 660 GLU cc_start: 0.8382 (mt-10) cc_final: 0.7910 (mt-10) REVERT: A 680 ARG cc_start: 0.7576 (ttp80) cc_final: 0.7295 (mtm110) REVERT: A 691 PHE cc_start: 0.8588 (t80) cc_final: 0.8348 (t80) REVERT: A 803 MET cc_start: 0.8832 (mmm) cc_final: 0.8584 (mmt) REVERT: A 818 LYS cc_start: 0.8383 (tttt) cc_final: 0.7879 (mmmm) REVERT: A 857 GLU cc_start: 0.7625 (tp30) cc_final: 0.7231 (tm-30) REVERT: A 981 ASP cc_start: 0.8159 (t70) cc_final: 0.7931 (t0) REVERT: A 989 SER cc_start: 0.8691 (m) cc_final: 0.8437 (p) REVERT: A 1031 LYS cc_start: 0.8684 (tttt) cc_final: 0.8449 (tmmm) REVERT: A 1034 GLU cc_start: 0.7748 (mm-30) cc_final: 0.7544 (mm-30) REVERT: A 1036 GLU cc_start: 0.7660 (mm-30) cc_final: 0.7341 (mt-10) REVERT: A 1068 LYS cc_start: 0.8392 (tttp) cc_final: 0.8116 (mmmm) REVERT: A 1179 ASP cc_start: 0.7918 (m-30) cc_final: 0.7509 (m-30) REVERT: A 1239 ASP cc_start: 0.7071 (m-30) cc_final: 0.6787 (m-30) REVERT: A 1246 ARG cc_start: 0.8072 (mtt180) cc_final: 0.7836 (mtp-110) REVERT: A 1254 GLU cc_start: 0.8010 (mm-30) cc_final: 0.7591 (tp30) REVERT: A 1260 LEU cc_start: 0.9079 (mt) cc_final: 0.8841 (mm) REVERT: A 1283 SER cc_start: 0.8821 (t) cc_final: 0.8393 (p) REVERT: A 1296 ASP cc_start: 0.8439 (m-30) cc_final: 0.8169 (m-30) REVERT: A 1336 ILE cc_start: 0.8235 (pt) cc_final: 0.8009 (mp) REVERT: A 1341 LYS cc_start: 0.8986 (tttt) cc_final: 0.8537 (ttpp) REVERT: A 1383 ASP cc_start: 0.8069 (m-30) cc_final: 0.7847 (m-30) REVERT: A 1524 ASP cc_start: 0.7671 (m-30) cc_final: 0.7336 (m-30) REVERT: A 1533 LEU cc_start: 0.9161 (mt) cc_final: 0.8535 (mp) REVERT: A 1553 GLU cc_start: 0.7962 (mt-10) cc_final: 0.7723 (mt-10) REVERT: A 1648 LYS cc_start: 0.8315 (mttt) cc_final: 0.7899 (mttm) REVERT: A 1708 VAL cc_start: 0.7984 (t) cc_final: 0.7715 (p) REVERT: A 1727 VAL cc_start: 0.7957 (t) cc_final: 0.7650 (t) REVERT: A 1734 ARG cc_start: 0.7690 (ptt-90) cc_final: 0.7288 (pmm-80) REVERT: A 1768 GLU cc_start: 0.8027 (mt-10) cc_final: 0.7481 (tt0) REVERT: A 1864 HIS cc_start: 0.8358 (m90) cc_final: 0.8094 (m90) REVERT: A 1906 LYS cc_start: 0.8748 (tttt) cc_final: 0.8370 (ttpp) REVERT: A 2038 ASN cc_start: 0.7821 (m-40) cc_final: 0.7363 (m110) REVERT: A 2067 SER cc_start: 0.8886 (t) cc_final: 0.8641 (p) REVERT: A 2071 LEU cc_start: 0.8727 (tp) cc_final: 0.8478 (tp) REVERT: A 2091 ILE cc_start: 0.8103 (mt) cc_final: 0.7866 (tt) REVERT: A 2096 LYS cc_start: 0.8600 (tttt) cc_final: 0.8361 (tttt) REVERT: A 2116 LYS cc_start: 0.8592 (tttt) cc_final: 0.7892 (mtpp) REVERT: A 2124 LYS cc_start: 0.8535 (mttt) cc_final: 0.8188 (mttm) REVERT: A 2209 MET cc_start: 0.7713 (mtm) cc_final: 0.7432 (mtm) REVERT: A 2221 LEU cc_start: 0.8373 (tp) cc_final: 0.8168 (tm) REVERT: A 2298 ASP cc_start: 0.8612 (t0) cc_final: 0.8246 (t0) REVERT: A 2368 ILE cc_start: 0.8649 (mm) cc_final: 0.8403 (mp) REVERT: B 29 GLN cc_start: 0.5210 (mm-40) cc_final: 0.4866 (tm-30) REVERT: B 148 ASN cc_start: 0.7640 (m-40) cc_final: 0.7295 (m110) REVERT: C 354 ILE cc_start: 0.8074 (mt) cc_final: 0.7831 (mt) REVERT: C 384 ASP cc_start: 0.7806 (m-30) cc_final: 0.7571 (m-30) REVERT: C 394 PHE cc_start: 0.7726 (m-80) cc_final: 0.7361 (m-80) REVERT: C 482 SER cc_start: 0.7749 (t) cc_final: 0.7415 (p) REVERT: C 533 MET cc_start: 0.8162 (mmm) cc_final: 0.7952 (mmm) REVERT: C 713 ASP cc_start: 0.7673 (t0) cc_final: 0.7419 (t70) REVERT: C 821 PHE cc_start: 0.8046 (m-80) cc_final: 0.7829 (m-10) REVERT: C 839 LYS cc_start: 0.7858 (mtpp) cc_final: 0.7380 (pmmt) REVERT: C 848 MET cc_start: 0.6706 (mtp) cc_final: 0.6328 (mtp) REVERT: C 903 MET cc_start: 0.7227 (mtt) cc_final: 0.6971 (mtp) REVERT: C 982 MET cc_start: 0.7483 (mmm) cc_final: 0.7187 (mmm) REVERT: C 1002 GLN cc_start: 0.7743 (tt0) cc_final: 0.7519 (tt0) REVERT: C 1025 LEU cc_start: 0.8034 (mt) cc_final: 0.7791 (mt) REVERT: C 1069 GLU cc_start: 0.7373 (tt0) cc_final: 0.7103 (tt0) REVERT: C 1079 LYS cc_start: 0.8647 (tttt) cc_final: 0.8360 (tttp) REVERT: C 1133 ASN cc_start: 0.7288 (m-40) cc_final: 0.7088 (m110) REVERT: C 1209 GLU cc_start: 0.6245 (mm-30) cc_final: 0.6013 (mm-30) REVERT: C 1406 ILE cc_start: 0.7632 (mm) cc_final: 0.7419 (mm) REVERT: D 17 ASN cc_start: 0.7599 (t0) cc_final: 0.7193 (p0) REVERT: D 23 ARG cc_start: 0.8067 (ttm110) cc_final: 0.6109 (ttp-170) REVERT: D 85 LYS cc_start: 0.8767 (mmtt) cc_final: 0.8462 (mmmm) REVERT: D 127 LEU cc_start: 0.8306 (mt) cc_final: 0.8010 (tp) REVERT: D 193 ILE cc_start: 0.8469 (mt) cc_final: 0.8078 (mm) REVERT: E 497 ASN cc_start: 0.8164 (m-40) cc_final: 0.7962 (m110) REVERT: G 52 MET cc_start: 0.6751 (ttp) cc_final: 0.6400 (ttp) REVERT: H 1265 ASP cc_start: 0.7304 (m-30) cc_final: 0.7008 (m-30) outliers start: 0 outliers final: 2 residues processed: 1077 average time/residue: 0.7107 time to fit residues: 910.2242 Evaluate side-chains 798 residues out of total 3758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 796 time to evaluate : 1.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 924 LEU Chi-restraints excluded: chain C residue 1052 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 197 optimal weight: 0.5980 chunk 388 optimal weight: 0.5980 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 0.1980 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 1.9990 chunk 401 optimal weight: 1.9990 chunk 155 optimal weight: 0.6980 chunk 244 optimal weight: 5.9990 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 498 GLN A 585 HIS A 587 GLN A 859 ASN A 996 GLN A1001 HIS A1657 GLN A1977 GLN A1982 HIS A2238 GLN A2343 ASN A2462 ASN B 77 ASN B 127 ASN ** B 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 511 ASN C 692 GLN ** C 843 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 889 HIS C 988 GLN C1053 ASN C1396 HIS D 67 HIS D 108 ASN D 163 ASN D 192 ASN E 294 HIS E 320 ASN E 391 GLN E 498 GLN ** G 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.158484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.125172 restraints weight = 67825.150| |-----------------------------------------------------------------------------| r_work (start): 0.3726 rms_B_bonded: 2.64 r_work: 0.3587 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.2464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 34200 Z= 0.151 Angle : 0.623 17.185 46258 Z= 0.307 Chirality : 0.044 1.006 5293 Planarity : 0.004 0.059 5844 Dihedral : 4.841 80.080 4522 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.82 % Allowed : 13.07 % Favored : 84.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.20 (0.13), residues: 4102 helix: 1.44 (0.10), residues: 2805 sheet: -0.25 (0.39), residues: 175 loop : -0.56 (0.19), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 15 TYR 0.024 0.002 TYR B 113 PHE 0.033 0.001 PHE E 355 TRP 0.032 0.002 TRP A1229 HIS 0.014 0.001 HIS C1396 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.15 (34200) covalent geometry : angle 0.62279 / 0.31 (46258) hydrogen bonds : bond 0.03949 / 2.73 ( 2045) hydrogen bonds : angle 4.07659 / 2.93 ( 6033) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8204 Ramachandran restraints generated. 4102 Oldfield, 0 Emsley, 4102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8204 Ramachandran restraints generated. 4102 Oldfield, 0 Emsley, 4102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 949 residues out of total 3758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 843 time to evaluate : 1.364 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 347 LYS cc_start: 0.8038 (mmtt) cc_final: 0.7772 (mmmm) REVERT: A 376 LEU cc_start: 0.8874 (mt) cc_final: 0.8534 (mt) REVERT: A 395 VAL cc_start: 0.8738 (t) cc_final: 0.8279 (m) REVERT: A 432 ILE cc_start: 0.8230 (tp) cc_final: 0.7045 (mp) REVERT: A 436 MET cc_start: 0.6861 (mmm) cc_final: 0.6379 (mmm) REVERT: A 504 LEU cc_start: 0.7929 (mt) cc_final: 0.7630 (mm) REVERT: A 508 ILE cc_start: 0.8312 (mt) cc_final: 0.7939 (tt) REVERT: A 557 PHE cc_start: 0.5941 (OUTLIER) cc_final: 0.5651 (t80) REVERT: A 559 LYS cc_start: 0.7638 (tptp) cc_final: 0.7025 (mmpt) REVERT: A 565 ASN cc_start: 0.5181 (t0) cc_final: 0.4598 (t0) REVERT: A 573 ILE cc_start: 0.7813 (tp) cc_final: 0.7610 (tt) REVERT: A 625 ASP cc_start: 0.8143 (m-30) cc_final: 0.7937 (p0) REVERT: A 640 GLU cc_start: 0.8140 (tt0) cc_final: 0.7757 (tm-30) REVERT: A 680 ARG cc_start: 0.7836 (ttp80) cc_final: 0.7514 (mtm110) REVERT: A 808 ASN cc_start: 0.8141 (m-40) cc_final: 0.7880 (m-40) REVERT: A 818 LYS cc_start: 0.8540 (tttt) cc_final: 0.8104 (mmmm) REVERT: A 927 MET cc_start: 0.8676 (mmm) cc_final: 0.7918 (mpp) REVERT: A 981 ASP cc_start: 0.8150 (t70) cc_final: 0.7932 (t0) REVERT: A 1031 LYS cc_start: 0.8882 (tttt) cc_final: 0.8567 (tmmm) REVERT: A 1034 GLU cc_start: 0.7755 (mm-30) cc_final: 0.7491 (mm-30) REVERT: A 1036 GLU cc_start: 0.7902 (mm-30) cc_final: 0.7551 (mt-10) REVERT: A 1173 ILE cc_start: 0.8612 (OUTLIER) cc_final: 0.8347 (mp) REVERT: A 1179 ASP cc_start: 0.7931 (m-30) cc_final: 0.6964 (m-30) REVERT: A 1183 ASN cc_start: 0.8200 (m-40) cc_final: 0.7485 (m110) REVERT: A 1246 ARG cc_start: 0.8412 (mtt180) cc_final: 0.8071 (mtp-110) REVERT: A 1250 GLN cc_start: 0.7891 (mp10) cc_final: 0.7482 (mp10) REVERT: A 1254 GLU cc_start: 0.8062 (mm-30) cc_final: 0.7538 (tp30) REVERT: A 1276 GLU cc_start: 0.8375 (OUTLIER) cc_final: 0.8055 (mp0) REVERT: A 1283 SER cc_start: 0.8832 (t) cc_final: 0.8326 (p) REVERT: A 1296 ASP cc_start: 0.8557 (m-30) cc_final: 0.8333 (m-30) REVERT: A 1298 ILE cc_start: 0.8605 (mm) cc_final: 0.8264 (mp) REVERT: A 1357 GLU cc_start: 0.8100 (mt-10) cc_final: 0.7856 (mm-30) REVERT: A 1438 SER cc_start: 0.8719 (m) cc_final: 0.8497 (p) REVERT: A 1447 GLU cc_start: 0.8666 (OUTLIER) cc_final: 0.8075 (mp0) REVERT: A 1529 GLU cc_start: 0.8249 (tm-30) cc_final: 0.7977 (tp30) REVERT: A 1533 LEU cc_start: 0.9019 (mt) cc_final: 0.8719 (mm) REVERT: A 1636 GLU cc_start: 0.7030 (tp30) cc_final: 0.6658 (tp30) REVERT: A 1648 LYS cc_start: 0.8505 (mttt) cc_final: 0.7862 (mttm) REVERT: A 1687 LEU cc_start: 0.8790 (mt) cc_final: 0.8504 (mp) REVERT: A 1708 VAL cc_start: 0.7973 (t) cc_final: 0.7694 (p) REVERT: A 1734 ARG cc_start: 0.8035 (ptt-90) cc_final: 0.7807 (pmm-80) REVERT: A 1768 GLU cc_start: 0.8258 (mt-10) cc_final: 0.7749 (tt0) REVERT: A 1864 HIS cc_start: 0.8555 (m90) cc_final: 0.8247 (m90) REVERT: A 1906 LYS cc_start: 0.8899 (tttt) cc_final: 0.8534 (ttpp) REVERT: A 1977 GLN cc_start: 0.7528 (mt0) cc_final: 0.6403 (mt0) REVERT: A 1986 LYS cc_start: 0.7398 (mmtt) cc_final: 0.6927 (tmtt) REVERT: A 1999 LYS cc_start: 0.8457 (mttt) cc_final: 0.8250 (mttt) REVERT: A 2000 ARG cc_start: 0.8010 (tpp80) cc_final: 0.7383 (tpp80) REVERT: A 2095 SER cc_start: 0.8805 (t) cc_final: 0.8543 (p) REVERT: A 2096 LYS cc_start: 0.8453 (tttt) cc_final: 0.8240 (tttt) REVERT: A 2116 LYS cc_start: 0.8586 (tttt) cc_final: 0.7729 (mmmm) REVERT: A 2124 LYS cc_start: 0.8640 (mttt) cc_final: 0.8361 (mttm) REVERT: A 2209 MET cc_start: 0.7688 (mtm) cc_final: 0.7401 (mtm) REVERT: A 2221 LEU cc_start: 0.8014 (tp) cc_final: 0.7716 (tm) REVERT: A 2238 GLN cc_start: 0.8724 (OUTLIER) cc_final: 0.8190 (mt0) REVERT: A 2298 ASP cc_start: 0.8643 (t0) cc_final: 0.8331 (t0) REVERT: A 2368 ILE cc_start: 0.8568 (mm) cc_final: 0.8324 (mp) REVERT: B 29 GLN cc_start: 0.5729 (mm-40) cc_final: 0.4977 (tm-30) REVERT: B 35 VAL cc_start: 0.8182 (t) cc_final: 0.7750 (p) REVERT: B 188 MET cc_start: -0.0244 (mmm) cc_final: -0.0844 (mmm) REVERT: B 198 LYS cc_start: 0.7954 (OUTLIER) cc_final: 0.7497 (tmmt) REVERT: B 241 LYS cc_start: 0.7954 (tppt) cc_final: 0.7578 (tppp) REVERT: C 314 PHE cc_start: 0.7072 (m-80) cc_final: 0.6703 (m-80) REVERT: C 354 ILE cc_start: 0.7752 (mt) cc_final: 0.7511 (mt) REVERT: C 384 ASP cc_start: 0.7774 (m-30) cc_final: 0.7498 (m-30) REVERT: C 402 ASP cc_start: 0.7791 (p0) cc_final: 0.7412 (m-30) REVERT: C 422 TYR cc_start: 0.8657 (m-80) cc_final: 0.8455 (m-80) REVERT: C 466 GLU cc_start: 0.7858 (tp30) cc_final: 0.7595 (tp30) REVERT: C 642 GLU cc_start: 0.7019 (tm-30) cc_final: 0.6651 (tm-30) REVERT: C 689 GLU cc_start: 0.8203 (tt0) cc_final: 0.7838 (tt0) REVERT: C 713 ASP cc_start: 0.7754 (t0) cc_final: 0.7502 (t70) REVERT: C 720 SER cc_start: 0.8285 (OUTLIER) cc_final: 0.7959 (m) REVERT: C 821 PHE cc_start: 0.8359 (m-80) cc_final: 0.7971 (m-10) REVERT: C 839 LYS cc_start: 0.7925 (mtpp) cc_final: 0.7548 (pmmt) REVERT: C 848 MET cc_start: 0.6802 (mtp) cc_final: 0.6368 (mtp) REVERT: C 903 MET cc_start: 0.7659 (mtt) cc_final: 0.7327 (mtp) REVERT: C 958 LYS cc_start: 0.7917 (mtmp) cc_final: 0.7666 (mtmm) REVERT: C 982 MET cc_start: 0.7749 (mmm) cc_final: 0.7417 (mmm) REVERT: C 1002 GLN cc_start: 0.8034 (tt0) cc_final: 0.7804 (tt0) REVERT: C 1042 ARG cc_start: 0.7849 (mpp80) cc_final: 0.7493 (mpp-170) REVERT: C 1044 TYR cc_start: 0.7637 (p90) cc_final: 0.7347 (p90) REVERT: C 1069 GLU cc_start: 0.7777 (tt0) cc_final: 0.7372 (tt0) REVERT: C 1079 LYS cc_start: 0.8702 (tttt) cc_final: 0.8484 (tttp) REVERT: C 1083 SER cc_start: 0.8527 (t) cc_final: 0.8129 (p) REVERT: C 1133 ASN cc_start: 0.7365 (m-40) cc_final: 0.7145 (m110) REVERT: C 1261 LYS cc_start: 0.7301 (OUTLIER) cc_final: 0.6829 (mptp) REVERT: C 1394 LYS cc_start: 0.8362 (OUTLIER) cc_final: 0.8115 (mttp) REVERT: C 1406 ILE cc_start: 0.7975 (mm) cc_final: 0.7678 (mm) REVERT: C 1409 ARG cc_start: 0.8373 (mtt-85) cc_final: 0.8058 (mpp80) REVERT: D 23 ARG cc_start: 0.8104 (ttm110) cc_final: 0.6145 (ttp-170) REVERT: D 85 LYS cc_start: 0.8805 (mmtt) cc_final: 0.8551 (mmmm) REVERT: D 88 GLU cc_start: 0.8386 (mt-10) cc_final: 0.8035 (mt-10) REVERT: D 115 ILE cc_start: 0.8087 (mt) cc_final: 0.7851 (mm) REVERT: D 125 LEU cc_start: 0.8056 (OUTLIER) cc_final: 0.7733 (tt) REVERT: D 163 ASN cc_start: 0.7580 (m-40) cc_final: 0.7379 (m110) REVERT: D 189 GLU cc_start: 0.8718 (tm-30) cc_final: 0.8512 (tm-30) REVERT: E 292 MET cc_start: 0.6327 (ptt) cc_final: 0.5972 (pp-130) REVERT: E 353 LEU cc_start: 0.6825 (tp) cc_final: 0.6418 (tt) REVERT: E 374 ILE cc_start: 0.8815 (mp) cc_final: 0.8425 (mp) REVERT: E 490 SER cc_start: 0.7952 (m) cc_final: 0.7374 (p) REVERT: G 51 TYR cc_start: 0.6604 (m-80) cc_final: 0.5801 (m-80) REVERT: G 52 MET cc_start: 0.6303 (ttp) cc_final: 0.5945 (ttp) outliers start: 106 outliers final: 37 residues processed: 896 average time/residue: 0.7239 time to fit residues: 768.5116 Evaluate side-chains 836 residues out of total 3758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 789 time to evaluate : 1.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 HIS Chi-restraints excluded: chain A residue 435 TYR Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 557 PHE Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 618 CYS Chi-restraints excluded: chain A residue 677 ASP Chi-restraints excluded: chain A residue 750 SER Chi-restraints excluded: chain A residue 1173 ILE Chi-restraints excluded: chain A residue 1255 SER Chi-restraints excluded: chain A residue 1265 SER Chi-restraints excluded: chain A residue 1269 VAL Chi-restraints excluded: chain A residue 1276 GLU Chi-restraints excluded: chain A residue 1303 LYS Chi-restraints excluded: chain A residue 1447 GLU Chi-restraints excluded: chain A residue 1451 LEU Chi-restraints excluded: chain A residue 1482 ASP Chi-restraints excluded: chain A residue 1668 ASP Chi-restraints excluded: chain A residue 1773 LEU Chi-restraints excluded: chain A residue 1944 VAL Chi-restraints excluded: chain A residue 2060 THR Chi-restraints excluded: chain A residue 2238 GLN Chi-restraints excluded: chain A residue 2288 ASP Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 198 LYS Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain C residue 436 SER Chi-restraints excluded: chain C residue 720 SER Chi-restraints excluded: chain C residue 722 SER Chi-restraints excluded: chain C residue 924 LEU Chi-restraints excluded: chain C residue 1031 ILE Chi-restraints excluded: chain C residue 1052 ILE Chi-restraints excluded: chain C residue 1053 ASN Chi-restraints excluded: chain C residue 1080 LYS Chi-restraints excluded: chain C residue 1261 LYS Chi-restraints excluded: chain C residue 1347 VAL Chi-restraints excluded: chain C residue 1358 HIS Chi-restraints excluded: chain C residue 1394 LYS Chi-restraints excluded: chain D residue 2 LEU Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain D residue 37 SER Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain E residue 467 CYS Chi-restraints excluded: chain E residue 474 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 104 optimal weight: 0.7980 chunk 127 optimal weight: 1.9990 chunk 202 optimal weight: 0.5980 chunk 173 optimal weight: 1.9990 chunk 318 optimal weight: 1.9990 chunk 168 optimal weight: 0.9990 chunk 183 optimal weight: 0.8980 chunk 45 optimal weight: 4.9990 chunk 329 optimal weight: 1.9990 chunk 164 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 587 GLN A1376 ASN A2036 ASN A2238 GLN B 148 ASN ** B 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 495 GLN C 511 ASN C 534 GLN C 692 GLN ** C 843 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 988 GLN C1053 ASN C1352 ASN D 108 ASN E 523 GLN ** G 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 621 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.156692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.123323 restraints weight = 67142.532| |-----------------------------------------------------------------------------| r_work (start): 0.3699 rms_B_bonded: 2.69 r_work: 0.3553 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.3165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 34200 Z= 0.192 Angle : 0.619 16.318 46258 Z= 0.311 Chirality : 0.042 0.362 5293 Planarity : 0.004 0.047 5844 Dihedral : 4.607 80.176 4522 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 3.49 % Allowed : 15.86 % Favored : 80.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.42 (0.13), residues: 4102 helix: 1.60 (0.10), residues: 2788 sheet: -0.07 (0.39), residues: 174 loop : -0.44 (0.19), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A1039 TYR 0.028 0.002 TYR B 113 PHE 0.049 0.002 PHE E 496 TRP 0.035 0.002 TRP C 894 HIS 0.010 0.001 HIS A 479 Details of bonding type rmsd/Z covalent geometry : bond 0.00458 / 0.19 (34200) covalent geometry : angle 0.61919 / 0.31 (46258) hydrogen bonds : bond 0.03918 / 2.70 ( 2045) hydrogen bonds : angle 4.07156 / 2.92 ( 6033) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8204 Ramachandran restraints generated. 4102 Oldfield, 0 Emsley, 4102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8204 Ramachandran restraints generated. 4102 Oldfield, 0 Emsley, 4102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 948 residues out of total 3758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 817 time to evaluate : 1.299 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 347 LYS cc_start: 0.7987 (mmtt) cc_final: 0.7747 (mmmm) REVERT: A 413 ASP cc_start: 0.3527 (OUTLIER) cc_final: 0.2205 (m-30) REVERT: A 432 ILE cc_start: 0.8327 (tp) cc_final: 0.7263 (mp) REVERT: A 436 MET cc_start: 0.6950 (mmm) cc_final: 0.6513 (mmm) REVERT: A 499 GLU cc_start: 0.8428 (tm-30) cc_final: 0.8184 (tm-30) REVERT: A 508 ILE cc_start: 0.8650 (mt) cc_final: 0.8282 (tt) REVERT: A 557 PHE cc_start: 0.5699 (OUTLIER) cc_final: 0.5495 (t80) REVERT: A 565 ASN cc_start: 0.4873 (t0) cc_final: 0.4519 (t0) REVERT: A 621 PHE cc_start: 0.8524 (t80) cc_final: 0.8323 (t80) REVERT: A 622 ILE cc_start: 0.8903 (OUTLIER) cc_final: 0.8671 (mt) REVERT: A 640 GLU cc_start: 0.8379 (tt0) cc_final: 0.7893 (tm-30) REVERT: A 680 ARG cc_start: 0.7936 (ttp80) cc_final: 0.7562 (mtm110) REVERT: A 703 ARG cc_start: 0.8723 (ttp-110) cc_final: 0.8450 (ttm-80) REVERT: A 808 ASN cc_start: 0.8146 (m-40) cc_final: 0.7848 (m-40) REVERT: A 818 LYS cc_start: 0.8603 (tttt) cc_final: 0.8196 (mmmm) REVERT: A 927 MET cc_start: 0.8691 (mmm) cc_final: 0.7981 (mpp) REVERT: A 981 ASP cc_start: 0.8099 (t70) cc_final: 0.7887 (t0) REVERT: A 1036 GLU cc_start: 0.7962 (mm-30) cc_final: 0.7550 (mt-10) REVERT: A 1173 ILE cc_start: 0.8731 (mp) cc_final: 0.8449 (mp) REVERT: A 1179 ASP cc_start: 0.8142 (m-30) cc_final: 0.7248 (m-30) REVERT: A 1183 ASN cc_start: 0.8184 (m-40) cc_final: 0.7648 (m110) REVERT: A 1221 ASN cc_start: 0.8187 (t0) cc_final: 0.7848 (t0) REVERT: A 1222 GLN cc_start: 0.8066 (mp10) cc_final: 0.7808 (mp10) REVERT: A 1246 ARG cc_start: 0.8431 (mtt180) cc_final: 0.8019 (mtp-110) REVERT: A 1250 GLN cc_start: 0.8005 (mp10) cc_final: 0.7424 (mp10) REVERT: A 1254 GLU cc_start: 0.8159 (mm-30) cc_final: 0.7558 (tp30) REVERT: A 1283 SER cc_start: 0.8892 (t) cc_final: 0.8371 (p) REVERT: A 1296 ASP cc_start: 0.8644 (m-30) cc_final: 0.8414 (m-30) REVERT: A 1298 ILE cc_start: 0.8723 (mm) cc_final: 0.8459 (mm) REVERT: A 1336 ILE cc_start: 0.8274 (mp) cc_final: 0.8072 (mt) REVERT: A 1378 GLN cc_start: 0.8342 (mt0) cc_final: 0.8030 (mt0) REVERT: A 1438 SER cc_start: 0.8830 (m) cc_final: 0.8547 (p) REVERT: A 1447 GLU cc_start: 0.8722 (OUTLIER) cc_final: 0.8421 (mm-30) REVERT: A 1450 LYS cc_start: 0.8590 (OUTLIER) cc_final: 0.8222 (ttpt) REVERT: A 1529 GLU cc_start: 0.8336 (tm-30) cc_final: 0.8074 (tm-30) REVERT: A 1533 LEU cc_start: 0.9061 (mt) cc_final: 0.8675 (mm) REVERT: A 1636 GLU cc_start: 0.7220 (tp30) cc_final: 0.6721 (tp30) REVERT: A 1648 LYS cc_start: 0.8535 (mttt) cc_final: 0.7985 (mtpm) REVERT: A 1687 LEU cc_start: 0.8873 (mt) cc_final: 0.8583 (mp) REVERT: A 1695 GLN cc_start: 0.8081 (mp10) cc_final: 0.7850 (mp10) REVERT: A 1734 ARG cc_start: 0.8172 (ptt-90) cc_final: 0.7859 (pmm-80) REVERT: A 1764 LEU cc_start: 0.8541 (OUTLIER) cc_final: 0.8301 (mp) REVERT: A 1768 GLU cc_start: 0.8266 (mt-10) cc_final: 0.7626 (tt0) REVERT: A 1860 THR cc_start: 0.9037 (t) cc_final: 0.8033 (t) REVERT: A 1864 HIS cc_start: 0.8649 (m90) cc_final: 0.8118 (m90) REVERT: A 1906 LYS cc_start: 0.8953 (tttt) cc_final: 0.8567 (ttpp) REVERT: A 1959 MET cc_start: 0.8530 (mtp) cc_final: 0.8282 (mtp) REVERT: A 2000 ARG cc_start: 0.8195 (tpp80) cc_final: 0.7579 (tpp80) REVERT: A 2067 SER cc_start: 0.8667 (t) cc_final: 0.8282 (p) REVERT: A 2092 VAL cc_start: 0.8393 (t) cc_final: 0.7988 (p) REVERT: A 2095 SER cc_start: 0.8884 (t) cc_final: 0.8572 (p) REVERT: A 2096 LYS cc_start: 0.8393 (tttt) cc_final: 0.8172 (tttt) REVERT: A 2116 LYS cc_start: 0.8521 (tttt) cc_final: 0.8020 (tttt) REVERT: A 2124 LYS cc_start: 0.8675 (mttt) cc_final: 0.8358 (mttm) REVERT: A 2131 GLU cc_start: 0.7499 (mp0) cc_final: 0.7265 (mp0) REVERT: A 2203 ASN cc_start: 0.8221 (m-40) cc_final: 0.7800 (p0) REVERT: A 2221 LEU cc_start: 0.8050 (tp) cc_final: 0.7790 (tm) REVERT: A 2298 ASP cc_start: 0.8588 (t0) cc_final: 0.8258 (t0) REVERT: A 2368 ILE cc_start: 0.8589 (mm) cc_final: 0.8345 (mp) REVERT: A 2424 LEU cc_start: 0.8651 (mm) cc_final: 0.8195 (mp) REVERT: A 2439 ARG cc_start: 0.7844 (ttm110) cc_final: 0.7341 (ttm110) REVERT: B 7 SER cc_start: 0.4958 (p) cc_final: 0.4719 (m) REVERT: B 23 VAL cc_start: 0.6863 (p) cc_final: 0.6496 (m) REVERT: B 29 GLN cc_start: 0.5946 (mm-40) cc_final: 0.4995 (tm-30) REVERT: B 113 TYR cc_start: 0.3810 (OUTLIER) cc_final: 0.3474 (m-80) REVERT: B 167 MET cc_start: 0.5077 (tpt) cc_final: 0.4339 (tpt) REVERT: B 222 LEU cc_start: 0.6927 (OUTLIER) cc_final: 0.6717 (mt) REVERT: B 282 ARG cc_start: 0.7892 (mpp-170) cc_final: 0.7581 (mtm-85) REVERT: C 311 MET cc_start: 0.8387 (ppp) cc_final: 0.8100 (pp-130) REVERT: C 324 ILE cc_start: 0.7901 (OUTLIER) cc_final: 0.7639 (tp) REVERT: C 354 ILE cc_start: 0.7760 (mt) cc_final: 0.7441 (mt) REVERT: C 384 ASP cc_start: 0.7854 (m-30) cc_final: 0.7499 (m-30) REVERT: C 402 ASP cc_start: 0.7799 (p0) cc_final: 0.7484 (m-30) REVERT: C 418 ARG cc_start: 0.7753 (tpp-160) cc_final: 0.7434 (tpt90) REVERT: C 437 CYS cc_start: 0.8678 (m) cc_final: 0.8310 (m) REVERT: C 533 MET cc_start: 0.8101 (OUTLIER) cc_final: 0.7896 (mmt) REVERT: C 642 GLU cc_start: 0.7181 (tm-30) cc_final: 0.6713 (tm-30) REVERT: C 695 LYS cc_start: 0.8438 (OUTLIER) cc_final: 0.8054 (mtmm) REVERT: C 713 ASP cc_start: 0.7791 (t0) cc_final: 0.7546 (t70) REVERT: C 821 PHE cc_start: 0.8504 (m-80) cc_final: 0.8002 (m-10) REVERT: C 835 MET cc_start: 0.7561 (tmt) cc_final: 0.7232 (tmm) REVERT: C 839 LYS cc_start: 0.7974 (mtpp) cc_final: 0.7522 (pmmt) REVERT: C 848 MET cc_start: 0.6875 (mtp) cc_final: 0.6404 (mtp) REVERT: C 902 LYS cc_start: 0.8169 (ptpt) cc_final: 0.7688 (pttp) REVERT: C 903 MET cc_start: 0.7453 (mtt) cc_final: 0.6967 (mtp) REVERT: C 915 LEU cc_start: 0.8279 (tp) cc_final: 0.8026 (tp) REVERT: C 951 LYS cc_start: 0.7873 (mttp) cc_final: 0.7595 (mmmm) REVERT: C 958 LYS cc_start: 0.7911 (mtmp) cc_final: 0.7635 (mtmm) REVERT: C 982 MET cc_start: 0.7854 (mmm) cc_final: 0.7528 (mmm) REVERT: C 1002 GLN cc_start: 0.8115 (tt0) cc_final: 0.7857 (tt0) REVERT: C 1015 GLU cc_start: 0.6855 (tp30) cc_final: 0.6425 (tp30) REVERT: C 1069 GLU cc_start: 0.7859 (tt0) cc_final: 0.7424 (tt0) REVERT: C 1079 LYS cc_start: 0.8698 (tttt) cc_final: 0.8373 (tttp) REVERT: C 1083 SER cc_start: 0.8667 (t) cc_final: 0.8237 (p) REVERT: C 1261 LYS cc_start: 0.7373 (OUTLIER) cc_final: 0.6945 (mptp) REVERT: C 1406 ILE cc_start: 0.7998 (mm) cc_final: 0.7758 (mt) REVERT: C 1409 ARG cc_start: 0.8429 (mtt-85) cc_final: 0.8092 (mpp80) REVERT: D 23 ARG cc_start: 0.8272 (ttm110) cc_final: 0.6192 (ttp-170) REVERT: D 36 ASP cc_start: 0.8600 (t0) cc_final: 0.8378 (t0) REVERT: D 85 LYS cc_start: 0.8884 (mmtt) cc_final: 0.8562 (mmmm) REVERT: D 120 ASP cc_start: 0.7843 (t0) cc_final: 0.7575 (t0) REVERT: D 125 LEU cc_start: 0.8053 (OUTLIER) cc_final: 0.7781 (tt) REVERT: E 292 MET cc_start: 0.6252 (ptt) cc_final: 0.5901 (pp-130) REVERT: E 314 GLU cc_start: 0.3493 (tm-30) cc_final: 0.2683 (tp30) REVERT: E 334 PHE cc_start: 0.7140 (m-80) cc_final: 0.6548 (m-80) REVERT: E 353 LEU cc_start: 0.6877 (tp) cc_final: 0.6479 (tt) REVERT: E 374 ILE cc_start: 0.8786 (mt) cc_final: 0.8445 (mp) REVERT: E 463 LEU cc_start: 0.7678 (mp) cc_final: 0.7375 (mm) REVERT: E 467 CYS cc_start: 0.8272 (OUTLIER) cc_final: 0.8063 (t) REVERT: E 490 SER cc_start: 0.7970 (m) cc_final: 0.7299 (p) REVERT: E 509 LYS cc_start: 0.8711 (mttt) cc_final: 0.8453 (mppt) REVERT: G 52 MET cc_start: 0.6267 (ttp) cc_final: 0.5916 (ttp) outliers start: 131 outliers final: 54 residues processed: 878 average time/residue: 0.7556 time to fit residues: 792.8815 Evaluate side-chains 834 residues out of total 3758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 766 time to evaluate : 1.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 HIS Chi-restraints excluded: chain A residue 413 ASP Chi-restraints excluded: chain A residue 435 TYR Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 503 ILE Chi-restraints excluded: chain A residue 521 ASN Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain A residue 557 PHE Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 618 CYS Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 657 ILE Chi-restraints excluded: chain A residue 677 ASP Chi-restraints excluded: chain A residue 750 SER Chi-restraints excluded: chain A residue 753 VAL Chi-restraints excluded: chain A residue 957 CYS Chi-restraints excluded: chain A residue 996 GLN Chi-restraints excluded: chain A residue 1024 SER Chi-restraints excluded: chain A residue 1068 LYS Chi-restraints excluded: chain A residue 1220 VAL Chi-restraints excluded: chain A residue 1255 SER Chi-restraints excluded: chain A residue 1265 SER Chi-restraints excluded: chain A residue 1269 VAL Chi-restraints excluded: chain A residue 1276 GLU Chi-restraints excluded: chain A residue 1382 THR Chi-restraints excluded: chain A residue 1447 GLU Chi-restraints excluded: chain A residue 1450 LYS Chi-restraints excluded: chain A residue 1451 LEU Chi-restraints excluded: chain A residue 1526 LEU Chi-restraints excluded: chain A residue 1657 GLN Chi-restraints excluded: chain A residue 1764 LEU Chi-restraints excluded: chain A residue 1773 LEU Chi-restraints excluded: chain A residue 1944 VAL Chi-restraints excluded: chain A residue 2004 THR Chi-restraints excluded: chain A residue 2060 THR Chi-restraints excluded: chain A residue 2100 VAL Chi-restraints excluded: chain A residue 2417 ILE Chi-restraints excluded: chain A residue 2445 ASP Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 113 TYR Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain C residue 324 ILE Chi-restraints excluded: chain C residue 533 MET Chi-restraints excluded: chain C residue 695 LYS Chi-restraints excluded: chain C residue 718 ILE Chi-restraints excluded: chain C residue 722 SER Chi-restraints excluded: chain C residue 924 LEU Chi-restraints excluded: chain C residue 980 PHE Chi-restraints excluded: chain C residue 995 SER Chi-restraints excluded: chain C residue 1080 LYS Chi-restraints excluded: chain C residue 1261 LYS Chi-restraints excluded: chain C residue 1358 HIS Chi-restraints excluded: chain C residue 1415 ILE Chi-restraints excluded: chain D residue 2 LEU Chi-restraints excluded: chain D residue 7 VAL Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain D residue 37 SER Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain E residue 291 SER Chi-restraints excluded: chain E residue 324 ASN Chi-restraints excluded: chain E residue 467 CYS Chi-restraints excluded: chain E residue 474 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 283 optimal weight: 0.4980 chunk 192 optimal weight: 3.9990 chunk 316 optimal weight: 0.9990 chunk 69 optimal weight: 0.5980 chunk 198 optimal weight: 0.7980 chunk 4 optimal weight: 40.0000 chunk 260 optimal weight: 0.9980 chunk 17 optimal weight: 5.9990 chunk 266 optimal weight: 0.0370 chunk 23 optimal weight: 5.9990 chunk 278 optimal weight: 1.9990 overall best weight: 0.5858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 694 GLN A1380 HIS A2183 ASN A2238 GLN B 77 ASN B 116 ASN B 148 ASN C 511 ASN C 557 ASN C 692 GLN ** C 843 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 988 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1053 ASN C1133 ASN D 96 GLN D 104 HIS ** E 528 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.156630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.123234 restraints weight = 66904.714| |-----------------------------------------------------------------------------| r_work (start): 0.3717 rms_B_bonded: 2.74 r_work: 0.3572 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.3485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 34200 Z= 0.136 Angle : 0.592 17.522 46258 Z= 0.295 Chirality : 0.040 0.312 5293 Planarity : 0.004 0.059 5844 Dihedral : 4.442 79.624 4520 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.41 % Favored : 97.56 % Rotamer: Outliers : 3.11 % Allowed : 17.67 % Favored : 79.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.56 (0.13), residues: 4102 helix: 1.75 (0.10), residues: 2788 sheet: 0.03 (0.39), residues: 174 loop : -0.52 (0.19), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A1136 TYR 0.030 0.002 TYR A 352 PHE 0.056 0.001 PHE E 496 TRP 0.023 0.001 TRP A1229 HIS 0.009 0.001 HIS A 633 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 (34200) covalent geometry : angle 0.59197 / 0.29 (46258) hydrogen bonds : bond 0.03535 / 2.44 ( 2045) hydrogen bonds : angle 3.97107 / 2.85 ( 6033) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8204 Ramachandran restraints generated. 4102 Oldfield, 0 Emsley, 4102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8204 Ramachandran restraints generated. 4102 Oldfield, 0 Emsley, 4102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 909 residues out of total 3758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 792 time to evaluate : 1.290 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 351 ILE cc_start: 0.7700 (mm) cc_final: 0.7428 (mp) REVERT: A 371 TYR cc_start: 0.7577 (m-10) cc_final: 0.7328 (m-10) REVERT: A 380 PHE cc_start: 0.6937 (t80) cc_final: 0.6716 (t80) REVERT: A 397 TYR cc_start: 0.8037 (m-80) cc_final: 0.7750 (m-80) REVERT: A 432 ILE cc_start: 0.8393 (tp) cc_final: 0.7346 (mp) REVERT: A 436 MET cc_start: 0.6828 (mmm) cc_final: 0.6405 (mmm) REVERT: A 499 GLU cc_start: 0.8363 (tm-30) cc_final: 0.8121 (tm-30) REVERT: A 508 ILE cc_start: 0.8691 (mt) cc_final: 0.8306 (tt) REVERT: A 565 ASN cc_start: 0.4953 (t0) cc_final: 0.4678 (t0) REVERT: A 621 PHE cc_start: 0.8611 (t80) cc_final: 0.8409 (t80) REVERT: A 622 ILE cc_start: 0.8856 (OUTLIER) cc_final: 0.8651 (mt) REVERT: A 640 GLU cc_start: 0.8275 (tt0) cc_final: 0.7869 (tm-30) REVERT: A 680 ARG cc_start: 0.7887 (ttp80) cc_final: 0.7561 (mtm110) REVERT: A 808 ASN cc_start: 0.8142 (m-40) cc_final: 0.7868 (m-40) REVERT: A 818 LYS cc_start: 0.8567 (tttt) cc_final: 0.8247 (mmmm) REVERT: A 855 LYS cc_start: 0.7252 (mtmt) cc_final: 0.6825 (mttt) REVERT: A 1028 SER cc_start: 0.8801 (m) cc_final: 0.8468 (m) REVERT: A 1036 GLU cc_start: 0.7928 (mm-30) cc_final: 0.7567 (mt-10) REVERT: A 1171 ASN cc_start: 0.7878 (OUTLIER) cc_final: 0.7666 (m110) REVERT: A 1173 ILE cc_start: 0.8650 (OUTLIER) cc_final: 0.8388 (mp) REVERT: A 1179 ASP cc_start: 0.8163 (m-30) cc_final: 0.7251 (m-30) REVERT: A 1183 ASN cc_start: 0.8221 (m-40) cc_final: 0.7691 (m110) REVERT: A 1242 GLU cc_start: 0.7919 (tp30) cc_final: 0.7698 (tm-30) REVERT: A 1250 GLN cc_start: 0.7971 (mp10) cc_final: 0.7427 (mp10) REVERT: A 1283 SER cc_start: 0.8914 (t) cc_final: 0.8453 (p) REVERT: A 1296 ASP cc_start: 0.8516 (m-30) cc_final: 0.8291 (m-30) REVERT: A 1298 ILE cc_start: 0.8653 (mm) cc_final: 0.8407 (mm) REVERT: A 1378 GLN cc_start: 0.8226 (mt0) cc_final: 0.7769 (mt0) REVERT: A 1438 SER cc_start: 0.8866 (m) cc_final: 0.8593 (p) REVERT: A 1533 LEU cc_start: 0.9046 (mt) cc_final: 0.8830 (mm) REVERT: A 1636 GLU cc_start: 0.7251 (tp30) cc_final: 0.6742 (tp30) REVERT: A 1648 LYS cc_start: 0.8582 (mttt) cc_final: 0.8030 (mttm) REVERT: A 1687 LEU cc_start: 0.8908 (mt) cc_final: 0.8614 (mp) REVERT: A 1695 GLN cc_start: 0.8057 (mp10) cc_final: 0.7808 (mp10) REVERT: A 1734 ARG cc_start: 0.8192 (ptt-90) cc_final: 0.7870 (pmm-80) REVERT: A 1735 LEU cc_start: 0.8876 (mm) cc_final: 0.8665 (mt) REVERT: A 1764 LEU cc_start: 0.8621 (OUTLIER) cc_final: 0.8374 (mp) REVERT: A 1768 GLU cc_start: 0.8280 (mt-10) cc_final: 0.7660 (tt0) REVERT: A 1799 MET cc_start: 0.8144 (mmp) cc_final: 0.7730 (tpp) REVERT: A 1860 THR cc_start: 0.9071 (t) cc_final: 0.7999 (t) REVERT: A 1864 HIS cc_start: 0.8604 (m90) cc_final: 0.8098 (m90) REVERT: A 1906 LYS cc_start: 0.8955 (tttt) cc_final: 0.8609 (ttpp) REVERT: A 1959 MET cc_start: 0.8554 (mtp) cc_final: 0.8246 (mtm) REVERT: A 2000 ARG cc_start: 0.8210 (tpp80) cc_final: 0.7637 (tpp80) REVERT: A 2062 GLU cc_start: 0.8476 (mt-10) cc_final: 0.8177 (mm-30) REVERT: A 2067 SER cc_start: 0.8669 (t) cc_final: 0.8340 (p) REVERT: A 2092 VAL cc_start: 0.8414 (t) cc_final: 0.8030 (p) REVERT: A 2095 SER cc_start: 0.8890 (t) cc_final: 0.8599 (p) REVERT: A 2096 LYS cc_start: 0.8442 (tttt) cc_final: 0.8180 (tttt) REVERT: A 2116 LYS cc_start: 0.8535 (tttt) cc_final: 0.8081 (tttt) REVERT: A 2124 LYS cc_start: 0.8665 (mttt) cc_final: 0.8379 (mttm) REVERT: A 2203 ASN cc_start: 0.8083 (m-40) cc_final: 0.7607 (p0) REVERT: A 2221 LEU cc_start: 0.8128 (tp) cc_final: 0.7883 (tm) REVERT: A 2223 GLN cc_start: 0.8463 (mt0) cc_final: 0.8189 (pt0) REVERT: A 2298 ASP cc_start: 0.8556 (t0) cc_final: 0.8234 (t0) REVERT: A 2368 ILE cc_start: 0.8576 (mm) cc_final: 0.8356 (mp) REVERT: A 2439 ARG cc_start: 0.7800 (ttm110) cc_final: 0.7321 (ttm110) REVERT: B 23 VAL cc_start: 0.6932 (p) cc_final: 0.6580 (m) REVERT: B 29 GLN cc_start: 0.6198 (mm-40) cc_final: 0.5106 (tm-30) REVERT: B 68 VAL cc_start: 0.7467 (OUTLIER) cc_final: 0.7187 (p) REVERT: B 212 ARG cc_start: 0.6137 (tpt-90) cc_final: 0.5624 (tpp-160) REVERT: B 222 LEU cc_start: 0.6996 (OUTLIER) cc_final: 0.6671 (pp) REVERT: B 241 LYS cc_start: 0.7885 (tppt) cc_final: 0.7683 (tptp) REVERT: B 293 LYS cc_start: 0.8180 (mmtt) cc_final: 0.7971 (mmtt) REVERT: C 311 MET cc_start: 0.8424 (ppp) cc_final: 0.8102 (pp-130) REVERT: C 354 ILE cc_start: 0.7778 (mt) cc_final: 0.7449 (mt) REVERT: C 384 ASP cc_start: 0.7873 (m-30) cc_final: 0.7383 (m-30) REVERT: C 418 ARG cc_start: 0.7857 (tpp-160) cc_final: 0.7567 (tpt90) REVERT: C 437 CYS cc_start: 0.8620 (m) cc_final: 0.8296 (m) REVERT: C 451 GLU cc_start: 0.7483 (tm-30) cc_final: 0.7275 (tm-30) REVERT: C 470 MET cc_start: 0.8746 (OUTLIER) cc_final: 0.8363 (tpp) REVERT: C 642 GLU cc_start: 0.7276 (tm-30) cc_final: 0.6787 (tm-30) REVERT: C 695 LYS cc_start: 0.8473 (ttmt) cc_final: 0.8096 (mtmm) REVERT: C 713 ASP cc_start: 0.7846 (t0) cc_final: 0.7590 (t70) REVERT: C 720 SER cc_start: 0.8398 (OUTLIER) cc_final: 0.8068 (m) REVERT: C 725 ILE cc_start: 0.8122 (OUTLIER) cc_final: 0.7899 (mt) REVERT: C 821 PHE cc_start: 0.8416 (m-80) cc_final: 0.7943 (m-10) REVERT: C 839 LYS cc_start: 0.7937 (mtpp) cc_final: 0.7512 (pmmt) REVERT: C 848 MET cc_start: 0.6743 (mtp) cc_final: 0.6322 (mtp) REVERT: C 902 LYS cc_start: 0.8228 (ptpt) cc_final: 0.7840 (pttp) REVERT: C 903 MET cc_start: 0.7385 (mtt) cc_final: 0.6884 (mtp) REVERT: C 915 LEU cc_start: 0.8299 (tp) cc_final: 0.8039 (tp) REVERT: C 951 LYS cc_start: 0.7886 (mttp) cc_final: 0.7583 (mmmm) REVERT: C 958 LYS cc_start: 0.7923 (mtmp) cc_final: 0.7655 (mtmm) REVERT: C 982 MET cc_start: 0.7700 (mmm) cc_final: 0.7389 (mmm) REVERT: C 1002 GLN cc_start: 0.8086 (tt0) cc_final: 0.7836 (tt0) REVERT: C 1069 GLU cc_start: 0.7916 (tt0) cc_final: 0.7526 (tt0) REVERT: C 1079 LYS cc_start: 0.8725 (tttt) cc_final: 0.8415 (tttp) REVERT: C 1080 LYS cc_start: 0.8978 (OUTLIER) cc_final: 0.8727 (ttpp) REVERT: C 1083 SER cc_start: 0.8690 (t) cc_final: 0.8263 (p) REVERT: C 1261 LYS cc_start: 0.7433 (OUTLIER) cc_final: 0.6931 (mptp) REVERT: C 1406 ILE cc_start: 0.8100 (mm) cc_final: 0.7893 (mt) REVERT: C 1409 ARG cc_start: 0.8334 (mtt-85) cc_final: 0.8053 (mpp80) REVERT: D 23 ARG cc_start: 0.8367 (ttm110) cc_final: 0.6284 (ttp-170) REVERT: D 69 LEU cc_start: 0.8891 (tt) cc_final: 0.8660 (tm) REVERT: D 85 LYS cc_start: 0.8893 (mmtt) cc_final: 0.8564 (mmmm) REVERT: D 88 GLU cc_start: 0.8399 (mt-10) cc_final: 0.8114 (mt-10) REVERT: D 120 ASP cc_start: 0.7770 (t0) cc_final: 0.7562 (t0) REVERT: D 125 LEU cc_start: 0.8093 (OUTLIER) cc_final: 0.7846 (tt) REVERT: E 292 MET cc_start: 0.6359 (ptt) cc_final: 0.5997 (pp-130) REVERT: E 303 LEU cc_start: 0.8195 (OUTLIER) cc_final: 0.7845 (mt) REVERT: E 314 GLU cc_start: 0.3454 (tm-30) cc_final: 0.2635 (tp30) REVERT: E 334 PHE cc_start: 0.7021 (m-80) cc_final: 0.6681 (m-80) REVERT: E 467 CYS cc_start: 0.8264 (m) cc_final: 0.8041 (t) REVERT: E 490 SER cc_start: 0.7955 (OUTLIER) cc_final: 0.7303 (p) REVERT: E 509 LYS cc_start: 0.8661 (mttt) cc_final: 0.8438 (mppt) REVERT: G 52 MET cc_start: 0.6287 (ttp) cc_final: 0.5952 (ttp) outliers start: 117 outliers final: 46 residues processed: 841 average time/residue: 0.7287 time to fit residues: 725.4092 Evaluate side-chains 819 residues out of total 3758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 759 time to evaluate : 1.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 HIS Chi-restraints excluded: chain A residue 435 TYR Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 503 ILE Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain A residue 618 CYS Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 677 ASP Chi-restraints excluded: chain A residue 1024 SER Chi-restraints excluded: chain A residue 1171 ASN Chi-restraints excluded: chain A residue 1173 ILE Chi-restraints excluded: chain A residue 1177 VAL Chi-restraints excluded: chain A residue 1188 ASN Chi-restraints excluded: chain A residue 1255 SER Chi-restraints excluded: chain A residue 1265 SER Chi-restraints excluded: chain A residue 1269 VAL Chi-restraints excluded: chain A residue 1276 GLU Chi-restraints excluded: chain A residue 1305 LEU Chi-restraints excluded: chain A residue 1451 LEU Chi-restraints excluded: chain A residue 1482 ASP Chi-restraints excluded: chain A residue 1657 GLN Chi-restraints excluded: chain A residue 1764 LEU Chi-restraints excluded: chain A residue 1871 GLN Chi-restraints excluded: chain A residue 1892 ILE Chi-restraints excluded: chain A residue 1944 VAL Chi-restraints excluded: chain A residue 2199 LYS Chi-restraints excluded: chain A residue 2236 GLU Chi-restraints excluded: chain A residue 2417 ILE Chi-restraints excluded: chain A residue 2437 ASP Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain C residue 470 MET Chi-restraints excluded: chain C residue 720 SER Chi-restraints excluded: chain C residue 722 SER Chi-restraints excluded: chain C residue 725 ILE Chi-restraints excluded: chain C residue 832 LYS Chi-restraints excluded: chain C residue 924 LEU Chi-restraints excluded: chain C residue 980 PHE Chi-restraints excluded: chain C residue 1053 ASN Chi-restraints excluded: chain C residue 1080 LYS Chi-restraints excluded: chain C residue 1117 GLN Chi-restraints excluded: chain C residue 1261 LYS Chi-restraints excluded: chain C residue 1271 LEU Chi-restraints excluded: chain C residue 1358 HIS Chi-restraints excluded: chain C residue 1415 ILE Chi-restraints excluded: chain D residue 2 LEU Chi-restraints excluded: chain D residue 37 SER Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain D residue 155 ILE Chi-restraints excluded: chain E residue 303 LEU Chi-restraints excluded: chain E residue 324 ASN Chi-restraints excluded: chain E residue 490 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 319 optimal weight: 3.9990 chunk 158 optimal weight: 1.9990 chunk 360 optimal weight: 1.9990 chunk 105 optimal weight: 0.0050 chunk 246 optimal weight: 1.9990 chunk 405 optimal weight: 0.9980 chunk 82 optimal weight: 1.9990 chunk 386 optimal weight: 3.9990 chunk 288 optimal weight: 0.5980 chunk 245 optimal weight: 8.9990 chunk 390 optimal weight: 4.9990 overall best weight: 1.1198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 396 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 859 ASN A1380 HIS A2238 GLN A2462 ASN B 148 ASN B 221 HIS C 411 GLN C 495 GLN C 511 ASN C 557 ASN C 692 GLN ** C 843 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 988 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1133 ASN D 17 ASN D 96 GLN G 23 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.154943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.121364 restraints weight = 66689.436| |-----------------------------------------------------------------------------| r_work (start): 0.3670 rms_B_bonded: 2.68 r_work: 0.3525 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.3818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 34200 Z= 0.195 Angle : 0.614 13.334 46258 Z= 0.311 Chirality : 0.042 0.343 5293 Planarity : 0.004 0.054 5844 Dihedral : 4.465 80.902 4520 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.51 % Favored : 97.46 % Rotamer: Outliers : 3.54 % Allowed : 18.15 % Favored : 78.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.51 (0.13), residues: 4102 helix: 1.69 (0.10), residues: 2789 sheet: 0.04 (0.39), residues: 169 loop : -0.51 (0.19), residues: 1144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A1136 TYR 0.031 0.002 TYR A 361 PHE 0.055 0.002 PHE E 496 TRP 0.024 0.002 TRP A1481 HIS 0.014 0.001 HIS C 338 Details of bonding type rmsd/Z covalent geometry : bond 0.00468 / 0.19 (34200) covalent geometry : angle 0.61448 / 0.31 (46258) hydrogen bonds : bond 0.03804 / 2.62 ( 2045) hydrogen bonds : angle 4.04577 / 2.90 ( 6033) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8204 Ramachandran restraints generated. 4102 Oldfield, 0 Emsley, 4102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8204 Ramachandran restraints generated. 4102 Oldfield, 0 Emsley, 4102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 916 residues out of total 3758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 783 time to evaluate : 1.175 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 351 ILE cc_start: 0.7726 (mm) cc_final: 0.7479 (mp) REVERT: A 380 PHE cc_start: 0.7129 (t80) cc_final: 0.6865 (t80) REVERT: A 413 ASP cc_start: 0.3545 (OUTLIER) cc_final: 0.2587 (m-30) REVERT: A 432 ILE cc_start: 0.8378 (tp) cc_final: 0.7360 (mp) REVERT: A 436 MET cc_start: 0.7024 (mmm) cc_final: 0.6541 (mmm) REVERT: A 497 MET cc_start: 0.7220 (ttp) cc_final: 0.6819 (ttp) REVERT: A 499 GLU cc_start: 0.8419 (tm-30) cc_final: 0.8149 (tm-30) REVERT: A 508 ILE cc_start: 0.8776 (mt) cc_final: 0.8377 (tt) REVERT: A 626 ILE cc_start: 0.8595 (tt) cc_final: 0.8304 (tp) REVERT: A 640 GLU cc_start: 0.8451 (tt0) cc_final: 0.7949 (tm-30) REVERT: A 680 ARG cc_start: 0.7964 (ttp80) cc_final: 0.7562 (mtp-110) REVERT: A 808 ASN cc_start: 0.8134 (m-40) cc_final: 0.7847 (m-40) REVERT: A 818 LYS cc_start: 0.8598 (tttt) cc_final: 0.8232 (mmmm) REVERT: A 855 LYS cc_start: 0.7283 (mtmt) cc_final: 0.6909 (mttt) REVERT: A 927 MET cc_start: 0.8773 (mmm) cc_final: 0.8369 (mpp) REVERT: A 1028 SER cc_start: 0.8801 (m) cc_final: 0.8450 (m) REVERT: A 1036 GLU cc_start: 0.7960 (mm-30) cc_final: 0.7549 (mt-10) REVERT: A 1174 GLN cc_start: 0.8281 (tm-30) cc_final: 0.7744 (tm-30) REVERT: A 1179 ASP cc_start: 0.8243 (m-30) cc_final: 0.7379 (m-30) REVERT: A 1183 ASN cc_start: 0.8158 (m-40) cc_final: 0.7639 (m110) REVERT: A 1184 LYS cc_start: 0.8519 (OUTLIER) cc_final: 0.8121 (mtpp) REVERT: A 1242 GLU cc_start: 0.7933 (tp30) cc_final: 0.7667 (tm-30) REVERT: A 1250 GLN cc_start: 0.8162 (mp10) cc_final: 0.7467 (mp10) REVERT: A 1283 SER cc_start: 0.8940 (t) cc_final: 0.8386 (p) REVERT: A 1296 ASP cc_start: 0.8645 (m-30) cc_final: 0.8404 (m-30) REVERT: A 1344 GLN cc_start: 0.8407 (tt0) cc_final: 0.8085 (tp-100) REVERT: A 1357 GLU cc_start: 0.8160 (mm-30) cc_final: 0.7957 (tp30) REVERT: A 1378 GLN cc_start: 0.8340 (mt0) cc_final: 0.7805 (mt0) REVERT: A 1438 SER cc_start: 0.8866 (m) cc_final: 0.8492 (p) REVERT: A 1529 GLU cc_start: 0.8414 (tm-30) cc_final: 0.8071 (tm-30) REVERT: A 1533 LEU cc_start: 0.9162 (mt) cc_final: 0.8820 (mp) REVERT: A 1587 ASN cc_start: 0.8547 (t0) cc_final: 0.8278 (t0) REVERT: A 1603 LYS cc_start: 0.8440 (OUTLIER) cc_final: 0.8187 (mtmm) REVERT: A 1636 GLU cc_start: 0.7279 (tp30) cc_final: 0.6645 (tp30) REVERT: A 1648 LYS cc_start: 0.8629 (mttt) cc_final: 0.8073 (mttm) REVERT: A 1687 LEU cc_start: 0.8908 (mt) cc_final: 0.8609 (mp) REVERT: A 1735 LEU cc_start: 0.8778 (mm) cc_final: 0.8551 (mt) REVERT: A 1764 LEU cc_start: 0.8546 (OUTLIER) cc_final: 0.8305 (mp) REVERT: A 1817 ILE cc_start: 0.8234 (mm) cc_final: 0.8027 (mp) REVERT: A 1826 LYS cc_start: 0.8731 (mttt) cc_final: 0.8451 (mttp) REVERT: A 1860 THR cc_start: 0.9077 (t) cc_final: 0.8066 (t) REVERT: A 1864 HIS cc_start: 0.8645 (m90) cc_final: 0.8077 (m90) REVERT: A 1906 LYS cc_start: 0.8993 (tttt) cc_final: 0.8649 (ttpp) REVERT: A 1999 LYS cc_start: 0.8318 (mttp) cc_final: 0.8070 (mttp) REVERT: A 2000 ARG cc_start: 0.8310 (tpp80) cc_final: 0.7699 (tpp80) REVERT: A 2062 GLU cc_start: 0.8489 (mt-10) cc_final: 0.8151 (mm-30) REVERT: A 2067 SER cc_start: 0.8691 (t) cc_final: 0.8429 (p) REVERT: A 2092 VAL cc_start: 0.8419 (t) cc_final: 0.8001 (p) REVERT: A 2095 SER cc_start: 0.8891 (t) cc_final: 0.8561 (p) REVERT: A 2096 LYS cc_start: 0.8432 (tttt) cc_final: 0.8155 (tttt) REVERT: A 2116 LYS cc_start: 0.8477 (tttt) cc_final: 0.7974 (tttt) REVERT: A 2124 LYS cc_start: 0.8674 (mttt) cc_final: 0.8381 (mttm) REVERT: A 2131 GLU cc_start: 0.7617 (mp0) cc_final: 0.7327 (mp0) REVERT: A 2203 ASN cc_start: 0.8179 (m-40) cc_final: 0.7676 (p0) REVERT: A 2221 LEU cc_start: 0.8137 (tp) cc_final: 0.7876 (tm) REVERT: A 2223 GLN cc_start: 0.8485 (mt0) cc_final: 0.8204 (pt0) REVERT: A 2226 GLU cc_start: 0.7522 (tt0) cc_final: 0.7305 (tp30) REVERT: A 2298 ASP cc_start: 0.8532 (t0) cc_final: 0.8210 (t0) REVERT: A 2368 ILE cc_start: 0.8557 (mm) cc_final: 0.8267 (mp) REVERT: A 2439 ARG cc_start: 0.7954 (ttm110) cc_final: 0.7467 (ttm110) REVERT: B 29 GLN cc_start: 0.6221 (mm-40) cc_final: 0.5170 (tm-30) REVERT: B 68 VAL cc_start: 0.7465 (OUTLIER) cc_final: 0.7243 (p) REVERT: B 167 MET cc_start: 0.4902 (tpt) cc_final: 0.4422 (tpt) REVERT: B 212 ARG cc_start: 0.6179 (tpt-90) cc_final: 0.5890 (tpp-160) REVERT: B 222 LEU cc_start: 0.6954 (OUTLIER) cc_final: 0.6636 (pp) REVERT: B 293 LYS cc_start: 0.8194 (mmtt) cc_final: 0.7886 (mmtt) REVERT: C 311 MET cc_start: 0.8454 (ppp) cc_final: 0.8121 (pp-130) REVERT: C 314 PHE cc_start: 0.8630 (t80) cc_final: 0.8202 (t80) REVERT: C 354 ILE cc_start: 0.7883 (mt) cc_final: 0.7462 (mt) REVERT: C 357 LEU cc_start: 0.7997 (mt) cc_final: 0.7549 (mp) REVERT: C 384 ASP cc_start: 0.7912 (m-30) cc_final: 0.7405 (m-30) REVERT: C 418 ARG cc_start: 0.7965 (tpp-160) cc_final: 0.7716 (tpt90) REVERT: C 437 CYS cc_start: 0.8664 (m) cc_final: 0.8302 (m) REVERT: C 440 LYS cc_start: 0.7657 (tttm) cc_final: 0.6907 (tttm) REVERT: C 443 ASP cc_start: 0.7551 (m-30) cc_final: 0.6892 (m-30) REVERT: C 451 GLU cc_start: 0.7458 (tm-30) cc_final: 0.7142 (tm-30) REVERT: C 470 MET cc_start: 0.8689 (OUTLIER) cc_final: 0.8379 (tpp) REVERT: C 642 GLU cc_start: 0.7312 (tm-30) cc_final: 0.6737 (tm-30) REVERT: C 695 LYS cc_start: 0.8478 (OUTLIER) cc_final: 0.8109 (mtmm) REVERT: C 713 ASP cc_start: 0.7847 (t0) cc_final: 0.7589 (t70) REVERT: C 794 ARG cc_start: 0.7230 (mtp-110) cc_final: 0.7019 (mmt90) REVERT: C 821 PHE cc_start: 0.8492 (m-80) cc_final: 0.7992 (m-10) REVERT: C 835 MET cc_start: 0.7491 (tmt) cc_final: 0.7186 (tmm) REVERT: C 848 MET cc_start: 0.6736 (mtp) cc_final: 0.6355 (mtp) REVERT: C 894 TRP cc_start: 0.6163 (m100) cc_final: 0.5824 (t60) REVERT: C 903 MET cc_start: 0.7545 (mtt) cc_final: 0.7302 (mtp) REVERT: C 946 ARG cc_start: 0.6429 (mtm-85) cc_final: 0.6156 (ttm110) REVERT: C 951 LYS cc_start: 0.7969 (mttp) cc_final: 0.7691 (mmmm) REVERT: C 958 LYS cc_start: 0.7921 (mtmp) cc_final: 0.7678 (mtmm) REVERT: C 982 MET cc_start: 0.7859 (mmm) cc_final: 0.7573 (mmm) REVERT: C 1002 GLN cc_start: 0.8084 (tt0) cc_final: 0.7839 (tt0) REVERT: C 1032 ARG cc_start: 0.8058 (mmm-85) cc_final: 0.7829 (mmm160) REVERT: C 1069 GLU cc_start: 0.7970 (tt0) cc_final: 0.7537 (tt0) REVERT: C 1079 LYS cc_start: 0.8629 (tttt) cc_final: 0.8367 (tttp) REVERT: C 1083 SER cc_start: 0.8733 (t) cc_final: 0.8297 (p) REVERT: C 1261 LYS cc_start: 0.7526 (OUTLIER) cc_final: 0.7046 (mptp) REVERT: C 1394 LYS cc_start: 0.8137 (OUTLIER) cc_final: 0.7858 (mtmm) REVERT: C 1409 ARG cc_start: 0.8393 (mtt-85) cc_final: 0.8082 (mpp80) REVERT: D 23 ARG cc_start: 0.8359 (ttm110) cc_final: 0.6200 (ttp-170) REVERT: D 69 LEU cc_start: 0.8923 (tt) cc_final: 0.8656 (tm) REVERT: D 85 LYS cc_start: 0.8903 (mmtt) cc_final: 0.8620 (mmmm) REVERT: D 96 GLN cc_start: 0.7707 (OUTLIER) cc_final: 0.7349 (pm20) REVERT: D 118 MET cc_start: 0.7396 (mtp) cc_final: 0.7129 (ptp) REVERT: D 120 ASP cc_start: 0.7843 (t0) cc_final: 0.7565 (t0) REVERT: D 125 LEU cc_start: 0.8025 (OUTLIER) cc_final: 0.7795 (tt) REVERT: E 303 LEU cc_start: 0.8137 (OUTLIER) cc_final: 0.7911 (pp) REVERT: E 314 GLU cc_start: 0.3484 (tm-30) cc_final: 0.2672 (tp30) REVERT: E 334 PHE cc_start: 0.7082 (m-80) cc_final: 0.6709 (m-80) REVERT: E 466 MET cc_start: 0.7552 (OUTLIER) cc_final: 0.7320 (ptp) REVERT: E 490 SER cc_start: 0.7902 (OUTLIER) cc_final: 0.7486 (p) REVERT: G 52 MET cc_start: 0.6062 (ttp) cc_final: 0.5748 (ttp) outliers start: 133 outliers final: 63 residues processed: 840 average time/residue: 0.7419 time to fit residues: 736.7544 Evaluate side-chains 841 residues out of total 3758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 763 time to evaluate : 1.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 HIS Chi-restraints excluded: chain A residue 413 ASP Chi-restraints excluded: chain A residue 435 TYR Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain A residue 618 CYS Chi-restraints excluded: chain A residue 647 MET Chi-restraints excluded: chain A residue 677 ASP Chi-restraints excluded: chain A residue 753 VAL Chi-restraints excluded: chain A residue 955 LEU Chi-restraints excluded: chain A residue 996 GLN Chi-restraints excluded: chain A residue 1008 VAL Chi-restraints excluded: chain A residue 1024 SER Chi-restraints excluded: chain A residue 1177 VAL Chi-restraints excluded: chain A residue 1184 LYS Chi-restraints excluded: chain A residue 1220 VAL Chi-restraints excluded: chain A residue 1249 ILE Chi-restraints excluded: chain A residue 1255 SER Chi-restraints excluded: chain A residue 1265 SER Chi-restraints excluded: chain A residue 1269 VAL Chi-restraints excluded: chain A residue 1276 GLU Chi-restraints excluded: chain A residue 1305 LEU Chi-restraints excluded: chain A residue 1382 THR Chi-restraints excluded: chain A residue 1451 LEU Chi-restraints excluded: chain A residue 1603 LYS Chi-restraints excluded: chain A residue 1764 LEU Chi-restraints excluded: chain A residue 1871 GLN Chi-restraints excluded: chain A residue 1892 ILE Chi-restraints excluded: chain A residue 1923 GLU Chi-restraints excluded: chain A residue 2199 LYS Chi-restraints excluded: chain A residue 2204 ILE Chi-restraints excluded: chain A residue 2331 SER Chi-restraints excluded: chain A residue 2417 ILE Chi-restraints excluded: chain A residue 2445 ASP Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 77 ASN Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 113 TYR Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 244 THR Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain C residue 436 SER Chi-restraints excluded: chain C residue 463 MET Chi-restraints excluded: chain C residue 470 MET Chi-restraints excluded: chain C residue 695 LYS Chi-restraints excluded: chain C residue 718 ILE Chi-restraints excluded: chain C residue 720 SER Chi-restraints excluded: chain C residue 742 MET Chi-restraints excluded: chain C residue 832 LYS Chi-restraints excluded: chain C residue 872 PHE Chi-restraints excluded: chain C residue 924 LEU Chi-restraints excluded: chain C residue 980 PHE Chi-restraints excluded: chain C residue 1053 ASN Chi-restraints excluded: chain C residue 1080 LYS Chi-restraints excluded: chain C residue 1261 LYS Chi-restraints excluded: chain C residue 1271 LEU Chi-restraints excluded: chain C residue 1358 HIS Chi-restraints excluded: chain C residue 1394 LYS Chi-restraints excluded: chain C residue 1415 ILE Chi-restraints excluded: chain D residue 2 LEU Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain D residue 96 GLN Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 155 ILE Chi-restraints excluded: chain E residue 291 SER Chi-restraints excluded: chain E residue 303 LEU Chi-restraints excluded: chain E residue 324 ASN Chi-restraints excluded: chain E residue 458 TYR Chi-restraints excluded: chain E residue 466 MET Chi-restraints excluded: chain E residue 490 SER Chi-restraints excluded: chain G residue 632 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 387 optimal weight: 7.9990 chunk 230 optimal weight: 8.9990 chunk 301 optimal weight: 0.0270 chunk 345 optimal weight: 0.5980 chunk 149 optimal weight: 0.7980 chunk 197 optimal weight: 0.5980 chunk 244 optimal weight: 9.9990 chunk 109 optimal weight: 0.7980 chunk 273 optimal weight: 0.6980 chunk 298 optimal weight: 2.9990 chunk 147 optimal weight: 1.9990 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 396 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 479 HIS A 633 HIS A 859 ASN A1171 ASN A1380 HIS A2462 ASN B 148 ASN C 495 GLN C 511 ASN C 557 ASN C 692 GLN ** C 843 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 988 GLN C1053 ASN D 17 ASN D 96 GLN E 523 GLN G 23 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.156423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.123367 restraints weight = 66676.041| |-----------------------------------------------------------------------------| r_work (start): 0.3706 rms_B_bonded: 2.67 r_work: 0.3584 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.3973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 34200 Z= 0.135 Angle : 0.614 19.251 46258 Z= 0.305 Chirality : 0.041 0.373 5293 Planarity : 0.004 0.061 5844 Dihedral : 4.419 80.143 4520 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.29 % Favored : 97.68 % Rotamer: Outliers : 3.06 % Allowed : 19.74 % Favored : 77.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.63 (0.13), residues: 4102 helix: 1.79 (0.10), residues: 2787 sheet: 0.27 (0.38), residues: 174 loop : -0.53 (0.19), residues: 1141 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A1136 TYR 0.028 0.001 TYR D 49 PHE 0.039 0.001 PHE E 349 TRP 0.025 0.001 TRP A1229 HIS 0.014 0.001 HIS C 338 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 (34200) covalent geometry : angle 0.61385 / 0.31 (46258) hydrogen bonds : bond 0.03532 / 2.42 ( 2045) hydrogen bonds : angle 3.96332 / 2.84 ( 6033) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8204 Ramachandran restraints generated. 4102 Oldfield, 0 Emsley, 4102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8204 Ramachandran restraints generated. 4102 Oldfield, 0 Emsley, 4102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 889 residues out of total 3758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 774 time to evaluate : 1.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 351 ILE cc_start: 0.7708 (mm) cc_final: 0.7455 (mp) REVERT: A 432 ILE cc_start: 0.8335 (tp) cc_final: 0.7345 (mp) REVERT: A 436 MET cc_start: 0.6960 (mmm) cc_final: 0.6507 (mmm) REVERT: A 499 GLU cc_start: 0.8392 (tm-30) cc_final: 0.8121 (tm-30) REVERT: A 508 ILE cc_start: 0.8652 (mt) cc_final: 0.8232 (tt) REVERT: A 519 ILE cc_start: 0.8085 (mt) cc_final: 0.7859 (tt) REVERT: A 626 ILE cc_start: 0.8493 (tt) cc_final: 0.8197 (tp) REVERT: A 640 GLU cc_start: 0.8372 (tt0) cc_final: 0.7904 (tm-30) REVERT: A 679 LEU cc_start: 0.8608 (OUTLIER) cc_final: 0.8397 (mm) REVERT: A 680 ARG cc_start: 0.7922 (ttp80) cc_final: 0.7564 (mtm110) REVERT: A 794 GLU cc_start: 0.7952 (mp0) cc_final: 0.7693 (mp0) REVERT: A 808 ASN cc_start: 0.8140 (m-40) cc_final: 0.7847 (m-40) REVERT: A 818 LYS cc_start: 0.8532 (tttt) cc_final: 0.8235 (mmmm) REVERT: A 927 MET cc_start: 0.8721 (mmm) cc_final: 0.8029 (mpp) REVERT: A 1028 SER cc_start: 0.8827 (m) cc_final: 0.8492 (m) REVERT: A 1036 GLU cc_start: 0.7976 (mm-30) cc_final: 0.7568 (mt-10) REVERT: A 1171 ASN cc_start: 0.7682 (OUTLIER) cc_final: 0.7465 (m110) REVERT: A 1173 ILE cc_start: 0.8734 (OUTLIER) cc_final: 0.8424 (mp) REVERT: A 1174 GLN cc_start: 0.8192 (tm-30) cc_final: 0.7625 (tm-30) REVERT: A 1179 ASP cc_start: 0.8213 (m-30) cc_final: 0.7341 (m-30) REVERT: A 1183 ASN cc_start: 0.8144 (m-40) cc_final: 0.7632 (m110) REVERT: A 1184 LYS cc_start: 0.8516 (OUTLIER) cc_final: 0.8044 (mtpp) REVERT: A 1242 GLU cc_start: 0.7926 (tp30) cc_final: 0.7513 (tm-30) REVERT: A 1250 GLN cc_start: 0.8201 (mp10) cc_final: 0.7525 (mp10) REVERT: A 1283 SER cc_start: 0.8866 (t) cc_final: 0.8326 (p) REVERT: A 1296 ASP cc_start: 0.8608 (m-30) cc_final: 0.8359 (m-30) REVERT: A 1344 GLN cc_start: 0.8314 (tt0) cc_final: 0.8093 (tp-100) REVERT: A 1357 GLU cc_start: 0.8175 (OUTLIER) cc_final: 0.7942 (mm-30) REVERT: A 1378 GLN cc_start: 0.8229 (mt0) cc_final: 0.7714 (mt0) REVERT: A 1438 SER cc_start: 0.8849 (m) cc_final: 0.8485 (p) REVERT: A 1529 GLU cc_start: 0.8369 (tm-30) cc_final: 0.8109 (tm-30) REVERT: A 1533 LEU cc_start: 0.9119 (mt) cc_final: 0.8758 (mp) REVERT: A 1636 GLU cc_start: 0.7275 (tp30) cc_final: 0.6627 (tp30) REVERT: A 1648 LYS cc_start: 0.8652 (mttt) cc_final: 0.8093 (mttm) REVERT: A 1687 LEU cc_start: 0.8934 (mt) cc_final: 0.8655 (mp) REVERT: A 1735 LEU cc_start: 0.8776 (mm) cc_final: 0.8546 (mt) REVERT: A 1764 LEU cc_start: 0.8562 (OUTLIER) cc_final: 0.8297 (mp) REVERT: A 1799 MET cc_start: 0.8160 (mmp) cc_final: 0.7820 (tpp) REVERT: A 1817 ILE cc_start: 0.8169 (mm) cc_final: 0.7968 (mp) REVERT: A 1826 LYS cc_start: 0.8740 (mttt) cc_final: 0.8474 (mttp) REVERT: A 1860 THR cc_start: 0.9107 (t) cc_final: 0.8126 (t) REVERT: A 1864 HIS cc_start: 0.8520 (m90) cc_final: 0.8064 (m90) REVERT: A 1906 LYS cc_start: 0.9000 (tttt) cc_final: 0.8668 (ttpp) REVERT: A 1959 MET cc_start: 0.8503 (OUTLIER) cc_final: 0.8252 (mtm) REVERT: A 1999 LYS cc_start: 0.8300 (mttp) cc_final: 0.8060 (mttp) REVERT: A 2060 THR cc_start: 0.8597 (m) cc_final: 0.8346 (t) REVERT: A 2062 GLU cc_start: 0.8484 (mt-10) cc_final: 0.8158 (mm-30) REVERT: A 2067 SER cc_start: 0.8684 (t) cc_final: 0.8407 (p) REVERT: A 2092 VAL cc_start: 0.8429 (t) cc_final: 0.8023 (p) REVERT: A 2095 SER cc_start: 0.8920 (t) cc_final: 0.8610 (p) REVERT: A 2096 LYS cc_start: 0.8425 (tttt) cc_final: 0.8191 (tttt) REVERT: A 2116 LYS cc_start: 0.8477 (tttt) cc_final: 0.7993 (tttt) REVERT: A 2124 LYS cc_start: 0.8665 (mttt) cc_final: 0.8374 (mttm) REVERT: A 2131 GLU cc_start: 0.7589 (mp0) cc_final: 0.7316 (mp0) REVERT: A 2203 ASN cc_start: 0.8245 (m-40) cc_final: 0.7616 (p0) REVERT: A 2223 GLN cc_start: 0.8464 (mt0) cc_final: 0.8094 (pt0) REVERT: A 2298 ASP cc_start: 0.8496 (t0) cc_final: 0.8170 (t0) REVERT: B 29 GLN cc_start: 0.6250 (mm-40) cc_final: 0.5223 (tm-30) REVERT: B 167 MET cc_start: 0.4805 (tpt) cc_final: 0.4329 (tpt) REVERT: B 212 ARG cc_start: 0.6164 (tpt-90) cc_final: 0.5899 (tpp-160) REVERT: B 222 LEU cc_start: 0.7037 (OUTLIER) cc_final: 0.6737 (pp) REVERT: B 241 LYS cc_start: 0.7772 (tppt) cc_final: 0.7571 (tptt) REVERT: C 311 MET cc_start: 0.8367 (ppp) cc_final: 0.8110 (pp-130) REVERT: C 314 PHE cc_start: 0.8468 (t80) cc_final: 0.8160 (t80) REVERT: C 354 ILE cc_start: 0.7840 (mt) cc_final: 0.7456 (mt) REVERT: C 357 LEU cc_start: 0.7976 (mt) cc_final: 0.7538 (mp) REVERT: C 384 ASP cc_start: 0.7861 (m-30) cc_final: 0.7357 (m-30) REVERT: C 440 LYS cc_start: 0.7680 (tttm) cc_final: 0.7164 (tttm) REVERT: C 451 GLU cc_start: 0.7438 (tm-30) cc_final: 0.7174 (tm-30) REVERT: C 642 GLU cc_start: 0.7368 (tm-30) cc_final: 0.6773 (tm-30) REVERT: C 695 LYS cc_start: 0.8448 (OUTLIER) cc_final: 0.8068 (mtmm) REVERT: C 713 ASP cc_start: 0.7747 (t0) cc_final: 0.7484 (t70) REVERT: C 716 GLN cc_start: 0.8158 (mm-40) cc_final: 0.7742 (tm-30) REVERT: C 794 ARG cc_start: 0.7051 (mtp-110) cc_final: 0.6649 (mtp-110) REVERT: C 821 PHE cc_start: 0.8185 (m-80) cc_final: 0.7804 (m-10) REVERT: C 839 LYS cc_start: 0.7920 (mtpp) cc_final: 0.7372 (ptpp) REVERT: C 848 MET cc_start: 0.6511 (mtp) cc_final: 0.6181 (mtp) REVERT: C 903 MET cc_start: 0.7433 (mtt) cc_final: 0.7201 (mtp) REVERT: C 951 LYS cc_start: 0.7968 (mttp) cc_final: 0.7738 (mmmm) REVERT: C 958 LYS cc_start: 0.7842 (mtmp) cc_final: 0.7621 (mtmm) REVERT: C 982 MET cc_start: 0.7818 (mmm) cc_final: 0.7513 (mmm) REVERT: C 1002 GLN cc_start: 0.8071 (tt0) cc_final: 0.7819 (tt0) REVERT: C 1069 GLU cc_start: 0.7937 (tt0) cc_final: 0.7518 (tt0) REVERT: C 1079 LYS cc_start: 0.8734 (tttt) cc_final: 0.8472 (tttp) REVERT: C 1080 LYS cc_start: 0.9019 (OUTLIER) cc_final: 0.8788 (ttpp) REVERT: C 1083 SER cc_start: 0.8687 (t) cc_final: 0.8272 (p) REVERT: C 1137 MET cc_start: 0.7751 (mtm) cc_final: 0.7513 (mtp) REVERT: C 1261 LYS cc_start: 0.7607 (OUTLIER) cc_final: 0.7072 (mptp) REVERT: C 1394 LYS cc_start: 0.8106 (OUTLIER) cc_final: 0.7818 (mtmm) REVERT: C 1409 ARG cc_start: 0.8368 (mtt-85) cc_final: 0.8102 (mpp80) REVERT: D 23 ARG cc_start: 0.8308 (ttm110) cc_final: 0.6210 (ttp-170) REVERT: D 69 LEU cc_start: 0.8951 (tt) cc_final: 0.8729 (tm) REVERT: D 85 LYS cc_start: 0.8920 (mmtt) cc_final: 0.8644 (mmmm) REVERT: D 120 ASP cc_start: 0.7832 (t0) cc_final: 0.7574 (t0) REVERT: D 125 LEU cc_start: 0.8065 (OUTLIER) cc_final: 0.7830 (tt) REVERT: E 292 MET cc_start: 0.5773 (ptt) cc_final: 0.5500 (pp-130) REVERT: E 303 LEU cc_start: 0.8090 (OUTLIER) cc_final: 0.7839 (pp) REVERT: E 314 GLU cc_start: 0.3448 (tm-30) cc_final: 0.2650 (tp30) REVERT: E 466 MET cc_start: 0.7436 (OUTLIER) cc_final: 0.7139 (ptp) REVERT: E 490 SER cc_start: 0.7732 (OUTLIER) cc_final: 0.7485 (p) REVERT: E 518 ILE cc_start: 0.8348 (tp) cc_final: 0.7890 (mp) REVERT: G 26 ARG cc_start: 0.7995 (mtm110) cc_final: 0.7777 (mtm110) REVERT: G 52 MET cc_start: 0.6050 (ttp) cc_final: 0.5739 (ttp) outliers start: 115 outliers final: 55 residues processed: 825 average time/residue: 0.7281 time to fit residues: 711.9697 Evaluate side-chains 825 residues out of total 3758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 754 time to evaluate : 1.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 HIS Chi-restraints excluded: chain A residue 435 TYR Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 503 ILE Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain A residue 576 GLN Chi-restraints excluded: chain A residue 618 CYS Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 647 MET Chi-restraints excluded: chain A residue 679 LEU Chi-restraints excluded: chain A residue 753 VAL Chi-restraints excluded: chain A residue 955 LEU Chi-restraints excluded: chain A residue 996 GLN Chi-restraints excluded: chain A residue 1008 VAL Chi-restraints excluded: chain A residue 1024 SER Chi-restraints excluded: chain A residue 1171 ASN Chi-restraints excluded: chain A residue 1173 ILE Chi-restraints excluded: chain A residue 1184 LYS Chi-restraints excluded: chain A residue 1220 VAL Chi-restraints excluded: chain A residue 1249 ILE Chi-restraints excluded: chain A residue 1255 SER Chi-restraints excluded: chain A residue 1269 VAL Chi-restraints excluded: chain A residue 1276 GLU Chi-restraints excluded: chain A residue 1305 LEU Chi-restraints excluded: chain A residue 1357 GLU Chi-restraints excluded: chain A residue 1382 THR Chi-restraints excluded: chain A residue 1764 LEU Chi-restraints excluded: chain A residue 1871 GLN Chi-restraints excluded: chain A residue 1892 ILE Chi-restraints excluded: chain A residue 1923 GLU Chi-restraints excluded: chain A residue 1944 VAL Chi-restraints excluded: chain A residue 1959 MET Chi-restraints excluded: chain A residue 2204 ILE Chi-restraints excluded: chain A residue 2268 MET Chi-restraints excluded: chain A residue 2331 SER Chi-restraints excluded: chain B residue 77 ASN Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 113 TYR Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 244 THR Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain C residue 463 MET Chi-restraints excluded: chain C residue 695 LYS Chi-restraints excluded: chain C residue 720 SER Chi-restraints excluded: chain C residue 722 SER Chi-restraints excluded: chain C residue 832 LYS Chi-restraints excluded: chain C residue 872 PHE Chi-restraints excluded: chain C residue 924 LEU Chi-restraints excluded: chain C residue 980 PHE Chi-restraints excluded: chain C residue 1053 ASN Chi-restraints excluded: chain C residue 1080 LYS Chi-restraints excluded: chain C residue 1117 GLN Chi-restraints excluded: chain C residue 1261 LYS Chi-restraints excluded: chain C residue 1358 HIS Chi-restraints excluded: chain C residue 1394 LYS Chi-restraints excluded: chain C residue 1415 ILE Chi-restraints excluded: chain D residue 2 LEU Chi-restraints excluded: chain D residue 71 LYS Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain D residue 155 ILE Chi-restraints excluded: chain E residue 291 SER Chi-restraints excluded: chain E residue 303 LEU Chi-restraints excluded: chain E residue 458 TYR Chi-restraints excluded: chain E residue 466 MET Chi-restraints excluded: chain E residue 467 CYS Chi-restraints excluded: chain E residue 490 SER Chi-restraints excluded: chain G residue 632 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 283 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 228 optimal weight: 9.9990 chunk 255 optimal weight: 0.9990 chunk 276 optimal weight: 1.9990 chunk 212 optimal weight: 0.0770 chunk 300 optimal weight: 8.9990 chunk 286 optimal weight: 0.3980 chunk 32 optimal weight: 1.9990 chunk 152 optimal weight: 0.7980 chunk 251 optimal weight: 6.9990 overall best weight: 0.8542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 479 HIS A1380 HIS ** A1977 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2462 ASN B 148 ASN C 495 GLN C 511 ASN C 557 ASN C 692 GLN ** C 843 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 988 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1053 ASN C1133 ASN C1171 ASN ** D 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 350 ASN G 23 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.155514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.122339 restraints weight = 67040.610| |-----------------------------------------------------------------------------| r_work (start): 0.3688 rms_B_bonded: 2.68 r_work: 0.3547 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.4179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 34200 Z= 0.165 Angle : 0.640 19.310 46258 Z= 0.317 Chirality : 0.042 0.392 5293 Planarity : 0.004 0.059 5844 Dihedral : 4.421 81.141 4520 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.44 % Favored : 97.54 % Rotamer: Outliers : 3.25 % Allowed : 20.38 % Favored : 76.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.60 (0.13), residues: 4102 helix: 1.77 (0.10), residues: 2784 sheet: 0.30 (0.39), residues: 169 loop : -0.53 (0.19), residues: 1149 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C1032 TYR 0.036 0.002 TYR B 113 PHE 0.037 0.001 PHE E 349 TRP 0.028 0.001 TRP A1229 HIS 0.014 0.001 HIS D 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.16 (34200) covalent geometry : angle 0.63961 / 0.32 (46258) hydrogen bonds : bond 0.03651 / 2.51 ( 2045) hydrogen bonds : angle 4.01253 / 2.87 ( 6033) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8204 Ramachandran restraints generated. 4102 Oldfield, 0 Emsley, 4102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8204 Ramachandran restraints generated. 4102 Oldfield, 0 Emsley, 4102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 892 residues out of total 3758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 770 time to evaluate : 1.343 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 351 ILE cc_start: 0.7762 (mm) cc_final: 0.7526 (mp) REVERT: A 380 PHE cc_start: 0.7127 (t80) cc_final: 0.6840 (t80) REVERT: A 432 ILE cc_start: 0.8419 (tp) cc_final: 0.7462 (mp) REVERT: A 436 MET cc_start: 0.6948 (mmm) cc_final: 0.6506 (mmm) REVERT: A 497 MET cc_start: 0.7128 (ttp) cc_final: 0.6813 (ttp) REVERT: A 499 GLU cc_start: 0.8416 (tm-30) cc_final: 0.8170 (tm-30) REVERT: A 508 ILE cc_start: 0.8795 (mt) cc_final: 0.8387 (tt) REVERT: A 530 GLU cc_start: 0.7603 (OUTLIER) cc_final: 0.7383 (tm-30) REVERT: A 559 LYS cc_start: 0.7716 (tmmt) cc_final: 0.6993 (mmpt) REVERT: A 626 ILE cc_start: 0.8567 (tt) cc_final: 0.8275 (tp) REVERT: A 640 GLU cc_start: 0.8495 (tt0) cc_final: 0.8000 (tm-30) REVERT: A 679 LEU cc_start: 0.8568 (OUTLIER) cc_final: 0.8337 (mm) REVERT: A 680 ARG cc_start: 0.8028 (ttp80) cc_final: 0.7658 (mtp-110) REVERT: A 794 GLU cc_start: 0.8008 (mp0) cc_final: 0.7800 (mp0) REVERT: A 808 ASN cc_start: 0.8181 (m-40) cc_final: 0.7886 (m-40) REVERT: A 818 LYS cc_start: 0.8600 (tttt) cc_final: 0.8306 (mmmm) REVERT: A 927 MET cc_start: 0.8741 (mmm) cc_final: 0.8015 (mpp) REVERT: A 951 GLN cc_start: 0.8360 (mm110) cc_final: 0.8051 (mm110) REVERT: A 1028 SER cc_start: 0.8840 (m) cc_final: 0.8513 (m) REVERT: A 1036 GLU cc_start: 0.7957 (mm-30) cc_final: 0.7566 (mt-10) REVERT: A 1174 GLN cc_start: 0.8309 (tm-30) cc_final: 0.7778 (tm-30) REVERT: A 1179 ASP cc_start: 0.8281 (m-30) cc_final: 0.7446 (m-30) REVERT: A 1183 ASN cc_start: 0.8190 (m-40) cc_final: 0.7679 (m110) REVERT: A 1184 LYS cc_start: 0.8515 (OUTLIER) cc_final: 0.8078 (mtpp) REVERT: A 1242 GLU cc_start: 0.7920 (tp30) cc_final: 0.7663 (tm-30) REVERT: A 1283 SER cc_start: 0.8892 (t) cc_final: 0.8365 (p) REVERT: A 1296 ASP cc_start: 0.8594 (m-30) cc_final: 0.8352 (m-30) REVERT: A 1298 ILE cc_start: 0.8815 (mm) cc_final: 0.8611 (mp) REVERT: A 1344 GLN cc_start: 0.8336 (tt0) cc_final: 0.8100 (tp-100) REVERT: A 1357 GLU cc_start: 0.8175 (OUTLIER) cc_final: 0.7940 (mm-30) REVERT: A 1378 GLN cc_start: 0.8296 (mt0) cc_final: 0.7793 (mt0) REVERT: A 1438 SER cc_start: 0.8903 (m) cc_final: 0.8521 (p) REVERT: A 1460 LYS cc_start: 0.8670 (mptt) cc_final: 0.8450 (mmtm) REVERT: A 1529 GLU cc_start: 0.8393 (tm-30) cc_final: 0.8167 (tm-30) REVERT: A 1533 LEU cc_start: 0.9115 (mt) cc_final: 0.8775 (mt) REVERT: A 1587 ASN cc_start: 0.8522 (t0) cc_final: 0.8265 (t0) REVERT: A 1636 GLU cc_start: 0.7301 (tp30) cc_final: 0.6638 (tp30) REVERT: A 1648 LYS cc_start: 0.8652 (mttt) cc_final: 0.8082 (mttm) REVERT: A 1687 LEU cc_start: 0.8940 (mt) cc_final: 0.8630 (mp) REVERT: A 1692 MET cc_start: 0.7357 (mmt) cc_final: 0.7090 (mmt) REVERT: A 1735 LEU cc_start: 0.8778 (mm) cc_final: 0.8546 (mt) REVERT: A 1764 LEU cc_start: 0.8554 (OUTLIER) cc_final: 0.8293 (mp) REVERT: A 1817 ILE cc_start: 0.8187 (mm) cc_final: 0.7978 (mp) REVERT: A 1826 LYS cc_start: 0.8772 (mttt) cc_final: 0.8499 (mttp) REVERT: A 1860 THR cc_start: 0.9081 (t) cc_final: 0.8168 (t) REVERT: A 1864 HIS cc_start: 0.8618 (m90) cc_final: 0.8054 (m90) REVERT: A 1906 LYS cc_start: 0.8970 (tttt) cc_final: 0.8635 (ttpp) REVERT: A 1959 MET cc_start: 0.8522 (OUTLIER) cc_final: 0.8253 (mtm) REVERT: A 1981 GLU cc_start: 0.7725 (tm-30) cc_final: 0.7338 (tm-30) REVERT: A 1999 LYS cc_start: 0.8290 (mttp) cc_final: 0.8057 (mttp) REVERT: A 2000 ARG cc_start: 0.8260 (tpp80) cc_final: 0.7722 (tpp80) REVERT: A 2029 LYS cc_start: 0.8550 (mmmm) cc_final: 0.8318 (mtpp) REVERT: A 2042 ASP cc_start: 0.8459 (t70) cc_final: 0.8098 (t0) REVERT: A 2060 THR cc_start: 0.8708 (m) cc_final: 0.8450 (t) REVERT: A 2062 GLU cc_start: 0.8449 (mt-10) cc_final: 0.8137 (mm-30) REVERT: A 2067 SER cc_start: 0.8699 (t) cc_final: 0.8440 (p) REVERT: A 2092 VAL cc_start: 0.8429 (t) cc_final: 0.8025 (p) REVERT: A 2095 SER cc_start: 0.8954 (t) cc_final: 0.8647 (p) REVERT: A 2096 LYS cc_start: 0.8455 (tttt) cc_final: 0.8227 (tttt) REVERT: A 2116 LYS cc_start: 0.8455 (tttt) cc_final: 0.7965 (tttt) REVERT: A 2124 LYS cc_start: 0.8663 (mttt) cc_final: 0.8368 (mttm) REVERT: A 2131 GLU cc_start: 0.7591 (mp0) cc_final: 0.7313 (mp0) REVERT: A 2203 ASN cc_start: 0.8206 (m-40) cc_final: 0.7704 (p0) REVERT: A 2223 GLN cc_start: 0.8482 (mt0) cc_final: 0.8179 (pt0) REVERT: A 2298 ASP cc_start: 0.8492 (t0) cc_final: 0.8155 (t0) REVERT: B 29 GLN cc_start: 0.6475 (mm-40) cc_final: 0.5452 (tm-30) REVERT: B 111 ARG cc_start: 0.4808 (OUTLIER) cc_final: 0.4518 (ppp80) REVERT: B 167 MET cc_start: 0.4791 (tpt) cc_final: 0.4464 (tpt) REVERT: B 187 GLU cc_start: 0.5841 (pp20) cc_final: 0.5624 (pp20) REVERT: B 212 ARG cc_start: 0.6128 (tpt-90) cc_final: 0.5876 (tpp-160) REVERT: B 222 LEU cc_start: 0.6917 (tt) cc_final: 0.6574 (pp) REVERT: C 311 MET cc_start: 0.8399 (ppp) cc_final: 0.8099 (pp-130) REVERT: C 314 PHE cc_start: 0.8654 (OUTLIER) cc_final: 0.8393 (t80) REVERT: C 354 ILE cc_start: 0.7839 (mt) cc_final: 0.7460 (mt) REVERT: C 357 LEU cc_start: 0.8119 (mt) cc_final: 0.7743 (mp) REVERT: C 384 ASP cc_start: 0.7921 (m-30) cc_final: 0.7415 (m-30) REVERT: C 437 CYS cc_start: 0.8571 (m) cc_final: 0.8229 (m) REVERT: C 440 LYS cc_start: 0.7721 (tttm) cc_final: 0.6873 (tttm) REVERT: C 443 ASP cc_start: 0.7512 (m-30) cc_final: 0.6703 (m-30) REVERT: C 451 GLU cc_start: 0.7550 (tm-30) cc_final: 0.7168 (tm-30) REVERT: C 470 MET cc_start: 0.8690 (OUTLIER) cc_final: 0.8302 (tpp) REVERT: C 642 GLU cc_start: 0.7394 (tm-30) cc_final: 0.6757 (tm-30) REVERT: C 695 LYS cc_start: 0.8489 (OUTLIER) cc_final: 0.8116 (mtmm) REVERT: C 713 ASP cc_start: 0.7846 (t0) cc_final: 0.7569 (t70) REVERT: C 716 GLN cc_start: 0.8207 (mm-40) cc_final: 0.7677 (mm-40) REVERT: C 719 LYS cc_start: 0.8229 (tmmt) cc_final: 0.7693 (ttpt) REVERT: C 721 PHE cc_start: 0.7971 (t80) cc_final: 0.7737 (t80) REVERT: C 794 ARG cc_start: 0.7315 (mtp-110) cc_final: 0.6918 (mtp-110) REVERT: C 821 PHE cc_start: 0.8476 (m-80) cc_final: 0.7994 (m-10) REVERT: C 839 LYS cc_start: 0.7998 (mtpp) cc_final: 0.7341 (ptpp) REVERT: C 848 MET cc_start: 0.6744 (mtp) cc_final: 0.6409 (mtp) REVERT: C 894 TRP cc_start: 0.6166 (m100) cc_final: 0.5883 (t60) REVERT: C 902 LYS cc_start: 0.8162 (ptpt) cc_final: 0.7776 (pttp) REVERT: C 903 MET cc_start: 0.7556 (mtt) cc_final: 0.7288 (mtp) REVERT: C 951 LYS cc_start: 0.7976 (mttp) cc_final: 0.7740 (mmmm) REVERT: C 982 MET cc_start: 0.7848 (mmm) cc_final: 0.7573 (mmm) REVERT: C 1002 GLN cc_start: 0.8100 (tt0) cc_final: 0.7830 (tt0) REVERT: C 1038 GLU cc_start: 0.7395 (OUTLIER) cc_final: 0.6643 (tm-30) REVERT: C 1069 GLU cc_start: 0.7997 (tt0) cc_final: 0.7555 (tt0) REVERT: C 1076 GLU cc_start: 0.7931 (tm-30) cc_final: 0.7688 (tm-30) REVERT: C 1079 LYS cc_start: 0.8658 (tttt) cc_final: 0.8385 (tttp) REVERT: C 1080 LYS cc_start: 0.8966 (OUTLIER) cc_final: 0.8746 (ttpp) REVERT: C 1083 SER cc_start: 0.8726 (t) cc_final: 0.8273 (p) REVERT: C 1130 LYS cc_start: 0.8731 (OUTLIER) cc_final: 0.8434 (ttpm) REVERT: C 1137 MET cc_start: 0.7855 (mtm) cc_final: 0.7623 (mtp) REVERT: C 1163 GLU cc_start: 0.8020 (mm-30) cc_final: 0.7770 (mm-30) REVERT: C 1261 LYS cc_start: 0.7603 (OUTLIER) cc_final: 0.7035 (mptp) REVERT: C 1394 LYS cc_start: 0.8114 (OUTLIER) cc_final: 0.7817 (mtmm) REVERT: C 1409 ARG cc_start: 0.8343 (mtt-85) cc_final: 0.8046 (mpp80) REVERT: D 23 ARG cc_start: 0.8358 (ttm110) cc_final: 0.6177 (ttp-170) REVERT: D 69 LEU cc_start: 0.8925 (tt) cc_final: 0.8666 (tm) REVERT: D 85 LYS cc_start: 0.8953 (mmtt) cc_final: 0.8631 (mmmm) REVERT: D 120 ASP cc_start: 0.7885 (t0) cc_final: 0.7609 (t0) REVERT: E 292 MET cc_start: 0.5776 (ptt) cc_final: 0.5271 (pp-130) REVERT: E 314 GLU cc_start: 0.3326 (tm-30) cc_final: 0.2554 (tp30) REVERT: E 334 PHE cc_start: 0.7126 (m-80) cc_final: 0.6685 (m-80) REVERT: E 518 ILE cc_start: 0.8358 (tp) cc_final: 0.7916 (mp) REVERT: E 543 ILE cc_start: 0.7506 (mm) cc_final: 0.7103 (tp) REVERT: G 52 MET cc_start: 0.6053 (ttp) cc_final: 0.5736 (ttp) REVERT: G 643 MET cc_start: 0.7478 (mtp) cc_final: 0.7227 (mtt) outliers start: 122 outliers final: 63 residues processed: 824 average time/residue: 0.7322 time to fit residues: 713.9542 Evaluate side-chains 830 residues out of total 3758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 752 time to evaluate : 1.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 HIS Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 435 TYR Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain A residue 530 GLU Chi-restraints excluded: chain A residue 618 CYS Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 647 MET Chi-restraints excluded: chain A residue 677 ASP Chi-restraints excluded: chain A residue 679 LEU Chi-restraints excluded: chain A residue 753 VAL Chi-restraints excluded: chain A residue 955 LEU Chi-restraints excluded: chain A residue 1008 VAL Chi-restraints excluded: chain A residue 1024 SER Chi-restraints excluded: chain A residue 1073 PHE Chi-restraints excluded: chain A residue 1171 ASN Chi-restraints excluded: chain A residue 1177 VAL Chi-restraints excluded: chain A residue 1184 LYS Chi-restraints excluded: chain A residue 1220 VAL Chi-restraints excluded: chain A residue 1249 ILE Chi-restraints excluded: chain A residue 1255 SER Chi-restraints excluded: chain A residue 1269 VAL Chi-restraints excluded: chain A residue 1276 GLU Chi-restraints excluded: chain A residue 1305 LEU Chi-restraints excluded: chain A residue 1357 GLU Chi-restraints excluded: chain A residue 1382 THR Chi-restraints excluded: chain A residue 1764 LEU Chi-restraints excluded: chain A residue 1871 GLN Chi-restraints excluded: chain A residue 1892 ILE Chi-restraints excluded: chain A residue 1923 GLU Chi-restraints excluded: chain A residue 1959 MET Chi-restraints excluded: chain A residue 2204 ILE Chi-restraints excluded: chain A residue 2331 SER Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 77 ASN Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 111 ARG Chi-restraints excluded: chain B residue 113 TYR Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 173 MET Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain C residue 314 PHE Chi-restraints excluded: chain C residue 463 MET Chi-restraints excluded: chain C residue 470 MET Chi-restraints excluded: chain C residue 695 LYS Chi-restraints excluded: chain C residue 832 LYS Chi-restraints excluded: chain C residue 872 PHE Chi-restraints excluded: chain C residue 924 LEU Chi-restraints excluded: chain C residue 980 PHE Chi-restraints excluded: chain C residue 1038 GLU Chi-restraints excluded: chain C residue 1053 ASN Chi-restraints excluded: chain C residue 1080 LYS Chi-restraints excluded: chain C residue 1117 GLN Chi-restraints excluded: chain C residue 1130 LYS Chi-restraints excluded: chain C residue 1261 LYS Chi-restraints excluded: chain C residue 1271 LEU Chi-restraints excluded: chain C residue 1358 HIS Chi-restraints excluded: chain C residue 1394 LYS Chi-restraints excluded: chain C residue 1415 ILE Chi-restraints excluded: chain D residue 2 LEU Chi-restraints excluded: chain D residue 7 VAL Chi-restraints excluded: chain D residue 19 LEU Chi-restraints excluded: chain D residue 37 SER Chi-restraints excluded: chain D residue 71 LYS Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain D residue 155 ILE Chi-restraints excluded: chain E residue 291 SER Chi-restraints excluded: chain E residue 324 ASN Chi-restraints excluded: chain E residue 458 TYR Chi-restraints excluded: chain E residue 467 CYS Chi-restraints excluded: chain G residue 32 ILE Chi-restraints excluded: chain G residue 632 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 294 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 183 optimal weight: 2.9990 chunk 21 optimal weight: 5.9990 chunk 33 optimal weight: 4.9990 chunk 332 optimal weight: 0.7980 chunk 164 optimal weight: 6.9990 chunk 76 optimal weight: 0.9980 chunk 314 optimal weight: 3.9990 chunk 123 optimal weight: 0.0970 chunk 157 optimal weight: 0.6980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 479 HIS A1171 ASN A1380 HIS A2462 ASN B 148 ASN C 495 GLN C 511 ASN C 557 ASN C 692 GLN C 703 ASN ** C 843 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 988 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1053 ASN C1133 ASN ** D 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 23 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.155269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.122267 restraints weight = 66670.425| |-----------------------------------------------------------------------------| r_work (start): 0.3683 rms_B_bonded: 2.66 r_work: 0.3536 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.4364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 34200 Z= 0.174 Angle : 0.659 16.578 46258 Z= 0.329 Chirality : 0.043 0.383 5293 Planarity : 0.004 0.076 5844 Dihedral : 4.450 82.512 4520 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.58 % Favored : 97.39 % Rotamer: Outliers : 3.19 % Allowed : 21.13 % Favored : 75.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.54 (0.13), residues: 4102 helix: 1.72 (0.10), residues: 2783 sheet: 0.29 (0.40), residues: 163 loop : -0.53 (0.19), residues: 1156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 946 TYR 0.031 0.001 TYR B 113 PHE 0.044 0.002 PHE E 416 TRP 0.032 0.001 TRP A1229 HIS 0.011 0.001 HIS C 952 Details of bonding type rmsd/Z covalent geometry : bond 0.00422 / 0.17 (34200) covalent geometry : angle 0.65869 / 0.33 (46258) hydrogen bonds : bond 0.03715 / 2.55 ( 2045) hydrogen bonds : angle 4.06657 / 2.92 ( 6033) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8204 Ramachandran restraints generated. 4102 Oldfield, 0 Emsley, 4102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8204 Ramachandran restraints generated. 4102 Oldfield, 0 Emsley, 4102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 892 residues out of total 3758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 772 time to evaluate : 1.335 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 351 ILE cc_start: 0.7766 (mm) cc_final: 0.7528 (mp) REVERT: A 361 TYR cc_start: 0.4478 (t80) cc_final: 0.4263 (t80) REVERT: A 380 PHE cc_start: 0.7201 (t80) cc_final: 0.6882 (t80) REVERT: A 406 MET cc_start: 0.5816 (ptm) cc_final: 0.5515 (pmm) REVERT: A 432 ILE cc_start: 0.8410 (tp) cc_final: 0.7513 (mp) REVERT: A 436 MET cc_start: 0.7017 (mmm) cc_final: 0.6644 (mmm) REVERT: A 499 GLU cc_start: 0.8377 (tm-30) cc_final: 0.8116 (tm-30) REVERT: A 508 ILE cc_start: 0.8817 (mt) cc_final: 0.8413 (tt) REVERT: A 559 LYS cc_start: 0.7820 (tmmt) cc_final: 0.7126 (mmpt) REVERT: A 580 MET cc_start: 0.7509 (mmm) cc_final: 0.7223 (mmm) REVERT: A 587 GLN cc_start: 0.8146 (tm-30) cc_final: 0.7909 (tp-100) REVERT: A 626 ILE cc_start: 0.8609 (tt) cc_final: 0.8313 (tp) REVERT: A 640 GLU cc_start: 0.8557 (tt0) cc_final: 0.8050 (tm-30) REVERT: A 679 LEU cc_start: 0.8572 (OUTLIER) cc_final: 0.8350 (mm) REVERT: A 794 GLU cc_start: 0.8027 (mp0) cc_final: 0.7787 (mp0) REVERT: A 808 ASN cc_start: 0.8199 (m-40) cc_final: 0.7899 (m-40) REVERT: A 818 LYS cc_start: 0.8615 (tttt) cc_final: 0.8345 (mmmm) REVERT: A 855 LYS cc_start: 0.7282 (mtmm) cc_final: 0.6834 (mttt) REVERT: A 951 GLN cc_start: 0.8381 (mm110) cc_final: 0.8058 (mm110) REVERT: A 1028 SER cc_start: 0.8848 (m) cc_final: 0.8505 (m) REVERT: A 1036 GLU cc_start: 0.7997 (mm-30) cc_final: 0.7602 (mt-10) REVERT: A 1174 GLN cc_start: 0.8297 (tm-30) cc_final: 0.7783 (tm-30) REVERT: A 1179 ASP cc_start: 0.8291 (m-30) cc_final: 0.7439 (m-30) REVERT: A 1183 ASN cc_start: 0.8189 (m-40) cc_final: 0.7661 (m110) REVERT: A 1184 LYS cc_start: 0.8447 (OUTLIER) cc_final: 0.8010 (mtpp) REVERT: A 1234 GLN cc_start: 0.7392 (OUTLIER) cc_final: 0.7151 (mp10) REVERT: A 1242 GLU cc_start: 0.7918 (tp30) cc_final: 0.7578 (tm-30) REVERT: A 1250 GLN cc_start: 0.8239 (OUTLIER) cc_final: 0.7493 (mp10) REVERT: A 1254 GLU cc_start: 0.7826 (mp0) cc_final: 0.7553 (mp0) REVERT: A 1283 SER cc_start: 0.8917 (t) cc_final: 0.8374 (p) REVERT: A 1296 ASP cc_start: 0.8640 (m-30) cc_final: 0.8377 (m-30) REVERT: A 1344 GLN cc_start: 0.8342 (tt0) cc_final: 0.8097 (tp-100) REVERT: A 1357 GLU cc_start: 0.8177 (OUTLIER) cc_final: 0.7947 (mm-30) REVERT: A 1367 SER cc_start: 0.8364 (p) cc_final: 0.8082 (t) REVERT: A 1378 GLN cc_start: 0.8309 (mt0) cc_final: 0.7801 (mt0) REVERT: A 1438 SER cc_start: 0.8946 (m) cc_final: 0.8511 (p) REVERT: A 1562 LYS cc_start: 0.9243 (OUTLIER) cc_final: 0.8892 (mtmm) REVERT: A 1587 ASN cc_start: 0.8535 (t0) cc_final: 0.8281 (t0) REVERT: A 1636 GLU cc_start: 0.7365 (tp30) cc_final: 0.6676 (tp30) REVERT: A 1648 LYS cc_start: 0.8652 (mttt) cc_final: 0.8027 (mttm) REVERT: A 1661 LEU cc_start: 0.8718 (OUTLIER) cc_final: 0.8511 (tp) REVERT: A 1687 LEU cc_start: 0.8937 (mt) cc_final: 0.8609 (mp) REVERT: A 1735 LEU cc_start: 0.8761 (mm) cc_final: 0.8543 (mt) REVERT: A 1764 LEU cc_start: 0.8552 (OUTLIER) cc_final: 0.8295 (mp) REVERT: A 1799 MET cc_start: 0.8158 (mmp) cc_final: 0.7791 (tpp) REVERT: A 1817 ILE cc_start: 0.8187 (mm) cc_final: 0.7969 (mp) REVERT: A 1826 LYS cc_start: 0.8790 (mttt) cc_final: 0.8517 (mttp) REVERT: A 1860 THR cc_start: 0.9116 (t) cc_final: 0.8248 (t) REVERT: A 1864 HIS cc_start: 0.8597 (m90) cc_final: 0.8065 (m90) REVERT: A 1906 LYS cc_start: 0.8994 (tttt) cc_final: 0.8651 (ttpp) REVERT: A 1959 MET cc_start: 0.8520 (OUTLIER) cc_final: 0.8253 (mtm) REVERT: A 1981 GLU cc_start: 0.7738 (tm-30) cc_final: 0.7288 (pp20) REVERT: A 1999 LYS cc_start: 0.8278 (mttp) cc_final: 0.8044 (mttp) REVERT: A 2000 ARG cc_start: 0.8335 (tpp80) cc_final: 0.7792 (tpp80) REVERT: A 2029 LYS cc_start: 0.8580 (mmmm) cc_final: 0.8343 (mtpp) REVERT: A 2060 THR cc_start: 0.8781 (m) cc_final: 0.8521 (t) REVERT: A 2062 GLU cc_start: 0.8458 (mt-10) cc_final: 0.8150 (mm-30) REVERT: A 2067 SER cc_start: 0.8710 (t) cc_final: 0.8445 (p) REVERT: A 2092 VAL cc_start: 0.8435 (t) cc_final: 0.8028 (p) REVERT: A 2095 SER cc_start: 0.8953 (t) cc_final: 0.8640 (p) REVERT: A 2096 LYS cc_start: 0.8454 (tttt) cc_final: 0.8236 (tttt) REVERT: A 2116 LYS cc_start: 0.8426 (tttt) cc_final: 0.7944 (tttt) REVERT: A 2124 LYS cc_start: 0.8685 (mttt) cc_final: 0.8398 (mttm) REVERT: A 2131 GLU cc_start: 0.7599 (mp0) cc_final: 0.7367 (mp0) REVERT: A 2203 ASN cc_start: 0.8254 (m-40) cc_final: 0.7766 (p0) REVERT: A 2223 GLN cc_start: 0.8428 (mt0) cc_final: 0.8106 (pt0) REVERT: A 2298 ASP cc_start: 0.8518 (t0) cc_final: 0.8177 (t0) REVERT: B 29 GLN cc_start: 0.6605 (mm-40) cc_final: 0.5618 (tm-30) REVERT: B 111 ARG cc_start: 0.4997 (OUTLIER) cc_final: 0.4708 (ppp80) REVERT: B 212 ARG cc_start: 0.6172 (tpt-90) cc_final: 0.5869 (tpp-160) REVERT: B 222 LEU cc_start: 0.6869 (tt) cc_final: 0.6534 (pp) REVERT: C 311 MET cc_start: 0.8368 (ppp) cc_final: 0.8112 (pp-130) REVERT: C 314 PHE cc_start: 0.8706 (OUTLIER) cc_final: 0.8278 (t80) REVERT: C 354 ILE cc_start: 0.7848 (mt) cc_final: 0.7469 (mt) REVERT: C 357 LEU cc_start: 0.8127 (mt) cc_final: 0.7740 (mp) REVERT: C 384 ASP cc_start: 0.7942 (m-30) cc_final: 0.7420 (m-30) REVERT: C 418 ARG cc_start: 0.8214 (tpp-160) cc_final: 0.7872 (tpt90) REVERT: C 437 CYS cc_start: 0.8570 (m) cc_final: 0.8233 (m) REVERT: C 440 LYS cc_start: 0.7752 (tttm) cc_final: 0.6953 (tttm) REVERT: C 443 ASP cc_start: 0.7557 (m-30) cc_final: 0.6907 (m-30) REVERT: C 451 GLU cc_start: 0.7540 (tm-30) cc_final: 0.7158 (tm-30) REVERT: C 470 MET cc_start: 0.8708 (OUTLIER) cc_final: 0.8306 (tpp) REVERT: C 642 GLU cc_start: 0.7425 (tm-30) cc_final: 0.6665 (tm-30) REVERT: C 695 LYS cc_start: 0.8501 (OUTLIER) cc_final: 0.8135 (mtmm) REVERT: C 713 ASP cc_start: 0.7870 (t0) cc_final: 0.7591 (t70) REVERT: C 716 GLN cc_start: 0.8203 (mm-40) cc_final: 0.7945 (mm-40) REVERT: C 719 LYS cc_start: 0.8256 (tmmt) cc_final: 0.7845 (ttpt) REVERT: C 721 PHE cc_start: 0.7985 (t80) cc_final: 0.7732 (t80) REVERT: C 794 ARG cc_start: 0.7347 (mtp-110) cc_final: 0.6957 (mtp-110) REVERT: C 821 PHE cc_start: 0.8524 (m-80) cc_final: 0.8035 (m-10) REVERT: C 835 MET cc_start: 0.7608 (tmt) cc_final: 0.7324 (tmm) REVERT: C 839 LYS cc_start: 0.7994 (mtpp) cc_final: 0.7344 (ptpp) REVERT: C 848 MET cc_start: 0.6832 (mtp) cc_final: 0.6450 (mtp) REVERT: C 894 TRP cc_start: 0.6273 (m100) cc_final: 0.5988 (t60) REVERT: C 902 LYS cc_start: 0.8127 (ptpt) cc_final: 0.7640 (pttm) REVERT: C 903 MET cc_start: 0.7634 (mtt) cc_final: 0.7407 (mtp) REVERT: C 982 MET cc_start: 0.7839 (mmm) cc_final: 0.7571 (mmm) REVERT: C 1002 GLN cc_start: 0.8101 (tt0) cc_final: 0.7835 (tt0) REVERT: C 1038 GLU cc_start: 0.7421 (OUTLIER) cc_final: 0.6677 (tm-30) REVERT: C 1069 GLU cc_start: 0.7969 (tt0) cc_final: 0.7522 (tt0) REVERT: C 1076 GLU cc_start: 0.7937 (tm-30) cc_final: 0.7699 (tm-30) REVERT: C 1079 LYS cc_start: 0.8671 (tttt) cc_final: 0.8290 (tttp) REVERT: C 1080 LYS cc_start: 0.8971 (OUTLIER) cc_final: 0.8751 (ttpp) REVERT: C 1083 SER cc_start: 0.8735 (t) cc_final: 0.8289 (p) REVERT: C 1130 LYS cc_start: 0.8749 (OUTLIER) cc_final: 0.8454 (ttpm) REVERT: C 1137 MET cc_start: 0.7888 (mtm) cc_final: 0.7662 (mtp) REVERT: C 1163 GLU cc_start: 0.8043 (mm-30) cc_final: 0.7795 (mm-30) REVERT: C 1261 LYS cc_start: 0.7509 (OUTLIER) cc_final: 0.6947 (mptp) REVERT: C 1394 LYS cc_start: 0.8099 (OUTLIER) cc_final: 0.7809 (mtmm) REVERT: C 1409 ARG cc_start: 0.8382 (mtt-85) cc_final: 0.8059 (mpp80) REVERT: D 20 ILE cc_start: 0.7460 (tt) cc_final: 0.7218 (pt) REVERT: D 23 ARG cc_start: 0.8352 (ttm110) cc_final: 0.6157 (ttp-170) REVERT: D 68 GLU cc_start: 0.8219 (tt0) cc_final: 0.7973 (tt0) REVERT: D 69 LEU cc_start: 0.8935 (tt) cc_final: 0.8670 (tm) REVERT: D 85 LYS cc_start: 0.8983 (mmtt) cc_final: 0.8672 (mmmm) REVERT: D 120 ASP cc_start: 0.7935 (t0) cc_final: 0.7645 (t0) REVERT: D 140 THR cc_start: 0.9079 (m) cc_final: 0.8651 (p) REVERT: E 292 MET cc_start: 0.5744 (ptt) cc_final: 0.5246 (pp-130) REVERT: E 314 GLU cc_start: 0.3411 (tm-30) cc_final: 0.2639 (tp30) REVERT: E 334 PHE cc_start: 0.7115 (m-80) cc_final: 0.6705 (m-80) REVERT: E 375 SER cc_start: 0.8291 (m) cc_final: 0.8039 (p) REVERT: E 543 ILE cc_start: 0.7579 (mm) cc_final: 0.7192 (tp) REVERT: G 52 MET cc_start: 0.6096 (ttp) cc_final: 0.5793 (ttp) REVERT: G 643 MET cc_start: 0.7509 (mtp) cc_final: 0.7240 (mtt) outliers start: 120 outliers final: 61 residues processed: 832 average time/residue: 0.7282 time to fit residues: 719.5367 Evaluate side-chains 833 residues out of total 3758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 754 time to evaluate : 1.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 HIS Chi-restraints excluded: chain A residue 435 TYR Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 521 ASN Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain A residue 552 SER Chi-restraints excluded: chain A residue 618 CYS Chi-restraints excluded: chain A residue 647 MET Chi-restraints excluded: chain A residue 677 ASP Chi-restraints excluded: chain A residue 679 LEU Chi-restraints excluded: chain A residue 753 VAL Chi-restraints excluded: chain A residue 955 LEU Chi-restraints excluded: chain A residue 996 GLN Chi-restraints excluded: chain A residue 1008 VAL Chi-restraints excluded: chain A residue 1024 SER Chi-restraints excluded: chain A residue 1177 VAL Chi-restraints excluded: chain A residue 1184 LYS Chi-restraints excluded: chain A residue 1220 VAL Chi-restraints excluded: chain A residue 1234 GLN Chi-restraints excluded: chain A residue 1249 ILE Chi-restraints excluded: chain A residue 1250 GLN Chi-restraints excluded: chain A residue 1255 SER Chi-restraints excluded: chain A residue 1265 SER Chi-restraints excluded: chain A residue 1269 VAL Chi-restraints excluded: chain A residue 1276 GLU Chi-restraints excluded: chain A residue 1305 LEU Chi-restraints excluded: chain A residue 1357 GLU Chi-restraints excluded: chain A residue 1382 THR Chi-restraints excluded: chain A residue 1562 LYS Chi-restraints excluded: chain A residue 1661 LEU Chi-restraints excluded: chain A residue 1764 LEU Chi-restraints excluded: chain A residue 1871 GLN Chi-restraints excluded: chain A residue 1892 ILE Chi-restraints excluded: chain A residue 1925 LEU Chi-restraints excluded: chain A residue 1959 MET Chi-restraints excluded: chain A residue 2098 GLU Chi-restraints excluded: chain A residue 2204 ILE Chi-restraints excluded: chain A residue 2331 SER Chi-restraints excluded: chain A residue 2437 ASP Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 77 ASN Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 111 ARG Chi-restraints excluded: chain B residue 113 TYR Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 244 THR Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain C residue 314 PHE Chi-restraints excluded: chain C residue 463 MET Chi-restraints excluded: chain C residue 470 MET Chi-restraints excluded: chain C residue 695 LYS Chi-restraints excluded: chain C residue 722 SER Chi-restraints excluded: chain C residue 832 LYS Chi-restraints excluded: chain C residue 872 PHE Chi-restraints excluded: chain C residue 924 LEU Chi-restraints excluded: chain C residue 980 PHE Chi-restraints excluded: chain C residue 1038 GLU Chi-restraints excluded: chain C residue 1053 ASN Chi-restraints excluded: chain C residue 1080 LYS Chi-restraints excluded: chain C residue 1117 GLN Chi-restraints excluded: chain C residue 1130 LYS Chi-restraints excluded: chain C residue 1261 LYS Chi-restraints excluded: chain C residue 1271 LEU Chi-restraints excluded: chain C residue 1358 HIS Chi-restraints excluded: chain C residue 1394 LYS Chi-restraints excluded: chain C residue 1415 ILE Chi-restraints excluded: chain D residue 2 LEU Chi-restraints excluded: chain D residue 7 VAL Chi-restraints excluded: chain D residue 37 SER Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain E residue 291 SER Chi-restraints excluded: chain E residue 324 ASN Chi-restraints excluded: chain E residue 467 CYS Chi-restraints excluded: chain G residue 32 ILE Chi-restraints excluded: chain G residue 632 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 361 optimal weight: 0.5980 chunk 96 optimal weight: 0.6980 chunk 21 optimal weight: 5.9990 chunk 402 optimal weight: 0.7980 chunk 192 optimal weight: 0.5980 chunk 19 optimal weight: 0.0030 chunk 261 optimal weight: 2.9990 chunk 230 optimal weight: 0.6980 chunk 293 optimal weight: 0.9990 chunk 406 optimal weight: 0.0050 chunk 294 optimal weight: 0.0870 overall best weight: 0.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 479 HIS A 496 HIS A 565 ASN A1171 ASN A1380 HIS ** A2141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2462 ASN B 148 ASN C 495 GLN C 511 ASN C 557 ASN C 666 ASN C 692 GLN ** C 843 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 988 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1053 ASN C1072 HIS C1133 ASN C1171 ASN ** D 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 123 GLN ** E 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 23 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.156365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.123522 restraints weight = 66728.339| |-----------------------------------------------------------------------------| r_work (start): 0.3705 rms_B_bonded: 2.70 r_work: 0.3560 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.4435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.089 34200 Z= 0.128 Angle : 0.664 18.157 46258 Z= 0.329 Chirality : 0.041 0.386 5293 Planarity : 0.004 0.082 5844 Dihedral : 4.364 81.163 4520 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.49 % Favored : 97.49 % Rotamer: Outliers : 2.53 % Allowed : 21.90 % Favored : 75.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.64 (0.13), residues: 4102 helix: 1.81 (0.10), residues: 2786 sheet: 0.25 (0.40), residues: 163 loop : -0.53 (0.19), residues: 1153 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C1032 TYR 0.031 0.001 TYR B 113 PHE 0.038 0.001 PHE E 349 TRP 0.038 0.001 TRP A1229 HIS 0.009 0.001 HIS A 479 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 (34200) covalent geometry : angle 0.66435 / 0.33 (46258) hydrogen bonds : bond 0.03417 / 2.34 ( 2045) hydrogen bonds : angle 3.98715 / 2.86 ( 6033) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8204 Ramachandran restraints generated. 4102 Oldfield, 0 Emsley, 4102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8204 Ramachandran restraints generated. 4102 Oldfield, 0 Emsley, 4102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 866 residues out of total 3758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 771 time to evaluate : 1.447 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 351 ILE cc_start: 0.7790 (mm) cc_final: 0.7555 (mp) REVERT: A 380 PHE cc_start: 0.7098 (t80) cc_final: 0.6786 (t80) REVERT: A 406 MET cc_start: 0.5791 (ptm) cc_final: 0.5346 (pmm) REVERT: A 432 ILE cc_start: 0.8330 (tp) cc_final: 0.7430 (mp) REVERT: A 436 MET cc_start: 0.6935 (mmm) cc_final: 0.6586 (mmm) REVERT: A 459 LYS cc_start: 0.8231 (tppp) cc_final: 0.7950 (tppt) REVERT: A 508 ILE cc_start: 0.8768 (mt) cc_final: 0.8371 (tt) REVERT: A 559 LYS cc_start: 0.7786 (tmmt) cc_final: 0.7094 (mmpt) REVERT: A 580 MET cc_start: 0.7455 (mmm) cc_final: 0.6989 (mmm) REVERT: A 587 GLN cc_start: 0.8084 (tm-30) cc_final: 0.7873 (tp-100) REVERT: A 626 ILE cc_start: 0.8464 (tt) cc_final: 0.8153 (tp) REVERT: A 640 GLU cc_start: 0.8468 (tt0) cc_final: 0.7994 (tm-30) REVERT: A 680 ARG cc_start: 0.8121 (ttp-110) cc_final: 0.7646 (mtp-110) REVERT: A 794 GLU cc_start: 0.8012 (mp0) cc_final: 0.7785 (mp0) REVERT: A 808 ASN cc_start: 0.8193 (m-40) cc_final: 0.7905 (m-40) REVERT: A 818 LYS cc_start: 0.8628 (tttt) cc_final: 0.8348 (mmmm) REVERT: A 951 GLN cc_start: 0.8327 (mm110) cc_final: 0.8023 (mm110) REVERT: A 1028 SER cc_start: 0.8832 (m) cc_final: 0.8504 (m) REVERT: A 1036 GLU cc_start: 0.7911 (mm-30) cc_final: 0.7579 (mt-10) REVERT: A 1174 GLN cc_start: 0.8236 (tm-30) cc_final: 0.7720 (tm-30) REVERT: A 1179 ASP cc_start: 0.8252 (m-30) cc_final: 0.7439 (m-30) REVERT: A 1183 ASN cc_start: 0.8224 (m-40) cc_final: 0.7699 (m110) REVERT: A 1184 LYS cc_start: 0.8438 (OUTLIER) cc_final: 0.8147 (mtpt) REVERT: A 1223 ASN cc_start: 0.8448 (t0) cc_final: 0.8174 (m-40) REVERT: A 1234 GLN cc_start: 0.7263 (OUTLIER) cc_final: 0.7043 (mp10) REVERT: A 1242 GLU cc_start: 0.7942 (tp30) cc_final: 0.7677 (tm-30) REVERT: A 1245 ARG cc_start: 0.8158 (ttm110) cc_final: 0.7762 (mtm-85) REVERT: A 1254 GLU cc_start: 0.7705 (mp0) cc_final: 0.7501 (mp0) REVERT: A 1283 SER cc_start: 0.8901 (t) cc_final: 0.8435 (p) REVERT: A 1296 ASP cc_start: 0.8523 (m-30) cc_final: 0.8293 (m-30) REVERT: A 1378 GLN cc_start: 0.8205 (mt0) cc_final: 0.7645 (mt0) REVERT: A 1438 SER cc_start: 0.8931 (m) cc_final: 0.8525 (p) REVERT: A 1460 LYS cc_start: 0.8678 (mptt) cc_final: 0.8471 (mmtm) REVERT: A 1636 GLU cc_start: 0.7288 (tp30) cc_final: 0.6692 (tp30) REVERT: A 1648 LYS cc_start: 0.8621 (mttt) cc_final: 0.8082 (mttm) REVERT: A 1661 LEU cc_start: 0.8759 (OUTLIER) cc_final: 0.8525 (tp) REVERT: A 1687 LEU cc_start: 0.8988 (mt) cc_final: 0.8670 (mp) REVERT: A 1735 LEU cc_start: 0.8797 (mm) cc_final: 0.8570 (mt) REVERT: A 1764 LEU cc_start: 0.8603 (OUTLIER) cc_final: 0.8252 (mp) REVERT: A 1768 GLU cc_start: 0.8206 (mt-10) cc_final: 0.7713 (mm-30) REVERT: A 1799 MET cc_start: 0.8082 (mmp) cc_final: 0.7711 (tpp) REVERT: A 1826 LYS cc_start: 0.8728 (mttt) cc_final: 0.8485 (mttp) REVERT: A 1860 THR cc_start: 0.9098 (t) cc_final: 0.8262 (t) REVERT: A 1864 HIS cc_start: 0.8552 (m90) cc_final: 0.8057 (m90) REVERT: A 1906 LYS cc_start: 0.8953 (tttt) cc_final: 0.8641 (ttpp) REVERT: A 1973 ASP cc_start: 0.8120 (t70) cc_final: 0.7868 (t0) REVERT: A 1981 GLU cc_start: 0.7631 (tm-30) cc_final: 0.7357 (pp20) REVERT: A 1999 LYS cc_start: 0.8271 (mttp) cc_final: 0.8034 (mttp) REVERT: A 2000 ARG cc_start: 0.8324 (tpp80) cc_final: 0.7804 (tpp80) REVERT: A 2060 THR cc_start: 0.8737 (m) cc_final: 0.8478 (t) REVERT: A 2062 GLU cc_start: 0.8438 (mt-10) cc_final: 0.8150 (mm-30) REVERT: A 2067 SER cc_start: 0.8686 (t) cc_final: 0.8408 (p) REVERT: A 2092 VAL cc_start: 0.8468 (t) cc_final: 0.8094 (p) REVERT: A 2095 SER cc_start: 0.9001 (t) cc_final: 0.8714 (p) REVERT: A 2116 LYS cc_start: 0.8459 (tttt) cc_final: 0.7985 (tttt) REVERT: A 2124 LYS cc_start: 0.8665 (mttt) cc_final: 0.8373 (mttm) REVERT: A 2203 ASN cc_start: 0.8118 (m-40) cc_final: 0.7670 (p0) REVERT: A 2298 ASP cc_start: 0.8503 (t0) cc_final: 0.8183 (t0) REVERT: B 15 ARG cc_start: 0.3277 (mmp80) cc_final: 0.2608 (mmp80) REVERT: B 29 GLN cc_start: 0.6552 (mm-40) cc_final: 0.5666 (tm-30) REVERT: B 212 ARG cc_start: 0.6135 (tpt-90) cc_final: 0.5893 (tpp-160) REVERT: B 222 LEU cc_start: 0.6874 (tt) cc_final: 0.6546 (pp) REVERT: B 241 LYS cc_start: 0.7755 (tppt) cc_final: 0.7424 (tptt) REVERT: C 311 MET cc_start: 0.8318 (ppp) cc_final: 0.8066 (pp-130) REVERT: C 314 PHE cc_start: 0.8654 (t80) cc_final: 0.8354 (t80) REVERT: C 354 ILE cc_start: 0.7815 (mt) cc_final: 0.7432 (mt) REVERT: C 357 LEU cc_start: 0.8111 (mt) cc_final: 0.7685 (mp) REVERT: C 384 ASP cc_start: 0.7893 (m-30) cc_final: 0.7380 (m-30) REVERT: C 418 ARG cc_start: 0.8185 (tpp-160) cc_final: 0.7865 (tpt90) REVERT: C 437 CYS cc_start: 0.8483 (m) cc_final: 0.8169 (m) REVERT: C 440 LYS cc_start: 0.7752 (tttm) cc_final: 0.6851 (tttm) REVERT: C 443 ASP cc_start: 0.7515 (m-30) cc_final: 0.6639 (m-30) REVERT: C 451 GLU cc_start: 0.7514 (tm-30) cc_final: 0.7220 (tm-30) REVERT: C 470 MET cc_start: 0.8731 (OUTLIER) cc_final: 0.8328 (tpp) REVERT: C 642 GLU cc_start: 0.7406 (tm-30) cc_final: 0.6916 (tm-30) REVERT: C 695 LYS cc_start: 0.8502 (OUTLIER) cc_final: 0.8130 (mtmm) REVERT: C 713 ASP cc_start: 0.7858 (t0) cc_final: 0.7592 (t70) REVERT: C 794 ARG cc_start: 0.7307 (mtp-110) cc_final: 0.6927 (mtp-110) REVERT: C 821 PHE cc_start: 0.8405 (m-80) cc_final: 0.7931 (m-10) REVERT: C 835 MET cc_start: 0.7536 (tmt) cc_final: 0.7255 (tmm) REVERT: C 839 LYS cc_start: 0.7903 (mtpp) cc_final: 0.7281 (ptpp) REVERT: C 848 MET cc_start: 0.6721 (mtp) cc_final: 0.6410 (mtp) REVERT: C 903 MET cc_start: 0.7479 (mtt) cc_final: 0.7249 (mtp) REVERT: C 904 PHE cc_start: 0.7221 (m-80) cc_final: 0.6802 (m-80) REVERT: C 982 MET cc_start: 0.7767 (mmm) cc_final: 0.7503 (mmm) REVERT: C 1038 GLU cc_start: 0.7406 (OUTLIER) cc_final: 0.6673 (tm-30) REVERT: C 1069 GLU cc_start: 0.7977 (tt0) cc_final: 0.7549 (tt0) REVERT: C 1076 GLU cc_start: 0.7990 (tm-30) cc_final: 0.7776 (tm-30) REVERT: C 1079 LYS cc_start: 0.8702 (tttt) cc_final: 0.8391 (tttp) REVERT: C 1080 LYS cc_start: 0.9011 (OUTLIER) cc_final: 0.8734 (tttp) REVERT: C 1083 SER cc_start: 0.8704 (t) cc_final: 0.8247 (p) REVERT: C 1163 GLU cc_start: 0.7981 (mm-30) cc_final: 0.7750 (mm-30) REVERT: C 1261 LYS cc_start: 0.7523 (OUTLIER) cc_final: 0.7163 (mptp) REVERT: C 1394 LYS cc_start: 0.8109 (OUTLIER) cc_final: 0.7817 (mtmm) REVERT: C 1409 ARG cc_start: 0.8274 (mtt-85) cc_final: 0.8005 (mpp80) REVERT: D 20 ILE cc_start: 0.7378 (tt) cc_final: 0.7174 (pt) REVERT: D 23 ARG cc_start: 0.8316 (ttm110) cc_final: 0.6187 (ttp-170) REVERT: D 68 GLU cc_start: 0.8112 (tt0) cc_final: 0.7873 (tt0) REVERT: D 69 LEU cc_start: 0.8909 (tt) cc_final: 0.8685 (tm) REVERT: D 85 LYS cc_start: 0.8973 (mmtt) cc_final: 0.8693 (mmmm) REVERT: D 120 ASP cc_start: 0.7860 (t0) cc_final: 0.7552 (t0) REVERT: D 140 THR cc_start: 0.9045 (m) cc_final: 0.8627 (p) REVERT: E 292 MET cc_start: 0.5790 (ptt) cc_final: 0.5318 (pp-130) REVERT: E 314 GLU cc_start: 0.3445 (tm-30) cc_final: 0.2588 (tp30) REVERT: E 334 PHE cc_start: 0.7118 (m-80) cc_final: 0.6712 (m-80) REVERT: E 375 SER cc_start: 0.8282 (m) cc_final: 0.8027 (p) REVERT: E 543 ILE cc_start: 0.7543 (mm) cc_final: 0.7176 (tp) REVERT: G 52 MET cc_start: 0.6087 (ttp) cc_final: 0.5775 (ttp) REVERT: G 643 MET cc_start: 0.7520 (mtp) cc_final: 0.7226 (mtt) outliers start: 95 outliers final: 44 residues processed: 819 average time/residue: 0.7313 time to fit residues: 708.6409 Evaluate side-chains 804 residues out of total 3758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 750 time to evaluate : 1.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 HIS Chi-restraints excluded: chain A residue 435 TYR Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain A residue 618 CYS Chi-restraints excluded: chain A residue 753 VAL Chi-restraints excluded: chain A residue 1008 VAL Chi-restraints excluded: chain A residue 1024 SER Chi-restraints excluded: chain A residue 1177 VAL Chi-restraints excluded: chain A residue 1184 LYS Chi-restraints excluded: chain A residue 1220 VAL Chi-restraints excluded: chain A residue 1234 GLN Chi-restraints excluded: chain A residue 1252 LEU Chi-restraints excluded: chain A residue 1255 SER Chi-restraints excluded: chain A residue 1276 GLU Chi-restraints excluded: chain A residue 1305 LEU Chi-restraints excluded: chain A residue 1382 THR Chi-restraints excluded: chain A residue 1661 LEU Chi-restraints excluded: chain A residue 1732 LYS Chi-restraints excluded: chain A residue 1764 LEU Chi-restraints excluded: chain A residue 1871 GLN Chi-restraints excluded: chain A residue 2098 GLU Chi-restraints excluded: chain A residue 2204 ILE Chi-restraints excluded: chain A residue 2331 SER Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 77 ASN Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 113 TYR Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 244 THR Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain C residue 470 MET Chi-restraints excluded: chain C residue 695 LYS Chi-restraints excluded: chain C residue 722 SER Chi-restraints excluded: chain C residue 832 LYS Chi-restraints excluded: chain C residue 872 PHE Chi-restraints excluded: chain C residue 924 LEU Chi-restraints excluded: chain C residue 1031 ILE Chi-restraints excluded: chain C residue 1038 GLU Chi-restraints excluded: chain C residue 1053 ASN Chi-restraints excluded: chain C residue 1080 LYS Chi-restraints excluded: chain C residue 1117 GLN Chi-restraints excluded: chain C residue 1261 LYS Chi-restraints excluded: chain C residue 1358 HIS Chi-restraints excluded: chain C residue 1394 LYS Chi-restraints excluded: chain C residue 1415 ILE Chi-restraints excluded: chain D residue 2 LEU Chi-restraints excluded: chain D residue 19 LEU Chi-restraints excluded: chain D residue 37 SER Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain E residue 324 ASN Chi-restraints excluded: chain G residue 32 ILE Chi-restraints excluded: chain G residue 632 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 119 optimal weight: 2.9990 chunk 195 optimal weight: 2.9990 chunk 207 optimal weight: 1.9990 chunk 173 optimal weight: 0.7980 chunk 245 optimal weight: 1.9990 chunk 315 optimal weight: 3.9990 chunk 340 optimal weight: 1.9990 chunk 276 optimal weight: 1.9990 chunk 251 optimal weight: 8.9990 chunk 250 optimal weight: 0.8980 chunk 248 optimal weight: 0.7980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 479 HIS ** A 859 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1171 ASN A1294 GLN A1380 HIS A1539 ASN A2183 ASN A2462 ASN B 112 ASN B 148 ASN ** B 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 495 GLN C 511 ASN C 557 ASN C 692 GLN ** C 843 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 988 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1053 ASN C1133 ASN ** D 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 294 HIS ** E 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 642 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.154046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.121058 restraints weight = 67112.134| |-----------------------------------------------------------------------------| r_work (start): 0.3658 rms_B_bonded: 2.68 r_work: 0.3510 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.4631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.089 34200 Z= 0.223 Angle : 0.741 17.987 46258 Z= 0.368 Chirality : 0.045 0.403 5293 Planarity : 0.005 0.070 5844 Dihedral : 4.508 84.546 4520 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.73 % Favored : 97.25 % Rotamer: Outliers : 2.21 % Allowed : 22.59 % Favored : 75.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.40 (0.13), residues: 4102 helix: 1.61 (0.10), residues: 2781 sheet: 0.16 (0.40), residues: 163 loop : -0.56 (0.19), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A1065 TYR 0.025 0.002 TYR B 113 PHE 0.042 0.002 PHE E 349 TRP 0.053 0.002 TRP C 894 HIS 0.010 0.001 HIS C 952 Details of bonding type rmsd/Z covalent geometry : bond 0.00545 / 0.22 (34200) covalent geometry : angle 0.74098 / 0.37 (46258) hydrogen bonds : bond 0.04010 / 2.75 ( 2045) hydrogen bonds : angle 4.19679 / 3.01 ( 6033) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8204 Ramachandran restraints generated. 4102 Oldfield, 0 Emsley, 4102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8204 Ramachandran restraints generated. 4102 Oldfield, 0 Emsley, 4102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 864 residues out of total 3758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 781 time to evaluate : 1.367 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 351 ILE cc_start: 0.7810 (mm) cc_final: 0.7588 (mp) REVERT: A 380 PHE cc_start: 0.7289 (t80) cc_final: 0.6937 (t80) REVERT: A 406 MET cc_start: 0.5844 (ptm) cc_final: 0.5516 (pmm) REVERT: A 432 ILE cc_start: 0.8378 (tp) cc_final: 0.7535 (mp) REVERT: A 436 MET cc_start: 0.7119 (mmm) cc_final: 0.6741 (mmm) REVERT: A 459 LYS cc_start: 0.8260 (tppp) cc_final: 0.8010 (tppt) REVERT: A 488 MET cc_start: 0.7987 (mtm) cc_final: 0.7695 (mtm) REVERT: A 508 ILE cc_start: 0.8838 (mt) cc_final: 0.8451 (tt) REVERT: A 559 LYS cc_start: 0.7858 (tmmt) cc_final: 0.7215 (mmpt) REVERT: A 580 MET cc_start: 0.7481 (mmm) cc_final: 0.7094 (mmm) REVERT: A 587 GLN cc_start: 0.8264 (tm-30) cc_final: 0.8063 (tp-100) REVERT: A 626 ILE cc_start: 0.8587 (tt) cc_final: 0.8305 (tp) REVERT: A 640 GLU cc_start: 0.8630 (tt0) cc_final: 0.8127 (tm-30) REVERT: A 680 ARG cc_start: 0.8238 (ttp-110) cc_final: 0.7966 (ptt90) REVERT: A 794 GLU cc_start: 0.8055 (mp0) cc_final: 0.7828 (mp0) REVERT: A 808 ASN cc_start: 0.8189 (m-40) cc_final: 0.7897 (m-40) REVERT: A 818 LYS cc_start: 0.8632 (tttt) cc_final: 0.8315 (mmmm) REVERT: A 855 LYS cc_start: 0.7342 (mtmm) cc_final: 0.7005 (mppt) REVERT: A 927 MET cc_start: 0.8738 (mmm) cc_final: 0.8130 (mpp) REVERT: A 951 GLN cc_start: 0.8426 (mm110) cc_final: 0.8104 (mm110) REVERT: A 1028 SER cc_start: 0.8837 (m) cc_final: 0.8504 (m) REVERT: A 1036 GLU cc_start: 0.8042 (mm-30) cc_final: 0.7631 (mt-10) REVERT: A 1065 ARG cc_start: 0.7961 (tpt90) cc_final: 0.7719 (tpt90) REVERT: A 1174 GLN cc_start: 0.8307 (tm-30) cc_final: 0.7807 (tm-30) REVERT: A 1179 ASP cc_start: 0.8305 (m-30) cc_final: 0.7438 (m-30) REVERT: A 1183 ASN cc_start: 0.8211 (m-40) cc_final: 0.7678 (m110) REVERT: A 1184 LYS cc_start: 0.8389 (OUTLIER) cc_final: 0.7943 (mtpp) REVERT: A 1223 ASN cc_start: 0.8537 (t0) cc_final: 0.8329 (m-40) REVERT: A 1234 GLN cc_start: 0.7473 (OUTLIER) cc_final: 0.7185 (mp10) REVERT: A 1242 GLU cc_start: 0.7981 (tp30) cc_final: 0.7622 (tm-30) REVERT: A 1254 GLU cc_start: 0.7848 (mp0) cc_final: 0.7559 (mp0) REVERT: A 1283 SER cc_start: 0.8950 (t) cc_final: 0.8386 (p) REVERT: A 1296 ASP cc_start: 0.8706 (m-30) cc_final: 0.8472 (m-30) REVERT: A 1367 SER cc_start: 0.8396 (p) cc_final: 0.8142 (t) REVERT: A 1378 GLN cc_start: 0.8205 (mt0) cc_final: 0.7828 (mt0) REVERT: A 1438 SER cc_start: 0.8970 (m) cc_final: 0.8517 (p) REVERT: A 1587 ASN cc_start: 0.8556 (t0) cc_final: 0.8339 (t0) REVERT: A 1636 GLU cc_start: 0.7389 (tp30) cc_final: 0.6712 (tp30) REVERT: A 1648 LYS cc_start: 0.8649 (mttt) cc_final: 0.8217 (mttm) REVERT: A 1661 LEU cc_start: 0.8712 (OUTLIER) cc_final: 0.8493 (tp) REVERT: A 1687 LEU cc_start: 0.8970 (mt) cc_final: 0.8654 (mp) REVERT: A 1734 ARG cc_start: 0.8524 (pmm-80) cc_final: 0.8181 (ptp-170) REVERT: A 1735 LEU cc_start: 0.8747 (mm) cc_final: 0.8545 (mt) REVERT: A 1764 LEU cc_start: 0.8533 (OUTLIER) cc_final: 0.8206 (mp) REVERT: A 1768 GLU cc_start: 0.8199 (mt-10) cc_final: 0.7773 (mm-30) REVERT: A 1799 MET cc_start: 0.8203 (mmp) cc_final: 0.7823 (tpp) REVERT: A 1817 ILE cc_start: 0.8204 (mm) cc_final: 0.7952 (mp) REVERT: A 1826 LYS cc_start: 0.8849 (mttt) cc_final: 0.8546 (mttp) REVERT: A 1860 THR cc_start: 0.9115 (t) cc_final: 0.8297 (t) REVERT: A 1864 HIS cc_start: 0.8636 (m90) cc_final: 0.8116 (m90) REVERT: A 1906 LYS cc_start: 0.8996 (tttt) cc_final: 0.8651 (ttpp) REVERT: A 1961 VAL cc_start: 0.8845 (t) cc_final: 0.8475 (p) REVERT: A 1973 ASP cc_start: 0.8088 (t70) cc_final: 0.7858 (t0) REVERT: A 1981 GLU cc_start: 0.7694 (tm-30) cc_final: 0.7281 (pp20) REVERT: A 1999 LYS cc_start: 0.8281 (mttp) cc_final: 0.8046 (mttp) REVERT: A 2000 ARG cc_start: 0.8383 (tpp80) cc_final: 0.7823 (tpp80) REVERT: A 2060 THR cc_start: 0.8842 (m) cc_final: 0.8585 (t) REVERT: A 2062 GLU cc_start: 0.8482 (mt-10) cc_final: 0.8160 (mm-30) REVERT: A 2067 SER cc_start: 0.8771 (t) cc_final: 0.8482 (p) REVERT: A 2092 VAL cc_start: 0.8400 (t) cc_final: 0.8008 (p) REVERT: A 2095 SER cc_start: 0.8986 (t) cc_final: 0.8659 (p) REVERT: A 2096 LYS cc_start: 0.8539 (tttm) cc_final: 0.8267 (tttt) REVERT: A 2116 LYS cc_start: 0.8423 (tttt) cc_final: 0.7980 (tttt) REVERT: A 2124 LYS cc_start: 0.8684 (mttt) cc_final: 0.8415 (mttm) REVERT: A 2203 ASN cc_start: 0.8290 (m-40) cc_final: 0.7855 (p0) REVERT: A 2226 GLU cc_start: 0.7698 (tp30) cc_final: 0.6916 (tp30) REVERT: A 2298 ASP cc_start: 0.8525 (t0) cc_final: 0.8177 (t0) REVERT: B 15 ARG cc_start: 0.3496 (mmp80) cc_final: 0.2793 (mmp80) REVERT: B 29 GLN cc_start: 0.6756 (mm-40) cc_final: 0.5872 (tm-30) REVERT: B 54 ASN cc_start: 0.4022 (p0) cc_final: 0.3727 (t0) REVERT: B 212 ARG cc_start: 0.6210 (tpt-90) cc_final: 0.5899 (tpp-160) REVERT: B 222 LEU cc_start: 0.6846 (tt) cc_final: 0.6497 (pp) REVERT: C 311 MET cc_start: 0.8376 (ppp) cc_final: 0.8090 (pp-130) REVERT: C 314 PHE cc_start: 0.8780 (OUTLIER) cc_final: 0.8290 (t80) REVERT: C 354 ILE cc_start: 0.7948 (mt) cc_final: 0.7595 (mt) REVERT: C 357 LEU cc_start: 0.8155 (mt) cc_final: 0.7787 (mp) REVERT: C 362 ASN cc_start: 0.7481 (t0) cc_final: 0.7098 (t0) REVERT: C 384 ASP cc_start: 0.7968 (m-30) cc_final: 0.7443 (m-30) REVERT: C 418 ARG cc_start: 0.8255 (tpp-160) cc_final: 0.7703 (mmm160) REVERT: C 431 MET cc_start: 0.8124 (tpp) cc_final: 0.7909 (tpp) REVERT: C 440 LYS cc_start: 0.7797 (tttm) cc_final: 0.6963 (tttm) REVERT: C 443 ASP cc_start: 0.7558 (m-30) cc_final: 0.6892 (m-30) REVERT: C 451 GLU cc_start: 0.7538 (tm-30) cc_final: 0.7182 (tm-30) REVERT: C 470 MET cc_start: 0.8733 (OUTLIER) cc_final: 0.8341 (tpp) REVERT: C 508 GLU cc_start: 0.8459 (tp30) cc_final: 0.8050 (tp30) REVERT: C 603 LYS cc_start: 0.8645 (OUTLIER) cc_final: 0.8443 (tttt) REVERT: C 642 GLU cc_start: 0.7439 (tm-30) cc_final: 0.6898 (tm-30) REVERT: C 695 LYS cc_start: 0.8488 (OUTLIER) cc_final: 0.8125 (mtmm) REVERT: C 713 ASP cc_start: 0.7859 (t0) cc_final: 0.7594 (t70) REVERT: C 716 GLN cc_start: 0.8237 (mm-40) cc_final: 0.7902 (tm-30) REVERT: C 719 LYS cc_start: 0.8299 (tmmt) cc_final: 0.8097 (ttpp) REVERT: C 721 PHE cc_start: 0.7882 (t80) cc_final: 0.7337 (t80) REVERT: C 794 ARG cc_start: 0.7300 (mtp-110) cc_final: 0.7097 (ttt90) REVERT: C 821 PHE cc_start: 0.8539 (m-80) cc_final: 0.8039 (m-10) REVERT: C 835 MET cc_start: 0.7589 (tmt) cc_final: 0.7307 (tmm) REVERT: C 839 LYS cc_start: 0.8046 (mtpp) cc_final: 0.7653 (pptt) REVERT: C 848 MET cc_start: 0.6871 (mtp) cc_final: 0.6545 (mtp) REVERT: C 902 LYS cc_start: 0.8157 (ptpt) cc_final: 0.7772 (pttp) REVERT: C 903 MET cc_start: 0.7623 (mtt) cc_final: 0.7376 (mtp) REVERT: C 904 PHE cc_start: 0.7416 (m-80) cc_final: 0.7098 (m-80) REVERT: C 982 MET cc_start: 0.7800 (mmm) cc_final: 0.7559 (mmm) REVERT: C 1002 GLN cc_start: 0.8186 (tt0) cc_final: 0.7912 (tt0) REVERT: C 1038 GLU cc_start: 0.7439 (OUTLIER) cc_final: 0.6702 (tm-30) REVERT: C 1069 GLU cc_start: 0.8002 (tt0) cc_final: 0.7554 (tt0) REVERT: C 1076 GLU cc_start: 0.7942 (tm-30) cc_final: 0.7709 (tm-30) REVERT: C 1079 LYS cc_start: 0.8636 (tttt) cc_final: 0.8317 (tttp) REVERT: C 1080 LYS cc_start: 0.9007 (OUTLIER) cc_final: 0.8791 (ttpp) REVERT: C 1083 SER cc_start: 0.8765 (t) cc_final: 0.8320 (p) REVERT: C 1163 GLU cc_start: 0.8060 (mm-30) cc_final: 0.7813 (mm-30) REVERT: C 1214 MET cc_start: 0.8408 (OUTLIER) cc_final: 0.7660 (mpp) REVERT: C 1407 ASN cc_start: 0.8271 (t0) cc_final: 0.7860 (t0) REVERT: C 1409 ARG cc_start: 0.8398 (mtt-85) cc_final: 0.8169 (mpp80) REVERT: D 20 ILE cc_start: 0.7276 (tt) cc_final: 0.7061 (pt) REVERT: D 23 ARG cc_start: 0.8342 (ttm110) cc_final: 0.6128 (ttp-170) REVERT: D 68 GLU cc_start: 0.8265 (tt0) cc_final: 0.8008 (tt0) REVERT: D 85 LYS cc_start: 0.9004 (mmtt) cc_final: 0.8667 (mmmm) REVERT: D 120 ASP cc_start: 0.7971 (t0) cc_final: 0.7670 (t0) REVERT: D 140 THR cc_start: 0.9090 (m) cc_final: 0.8679 (p) REVERT: E 292 MET cc_start: 0.5831 (ptt) cc_final: 0.5602 (pp-130) REVERT: E 314 GLU cc_start: 0.3420 (tm-30) cc_final: 0.2647 (tp30) REVERT: E 334 PHE cc_start: 0.7115 (m-80) cc_final: 0.6736 (m-80) REVERT: E 375 SER cc_start: 0.8322 (m) cc_final: 0.8077 (p) REVERT: E 543 ILE cc_start: 0.7649 (mm) cc_final: 0.7288 (tp) REVERT: G 52 MET cc_start: 0.6135 (ttp) cc_final: 0.5853 (ttp) REVERT: G 643 MET cc_start: 0.7467 (mtp) cc_final: 0.7198 (mtt) outliers start: 83 outliers final: 51 residues processed: 817 average time/residue: 0.7460 time to fit residues: 720.9527 Evaluate side-chains 825 residues out of total 3758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 763 time to evaluate : 1.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 HIS Chi-restraints excluded: chain A residue 435 TYR Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 521 ASN Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain A residue 552 SER Chi-restraints excluded: chain A residue 677 ASP Chi-restraints excluded: chain A residue 753 VAL Chi-restraints excluded: chain A residue 1008 VAL Chi-restraints excluded: chain A residue 1024 SER Chi-restraints excluded: chain A residue 1068 LYS Chi-restraints excluded: chain A residue 1177 VAL Chi-restraints excluded: chain A residue 1184 LYS Chi-restraints excluded: chain A residue 1220 VAL Chi-restraints excluded: chain A residue 1234 GLN Chi-restraints excluded: chain A residue 1255 SER Chi-restraints excluded: chain A residue 1265 SER Chi-restraints excluded: chain A residue 1276 GLU Chi-restraints excluded: chain A residue 1298 ILE Chi-restraints excluded: chain A residue 1305 LEU Chi-restraints excluded: chain A residue 1382 THR Chi-restraints excluded: chain A residue 1661 LEU Chi-restraints excluded: chain A residue 1732 LYS Chi-restraints excluded: chain A residue 1764 LEU Chi-restraints excluded: chain A residue 1776 VAL Chi-restraints excluded: chain A residue 1871 GLN Chi-restraints excluded: chain A residue 1923 GLU Chi-restraints excluded: chain A residue 2204 ILE Chi-restraints excluded: chain A residue 2331 SER Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 113 TYR Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 187 GLU Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain C residue 314 PHE Chi-restraints excluded: chain C residue 470 MET Chi-restraints excluded: chain C residue 603 LYS Chi-restraints excluded: chain C residue 695 LYS Chi-restraints excluded: chain C residue 722 SER Chi-restraints excluded: chain C residue 832 LYS Chi-restraints excluded: chain C residue 872 PHE Chi-restraints excluded: chain C residue 924 LEU Chi-restraints excluded: chain C residue 1038 GLU Chi-restraints excluded: chain C residue 1053 ASN Chi-restraints excluded: chain C residue 1080 LYS Chi-restraints excluded: chain C residue 1214 MET Chi-restraints excluded: chain C residue 1271 LEU Chi-restraints excluded: chain C residue 1358 HIS Chi-restraints excluded: chain C residue 1415 ILE Chi-restraints excluded: chain D residue 2 LEU Chi-restraints excluded: chain D residue 19 LEU Chi-restraints excluded: chain D residue 37 SER Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain E residue 291 SER Chi-restraints excluded: chain E residue 324 ASN Chi-restraints excluded: chain E residue 467 CYS Chi-restraints excluded: chain G residue 27 ILE Chi-restraints excluded: chain G residue 32 ILE Chi-restraints excluded: chain G residue 632 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 401 optimal weight: 0.6980 chunk 186 optimal weight: 1.9990 chunk 221 optimal weight: 0.0870 chunk 225 optimal weight: 0.7980 chunk 37 optimal weight: 2.9990 chunk 160 optimal weight: 0.5980 chunk 127 optimal weight: 1.9990 chunk 152 optimal weight: 0.9990 chunk 91 optimal weight: 0.9990 chunk 15 optimal weight: 30.0000 chunk 323 optimal weight: 8.9990 overall best weight: 0.6360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 479 HIS A1171 ASN A1380 HIS A2462 ASN B 112 ASN B 148 ASN C 511 ASN C 557 ASN C 692 GLN ** C 988 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1053 ASN C1133 ASN C1171 ASN ** D 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.154982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.122094 restraints weight = 66655.264| |-----------------------------------------------------------------------------| r_work (start): 0.3681 rms_B_bonded: 2.67 r_work: 0.3535 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.4721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 34200 Z= 0.156 Angle : 0.728 19.577 46258 Z= 0.358 Chirality : 0.043 0.384 5293 Planarity : 0.005 0.072 5844 Dihedral : 4.498 84.316 4520 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.66 % Favored : 97.32 % Rotamer: Outliers : 2.02 % Allowed : 23.04 % Favored : 74.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.45 (0.13), residues: 4102 helix: 1.66 (0.10), residues: 2786 sheet: 0.09 (0.40), residues: 163 loop : -0.56 (0.19), residues: 1153 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C1032 TYR 0.026 0.001 TYR B 113 PHE 0.040 0.001 PHE E 349 TRP 0.048 0.001 TRP A1229 HIS 0.011 0.001 HIS A 479 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.16 (34200) covalent geometry : angle 0.72753 / 0.36 (46258) hydrogen bonds : bond 0.03719 / 2.56 ( 2045) hydrogen bonds : angle 4.15580 / 2.98 ( 6033) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16493.09 seconds wall clock time: 280 minutes 32.26 seconds (16832.26 seconds total)