Starting phenix.real_space_refine on Wed Aug 27 01:43:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7sid_25141/08_2025/7sid_25141.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sid_25141/08_2025/7sid_25141.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.53 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7sid_25141/08_2025/7sid_25141.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sid_25141/08_2025/7sid_25141.map" model { file = "/net/cci-nas-00/data/ceres_data/7sid_25141/08_2025/7sid_25141.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sid_25141/08_2025/7sid_25141.cif" } resolution = 2.53 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 306 5.16 5 C 28526 2.51 5 N 7588 2.21 5 O 8222 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 60 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 44650 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 22210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2773, 22210 Classifications: {'peptide': 2773} Incomplete info: {'truncation_to_alanine': 51} Link IDs: {'PTRANS': 88, 'TRANS': 2684} Chain breaks: 18 Unresolved non-hydrogen bonds: 174 Unresolved non-hydrogen angles: 214 Unresolved non-hydrogen dihedrals: 136 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'ASN:plan1': 3, 'ASP:plan': 7, 'ARG:plan': 5, 'GLN:plan1': 3, 'GLU:plan': 10, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 112 Chain: "B" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 83 Classifications: {'peptide': 10} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 8} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "C" Number of atoms: 22210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2773, 22210 Classifications: {'peptide': 2773} Incomplete info: {'truncation_to_alanine': 51} Link IDs: {'PTRANS': 88, 'TRANS': 2684} Chain breaks: 18 Unresolved non-hydrogen bonds: 174 Unresolved non-hydrogen angles: 214 Unresolved non-hydrogen dihedrals: 136 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'ASN:plan1': 3, 'ASP:plan': 7, 'ARG:plan': 5, 'GLN:plan1': 3, 'GLU:plan': 10, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 112 Chain: "D" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 83 Classifications: {'peptide': 10} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 8} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 8.81, per 1000 atoms: 0.20 Number of scatterers: 44650 At special positions: 0 Unit cell: (225.302, 113.19, 216.678, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 306 16.00 P 6 15.00 Mg 2 11.99 O 8222 8.00 N 7588 7.00 C 28526 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: 3.28 Conformation dependent library (CDL) restraints added in 1.4 seconds Enol-peptide restraints added in 715.3 nanoseconds 10972 Ramachandran restraints generated. 5486 Oldfield, 0 Emsley, 5486 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10708 Finding SS restraints... Secondary structure from input PDB file: 324 helices and 10 sheets defined 76.1% alpha, 1.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.94 Creating SS restraints... Processing helix chain 'A' and resid 5 through 16 Processing helix chain 'A' and resid 21 through 33 removed outlier: 3.972A pdb=" N LYS A 25 " --> pdb=" O THR A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 35 through 43 removed outlier: 3.507A pdb=" N LEU A 43 " --> pdb=" O THR A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 74 Processing helix chain 'A' and resid 88 through 109 Processing helix chain 'A' and resid 116 through 130 removed outlier: 3.708A pdb=" N LEU A 120 " --> pdb=" O LYS A 116 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ASP A 130 " --> pdb=" O ASP A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 149 Processing helix chain 'A' and resid 152 through 159 removed outlier: 3.577A pdb=" N ILE A 159 " --> pdb=" O TYR A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 174 Processing helix chain 'A' and resid 182 through 201 removed outlier: 4.298A pdb=" N LEU A 186 " --> pdb=" O VAL A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 208 No H-bonds generated for 'chain 'A' and resid 206 through 208' Processing helix chain 'A' and resid 209 through 223 removed outlier: 3.688A pdb=" N PHE A 213 " --> pdb=" O PHE A 209 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLN A 222 " --> pdb=" O GLN A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 244 Processing helix chain 'A' and resid 247 through 269 Proline residue: A 260 - end of helix Processing helix chain 'A' and resid 272 through 291 removed outlier: 3.536A pdb=" N LYS A 276 " --> pdb=" O ASN A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 301 Processing helix chain 'A' and resid 305 through 324 removed outlier: 3.776A pdb=" N SER A 324 " --> pdb=" O VAL A 320 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 357 Processing helix chain 'A' and resid 392 through 403 removed outlier: 3.982A pdb=" N ILE A 396 " --> pdb=" O GLY A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 408 Processing helix chain 'A' and resid 409 through 423 Processing helix chain 'A' and resid 424 through 427 removed outlier: 3.672A pdb=" N LEU A 427 " --> pdb=" O PRO A 424 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 424 through 427' Processing helix chain 'A' and resid 428 through 430 No H-bonds generated for 'chain 'A' and resid 428 through 430' Processing helix chain 'A' and resid 431 through 443 removed outlier: 3.504A pdb=" N GLN A 441 " --> pdb=" O MET A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 468 removed outlier: 3.665A pdb=" N LYS A 468 " --> pdb=" O LEU A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 493 removed outlier: 3.858A pdb=" N ARG A 493 " --> pdb=" O CYS A 489 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 499 No H-bonds generated for 'chain 'A' and resid 497 through 499' Processing helix chain 'A' and resid 500 through 514 removed outlier: 3.710A pdb=" N PHE A 505 " --> pdb=" O GLN A 501 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N GLY A 506 " --> pdb=" O ALA A 502 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLY A 514 " --> pdb=" O ALA A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 528 removed outlier: 4.090A pdb=" N TRP A 524 " --> pdb=" O ASP A 520 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LYS A 525 " --> pdb=" O ARG A 521 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU A 526 " --> pdb=" O GLU A 522 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N PHE A 527 " --> pdb=" O PHE A 523 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N THR A 528 " --> pdb=" O TRP A 524 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 520 through 528' Processing helix chain 'A' and resid 535 through 548 Processing helix chain 'A' and resid 572 through 581 Processing helix chain 'A' and resid 596 through 601 Processing helix chain 'A' and resid 607 through 617 removed outlier: 3.580A pdb=" N THR A 616 " --> pdb=" O LEU A 612 " (cutoff:3.500A) Processing helix chain 'A' and resid 619 through 629 Processing helix chain 'A' and resid 645 through 656 Processing helix chain 'A' and resid 683 through 704 Processing helix chain 'A' and resid 711 through 732 removed outlier: 4.210A pdb=" N LEU A 715 " --> pdb=" O ASN A 711 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL A 716 " --> pdb=" O SER A 712 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N MET A 732 " --> pdb=" O CYS A 728 " (cutoff:3.500A) Processing helix chain 'A' and resid 736 through 742 removed outlier: 3.731A pdb=" N TYR A 741 " --> pdb=" O GLU A 737 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N LYS A 742 " --> pdb=" O GLU A 738 " (cutoff:3.500A) Processing helix chain 'A' and resid 743 through 766 removed outlier: 3.936A pdb=" N GLU A 758 " --> pdb=" O GLN A 754 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N SER A 759 " --> pdb=" O CYS A 755 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N ILE A 760 " --> pdb=" O ALA A 756 " (cutoff:3.500A) Processing helix chain 'A' and resid 772 through 787 Processing helix chain 'A' and resid 794 through 807 removed outlier: 3.553A pdb=" N LEU A 807 " --> pdb=" O PHE A 803 " (cutoff:3.500A) Processing helix chain 'A' and resid 808 through 825 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 891 through 912 removed outlier: 3.769A pdb=" N GLN A 912 " --> pdb=" O VAL A 908 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 930 removed outlier: 3.656A pdb=" N LEU A 930 " --> pdb=" O LYS A 926 " (cutoff:3.500A) Processing helix chain 'A' and resid 940 through 954 Processing helix chain 'A' and resid 962 through 971 Processing helix chain 'A' and resid 972 through 980 Processing helix chain 'A' and resid 983 through 995 Processing helix chain 'A' and resid 997 through 1002 Processing helix chain 'A' and resid 1008 through 1031 removed outlier: 3.620A pdb=" N ARG A1012 " --> pdb=" O SER A1008 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N VAL A1021 " --> pdb=" O GLN A1017 " (cutoff:3.500A) Processing helix chain 'A' and resid 1035 through 1053 Processing helix chain 'A' and resid 1070 through 1075 removed outlier: 3.597A pdb=" N THR A1075 " --> pdb=" O ASN A1071 " (cutoff:3.500A) Processing helix chain 'A' and resid 1076 through 1080 Processing helix chain 'A' and resid 1082 through 1093 Processing helix chain 'A' and resid 1094 through 1097 Processing helix chain 'A' and resid 1112 through 1133 removed outlier: 3.565A pdb=" N MET A1131 " --> pdb=" O ALA A1127 " (cutoff:3.500A) Processing helix chain 'A' and resid 1143 through 1165 removed outlier: 3.653A pdb=" N ILE A1147 " --> pdb=" O THR A1143 " (cutoff:3.500A) Processing helix chain 'A' and resid 1168 through 1183 removed outlier: 4.120A pdb=" N LYS A1181 " --> pdb=" O CYS A1177 " (cutoff:3.500A) Processing helix chain 'A' and resid 1186 through 1202 Processing helix chain 'A' and resid 1205 through 1225 removed outlier: 3.666A pdb=" N PHE A1209 " --> pdb=" O ARG A1205 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N HIS A1213 " --> pdb=" O PHE A1209 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N ASP A1215 " --> pdb=" O ALA A1211 " (cutoff:3.500A) removed outlier: 5.773A pdb=" N TYR A1216 " --> pdb=" O SER A1212 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLN A1225 " --> pdb=" O TRP A1221 " (cutoff:3.500A) Processing helix chain 'A' and resid 1236 through 1240 Processing helix chain 'A' and resid 1243 through 1262 removed outlier: 6.607A pdb=" N LYS A1253 " --> pdb=" O ARG A1249 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N VAL A1254 " --> pdb=" O SER A1250 " (cutoff:3.500A) Proline residue: A1257 - end of helix Processing helix chain 'A' and resid 1264 through 1274 removed outlier: 3.753A pdb=" N VAL A1268 " --> pdb=" O HIS A1264 " (cutoff:3.500A) Processing helix chain 'A' and resid 1278 through 1286 removed outlier: 3.552A pdb=" N CYS A1286 " --> pdb=" O LEU A1282 " (cutoff:3.500A) Processing helix chain 'A' and resid 1286 through 1292 Processing helix chain 'A' and resid 1294 through 1299 removed outlier: 3.863A pdb=" N PHE A1298 " --> pdb=" O ILE A1294 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ALA A1299 " --> pdb=" O LEU A1295 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1294 through 1299' Processing helix chain 'A' and resid 1305 through 1323 Processing helix chain 'A' and resid 1327 through 1330 removed outlier: 4.251A pdb=" N LYS A1330 " --> pdb=" O LEU A1327 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1327 through 1330' Processing helix chain 'A' and resid 1331 through 1339 removed outlier: 3.605A pdb=" N ASN A1339 " --> pdb=" O LEU A1335 " (cutoff:3.500A) Processing helix chain 'A' and resid 1340 through 1349 Processing helix chain 'A' and resid 1382 through 1397 removed outlier: 3.522A pdb=" N HIS A1397 " --> pdb=" O ILE A1393 " (cutoff:3.500A) Processing helix chain 'A' and resid 1403 through 1409 removed outlier: 3.887A pdb=" N ILE A1407 " --> pdb=" O SER A1403 " (cutoff:3.500A) Processing helix chain 'A' and resid 1413 through 1429 Processing helix chain 'A' and resid 1431 through 1452 removed outlier: 4.055A pdb=" N ASP A1452 " --> pdb=" O LEU A1448 " (cutoff:3.500A) Processing helix chain 'A' and resid 1453 through 1456 Processing helix chain 'A' and resid 1460 through 1478 Processing helix chain 'A' and resid 1484 through 1509 Processing helix chain 'A' and resid 1516 through 1525 Processing helix chain 'A' and resid 1526 through 1528 No H-bonds generated for 'chain 'A' and resid 1526 through 1528' Processing helix chain 'A' and resid 1534 through 1547 Processing helix chain 'A' and resid 1552 through 1561 removed outlier: 3.961A pdb=" N ILE A1557 " --> pdb=" O GLU A1553 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N THR A1558 " --> pdb=" O ASN A1554 " (cutoff:3.500A) Processing helix chain 'A' and resid 1568 through 1570 No H-bonds generated for 'chain 'A' and resid 1568 through 1570' Processing helix chain 'A' and resid 1571 through 1583 Processing helix chain 'A' and resid 1589 through 1602 removed outlier: 3.724A pdb=" N VAL A1602 " --> pdb=" O LEU A1598 " (cutoff:3.500A) Processing helix chain 'A' and resid 1606 through 1609 Processing helix chain 'A' and resid 1610 through 1623 removed outlier: 3.662A pdb=" N LYS A1615 " --> pdb=" O LEU A1611 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N LEU A1623 " --> pdb=" O ARG A1619 " (cutoff:3.500A) Processing helix chain 'A' and resid 1624 through 1635 Processing helix chain 'A' and resid 1636 through 1637 No H-bonds generated for 'chain 'A' and resid 1636 through 1637' Processing helix chain 'A' and resid 1638 through 1641 Processing helix chain 'A' and resid 1642 through 1658 Processing helix chain 'A' and resid 1663 through 1678 removed outlier: 3.849A pdb=" N VAL A1667 " --> pdb=" O GLY A1663 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N VAL A1678 " --> pdb=" O CYS A1674 " (cutoff:3.500A) Processing helix chain 'A' and resid 1693 through 1703 removed outlier: 3.875A pdb=" N PHE A1703 " --> pdb=" O ALA A1699 " (cutoff:3.500A) Processing helix chain 'A' and resid 1705 through 1722 Processing helix chain 'A' and resid 1726 through 1742 removed outlier: 3.605A pdb=" N ARG A1730 " --> pdb=" O CYS A1726 " (cutoff:3.500A) Processing helix chain 'A' and resid 1743 through 1754 removed outlier: 3.606A pdb=" N ILE A1752 " --> pdb=" O SER A1748 " (cutoff:3.500A) Processing helix chain 'A' and resid 1758 through 1765 removed outlier: 3.901A pdb=" N ALA A1762 " --> pdb=" O ASP A1758 " (cutoff:3.500A) Processing helix chain 'A' and resid 1785 through 1790 removed outlier: 4.255A pdb=" N LEU A1789 " --> pdb=" O PRO A1785 " (cutoff:3.500A) Processing helix chain 'A' and resid 1791 through 1796 removed outlier: 3.644A pdb=" N TRP A1795 " --> pdb=" O ASP A1791 " (cutoff:3.500A) Processing helix chain 'A' and resid 1801 through 1816 removed outlier: 3.501A pdb=" N SER A1816 " --> pdb=" O ALA A1812 " (cutoff:3.500A) Processing helix chain 'A' and resid 1823 through 1826 Processing helix chain 'A' and resid 1827 through 1832 Processing helix chain 'A' and resid 1834 through 1852 removed outlier: 3.631A pdb=" N CYS A1838 " --> pdb=" O LYS A1834 " (cutoff:3.500A) Proline residue: A1843 - end of helix removed outlier: 3.656A pdb=" N GLN A1852 " --> pdb=" O ASP A1848 " (cutoff:3.500A) Processing helix chain 'A' and resid 1857 through 1876 removed outlier: 3.827A pdb=" N HIS A1876 " --> pdb=" O SER A1872 " (cutoff:3.500A) Processing helix chain 'A' and resid 1902 through 1918 removed outlier: 3.516A pdb=" N GLN A1906 " --> pdb=" O ASP A1902 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ARG A1918 " --> pdb=" O ASP A1914 " (cutoff:3.500A) Processing helix chain 'A' and resid 1928 through 1932 Processing helix chain 'A' and resid 1937 through 1948 removed outlier: 3.517A pdb=" N VAL A1941 " --> pdb=" O ASN A1937 " (cutoff:3.500A) Processing helix chain 'A' and resid 1950 through 1974 Processing helix chain 'A' and resid 1985 through 1997 Processing helix chain 'A' and resid 2000 through 2013 Processing helix chain 'A' and resid 2015 through 2020 Processing helix chain 'A' and resid 2028 through 2039 Processing helix chain 'A' and resid 2041 through 2052 Processing helix chain 'A' and resid 2056 through 2071 Processing helix chain 'A' and resid 2073 through 2088 Processing helix chain 'A' and resid 2092 through 2107 Processing helix chain 'A' and resid 2123 through 2137 Processing helix chain 'A' and resid 2139 through 2161 removed outlier: 3.946A pdb=" N ARG A2161 " --> pdb=" O GLU A2157 " (cutoff:3.500A) Processing helix chain 'A' and resid 2165 through 2168 Processing helix chain 'A' and resid 2169 through 2191 removed outlier: 3.839A pdb=" N GLU A2187 " --> pdb=" O GLU A2183 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N LEU A2188 " --> pdb=" O SER A2184 " (cutoff:3.500A) Processing helix chain 'A' and resid 2194 through 2212 Processing helix chain 'A' and resid 2216 through 2237 Proline residue: A2222 - end of helix Processing helix chain 'A' and resid 2243 through 2265 removed outlier: 3.785A pdb=" N ILE A2247 " --> pdb=" O GLN A2243 " (cutoff:3.500A) Processing helix chain 'A' and resid 2268 through 2282 removed outlier: 3.910A pdb=" N GLU A2272 " --> pdb=" O THR A2268 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N TYR A2281 " --> pdb=" O GLN A2277 " (cutoff:3.500A) Processing helix chain 'A' and resid 2289 through 2302 removed outlier: 3.761A pdb=" N LEU A2293 " --> pdb=" O SER A2289 " (cutoff:3.500A) Processing helix chain 'A' and resid 2304 through 2323 removed outlier: 3.902A pdb=" N ALA A2321 " --> pdb=" O LYS A2317 " (cutoff:3.500A) Processing helix chain 'A' and resid 2327 through 2349 Processing helix chain 'A' and resid 2352 through 2360 Processing helix chain 'A' and resid 2360 through 2371 removed outlier: 3.512A pdb=" N VAL A2365 " --> pdb=" O LEU A2361 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N TYR A2371 " --> pdb=" O VAL A2367 " (cutoff:3.500A) Processing helix chain 'A' and resid 2377 through 2406 Processing helix chain 'A' and resid 2407 through 2422 removed outlier: 3.623A pdb=" N GLU A2411 " --> pdb=" O SER A2407 " (cutoff:3.500A) Processing helix chain 'A' and resid 2437 through 2477 removed outlier: 3.506A pdb=" N GLY A2477 " --> pdb=" O CYS A2473 " (cutoff:3.500A) Processing helix chain 'A' and resid 2480 through 2482 No H-bonds generated for 'chain 'A' and resid 2480 through 2482' Processing helix chain 'A' and resid 2483 through 2493 removed outlier: 3.721A pdb=" N GLU A2493 " --> pdb=" O SER A2489 " (cutoff:3.500A) Processing helix chain 'A' and resid 2497 through 2508 removed outlier: 3.556A pdb=" N ASN A2501 " --> pdb=" O VAL A2497 " (cutoff:3.500A) Processing helix chain 'A' and resid 2509 through 2511 No H-bonds generated for 'chain 'A' and resid 2509 through 2511' Processing helix chain 'A' and resid 2512 through 2518 Proline residue: A2518 - end of helix Processing helix chain 'A' and resid 2519 through 2525 removed outlier: 3.602A pdb=" N ALA A2525 " --> pdb=" O TYR A2521 " (cutoff:3.500A) Processing helix chain 'A' and resid 2536 through 2552 Processing helix chain 'A' and resid 2552 through 2565 removed outlier: 3.540A pdb=" N THR A2556 " --> pdb=" O HIS A2552 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N PHE A2558 " --> pdb=" O HIS A2554 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N ILE A2559 " --> pdb=" O HIS A2555 " (cutoff:3.500A) Processing helix chain 'A' and resid 2567 through 2573 removed outlier: 4.021A pdb=" N PHE A2571 " --> pdb=" O ASN A2567 " (cutoff:3.500A) Processing helix chain 'A' and resid 2592 through 2611 removed outlier: 3.511A pdb=" N GLU A2596 " --> pdb=" O SER A2592 " (cutoff:3.500A) Processing helix chain 'A' and resid 2613 through 2632 Processing helix chain 'A' and resid 2651 through 2655 Processing helix chain 'A' and resid 2722 through 2741 removed outlier: 3.588A pdb=" N ARG A2741 " --> pdb=" O THR A2737 " (cutoff:3.500A) Processing helix chain 'A' and resid 2742 through 2748 removed outlier: 3.570A pdb=" N ARG A2748 " --> pdb=" O GLU A2744 " (cutoff:3.500A) Processing helix chain 'A' and resid 2776 through 2782 removed outlier: 3.763A pdb=" N ASN A2782 " --> pdb=" O GLU A2778 " (cutoff:3.500A) Processing helix chain 'A' and resid 2786 through 2792 Processing helix chain 'A' and resid 2797 through 2807 Processing helix chain 'A' and resid 2812 through 2826 Processing helix chain 'A' and resid 2830 through 2834 Processing helix chain 'A' and resid 2841 through 2867 Processing helix chain 'A' and resid 2872 through 2874 No H-bonds generated for 'chain 'A' and resid 2872 through 2874' Processing helix chain 'A' and resid 2895 through 2899 removed outlier: 3.571A pdb=" N LYS A2898 " --> pdb=" O GLU A2895 " (cutoff:3.500A) Processing helix chain 'A' and resid 2911 through 2917 Processing helix chain 'A' and resid 2925 through 2941 Processing helix chain 'A' and resid 2941 through 2954 removed outlier: 3.590A pdb=" N TYR A2954 " --> pdb=" O GLU A2950 " (cutoff:3.500A) Processing helix chain 'A' and resid 2963 through 2971 Processing helix chain 'A' and resid 3002 through 3018 Processing helix chain 'A' and resid 3027 through 3040 Processing helix chain 'A' and resid 3041 through 3047 removed outlier: 3.609A pdb=" N ARG A3047 " --> pdb=" O LYS A3043 " (cutoff:3.500A) Processing helix chain 'A' and resid 3048 through 3053 removed outlier: 6.061A pdb=" N GLY A3051 " --> pdb=" O LEU A3048 " (cutoff:3.500A) Processing helix chain 'C' and resid 6 through 16 Processing helix chain 'C' and resid 21 through 33 removed outlier: 3.972A pdb=" N LYS C 25 " --> pdb=" O THR C 21 " (cutoff:3.500A) Processing helix chain 'C' and resid 35 through 43 removed outlier: 3.507A pdb=" N LEU C 43 " --> pdb=" O THR C 39 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 74 Processing helix chain 'C' and resid 88 through 109 Processing helix chain 'C' and resid 116 through 130 removed outlier: 3.708A pdb=" N LEU C 120 " --> pdb=" O LYS C 116 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ASP C 130 " --> pdb=" O ASP C 126 " (cutoff:3.500A) Processing helix chain 'C' and resid 134 through 149 Processing helix chain 'C' and resid 152 through 159 removed outlier: 3.578A pdb=" N ILE C 159 " --> pdb=" O TYR C 155 " (cutoff:3.500A) Processing helix chain 'C' and resid 160 through 174 Processing helix chain 'C' and resid 182 through 201 removed outlier: 4.298A pdb=" N LEU C 186 " --> pdb=" O VAL C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 208 No H-bonds generated for 'chain 'C' and resid 206 through 208' Processing helix chain 'C' and resid 209 through 223 removed outlier: 3.688A pdb=" N PHE C 213 " --> pdb=" O PHE C 209 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLN C 222 " --> pdb=" O GLN C 218 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 244 Processing helix chain 'C' and resid 247 through 269 Proline residue: C 260 - end of helix Processing helix chain 'C' and resid 272 through 291 removed outlier: 3.536A pdb=" N LYS C 276 " --> pdb=" O ASN C 272 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 301 Processing helix chain 'C' and resid 305 through 324 removed outlier: 3.776A pdb=" N SER C 324 " --> pdb=" O VAL C 320 " (cutoff:3.500A) Processing helix chain 'C' and resid 342 through 357 Processing helix chain 'C' and resid 392 through 403 removed outlier: 3.983A pdb=" N ILE C 396 " --> pdb=" O GLY C 392 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 408 Processing helix chain 'C' and resid 409 through 423 Processing helix chain 'C' and resid 424 through 427 removed outlier: 3.672A pdb=" N LEU C 427 " --> pdb=" O PRO C 424 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 424 through 427' Processing helix chain 'C' and resid 428 through 430 No H-bonds generated for 'chain 'C' and resid 428 through 430' Processing helix chain 'C' and resid 431 through 443 removed outlier: 3.504A pdb=" N GLN C 441 " --> pdb=" O MET C 437 " (cutoff:3.500A) Processing helix chain 'C' and resid 451 through 468 removed outlier: 3.665A pdb=" N LYS C 468 " --> pdb=" O LEU C 464 " (cutoff:3.500A) Processing helix chain 'C' and resid 473 through 493 removed outlier: 3.858A pdb=" N ARG C 493 " --> pdb=" O CYS C 489 " (cutoff:3.500A) Processing helix chain 'C' and resid 497 through 499 No H-bonds generated for 'chain 'C' and resid 497 through 499' Processing helix chain 'C' and resid 500 through 514 removed outlier: 3.710A pdb=" N PHE C 505 " --> pdb=" O GLN C 501 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N GLY C 506 " --> pdb=" O ALA C 502 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLY C 514 " --> pdb=" O ALA C 510 " (cutoff:3.500A) Processing helix chain 'C' and resid 520 through 528 removed outlier: 4.090A pdb=" N TRP C 524 " --> pdb=" O ASP C 520 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LYS C 525 " --> pdb=" O ARG C 521 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU C 526 " --> pdb=" O GLU C 522 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N PHE C 527 " --> pdb=" O PHE C 523 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N THR C 528 " --> pdb=" O TRP C 524 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 520 through 528' Processing helix chain 'C' and resid 535 through 548 Processing helix chain 'C' and resid 572 through 581 Processing helix chain 'C' and resid 596 through 601 Processing helix chain 'C' and resid 607 through 617 removed outlier: 3.580A pdb=" N THR C 616 " --> pdb=" O LEU C 612 " (cutoff:3.500A) Processing helix chain 'C' and resid 619 through 629 Processing helix chain 'C' and resid 645 through 656 Processing helix chain 'C' and resid 683 through 704 Processing helix chain 'C' and resid 711 through 732 removed outlier: 4.210A pdb=" N LEU C 715 " --> pdb=" O ASN C 711 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL C 716 " --> pdb=" O SER C 712 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N MET C 732 " --> pdb=" O CYS C 728 " (cutoff:3.500A) Processing helix chain 'C' and resid 736 through 742 removed outlier: 3.731A pdb=" N TYR C 741 " --> pdb=" O GLU C 737 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N LYS C 742 " --> pdb=" O GLU C 738 " (cutoff:3.500A) Processing helix chain 'C' and resid 743 through 766 removed outlier: 3.936A pdb=" N GLU C 758 " --> pdb=" O GLN C 754 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N SER C 759 " --> pdb=" O CYS C 755 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N ILE C 760 " --> pdb=" O ALA C 756 " (cutoff:3.500A) Processing helix chain 'C' and resid 772 through 787 Processing helix chain 'C' and resid 794 through 807 removed outlier: 3.553A pdb=" N LEU C 807 " --> pdb=" O PHE C 803 " (cutoff:3.500A) Processing helix chain 'C' and resid 808 through 825 Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 891 through 912 removed outlier: 3.769A pdb=" N GLN C 912 " --> pdb=" O VAL C 908 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 930 removed outlier: 3.656A pdb=" N LEU C 930 " --> pdb=" O LYS C 926 " (cutoff:3.500A) Processing helix chain 'C' and resid 940 through 954 Processing helix chain 'C' and resid 962 through 971 Processing helix chain 'C' and resid 972 through 980 Processing helix chain 'C' and resid 983 through 995 Processing helix chain 'C' and resid 997 through 1002 Processing helix chain 'C' and resid 1008 through 1031 removed outlier: 3.620A pdb=" N ARG C1012 " --> pdb=" O SER C1008 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N VAL C1021 " --> pdb=" O GLN C1017 " (cutoff:3.500A) Processing helix chain 'C' and resid 1035 through 1053 Processing helix chain 'C' and resid 1070 through 1075 removed outlier: 3.597A pdb=" N THR C1075 " --> pdb=" O ASN C1071 " (cutoff:3.500A) Processing helix chain 'C' and resid 1076 through 1080 Processing helix chain 'C' and resid 1082 through 1093 Processing helix chain 'C' and resid 1094 through 1097 Processing helix chain 'C' and resid 1112 through 1133 removed outlier: 3.565A pdb=" N MET C1131 " --> pdb=" O ALA C1127 " (cutoff:3.500A) Processing helix chain 'C' and resid 1143 through 1165 removed outlier: 3.653A pdb=" N ILE C1147 " --> pdb=" O THR C1143 " (cutoff:3.500A) Processing helix chain 'C' and resid 1168 through 1183 removed outlier: 4.120A pdb=" N LYS C1181 " --> pdb=" O CYS C1177 " (cutoff:3.500A) Processing helix chain 'C' and resid 1186 through 1202 Processing helix chain 'C' and resid 1205 through 1225 removed outlier: 3.667A pdb=" N PHE C1209 " --> pdb=" O ARG C1205 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N HIS C1213 " --> pdb=" O PHE C1209 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N ASP C1215 " --> pdb=" O ALA C1211 " (cutoff:3.500A) removed outlier: 5.773A pdb=" N TYR C1216 " --> pdb=" O SER C1212 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLN C1225 " --> pdb=" O TRP C1221 " (cutoff:3.500A) Processing helix chain 'C' and resid 1236 through 1240 Processing helix chain 'C' and resid 1243 through 1262 removed outlier: 6.607A pdb=" N LYS C1253 " --> pdb=" O ARG C1249 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N VAL C1254 " --> pdb=" O SER C1250 " (cutoff:3.500A) Proline residue: C1257 - end of helix Processing helix chain 'C' and resid 1264 through 1274 removed outlier: 3.753A pdb=" N VAL C1268 " --> pdb=" O HIS C1264 " (cutoff:3.500A) Processing helix chain 'C' and resid 1278 through 1286 removed outlier: 3.552A pdb=" N CYS C1286 " --> pdb=" O LEU C1282 " (cutoff:3.500A) Processing helix chain 'C' and resid 1286 through 1292 Processing helix chain 'C' and resid 1294 through 1299 removed outlier: 3.863A pdb=" N PHE C1298 " --> pdb=" O ILE C1294 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ALA C1299 " --> pdb=" O LEU C1295 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1294 through 1299' Processing helix chain 'C' and resid 1305 through 1323 Processing helix chain 'C' and resid 1327 through 1330 removed outlier: 4.251A pdb=" N LYS C1330 " --> pdb=" O LEU C1327 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1327 through 1330' Processing helix chain 'C' and resid 1331 through 1339 removed outlier: 3.605A pdb=" N ASN C1339 " --> pdb=" O LEU C1335 " (cutoff:3.500A) Processing helix chain 'C' and resid 1340 through 1349 Processing helix chain 'C' and resid 1382 through 1397 removed outlier: 3.522A pdb=" N HIS C1397 " --> pdb=" O ILE C1393 " (cutoff:3.500A) Processing helix chain 'C' and resid 1403 through 1409 removed outlier: 3.887A pdb=" N ILE C1407 " --> pdb=" O SER C1403 " (cutoff:3.500A) Processing helix chain 'C' and resid 1413 through 1429 Processing helix chain 'C' and resid 1431 through 1452 removed outlier: 4.055A pdb=" N ASP C1452 " --> pdb=" O LEU C1448 " (cutoff:3.500A) Processing helix chain 'C' and resid 1453 through 1456 Processing helix chain 'C' and resid 1460 through 1478 Processing helix chain 'C' and resid 1484 through 1509 Processing helix chain 'C' and resid 1516 through 1525 Processing helix chain 'C' and resid 1526 through 1528 No H-bonds generated for 'chain 'C' and resid 1526 through 1528' Processing helix chain 'C' and resid 1534 through 1547 Processing helix chain 'C' and resid 1552 through 1561 removed outlier: 3.961A pdb=" N ILE C1557 " --> pdb=" O GLU C1553 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N THR C1558 " --> pdb=" O ASN C1554 " (cutoff:3.500A) Processing helix chain 'C' and resid 1568 through 1570 No H-bonds generated for 'chain 'C' and resid 1568 through 1570' Processing helix chain 'C' and resid 1571 through 1583 Processing helix chain 'C' and resid 1589 through 1602 removed outlier: 3.724A pdb=" N VAL C1602 " --> pdb=" O LEU C1598 " (cutoff:3.500A) Processing helix chain 'C' and resid 1606 through 1609 Processing helix chain 'C' and resid 1610 through 1623 removed outlier: 3.662A pdb=" N LYS C1615 " --> pdb=" O LEU C1611 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N LEU C1623 " --> pdb=" O ARG C1619 " (cutoff:3.500A) Processing helix chain 'C' and resid 1624 through 1635 Processing helix chain 'C' and resid 1636 through 1637 No H-bonds generated for 'chain 'C' and resid 1636 through 1637' Processing helix chain 'C' and resid 1638 through 1641 Processing helix chain 'C' and resid 1642 through 1658 Processing helix chain 'C' and resid 1663 through 1678 removed outlier: 3.849A pdb=" N VAL C1667 " --> pdb=" O GLY C1663 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N VAL C1678 " --> pdb=" O CYS C1674 " (cutoff:3.500A) Processing helix chain 'C' and resid 1693 through 1703 removed outlier: 3.875A pdb=" N PHE C1703 " --> pdb=" O ALA C1699 " (cutoff:3.500A) Processing helix chain 'C' and resid 1705 through 1722 Processing helix chain 'C' and resid 1726 through 1742 removed outlier: 3.605A pdb=" N ARG C1730 " --> pdb=" O CYS C1726 " (cutoff:3.500A) Processing helix chain 'C' and resid 1743 through 1754 removed outlier: 3.606A pdb=" N ILE C1752 " --> pdb=" O SER C1748 " (cutoff:3.500A) Processing helix chain 'C' and resid 1758 through 1765 removed outlier: 3.901A pdb=" N ALA C1762 " --> pdb=" O ASP C1758 " (cutoff:3.500A) Processing helix chain 'C' and resid 1785 through 1790 removed outlier: 4.255A pdb=" N LEU C1789 " --> pdb=" O PRO C1785 " (cutoff:3.500A) Processing helix chain 'C' and resid 1791 through 1796 removed outlier: 3.644A pdb=" N TRP C1795 " --> pdb=" O ASP C1791 " (cutoff:3.500A) Processing helix chain 'C' and resid 1801 through 1816 removed outlier: 3.501A pdb=" N SER C1816 " --> pdb=" O ALA C1812 " (cutoff:3.500A) Processing helix chain 'C' and resid 1823 through 1826 Processing helix chain 'C' and resid 1827 through 1832 Processing helix chain 'C' and resid 1834 through 1852 removed outlier: 3.631A pdb=" N CYS C1838 " --> pdb=" O LYS C1834 " (cutoff:3.500A) Proline residue: C1843 - end of helix removed outlier: 3.656A pdb=" N GLN C1852 " --> pdb=" O ASP C1848 " (cutoff:3.500A) Processing helix chain 'C' and resid 1857 through 1876 removed outlier: 3.827A pdb=" N HIS C1876 " --> pdb=" O SER C1872 " (cutoff:3.500A) Processing helix chain 'C' and resid 1902 through 1918 removed outlier: 3.516A pdb=" N GLN C1906 " --> pdb=" O ASP C1902 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ARG C1918 " --> pdb=" O ASP C1914 " (cutoff:3.500A) Processing helix chain 'C' and resid 1928 through 1932 Processing helix chain 'C' and resid 1937 through 1948 removed outlier: 3.517A pdb=" N VAL C1941 " --> pdb=" O ASN C1937 " (cutoff:3.500A) Processing helix chain 'C' and resid 1950 through 1974 Processing helix chain 'C' and resid 1985 through 1997 Processing helix chain 'C' and resid 2000 through 2013 Processing helix chain 'C' and resid 2015 through 2020 Processing helix chain 'C' and resid 2028 through 2039 Processing helix chain 'C' and resid 2041 through 2052 Processing helix chain 'C' and resid 2056 through 2071 Processing helix chain 'C' and resid 2073 through 2088 Processing helix chain 'C' and resid 2092 through 2107 Processing helix chain 'C' and resid 2123 through 2137 Processing helix chain 'C' and resid 2139 through 2161 removed outlier: 3.946A pdb=" N ARG C2161 " --> pdb=" O GLU C2157 " (cutoff:3.500A) Processing helix chain 'C' and resid 2165 through 2168 Processing helix chain 'C' and resid 2169 through 2191 removed outlier: 3.839A pdb=" N GLU C2187 " --> pdb=" O GLU C2183 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N LEU C2188 " --> pdb=" O SER C2184 " (cutoff:3.500A) Processing helix chain 'C' and resid 2194 through 2212 Processing helix chain 'C' and resid 2216 through 2237 Proline residue: C2222 - end of helix Processing helix chain 'C' and resid 2243 through 2265 removed outlier: 3.785A pdb=" N ILE C2247 " --> pdb=" O GLN C2243 " (cutoff:3.500A) Processing helix chain 'C' and resid 2268 through 2282 removed outlier: 3.910A pdb=" N GLU C2272 " --> pdb=" O THR C2268 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N TYR C2281 " --> pdb=" O GLN C2277 " (cutoff:3.500A) Processing helix chain 'C' and resid 2289 through 2302 removed outlier: 3.761A pdb=" N LEU C2293 " --> pdb=" O SER C2289 " (cutoff:3.500A) Processing helix chain 'C' and resid 2304 through 2323 removed outlier: 3.902A pdb=" N ALA C2321 " --> pdb=" O LYS C2317 " (cutoff:3.500A) Processing helix chain 'C' and resid 2327 through 2349 Processing helix chain 'C' and resid 2352 through 2360 Processing helix chain 'C' and resid 2360 through 2371 removed outlier: 3.512A pdb=" N VAL C2365 " --> pdb=" O LEU C2361 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N TYR C2371 " --> pdb=" O VAL C2367 " (cutoff:3.500A) Processing helix chain 'C' and resid 2377 through 2406 Processing helix chain 'C' and resid 2407 through 2422 removed outlier: 3.623A pdb=" N GLU C2411 " --> pdb=" O SER C2407 " (cutoff:3.500A) Processing helix chain 'C' and resid 2437 through 2477 removed outlier: 3.506A pdb=" N GLY C2477 " --> pdb=" O CYS C2473 " (cutoff:3.500A) Processing helix chain 'C' and resid 2480 through 2482 No H-bonds generated for 'chain 'C' and resid 2480 through 2482' Processing helix chain 'C' and resid 2483 through 2493 removed outlier: 3.721A pdb=" N GLU C2493 " --> pdb=" O SER C2489 " (cutoff:3.500A) Processing helix chain 'C' and resid 2497 through 2508 removed outlier: 3.556A pdb=" N ASN C2501 " --> pdb=" O VAL C2497 " (cutoff:3.500A) Processing helix chain 'C' and resid 2509 through 2511 No H-bonds generated for 'chain 'C' and resid 2509 through 2511' Processing helix chain 'C' and resid 2512 through 2518 Proline residue: C2518 - end of helix Processing helix chain 'C' and resid 2519 through 2525 removed outlier: 3.602A pdb=" N ALA C2525 " --> pdb=" O TYR C2521 " (cutoff:3.500A) Processing helix chain 'C' and resid 2536 through 2552 Processing helix chain 'C' and resid 2552 through 2565 removed outlier: 3.540A pdb=" N THR C2556 " --> pdb=" O HIS C2552 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N PHE C2558 " --> pdb=" O HIS C2554 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N ILE C2559 " --> pdb=" O HIS C2555 " (cutoff:3.500A) Processing helix chain 'C' and resid 2567 through 2573 removed outlier: 4.021A pdb=" N PHE C2571 " --> pdb=" O ASN C2567 " (cutoff:3.500A) Processing helix chain 'C' and resid 2592 through 2611 removed outlier: 3.510A pdb=" N GLU C2596 " --> pdb=" O SER C2592 " (cutoff:3.500A) Processing helix chain 'C' and resid 2613 through 2632 Processing helix chain 'C' and resid 2651 through 2655 Processing helix chain 'C' and resid 2722 through 2741 removed outlier: 3.588A pdb=" N ARG C2741 " --> pdb=" O THR C2737 " (cutoff:3.500A) Processing helix chain 'C' and resid 2742 through 2748 removed outlier: 3.570A pdb=" N ARG C2748 " --> pdb=" O GLU C2744 " (cutoff:3.500A) Processing helix chain 'C' and resid 2776 through 2782 removed outlier: 3.763A pdb=" N ASN C2782 " --> pdb=" O GLU C2778 " (cutoff:3.500A) Processing helix chain 'C' and resid 2786 through 2792 Processing helix chain 'C' and resid 2797 through 2807 Processing helix chain 'C' and resid 2812 through 2826 Processing helix chain 'C' and resid 2830 through 2834 Processing helix chain 'C' and resid 2841 through 2867 Processing helix chain 'C' and resid 2872 through 2874 No H-bonds generated for 'chain 'C' and resid 2872 through 2874' Processing helix chain 'C' and resid 2895 through 2899 removed outlier: 3.571A pdb=" N LYS C2898 " --> pdb=" O GLU C2895 " (cutoff:3.500A) Processing helix chain 'C' and resid 2911 through 2917 Processing helix chain 'C' and resid 2925 through 2941 Processing helix chain 'C' and resid 2941 through 2954 removed outlier: 3.589A pdb=" N TYR C2954 " --> pdb=" O GLU C2950 " (cutoff:3.500A) Processing helix chain 'C' and resid 2963 through 2971 Processing helix chain 'C' and resid 3002 through 3018 Processing helix chain 'C' and resid 3027 through 3040 Processing helix chain 'C' and resid 3041 through 3047 removed outlier: 3.609A pdb=" N ARG C3047 " --> pdb=" O LYS C3043 " (cutoff:3.500A) Processing helix chain 'C' and resid 3048 through 3053 removed outlier: 6.061A pdb=" N GLY C3051 " --> pdb=" O LEU C3048 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 1060 through 1063 Processing sheet with id=AA2, first strand: chain 'A' and resid 2645 through 2646 removed outlier: 7.336A pdb=" N GLU A2689 " --> pdb=" O ASP A2703 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N ASP A2703 " --> pdb=" O GLU A2689 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 2645 through 2646 removed outlier: 7.336A pdb=" N GLU A2689 " --> pdb=" O ASP A2703 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N ASP A2703 " --> pdb=" O GLU A2689 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 2773 through 2775 Processing sheet with id=AA5, first strand: chain 'A' and resid 3020 through 3021 Processing sheet with id=AA6, first strand: chain 'C' and resid 1060 through 1063 Processing sheet with id=AA7, first strand: chain 'C' and resid 2645 through 2646 removed outlier: 7.336A pdb=" N GLU C2689 " --> pdb=" O ASP C2703 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N ASP C2703 " --> pdb=" O GLU C2689 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 2645 through 2646 removed outlier: 7.336A pdb=" N GLU C2689 " --> pdb=" O ASP C2703 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N ASP C2703 " --> pdb=" O GLU C2689 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 2773 through 2775 Processing sheet with id=AB1, first strand: chain 'C' and resid 3020 through 3021 2831 hydrogen bonds defined for protein. 8283 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: 9.73 Time building geometry restraints manager: 4.21 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: 14411 1.34 - 1.46: 9796 1.46 - 1.58: 20819 1.58 - 1.70: 8 1.70 - 1.82: 450 Bond restraints: 45484 Sorted by residual: bond pdb=" O3A ANP C3101 " pdb=" PB ANP C3101 " ideal model delta sigma weight residual 1.700 1.556 0.144 2.00e-02 2.50e+03 5.16e+01 bond pdb=" O3A ANP A3101 " pdb=" PB ANP A3101 " ideal model delta sigma weight residual 1.700 1.556 0.144 2.00e-02 2.50e+03 5.16e+01 bond pdb=" N3B ANP A3101 " pdb=" PG ANP A3101 " ideal model delta sigma weight residual 1.795 1.693 0.102 2.00e-02 2.50e+03 2.60e+01 bond pdb=" N3B ANP C3101 " pdb=" PG ANP C3101 " ideal model delta sigma weight residual 1.795 1.693 0.102 2.00e-02 2.50e+03 2.60e+01 bond pdb=" O5' ANP A3101 " pdb=" PA ANP A3101 " ideal model delta sigma weight residual 1.655 1.578 0.077 2.00e-02 2.50e+03 1.48e+01 ... (remaining 45479 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.49: 61280 3.49 - 6.99: 166 6.99 - 10.48: 12 10.48 - 13.98: 2 13.98 - 17.47: 4 Bond angle restraints: 61464 Sorted by residual: angle pdb=" CA GLU A1313 " pdb=" CB GLU A1313 " pdb=" CG GLU A1313 " ideal model delta sigma weight residual 114.10 130.17 -16.07 2.00e+00 2.50e-01 6.46e+01 angle pdb=" CA GLU C1313 " pdb=" CB GLU C1313 " pdb=" CG GLU C1313 " ideal model delta sigma weight residual 114.10 130.17 -16.07 2.00e+00 2.50e-01 6.46e+01 angle pdb=" PB ANP A3101 " pdb=" N3B ANP A3101 " pdb=" PG ANP A3101 " ideal model delta sigma weight residual 126.95 109.48 17.47 3.00e+00 1.11e-01 3.39e+01 angle pdb=" PB ANP C3101 " pdb=" N3B ANP C3101 " pdb=" PG ANP C3101 " ideal model delta sigma weight residual 126.95 109.48 17.47 3.00e+00 1.11e-01 3.39e+01 angle pdb=" N GLU C1313 " pdb=" CA GLU C1313 " pdb=" CB GLU C1313 " ideal model delta sigma weight residual 110.28 116.88 -6.60 1.55e+00 4.16e-01 1.81e+01 ... (remaining 61459 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 25013 17.98 - 35.96: 2231 35.96 - 53.94: 374 53.94 - 71.92: 106 71.92 - 89.91: 48 Dihedral angle restraints: 27772 sinusoidal: 11354 harmonic: 16418 Sorted by residual: dihedral pdb=" CD ARG A1262 " pdb=" NE ARG A1262 " pdb=" CZ ARG A1262 " pdb=" NH1 ARG A1262 " ideal model delta sinusoidal sigma weight residual 0.00 -88.30 88.30 1 1.00e+01 1.00e-02 9.32e+01 dihedral pdb=" CD ARG C1262 " pdb=" NE ARG C1262 " pdb=" CZ ARG C1262 " pdb=" NH1 ARG C1262 " ideal model delta sinusoidal sigma weight residual 0.00 -88.27 88.27 1 1.00e+01 1.00e-02 9.31e+01 dihedral pdb=" CA LEU C 443 " pdb=" C LEU C 443 " pdb=" N PRO C 444 " pdb=" CA PRO C 444 " ideal model delta harmonic sigma weight residual 180.00 -156.85 -23.15 0 5.00e+00 4.00e-02 2.14e+01 ... (remaining 27769 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 6077 0.054 - 0.109: 911 0.109 - 0.163: 51 0.163 - 0.218: 1 0.218 - 0.272: 4 Chirality restraints: 7044 Sorted by residual: chirality pdb=" C3' ANP C3101 " pdb=" C2' ANP C3101 " pdb=" C4' ANP C3101 " pdb=" O3' ANP C3101 " both_signs ideal model delta sigma weight residual False -2.36 -2.63 0.27 2.00e-01 2.50e+01 1.85e+00 chirality pdb=" C3' ANP A3101 " pdb=" C2' ANP A3101 " pdb=" C4' ANP A3101 " pdb=" O3' ANP A3101 " both_signs ideal model delta sigma weight residual False -2.36 -2.63 0.27 2.00e-01 2.50e+01 1.83e+00 chirality pdb=" CA GLU A1313 " pdb=" N GLU A1313 " pdb=" C GLU A1313 " pdb=" CB GLU A1313 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.82e+00 ... (remaining 7041 not shown) Planarity restraints: 7740 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A1262 " -1.028 9.50e-02 1.11e+02 4.61e-01 1.29e+02 pdb=" NE ARG A1262 " 0.067 2.00e-02 2.50e+03 pdb=" CZ ARG A1262 " 0.000 2.00e-02 2.50e+03 pdb=" NH1 ARG A1262 " -0.010 2.00e-02 2.50e+03 pdb=" NH2 ARG A1262 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C1262 " -1.028 9.50e-02 1.11e+02 4.61e-01 1.29e+02 pdb=" NE ARG C1262 " 0.067 2.00e-02 2.50e+03 pdb=" CZ ARG C1262 " 0.000 2.00e-02 2.50e+03 pdb=" NH1 ARG C1262 " -0.010 2.00e-02 2.50e+03 pdb=" NH2 ARG C1262 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 443 " 0.041 5.00e-02 4.00e+02 6.03e-02 5.82e+00 pdb=" N PRO A 444 " -0.104 5.00e-02 4.00e+02 pdb=" CA PRO A 444 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 444 " 0.034 5.00e-02 4.00e+02 ... (remaining 7737 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 300 2.64 - 3.20: 40725 3.20 - 3.77: 68710 3.77 - 4.33: 92365 4.33 - 4.90: 153385 Nonbonded interactions: 355485 Sorted by model distance: nonbonded pdb=" N GLU C1313 " pdb=" OE1 GLU C1313 " model vdw 2.072 3.120 nonbonded pdb=" N GLU A1313 " pdb=" OE1 GLU A1313 " model vdw 2.072 3.120 nonbonded pdb=" O ALA C1309 " pdb=" OE1 GLU C1313 " model vdw 2.244 3.040 nonbonded pdb=" O ALA A1309 " pdb=" OE1 GLU A1313 " model vdw 2.244 3.040 nonbonded pdb=" O PHE C1298 " pdb=" NH2 ARG C1312 " model vdw 2.266 3.120 ... (remaining 355480 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.840 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.690 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 37.040 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5911 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 0.144 45484 Z= 0.133 Angle : 0.529 17.475 61464 Z= 0.275 Chirality : 0.036 0.272 7044 Planarity : 0.008 0.461 7740 Dihedral : 14.384 89.906 17064 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 0.77 % Allowed : 0.36 % Favored : 98.87 % 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 aren not related in a simple way. whole: 2.49 (0.12), residues: 5486 helix: 2.47 (0.09), residues: 3820 sheet: 0.50 (0.61), residues: 62 loop : -0.35 (0.16), residues: 1604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C1262 TYR 0.010 0.001 TYR A1529 PHE 0.023 0.001 PHE A1491 TRP 0.016 0.001 TRP C2104 HIS 0.003 0.001 HIS A2099 Details of bonding type rmsd covalent geometry : bond 0.00260 (45484) covalent geometry : angle 0.52878 (61464) hydrogen bonds : bond 0.13303 ( 2823) hydrogen bonds : angle 4.49776 ( 8283) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10972 Ramachandran restraints generated. 5486 Oldfield, 0 Emsley, 5486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10972 Ramachandran restraints generated. 5486 Oldfield, 0 Emsley, 5486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 643 residues out of total 5058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 605 time to evaluate : 1.296 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 732 MET cc_start: 0.0712 (mtt) cc_final: 0.0348 (pmt) REVERT: A 780 MET cc_start: 0.1299 (mmt) cc_final: 0.1000 (tmm) REVERT: A 1134 MET cc_start: -0.0918 (mtm) cc_final: -0.1412 (ttm) REVERT: A 1145 ASP cc_start: 0.2028 (OUTLIER) cc_final: 0.1641 (t0) REVERT: A 1260 VAL cc_start: 0.5486 (t) cc_final: 0.5238 (p) REVERT: A 1313 GLU cc_start: 0.6186 (OUTLIER) cc_final: 0.5704 (mp0) REVERT: A 1321 MET cc_start: 0.4813 (ptt) cc_final: 0.4322 (ptm) REVERT: A 1410 LYS cc_start: 0.6547 (mttp) cc_final: 0.6201 (mmtt) REVERT: A 1556 TYR cc_start: 0.5508 (t80) cc_final: 0.5125 (t80) REVERT: A 1568 HIS cc_start: 0.6215 (m90) cc_final: 0.5816 (m-70) REVERT: A 1632 MET cc_start: 0.8392 (mmm) cc_final: 0.8040 (tpt) REVERT: A 1696 TYR cc_start: 0.6826 (t80) cc_final: 0.6380 (t80) REVERT: A 1753 TYR cc_start: 0.7493 (t80) cc_final: 0.7220 (t80) REVERT: A 1757 THR cc_start: 0.6103 (p) cc_final: 0.5805 (m) REVERT: A 2224 MET cc_start: 0.8398 (mmm) cc_final: 0.7640 (mmm) REVERT: A 2266 LYS cc_start: 0.8239 (mmtm) cc_final: 0.8022 (mmmt) REVERT: A 2290 GLU cc_start: 0.6776 (mm-30) cc_final: 0.6530 (tp30) REVERT: A 2303 LYS cc_start: 0.8310 (mmtp) cc_final: 0.8108 (mmtm) REVERT: A 2317 LYS cc_start: 0.8010 (tttm) cc_final: 0.7793 (ttpp) REVERT: A 2319 LEU cc_start: 0.6250 (mt) cc_final: 0.6041 (mt) REVERT: A 2411 GLU cc_start: 0.6123 (mt-10) cc_final: 0.5905 (mp0) REVERT: A 2418 LYS cc_start: 0.5556 (mmtt) cc_final: 0.5056 (mmtp) REVERT: A 2453 ARG cc_start: 0.5919 (mtm110) cc_final: 0.5573 (mtm110) REVERT: A 2457 GLU cc_start: 0.6394 (mm-30) cc_final: 0.6001 (mp0) REVERT: A 2527 MET cc_start: 0.7924 (mtm) cc_final: 0.7698 (mtm) REVERT: A 2531 MET cc_start: 0.5853 (mtp) cc_final: 0.5292 (mtp) REVERT: A 2606 ILE cc_start: 0.7748 (mm) cc_final: 0.7527 (mt) REVERT: A 2638 TRP cc_start: 0.6861 (m-90) cc_final: 0.6472 (m-90) REVERT: A 2667 MET cc_start: 0.7643 (mtm) cc_final: 0.7376 (mtp) REVERT: A 2691 ARG cc_start: 0.6901 (mpt180) cc_final: 0.6685 (mmt90) REVERT: A 2959 ASP cc_start: 0.7657 (t0) cc_final: 0.7435 (t0) REVERT: A 2962 MET cc_start: 0.8126 (tpp) cc_final: 0.7716 (tpp) REVERT: C 732 MET cc_start: 0.0716 (mtt) cc_final: 0.0351 (pmt) REVERT: C 780 MET cc_start: 0.1297 (mmt) cc_final: 0.0998 (tmm) REVERT: C 1134 MET cc_start: -0.0914 (mtm) cc_final: -0.1409 (ttm) REVERT: C 1145 ASP cc_start: 0.2030 (OUTLIER) cc_final: 0.1642 (t0) REVERT: C 1260 VAL cc_start: 0.5479 (t) cc_final: 0.5231 (p) REVERT: C 1313 GLU cc_start: 0.6175 (OUTLIER) cc_final: 0.5685 (mp0) REVERT: C 1321 MET cc_start: 0.4816 (ptt) cc_final: 0.4326 (ptm) REVERT: C 1410 LYS cc_start: 0.6544 (mttp) cc_final: 0.6197 (mmtt) REVERT: C 1556 TYR cc_start: 0.5509 (t80) cc_final: 0.5126 (t80) REVERT: C 1568 HIS cc_start: 0.6218 (m90) cc_final: 0.5813 (m-70) REVERT: C 1632 MET cc_start: 0.8389 (mmm) cc_final: 0.8038 (tpt) REVERT: C 1696 TYR cc_start: 0.6808 (t80) cc_final: 0.6361 (t80) REVERT: C 1720 ASN cc_start: 0.7648 (m-40) cc_final: 0.7234 (m110) REVERT: C 1753 TYR cc_start: 0.7488 (t80) cc_final: 0.7214 (t80) REVERT: C 1757 THR cc_start: 0.6112 (p) cc_final: 0.5813 (m) REVERT: C 2224 MET cc_start: 0.8403 (mmm) cc_final: 0.7644 (mmm) REVERT: C 2266 LYS cc_start: 0.8235 (mmtm) cc_final: 0.8021 (mmmt) REVERT: C 2290 GLU cc_start: 0.6776 (mm-30) cc_final: 0.6527 (tp30) REVERT: C 2303 LYS cc_start: 0.8301 (mmtp) cc_final: 0.8099 (mmtm) REVERT: C 2317 LYS cc_start: 0.8009 (tttm) cc_final: 0.7795 (ttpp) REVERT: C 2319 LEU cc_start: 0.6255 (mt) cc_final: 0.6047 (mt) REVERT: C 2411 GLU cc_start: 0.6126 (mt-10) cc_final: 0.5899 (mp0) REVERT: C 2418 LYS cc_start: 0.5528 (mmtt) cc_final: 0.5032 (mmtp) REVERT: C 2453 ARG cc_start: 0.5908 (mtm110) cc_final: 0.5562 (mtm110) REVERT: C 2457 GLU cc_start: 0.6391 (mm-30) cc_final: 0.5990 (mp0) REVERT: C 2527 MET cc_start: 0.7922 (mtm) cc_final: 0.7694 (mtm) REVERT: C 2531 MET cc_start: 0.5851 (mtp) cc_final: 0.5290 (mtp) REVERT: C 2606 ILE cc_start: 0.7746 (mm) cc_final: 0.7527 (mt) REVERT: C 2638 TRP cc_start: 0.6862 (m-90) cc_final: 0.6473 (m-90) REVERT: C 2667 MET cc_start: 0.7642 (mtm) cc_final: 0.7372 (mtp) REVERT: C 2691 ARG cc_start: 0.6906 (mpt180) cc_final: 0.6693 (mmt90) REVERT: C 2959 ASP cc_start: 0.7657 (t0) cc_final: 0.7434 (t0) REVERT: C 2962 MET cc_start: 0.8123 (tpp) cc_final: 0.7712 (tpp) outliers start: 38 outliers final: 6 residues processed: 636 average time/residue: 0.8053 time to fit residues: 616.3978 Evaluate side-chains 394 residues out of total 5058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 384 time to evaluate : 1.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 ARG Chi-restraints excluded: chain A residue 1145 ASP Chi-restraints excluded: chain A residue 1313 GLU Chi-restraints excluded: chain A residue 1386 ILE Chi-restraints excluded: chain A residue 1448 LEU Chi-restraints excluded: chain C residue 110 ARG Chi-restraints excluded: chain C residue 1145 ASP Chi-restraints excluded: chain C residue 1313 GLU Chi-restraints excluded: chain C residue 1386 ILE Chi-restraints excluded: chain C residue 1448 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 556 random chunks: chunk 394 optimal weight: 0.5980 chunk 430 optimal weight: 5.9990 chunk 41 optimal weight: 8.9990 chunk 265 optimal weight: 0.9980 chunk 523 optimal weight: 7.9990 chunk 497 optimal weight: 1.9990 chunk 414 optimal weight: 0.2980 chunk 310 optimal weight: 1.9990 chunk 488 optimal weight: 1.9990 chunk 366 optimal weight: 4.9990 chunk 223 optimal weight: 1.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 180 GLN A 654 GLN A1082 HIS A1128 GLN A1223 ASN A1380 HIS A1384 HIS A1578 GLN A2069 GLN A2108 GLN A2177 GLN A2243 GLN A2358 GLN A2697 ASN A3014 GLN C 65 GLN C 180 GLN C 654 GLN C1082 HIS C1128 GLN C1223 ASN C1380 HIS C1384 HIS C1578 GLN C2069 GLN C2108 GLN C2177 GLN C2243 GLN C2358 GLN C2697 ASN C3014 GLN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4663 r_free = 0.4663 target = 0.230454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.153558 restraints weight = 58394.865| |-----------------------------------------------------------------------------| r_work (start): 0.3792 rms_B_bonded: 5.23 r_work: 0.3263 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3130 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.1774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 45484 Z= 0.135 Angle : 0.533 9.472 61464 Z= 0.274 Chirality : 0.039 0.362 7044 Planarity : 0.004 0.108 7740 Dihedral : 5.145 88.829 6064 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 1.78 % Allowed : 7.79 % Favored : 90.43 % 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 aren not related in a simple way. whole: 2.56 (0.12), residues: 5486 helix: 2.47 (0.08), residues: 3868 sheet: 0.61 (0.61), residues: 62 loop : -0.28 (0.16), residues: 1556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C1312 TYR 0.013 0.001 TYR C1470 PHE 0.031 0.002 PHE C 897 TRP 0.017 0.001 TRP C2638 HIS 0.008 0.001 HIS A2125 Details of bonding type rmsd covalent geometry : bond 0.00295 (45484) covalent geometry : angle 0.53276 (61464) hydrogen bonds : bond 0.04490 ( 2823) hydrogen bonds : angle 3.59788 ( 8283) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10972 Ramachandran restraints generated. 5486 Oldfield, 0 Emsley, 5486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10972 Ramachandran restraints generated. 5486 Oldfield, 0 Emsley, 5486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 496 residues out of total 5058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 408 time to evaluate : 1.774 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: A 437 MET cc_start: 0.2981 (tpp) cc_final: 0.2665 (tmm) REVERT: A 780 MET cc_start: 0.1333 (mmt) cc_final: 0.0922 (tmm) REVERT: A 1134 MET cc_start: 0.0488 (mtm) cc_final: -0.0697 (mmm) REVERT: A 1215 ASP cc_start: 0.5676 (OUTLIER) cc_final: 0.5277 (m-30) REVERT: A 1338 SER cc_start: 0.6386 (t) cc_final: 0.5979 (p) REVERT: A 1433 TYR cc_start: 0.7106 (m-80) cc_final: 0.6865 (m-80) REVERT: A 1435 LYS cc_start: 0.7441 (mttp) cc_final: 0.7216 (ttmt) REVERT: A 1491 PHE cc_start: 0.6940 (t80) cc_final: 0.6683 (t80) REVERT: A 1510 LYS cc_start: 0.4933 (mmmt) cc_final: 0.4722 (mptt) REVERT: A 1556 TYR cc_start: 0.5621 (t80) cc_final: 0.5332 (t80) REVERT: A 1568 HIS cc_start: 0.6848 (m90) cc_final: 0.6204 (m-70) REVERT: A 1632 MET cc_start: 0.8609 (mmm) cc_final: 0.8197 (tpt) REVERT: A 1696 TYR cc_start: 0.6946 (t80) cc_final: 0.6570 (t80) REVERT: A 1792 ILE cc_start: 0.7345 (mm) cc_final: 0.6994 (tt) REVERT: A 1827 LEU cc_start: 0.7797 (mt) cc_final: 0.7579 (mt) REVERT: A 2028 GLN cc_start: 0.7971 (mt0) cc_final: 0.7346 (mt0) REVERT: A 2058 SER cc_start: 0.7267 (OUTLIER) cc_final: 0.6979 (m) REVERT: A 2290 GLU cc_start: 0.7849 (mm-30) cc_final: 0.7362 (tp30) REVERT: A 2411 GLU cc_start: 0.6888 (mt-10) cc_final: 0.6606 (mp0) REVERT: A 2418 LYS cc_start: 0.6029 (mmtt) cc_final: 0.5394 (mmtp) REVERT: A 2453 ARG cc_start: 0.6818 (mtm110) cc_final: 0.6518 (mtm110) REVERT: A 2457 GLU cc_start: 0.7485 (mm-30) cc_final: 0.7095 (mp0) REVERT: A 2458 ASP cc_start: 0.8363 (OUTLIER) cc_final: 0.7971 (t0) REVERT: A 2531 MET cc_start: 0.6399 (mtp) cc_final: 0.5774 (mtp) REVERT: A 2638 TRP cc_start: 0.6991 (m-90) cc_final: 0.6386 (m-90) REVERT: A 2660 GLU cc_start: 0.6502 (pt0) cc_final: 0.6244 (tp30) REVERT: A 2667 MET cc_start: 0.8216 (mtm) cc_final: 0.8010 (mtp) REVERT: A 2689 GLU cc_start: 0.7178 (pt0) cc_final: 0.6866 (mt-10) REVERT: A 2691 ARG cc_start: 0.7552 (mpt180) cc_final: 0.7307 (mmt90) REVERT: A 2697 ASN cc_start: 0.7270 (m-40) cc_final: 0.7053 (m110) REVERT: A 2719 ARG cc_start: 0.6674 (mtp180) cc_final: 0.6470 (mpp-170) REVERT: A 2799 PHE cc_start: 0.7832 (t80) cc_final: 0.7585 (t80) REVERT: A 2959 ASP cc_start: 0.8313 (t0) cc_final: 0.8066 (t70) REVERT: A 2962 MET cc_start: 0.8533 (tpp) cc_final: 0.8104 (tpp) REVERT: C 437 MET cc_start: 0.2982 (tpp) cc_final: 0.2667 (tmm) REVERT: C 780 MET cc_start: 0.1331 (mmt) cc_final: 0.0921 (tmm) REVERT: C 1134 MET cc_start: 0.0500 (mtm) cc_final: -0.0689 (mmm) REVERT: C 1215 ASP cc_start: 0.5676 (OUTLIER) cc_final: 0.5277 (m-30) REVERT: C 1338 SER cc_start: 0.6386 (t) cc_final: 0.5980 (p) REVERT: C 1433 TYR cc_start: 0.7105 (m-80) cc_final: 0.6867 (m-80) REVERT: C 1435 LYS cc_start: 0.7443 (mttp) cc_final: 0.7216 (ttmt) REVERT: C 1442 TYR cc_start: 0.7572 (t80) cc_final: 0.7309 (t80) REVERT: C 1491 PHE cc_start: 0.6936 (t80) cc_final: 0.6681 (t80) REVERT: C 1510 LYS cc_start: 0.4939 (mmmt) cc_final: 0.4729 (mptt) REVERT: C 1556 TYR cc_start: 0.5623 (t80) cc_final: 0.5334 (t80) REVERT: C 1568 HIS cc_start: 0.6847 (m90) cc_final: 0.6203 (m-70) REVERT: C 1632 MET cc_start: 0.8608 (mmm) cc_final: 0.8194 (tpt) REVERT: C 1696 TYR cc_start: 0.6947 (t80) cc_final: 0.6571 (t80) REVERT: C 1792 ILE cc_start: 0.7354 (mm) cc_final: 0.6993 (tt) REVERT: C 1827 LEU cc_start: 0.7792 (mt) cc_final: 0.7576 (mt) REVERT: C 2028 GLN cc_start: 0.7973 (mt0) cc_final: 0.7348 (mt0) REVERT: C 2058 SER cc_start: 0.7266 (OUTLIER) cc_final: 0.6979 (m) REVERT: C 2290 GLU cc_start: 0.7849 (mm-30) cc_final: 0.7361 (tp30) REVERT: C 2411 GLU cc_start: 0.6885 (mt-10) cc_final: 0.6652 (mp0) REVERT: C 2418 LYS cc_start: 0.6023 (mmtt) cc_final: 0.5391 (mmtp) REVERT: C 2453 ARG cc_start: 0.6829 (mtm110) cc_final: 0.6530 (mtm110) REVERT: C 2457 GLU cc_start: 0.7485 (mm-30) cc_final: 0.7096 (mp0) REVERT: C 2458 ASP cc_start: 0.8363 (OUTLIER) cc_final: 0.7970 (t0) REVERT: C 2531 MET cc_start: 0.6404 (mtp) cc_final: 0.5781 (mtp) REVERT: C 2638 TRP cc_start: 0.6983 (m-90) cc_final: 0.6383 (m-90) REVERT: C 2660 GLU cc_start: 0.6508 (pt0) cc_final: 0.6248 (tp30) REVERT: C 2667 MET cc_start: 0.8207 (mtm) cc_final: 0.8002 (mtp) REVERT: C 2689 GLU cc_start: 0.7173 (pt0) cc_final: 0.6864 (mt-10) REVERT: C 2691 ARG cc_start: 0.7546 (mpt180) cc_final: 0.7302 (mmt90) REVERT: C 2697 ASN cc_start: 0.7263 (m-40) cc_final: 0.7046 (m110) REVERT: C 2719 ARG cc_start: 0.6669 (mtp180) cc_final: 0.6467 (mpp-170) REVERT: C 2784 GLU cc_start: 0.7014 (pm20) cc_final: 0.6808 (pm20) REVERT: C 2799 PHE cc_start: 0.7833 (t80) cc_final: 0.7579 (t80) REVERT: C 2962 MET cc_start: 0.8531 (tpp) cc_final: 0.8095 (tpp) outliers start: 88 outliers final: 24 residues processed: 466 average time/residue: 0.8383 time to fit residues: 473.2065 Evaluate side-chains 382 residues out of total 5058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 352 time to evaluate : 1.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 ARG Chi-restraints excluded: chain A residue 433 SER Chi-restraints excluded: chain A residue 1215 ASP Chi-restraints excluded: chain A residue 1313 GLU Chi-restraints excluded: chain A residue 1384 HIS Chi-restraints excluded: chain A residue 1404 ILE Chi-restraints excluded: chain A residue 1678 VAL Chi-restraints excluded: chain A residue 1747 HIS Chi-restraints excluded: chain A residue 1825 GLN Chi-restraints excluded: chain A residue 2057 SER Chi-restraints excluded: chain A residue 2058 SER Chi-restraints excluded: chain A residue 2447 LEU Chi-restraints excluded: chain A residue 2458 ASP Chi-restraints excluded: chain A residue 3043 LYS Chi-restraints excluded: chain A residue 3052 TRP Chi-restraints excluded: chain C residue 110 ARG Chi-restraints excluded: chain C residue 433 SER Chi-restraints excluded: chain C residue 1215 ASP Chi-restraints excluded: chain C residue 1313 GLU Chi-restraints excluded: chain C residue 1384 HIS Chi-restraints excluded: chain C residue 1404 ILE Chi-restraints excluded: chain C residue 1678 VAL Chi-restraints excluded: chain C residue 1747 HIS Chi-restraints excluded: chain C residue 1825 GLN Chi-restraints excluded: chain C residue 2057 SER Chi-restraints excluded: chain C residue 2058 SER Chi-restraints excluded: chain C residue 2447 LEU Chi-restraints excluded: chain C residue 2458 ASP Chi-restraints excluded: chain C residue 3043 LYS Chi-restraints excluded: chain C residue 3052 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 556 random chunks: chunk 378 optimal weight: 7.9990 chunk 531 optimal weight: 1.9990 chunk 395 optimal weight: 0.8980 chunk 522 optimal weight: 0.8980 chunk 176 optimal weight: 6.9990 chunk 195 optimal weight: 3.9990 chunk 144 optimal weight: 2.9990 chunk 515 optimal weight: 0.0670 chunk 469 optimal weight: 1.9990 chunk 140 optimal weight: 0.7980 chunk 347 optimal weight: 10.0000 overall best weight: 0.9320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1128 GLN A1380 HIS A1384 HIS A1535 GLN A2069 GLN A2358 GLN C1128 GLN C1380 HIS C1384 HIS C1535 GLN C1660 ASN C2069 GLN C2358 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4657 r_free = 0.4657 target = 0.230101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.152857 restraints weight = 58640.939| |-----------------------------------------------------------------------------| r_work (start): 0.3792 rms_B_bonded: 4.56 r_work: 0.3253 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3123 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.2144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 45484 Z= 0.112 Angle : 0.483 10.526 61464 Z= 0.247 Chirality : 0.037 0.193 7044 Planarity : 0.003 0.051 7740 Dihedral : 4.710 86.999 6052 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.70 % Allowed : 9.91 % Favored : 88.39 % 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 aren not related in a simple way. whole: 2.66 (0.12), residues: 5486 helix: 2.58 (0.08), residues: 3840 sheet: 0.52 (0.59), residues: 62 loop : -0.29 (0.15), residues: 1584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C1086 TYR 0.013 0.001 TYR C1470 PHE 0.021 0.001 PHE A 897 TRP 0.013 0.001 TRP A2104 HIS 0.021 0.001 HIS A1384 Details of bonding type rmsd covalent geometry : bond 0.00240 (45484) covalent geometry : angle 0.48344 (61464) hydrogen bonds : bond 0.04057 ( 2823) hydrogen bonds : angle 3.45912 ( 8283) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10972 Ramachandran restraints generated. 5486 Oldfield, 0 Emsley, 5486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10972 Ramachandran restraints generated. 5486 Oldfield, 0 Emsley, 5486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 441 residues out of total 5058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 357 time to evaluate : 1.825 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 577 MET cc_start: 0.0653 (ttp) cc_final: -0.0117 (tmt) REVERT: A 780 MET cc_start: 0.1442 (mmt) cc_final: 0.1033 (tmm) REVERT: A 1134 MET cc_start: 0.0833 (mtm) cc_final: -0.0484 (mmm) REVERT: A 1308 MET cc_start: 0.3190 (tmt) cc_final: 0.2946 (ppp) REVERT: A 1321 MET cc_start: 0.4681 (ptt) cc_final: 0.4339 (ptm) REVERT: A 1433 TYR cc_start: 0.7064 (m-80) cc_final: 0.6795 (m-80) REVERT: A 1435 LYS cc_start: 0.7239 (mttp) cc_final: 0.6991 (ttmt) REVERT: A 1448 LEU cc_start: 0.7915 (OUTLIER) cc_final: 0.7559 (tt) REVERT: A 1491 PHE cc_start: 0.6924 (t80) cc_final: 0.6662 (t80) REVERT: A 1510 LYS cc_start: 0.4932 (mmmt) cc_final: 0.4716 (mptt) REVERT: A 1556 TYR cc_start: 0.5769 (t80) cc_final: 0.5430 (t80) REVERT: A 1568 HIS cc_start: 0.7053 (m90) cc_final: 0.6282 (m-70) REVERT: A 1632 MET cc_start: 0.8646 (mmm) cc_final: 0.8256 (tpt) REVERT: A 1696 TYR cc_start: 0.6991 (t80) cc_final: 0.6556 (t80) REVERT: A 1707 GLU cc_start: 0.7570 (OUTLIER) cc_final: 0.7179 (mp0) REVERT: A 1776 GLU cc_start: 0.6287 (mm-30) cc_final: 0.5827 (mp0) REVERT: A 1827 LEU cc_start: 0.7827 (mt) cc_final: 0.7361 (mt) REVERT: A 2028 GLN cc_start: 0.7961 (mt0) cc_final: 0.7281 (mt0) REVERT: A 2058 SER cc_start: 0.7369 (OUTLIER) cc_final: 0.7053 (m) REVERT: A 2290 GLU cc_start: 0.7865 (mm-30) cc_final: 0.7344 (tp30) REVERT: A 2411 GLU cc_start: 0.7185 (mt-10) cc_final: 0.6875 (mp0) REVERT: A 2418 LYS cc_start: 0.6090 (mmtt) cc_final: 0.5471 (mmtp) REVERT: A 2453 ARG cc_start: 0.6821 (mtm110) cc_final: 0.6498 (mtm110) REVERT: A 2457 GLU cc_start: 0.7597 (mm-30) cc_final: 0.7246 (mp0) REVERT: A 2458 ASP cc_start: 0.8404 (OUTLIER) cc_final: 0.7949 (t0) REVERT: A 2531 MET cc_start: 0.6407 (mtp) cc_final: 0.5778 (mtp) REVERT: A 2596 GLU cc_start: 0.7483 (OUTLIER) cc_final: 0.7158 (mm-30) REVERT: A 2636 THR cc_start: 0.7129 (t) cc_final: 0.6844 (m) REVERT: A 2638 TRP cc_start: 0.6913 (m-90) cc_final: 0.6608 (m-90) REVERT: A 2660 GLU cc_start: 0.6572 (pt0) cc_final: 0.6372 (tp30) REVERT: A 2667 MET cc_start: 0.8220 (mtm) cc_final: 0.8009 (mtp) REVERT: A 2691 ARG cc_start: 0.7612 (mpt180) cc_final: 0.7259 (mmt90) REVERT: A 2697 ASN cc_start: 0.7300 (m-40) cc_final: 0.7058 (m110) REVERT: A 2799 PHE cc_start: 0.7897 (t80) cc_final: 0.7628 (t80) REVERT: A 2962 MET cc_start: 0.8472 (tpp) cc_final: 0.8180 (tpp) REVERT: C 577 MET cc_start: 0.0655 (ttp) cc_final: -0.0117 (tmt) REVERT: C 780 MET cc_start: 0.1442 (mmt) cc_final: 0.1035 (tmm) REVERT: C 1134 MET cc_start: 0.0826 (mtm) cc_final: -0.0489 (mmm) REVERT: C 1308 MET cc_start: 0.3192 (tmt) cc_final: 0.2945 (ppp) REVERT: C 1321 MET cc_start: 0.4689 (ptt) cc_final: 0.4344 (ptm) REVERT: C 1433 TYR cc_start: 0.7064 (m-80) cc_final: 0.6792 (m-80) REVERT: C 1435 LYS cc_start: 0.7238 (mttp) cc_final: 0.6993 (ttmt) REVERT: C 1448 LEU cc_start: 0.7915 (OUTLIER) cc_final: 0.7559 (tt) REVERT: C 1491 PHE cc_start: 0.6930 (t80) cc_final: 0.6667 (t80) REVERT: C 1510 LYS cc_start: 0.4932 (mmmt) cc_final: 0.4715 (mptt) REVERT: C 1556 TYR cc_start: 0.5759 (t80) cc_final: 0.5420 (t80) REVERT: C 1568 HIS cc_start: 0.7061 (m90) cc_final: 0.6289 (m-70) REVERT: C 1632 MET cc_start: 0.8642 (mmm) cc_final: 0.8254 (tpt) REVERT: C 1696 TYR cc_start: 0.6981 (t80) cc_final: 0.6550 (t80) REVERT: C 1707 GLU cc_start: 0.7579 (OUTLIER) cc_final: 0.7192 (mp0) REVERT: C 1776 GLU cc_start: 0.6144 (mm-30) cc_final: 0.5717 (mp0) REVERT: C 1827 LEU cc_start: 0.7823 (mt) cc_final: 0.7361 (mt) REVERT: C 2028 GLN cc_start: 0.7963 (mt0) cc_final: 0.7281 (mt0) REVERT: C 2058 SER cc_start: 0.7372 (OUTLIER) cc_final: 0.7057 (m) REVERT: C 2290 GLU cc_start: 0.7857 (mm-30) cc_final: 0.7341 (tp30) REVERT: C 2411 GLU cc_start: 0.7186 (mt-10) cc_final: 0.6877 (mp0) REVERT: C 2418 LYS cc_start: 0.6079 (mmtt) cc_final: 0.5462 (mmtp) REVERT: C 2453 ARG cc_start: 0.6841 (mtm110) cc_final: 0.6519 (mtm110) REVERT: C 2457 GLU cc_start: 0.7600 (mm-30) cc_final: 0.7248 (mp0) REVERT: C 2458 ASP cc_start: 0.8407 (OUTLIER) cc_final: 0.7954 (t0) REVERT: C 2531 MET cc_start: 0.6403 (mtp) cc_final: 0.5770 (mtp) REVERT: C 2596 GLU cc_start: 0.7477 (OUTLIER) cc_final: 0.7147 (mm-30) REVERT: C 2636 THR cc_start: 0.7137 (t) cc_final: 0.6853 (m) REVERT: C 2638 TRP cc_start: 0.6904 (m-90) cc_final: 0.6601 (m-90) REVERT: C 2660 GLU cc_start: 0.6587 (pt0) cc_final: 0.6380 (tp30) REVERT: C 2667 MET cc_start: 0.8232 (mtm) cc_final: 0.8021 (mtp) REVERT: C 2691 ARG cc_start: 0.7610 (mpt180) cc_final: 0.7256 (mmt90) REVERT: C 2697 ASN cc_start: 0.7296 (m-40) cc_final: 0.7056 (m110) REVERT: C 2784 GLU cc_start: 0.6972 (pm20) cc_final: 0.6696 (pm20) REVERT: C 2799 PHE cc_start: 0.7895 (t80) cc_final: 0.7622 (t80) REVERT: C 2962 MET cc_start: 0.8469 (tpp) cc_final: 0.8172 (tpp) outliers start: 84 outliers final: 25 residues processed: 411 average time/residue: 0.8598 time to fit residues: 427.3944 Evaluate side-chains 369 residues out of total 5058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 334 time to evaluate : 1.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 433 SER Chi-restraints excluded: chain A residue 1313 GLU Chi-restraints excluded: chain A residue 1404 ILE Chi-restraints excluded: chain A residue 1448 LEU Chi-restraints excluded: chain A residue 1643 ILE Chi-restraints excluded: chain A residue 1707 GLU Chi-restraints excluded: chain A residue 1747 HIS Chi-restraints excluded: chain A residue 1836 ASP Chi-restraints excluded: chain A residue 1971 GLU Chi-restraints excluded: chain A residue 2057 SER Chi-restraints excluded: chain A residue 2058 SER Chi-restraints excluded: chain A residue 2447 LEU Chi-restraints excluded: chain A residue 2458 ASP Chi-restraints excluded: chain A residue 2596 GLU Chi-restraints excluded: chain A residue 2810 LYS Chi-restraints excluded: chain A residue 2946 LEU Chi-restraints excluded: chain A residue 3043 LYS Chi-restraints excluded: chain A residue 3052 TRP Chi-restraints excluded: chain C residue 433 SER Chi-restraints excluded: chain C residue 1313 GLU Chi-restraints excluded: chain C residue 1448 LEU Chi-restraints excluded: chain C residue 1643 ILE Chi-restraints excluded: chain C residue 1707 GLU Chi-restraints excluded: chain C residue 1747 HIS Chi-restraints excluded: chain C residue 1836 ASP Chi-restraints excluded: chain C residue 1971 GLU Chi-restraints excluded: chain C residue 2057 SER Chi-restraints excluded: chain C residue 2058 SER Chi-restraints excluded: chain C residue 2447 LEU Chi-restraints excluded: chain C residue 2458 ASP Chi-restraints excluded: chain C residue 2596 GLU Chi-restraints excluded: chain C residue 2810 LYS Chi-restraints excluded: chain C residue 2946 LEU Chi-restraints excluded: chain C residue 3043 LYS Chi-restraints excluded: chain C residue 3052 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 556 random chunks: chunk 412 optimal weight: 0.9990 chunk 311 optimal weight: 2.9990 chunk 313 optimal weight: 9.9990 chunk 12 optimal weight: 0.0570 chunk 158 optimal weight: 9.9990 chunk 278 optimal weight: 50.0000 chunk 443 optimal weight: 2.9990 chunk 299 optimal weight: 8.9990 chunk 370 optimal weight: 0.9990 chunk 359 optimal weight: 5.9990 chunk 186 optimal weight: 3.9990 overall best weight: 1.6106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 628 GLN A 945 HIS A1128 GLN A1331 GLN A1384 HIS A2069 GLN C 65 GLN C 628 GLN C 945 HIS C1128 GLN C1331 GLN C1384 HIS C1660 ASN C2069 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4641 r_free = 0.4641 target = 0.228352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.149089 restraints weight = 58400.393| |-----------------------------------------------------------------------------| r_work (start): 0.3732 rms_B_bonded: 4.84 r_work: 0.3228 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3097 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.2897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 45484 Z= 0.141 Angle : 0.542 8.817 61464 Z= 0.278 Chirality : 0.039 0.164 7044 Planarity : 0.004 0.050 7740 Dihedral : 4.867 81.633 6044 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.20 % Allowed : 11.43 % Favored : 86.37 % 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 aren not related in a simple way. whole: 2.17 (0.11), residues: 5486 helix: 2.23 (0.08), residues: 3860 sheet: 0.45 (0.59), residues: 62 loop : -0.55 (0.15), residues: 1564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A1575 TYR 0.019 0.002 TYR A1470 PHE 0.021 0.002 PHE A2143 TRP 0.014 0.002 TRP C2638 HIS 0.008 0.001 HIS A2208 Details of bonding type rmsd covalent geometry : bond 0.00319 (45484) covalent geometry : angle 0.54219 (61464) hydrogen bonds : bond 0.04799 ( 2823) hydrogen bonds : angle 3.62356 ( 8283) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10972 Ramachandran restraints generated. 5486 Oldfield, 0 Emsley, 5486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10972 Ramachandran restraints generated. 5486 Oldfield, 0 Emsley, 5486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 464 residues out of total 5058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 355 time to evaluate : 1.865 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: A 437 MET cc_start: 0.2768 (tpp) cc_final: 0.2376 (tmm) REVERT: A 577 MET cc_start: 0.0726 (ttp) cc_final: -0.0080 (tmt) REVERT: A 660 MET cc_start: 0.1431 (mmm) cc_final: 0.1225 (mtt) REVERT: A 780 MET cc_start: 0.1195 (mmt) cc_final: 0.0711 (ptp) REVERT: A 1131 MET cc_start: 0.1838 (mtm) cc_final: 0.1520 (mtm) REVERT: A 1134 MET cc_start: 0.1269 (mtm) cc_final: -0.0307 (mmm) REVERT: A 1308 MET cc_start: 0.3340 (tmt) cc_final: 0.3079 (ppp) REVERT: A 1321 MET cc_start: 0.4458 (ptt) cc_final: 0.4081 (ptm) REVERT: A 1353 GLU cc_start: 0.4563 (mm-30) cc_final: 0.3987 (mm-30) REVERT: A 1433 TYR cc_start: 0.7014 (m-80) cc_final: 0.6801 (m-80) REVERT: A 1491 PHE cc_start: 0.6964 (t80) cc_final: 0.6697 (t80) REVERT: A 1556 TYR cc_start: 0.5857 (t80) cc_final: 0.5520 (t80) REVERT: A 1563 ASP cc_start: 0.7604 (OUTLIER) cc_final: 0.7368 (m-30) REVERT: A 1632 MET cc_start: 0.8701 (mmm) cc_final: 0.8238 (tpt) REVERT: A 1707 GLU cc_start: 0.7703 (OUTLIER) cc_final: 0.7149 (mp0) REVERT: A 1776 GLU cc_start: 0.6278 (mm-30) cc_final: 0.5878 (mp0) REVERT: A 1827 LEU cc_start: 0.7863 (mt) cc_final: 0.7390 (mt) REVERT: A 1971 GLU cc_start: 0.5877 (OUTLIER) cc_final: 0.5618 (mm-30) REVERT: A 2028 GLN cc_start: 0.7831 (mt0) cc_final: 0.7354 (mt0) REVERT: A 2058 SER cc_start: 0.7607 (OUTLIER) cc_final: 0.7327 (m) REVERT: A 2094 GLU cc_start: 0.6830 (pm20) cc_final: 0.6318 (tt0) REVERT: A 2177 GLN cc_start: 0.9016 (OUTLIER) cc_final: 0.8502 (tt0) REVERT: A 2332 LEU cc_start: 0.7922 (OUTLIER) cc_final: 0.7492 (mp) REVERT: A 2411 GLU cc_start: 0.7114 (mt-10) cc_final: 0.6852 (mp0) REVERT: A 2418 LYS cc_start: 0.6117 (mmtt) cc_final: 0.5534 (mmtp) REVERT: A 2453 ARG cc_start: 0.6997 (mtm110) cc_final: 0.6607 (mtm110) REVERT: A 2457 GLU cc_start: 0.7647 (mm-30) cc_final: 0.7294 (mp0) REVERT: A 2458 ASP cc_start: 0.8414 (OUTLIER) cc_final: 0.7907 (t0) REVERT: A 2531 MET cc_start: 0.6498 (mtp) cc_final: 0.5942 (mtp) REVERT: A 2596 GLU cc_start: 0.7617 (OUTLIER) cc_final: 0.7335 (mm-30) REVERT: A 2636 THR cc_start: 0.7104 (t) cc_final: 0.6881 (m) REVERT: A 2638 TRP cc_start: 0.6961 (m-90) cc_final: 0.6681 (m-90) REVERT: A 2667 MET cc_start: 0.8069 (mtm) cc_final: 0.7849 (mtp) REVERT: A 2763 ARG cc_start: 0.7201 (mtp-110) cc_final: 0.6838 (ttm170) REVERT: A 2799 PHE cc_start: 0.7751 (t80) cc_final: 0.7379 (t80) REVERT: A 2962 MET cc_start: 0.8412 (tpp) cc_final: 0.8180 (tpp) REVERT: C 437 MET cc_start: 0.2770 (tpp) cc_final: 0.2380 (tmm) REVERT: C 577 MET cc_start: 0.0731 (ttp) cc_final: -0.0073 (tmt) REVERT: C 660 MET cc_start: 0.1426 (mmm) cc_final: 0.1223 (mtt) REVERT: C 780 MET cc_start: 0.1196 (mmt) cc_final: 0.0709 (ptp) REVERT: C 1131 MET cc_start: 0.1835 (mtm) cc_final: 0.1519 (mtm) REVERT: C 1134 MET cc_start: 0.1255 (mtm) cc_final: -0.0314 (mmm) REVERT: C 1308 MET cc_start: 0.3321 (tmt) cc_final: 0.3063 (ppp) REVERT: C 1321 MET cc_start: 0.4464 (ptt) cc_final: 0.4083 (ptm) REVERT: C 1353 GLU cc_start: 0.4566 (mm-30) cc_final: 0.3990 (mm-30) REVERT: C 1433 TYR cc_start: 0.7014 (m-80) cc_final: 0.6799 (m-80) REVERT: C 1491 PHE cc_start: 0.6964 (t80) cc_final: 0.6693 (t80) REVERT: C 1556 TYR cc_start: 0.5852 (t80) cc_final: 0.5514 (t80) REVERT: C 1563 ASP cc_start: 0.7597 (OUTLIER) cc_final: 0.7359 (m-30) REVERT: C 1632 MET cc_start: 0.8705 (mmm) cc_final: 0.8242 (tpt) REVERT: C 1707 GLU cc_start: 0.7717 (OUTLIER) cc_final: 0.7167 (mp0) REVERT: C 1776 GLU cc_start: 0.6291 (mm-30) cc_final: 0.5879 (mp0) REVERT: C 1827 LEU cc_start: 0.7876 (mt) cc_final: 0.7408 (mt) REVERT: C 1971 GLU cc_start: 0.5872 (OUTLIER) cc_final: 0.5613 (mm-30) REVERT: C 2028 GLN cc_start: 0.7839 (mt0) cc_final: 0.7367 (mt0) REVERT: C 2058 SER cc_start: 0.7604 (OUTLIER) cc_final: 0.7324 (m) REVERT: C 2094 GLU cc_start: 0.6946 (pm20) cc_final: 0.6461 (tt0) REVERT: C 2177 GLN cc_start: 0.9018 (OUTLIER) cc_final: 0.8502 (tt0) REVERT: C 2332 LEU cc_start: 0.7933 (OUTLIER) cc_final: 0.7505 (mp) REVERT: C 2411 GLU cc_start: 0.7159 (mt-10) cc_final: 0.6868 (mp0) REVERT: C 2418 LYS cc_start: 0.6102 (mmtt) cc_final: 0.5522 (mmtp) REVERT: C 2453 ARG cc_start: 0.7003 (mtm110) cc_final: 0.6609 (mtm110) REVERT: C 2457 GLU cc_start: 0.7655 (mm-30) cc_final: 0.7311 (mp0) REVERT: C 2458 ASP cc_start: 0.8412 (OUTLIER) cc_final: 0.7906 (t0) REVERT: C 2531 MET cc_start: 0.6504 (mtp) cc_final: 0.5949 (mtp) REVERT: C 2596 GLU cc_start: 0.7612 (OUTLIER) cc_final: 0.7326 (mm-30) REVERT: C 2636 THR cc_start: 0.7101 (t) cc_final: 0.6879 (m) REVERT: C 2638 TRP cc_start: 0.6959 (m-90) cc_final: 0.6679 (m-90) REVERT: C 2667 MET cc_start: 0.8086 (mtm) cc_final: 0.7865 (mtp) REVERT: C 2763 ARG cc_start: 0.7211 (mtp-110) cc_final: 0.6846 (ttm170) REVERT: C 2799 PHE cc_start: 0.7755 (t80) cc_final: 0.7381 (t80) REVERT: C 2962 MET cc_start: 0.8384 (tpp) cc_final: 0.8140 (tpp) outliers start: 109 outliers final: 32 residues processed: 430 average time/residue: 0.9535 time to fit residues: 494.2216 Evaluate side-chains 375 residues out of total 5058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 327 time to evaluate : 1.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 433 SER Chi-restraints excluded: chain A residue 937 GLU Chi-restraints excluded: chain A residue 1256 ILE Chi-restraints excluded: chain A residue 1313 GLU Chi-restraints excluded: chain A residue 1404 ILE Chi-restraints excluded: chain A residue 1563 ASP Chi-restraints excluded: chain A residue 1623 LEU Chi-restraints excluded: chain A residue 1678 VAL Chi-restraints excluded: chain A residue 1707 GLU Chi-restraints excluded: chain A residue 1727 VAL Chi-restraints excluded: chain A residue 1836 ASP Chi-restraints excluded: chain A residue 1971 GLU Chi-restraints excluded: chain A residue 2057 SER Chi-restraints excluded: chain A residue 2058 SER Chi-restraints excluded: chain A residue 2082 LYS Chi-restraints excluded: chain A residue 2177 GLN Chi-restraints excluded: chain A residue 2332 LEU Chi-restraints excluded: chain A residue 2447 LEU Chi-restraints excluded: chain A residue 2458 ASP Chi-restraints excluded: chain A residue 2596 GLU Chi-restraints excluded: chain A residue 2742 ASN Chi-restraints excluded: chain A residue 2806 MET Chi-restraints excluded: chain A residue 3043 LYS Chi-restraints excluded: chain C residue 97 ILE Chi-restraints excluded: chain C residue 433 SER Chi-restraints excluded: chain C residue 937 GLU Chi-restraints excluded: chain C residue 1256 ILE Chi-restraints excluded: chain C residue 1313 GLU Chi-restraints excluded: chain C residue 1404 ILE Chi-restraints excluded: chain C residue 1563 ASP Chi-restraints excluded: chain C residue 1623 LEU Chi-restraints excluded: chain C residue 1678 VAL Chi-restraints excluded: chain C residue 1707 GLU Chi-restraints excluded: chain C residue 1727 VAL Chi-restraints excluded: chain C residue 1836 ASP Chi-restraints excluded: chain C residue 1971 GLU Chi-restraints excluded: chain C residue 2057 SER Chi-restraints excluded: chain C residue 2058 SER Chi-restraints excluded: chain C residue 2082 LYS Chi-restraints excluded: chain C residue 2177 GLN Chi-restraints excluded: chain C residue 2332 LEU Chi-restraints excluded: chain C residue 2447 LEU Chi-restraints excluded: chain C residue 2458 ASP Chi-restraints excluded: chain C residue 2596 GLU Chi-restraints excluded: chain C residue 2742 ASN Chi-restraints excluded: chain C residue 2806 MET Chi-restraints excluded: chain C residue 3043 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 556 random chunks: chunk 160 optimal weight: 4.9990 chunk 472 optimal weight: 0.7980 chunk 107 optimal weight: 3.9990 chunk 317 optimal weight: 2.9990 chunk 352 optimal weight: 2.9990 chunk 290 optimal weight: 20.0000 chunk 430 optimal weight: 4.9990 chunk 328 optimal weight: 10.0000 chunk 475 optimal weight: 0.8980 chunk 45 optimal weight: 9.9990 chunk 485 optimal weight: 0.4980 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 GLN A1384 HIS A1660 ASN A2069 GLN A2070 ASN C 65 GLN C1384 HIS C1660 ASN C2069 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4641 r_free = 0.4641 target = 0.228359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.149219 restraints weight = 58303.439| |-----------------------------------------------------------------------------| r_work (start): 0.3742 rms_B_bonded: 4.59 r_work: 0.3240 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3109 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.3211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 45484 Z= 0.137 Angle : 0.521 10.185 61464 Z= 0.268 Chirality : 0.039 0.166 7044 Planarity : 0.004 0.045 7740 Dihedral : 4.878 84.641 6044 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 2.42 % Allowed : 12.47 % Favored : 85.10 % 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 aren not related in a simple way. whole: 2.18 (0.11), residues: 5486 helix: 2.24 (0.08), residues: 3840 sheet: 0.39 (0.60), residues: 62 loop : -0.53 (0.15), residues: 1584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C2604 TYR 0.013 0.001 TYR C1470 PHE 0.018 0.001 PHE A2143 TRP 0.015 0.002 TRP C2104 HIS 0.006 0.001 HIS A1083 Details of bonding type rmsd covalent geometry : bond 0.00315 (45484) covalent geometry : angle 0.52074 (61464) hydrogen bonds : bond 0.04432 ( 2823) hydrogen bonds : angle 3.56907 ( 8283) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10972 Ramachandran restraints generated. 5486 Oldfield, 0 Emsley, 5486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10972 Ramachandran restraints generated. 5486 Oldfield, 0 Emsley, 5486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 472 residues out of total 5058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 352 time to evaluate : 1.041 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: A 780 MET cc_start: 0.1234 (mmt) cc_final: 0.0830 (ptp) REVERT: A 1064 MET cc_start: 0.0868 (pmm) cc_final: 0.0424 (ptp) REVERT: A 1308 MET cc_start: 0.3413 (tmt) cc_final: 0.3102 (ppp) REVERT: A 1353 GLU cc_start: 0.4823 (mm-30) cc_final: 0.4180 (mm-30) REVERT: A 1491 PHE cc_start: 0.6928 (t80) cc_final: 0.6640 (t80) REVERT: A 1556 TYR cc_start: 0.5837 (t80) cc_final: 0.5514 (t80) REVERT: A 1563 ASP cc_start: 0.7641 (OUTLIER) cc_final: 0.7384 (m-30) REVERT: A 1632 MET cc_start: 0.8654 (mmm) cc_final: 0.8236 (tpt) REVERT: A 1707 GLU cc_start: 0.7704 (OUTLIER) cc_final: 0.7113 (mp0) REVERT: A 1776 GLU cc_start: 0.6337 (mm-30) cc_final: 0.5988 (mp0) REVERT: A 1827 LEU cc_start: 0.7986 (mt) cc_final: 0.7563 (mt) REVERT: A 2028 GLN cc_start: 0.7803 (mt0) cc_final: 0.7291 (mt0) REVERT: A 2058 SER cc_start: 0.7579 (OUTLIER) cc_final: 0.7294 (m) REVERT: A 2094 GLU cc_start: 0.6739 (pm20) cc_final: 0.6235 (tt0) REVERT: A 2177 GLN cc_start: 0.9007 (OUTLIER) cc_final: 0.8507 (tt0) REVERT: A 2279 LYS cc_start: 0.8569 (mttt) cc_final: 0.8249 (mtmp) REVERT: A 2332 LEU cc_start: 0.7852 (OUTLIER) cc_final: 0.7544 (mp) REVERT: A 2418 LYS cc_start: 0.6232 (mmtt) cc_final: 0.5540 (mmtp) REVERT: A 2453 ARG cc_start: 0.6978 (mtm110) cc_final: 0.6626 (mtm110) REVERT: A 2457 GLU cc_start: 0.7634 (mm-30) cc_final: 0.7312 (mp0) REVERT: A 2458 ASP cc_start: 0.8421 (OUTLIER) cc_final: 0.7865 (t0) REVERT: A 2531 MET cc_start: 0.6511 (mtp) cc_final: 0.5980 (mtp) REVERT: A 2596 GLU cc_start: 0.7623 (OUTLIER) cc_final: 0.7341 (mm-30) REVERT: A 2612 ARG cc_start: 0.6947 (ttm170) cc_final: 0.6533 (ttp-170) REVERT: A 2636 THR cc_start: 0.7016 (t) cc_final: 0.6779 (m) REVERT: A 2667 MET cc_start: 0.8053 (mtm) cc_final: 0.7827 (mtp) REVERT: A 2763 ARG cc_start: 0.7283 (mtp-110) cc_final: 0.6933 (ttm170) REVERT: A 2799 PHE cc_start: 0.7720 (t80) cc_final: 0.7323 (t80) REVERT: C 780 MET cc_start: 0.1238 (mmt) cc_final: 0.0833 (ptp) REVERT: C 1064 MET cc_start: 0.0868 (pmm) cc_final: 0.0423 (ptp) REVERT: C 1308 MET cc_start: 0.3409 (tmt) cc_final: 0.3097 (ppp) REVERT: C 1353 GLU cc_start: 0.4824 (mm-30) cc_final: 0.4220 (mm-30) REVERT: C 1491 PHE cc_start: 0.6924 (t80) cc_final: 0.6633 (t80) REVERT: C 1556 TYR cc_start: 0.5841 (t80) cc_final: 0.5518 (t80) REVERT: C 1563 ASP cc_start: 0.7642 (OUTLIER) cc_final: 0.7412 (m-30) REVERT: C 1632 MET cc_start: 0.8657 (mmm) cc_final: 0.8239 (tpt) REVERT: C 1707 GLU cc_start: 0.7707 (OUTLIER) cc_final: 0.7122 (mp0) REVERT: C 1776 GLU cc_start: 0.6338 (mm-30) cc_final: 0.5991 (mp0) REVERT: C 1827 LEU cc_start: 0.7997 (mt) cc_final: 0.7577 (mt) REVERT: C 2028 GLN cc_start: 0.7804 (mt0) cc_final: 0.7287 (mt0) REVERT: C 2058 SER cc_start: 0.7573 (OUTLIER) cc_final: 0.7288 (m) REVERT: C 2094 GLU cc_start: 0.6732 (pm20) cc_final: 0.6234 (tt0) REVERT: C 2177 GLN cc_start: 0.9009 (OUTLIER) cc_final: 0.8506 (tt0) REVERT: C 2279 LYS cc_start: 0.8567 (mttt) cc_final: 0.8248 (mtmp) REVERT: C 2332 LEU cc_start: 0.7865 (OUTLIER) cc_final: 0.7556 (mp) REVERT: C 2418 LYS cc_start: 0.6216 (mmtt) cc_final: 0.5527 (mmtp) REVERT: C 2453 ARG cc_start: 0.6989 (mtm110) cc_final: 0.6636 (mtm110) REVERT: C 2457 GLU cc_start: 0.7643 (mm-30) cc_final: 0.7322 (mp0) REVERT: C 2458 ASP cc_start: 0.8416 (OUTLIER) cc_final: 0.7863 (t0) REVERT: C 2531 MET cc_start: 0.6514 (mtp) cc_final: 0.5983 (mtp) REVERT: C 2596 GLU cc_start: 0.7620 (OUTLIER) cc_final: 0.7335 (mm-30) REVERT: C 2612 ARG cc_start: 0.6945 (ttm170) cc_final: 0.6529 (ttp-170) REVERT: C 2636 THR cc_start: 0.7012 (t) cc_final: 0.6771 (m) REVERT: C 2667 MET cc_start: 0.8077 (mtm) cc_final: 0.7836 (mtp) REVERT: C 2763 ARG cc_start: 0.7280 (mtp-110) cc_final: 0.6936 (ttm170) REVERT: C 2799 PHE cc_start: 0.7717 (t80) cc_final: 0.7314 (t80) outliers start: 120 outliers final: 39 residues processed: 435 average time/residue: 0.5435 time to fit residues: 290.2284 Evaluate side-chains 380 residues out of total 5058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 327 time to evaluate : 1.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 433 SER Chi-restraints excluded: chain A residue 517 VAL Chi-restraints excluded: chain A residue 767 THR Chi-restraints excluded: chain A residue 1256 ILE Chi-restraints excluded: chain A residue 1313 GLU Chi-restraints excluded: chain A residue 1563 ASP Chi-restraints excluded: chain A residue 1643 ILE Chi-restraints excluded: chain A residue 1678 VAL Chi-restraints excluded: chain A residue 1707 GLU Chi-restraints excluded: chain A residue 1727 VAL Chi-restraints excluded: chain A residue 1836 ASP Chi-restraints excluded: chain A residue 2057 SER Chi-restraints excluded: chain A residue 2058 SER Chi-restraints excluded: chain A residue 2061 GLN Chi-restraints excluded: chain A residue 2122 THR Chi-restraints excluded: chain A residue 2177 GLN Chi-restraints excluded: chain A residue 2268 THR Chi-restraints excluded: chain A residue 2332 LEU Chi-restraints excluded: chain A residue 2447 LEU Chi-restraints excluded: chain A residue 2458 ASP Chi-restraints excluded: chain A residue 2596 GLU Chi-restraints excluded: chain A residue 2742 ASN Chi-restraints excluded: chain A residue 2806 MET Chi-restraints excluded: chain A residue 2946 LEU Chi-restraints excluded: chain A residue 3043 LYS Chi-restraints excluded: chain C residue 97 ILE Chi-restraints excluded: chain C residue 433 SER Chi-restraints excluded: chain C residue 517 VAL Chi-restraints excluded: chain C residue 767 THR Chi-restraints excluded: chain C residue 1256 ILE Chi-restraints excluded: chain C residue 1313 GLU Chi-restraints excluded: chain C residue 1563 ASP Chi-restraints excluded: chain C residue 1643 ILE Chi-restraints excluded: chain C residue 1659 ILE Chi-restraints excluded: chain C residue 1678 VAL Chi-restraints excluded: chain C residue 1707 GLU Chi-restraints excluded: chain C residue 1727 VAL Chi-restraints excluded: chain C residue 1836 ASP Chi-restraints excluded: chain C residue 2057 SER Chi-restraints excluded: chain C residue 2058 SER Chi-restraints excluded: chain C residue 2061 GLN Chi-restraints excluded: chain C residue 2122 THR Chi-restraints excluded: chain C residue 2177 GLN Chi-restraints excluded: chain C residue 2268 THR Chi-restraints excluded: chain C residue 2332 LEU Chi-restraints excluded: chain C residue 2447 LEU Chi-restraints excluded: chain C residue 2458 ASP Chi-restraints excluded: chain C residue 2596 GLU Chi-restraints excluded: chain C residue 2742 ASN Chi-restraints excluded: chain C residue 2806 MET Chi-restraints excluded: chain C residue 2946 LEU Chi-restraints excluded: chain C residue 3043 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 556 random chunks: chunk 428 optimal weight: 0.3980 chunk 16 optimal weight: 10.0000 chunk 196 optimal weight: 0.9980 chunk 342 optimal weight: 5.9990 chunk 486 optimal weight: 0.9980 chunk 531 optimal weight: 2.9990 chunk 198 optimal weight: 0.9980 chunk 362 optimal weight: 8.9990 chunk 141 optimal weight: 0.6980 chunk 98 optimal weight: 5.9990 chunk 6 optimal weight: 5.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 GLN A1384 HIS A1640 GLN A1951 HIS A2069 GLN A2679 ASN C1384 HIS C1640 GLN C1951 HIS C2069 GLN C2679 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4648 r_free = 0.4648 target = 0.229296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.148587 restraints weight = 58363.433| |-----------------------------------------------------------------------------| r_work (start): 0.3735 rms_B_bonded: 4.84 r_work: 0.3276 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3145 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 moved from start: 0.3309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 45484 Z= 0.106 Angle : 0.481 11.841 61464 Z= 0.247 Chirality : 0.037 0.154 7044 Planarity : 0.003 0.035 7740 Dihedral : 4.698 85.959 6044 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.70 % Allowed : 14.11 % Favored : 84.19 % 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 aren not related in a simple way. whole: 2.47 (0.12), residues: 5486 helix: 2.48 (0.08), residues: 3840 sheet: 0.44 (0.60), residues: 62 loop : -0.48 (0.15), residues: 1584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A2691 TYR 0.011 0.001 TYR A1470 PHE 0.019 0.001 PHE A 897 TRP 0.015 0.001 TRP C2104 HIS 0.010 0.001 HIS C1083 Details of bonding type rmsd covalent geometry : bond 0.00225 (45484) covalent geometry : angle 0.48122 (61464) hydrogen bonds : bond 0.03794 ( 2823) hydrogen bonds : angle 3.44127 ( 8283) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10972 Ramachandran restraints generated. 5486 Oldfield, 0 Emsley, 5486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10972 Ramachandran restraints generated. 5486 Oldfield, 0 Emsley, 5486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 5058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 337 time to evaluate : 0.924 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: A 94 MET cc_start: 0.0297 (OUTLIER) cc_final: 0.0084 (ttt) REVERT: A 577 MET cc_start: 0.0814 (ttp) cc_final: -0.0080 (tmt) REVERT: A 660 MET cc_start: 0.1433 (mmm) cc_final: 0.1107 (mtt) REVERT: A 780 MET cc_start: 0.1314 (mmt) cc_final: 0.0942 (ptp) REVERT: A 1064 MET cc_start: 0.0902 (pmm) cc_final: 0.0461 (ptp) REVERT: A 1321 MET cc_start: 0.4356 (ptt) cc_final: 0.3536 (tmm) REVERT: A 1353 GLU cc_start: 0.4685 (mm-30) cc_final: 0.4048 (mm-30) REVERT: A 1448 LEU cc_start: 0.8100 (OUTLIER) cc_final: 0.7775 (tt) REVERT: A 1556 TYR cc_start: 0.5814 (t80) cc_final: 0.5483 (t80) REVERT: A 1563 ASP cc_start: 0.7574 (OUTLIER) cc_final: 0.7337 (m-30) REVERT: A 1573 ASP cc_start: 0.6419 (t0) cc_final: 0.6104 (t0) REVERT: A 1632 MET cc_start: 0.8621 (mmm) cc_final: 0.8233 (tpt) REVERT: A 1735 THR cc_start: 0.8064 (m) cc_final: 0.7649 (p) REVERT: A 1776 GLU cc_start: 0.6505 (mm-30) cc_final: 0.6133 (mp0) REVERT: A 1827 LEU cc_start: 0.8041 (mt) cc_final: 0.7614 (mt) REVERT: A 2028 GLN cc_start: 0.7696 (mt0) cc_final: 0.7152 (mt0) REVERT: A 2058 SER cc_start: 0.7540 (OUTLIER) cc_final: 0.7252 (m) REVERT: A 2279 LYS cc_start: 0.8547 (mttt) cc_final: 0.8266 (mtmp) REVERT: A 2315 MET cc_start: 0.7993 (mtp) cc_final: 0.7736 (mtp) REVERT: A 2332 LEU cc_start: 0.7846 (OUTLIER) cc_final: 0.7447 (mp) REVERT: A 2418 LYS cc_start: 0.6112 (mmtt) cc_final: 0.5585 (mmtp) REVERT: A 2453 ARG cc_start: 0.6989 (mtm110) cc_final: 0.6725 (mtm110) REVERT: A 2457 GLU cc_start: 0.7563 (mm-30) cc_final: 0.7259 (mp0) REVERT: A 2458 ASP cc_start: 0.8378 (OUTLIER) cc_final: 0.7816 (t0) REVERT: A 2519 LEU cc_start: 0.8757 (OUTLIER) cc_final: 0.8539 (pp) REVERT: A 2531 MET cc_start: 0.6426 (mtp) cc_final: 0.5776 (mtp) REVERT: A 2596 GLU cc_start: 0.7606 (OUTLIER) cc_final: 0.7277 (mm-30) REVERT: A 2612 ARG cc_start: 0.6983 (ttm170) cc_final: 0.6588 (ttp-170) REVERT: A 2638 TRP cc_start: 0.6659 (m-90) cc_final: 0.6364 (m-90) REVERT: A 2667 MET cc_start: 0.7987 (mtm) cc_final: 0.7768 (mtp) REVERT: A 2763 ARG cc_start: 0.7277 (mtp-110) cc_final: 0.6897 (ttm170) REVERT: A 2799 PHE cc_start: 0.7847 (t80) cc_final: 0.7456 (t80) REVERT: C 94 MET cc_start: 0.0292 (OUTLIER) cc_final: 0.0079 (ttt) REVERT: C 577 MET cc_start: 0.0812 (ttp) cc_final: -0.0081 (tmt) REVERT: C 660 MET cc_start: 0.1422 (mmm) cc_final: 0.1102 (mtt) REVERT: C 780 MET cc_start: 0.1302 (mmt) cc_final: 0.0934 (ptp) REVERT: C 1064 MET cc_start: 0.0904 (pmm) cc_final: 0.0462 (ptp) REVERT: C 1321 MET cc_start: 0.4363 (ptt) cc_final: 0.3539 (tmm) REVERT: C 1353 GLU cc_start: 0.4681 (mm-30) cc_final: 0.4044 (mm-30) REVERT: C 1448 LEU cc_start: 0.8095 (OUTLIER) cc_final: 0.7811 (tt) REVERT: C 1491 PHE cc_start: 0.7029 (t80) cc_final: 0.6810 (t80) REVERT: C 1556 TYR cc_start: 0.5811 (t80) cc_final: 0.5478 (t80) REVERT: C 1563 ASP cc_start: 0.7571 (OUTLIER) cc_final: 0.7333 (m-30) REVERT: C 1573 ASP cc_start: 0.6534 (t0) cc_final: 0.6153 (t0) REVERT: C 1632 MET cc_start: 0.8647 (mmm) cc_final: 0.8254 (tpt) REVERT: C 1735 THR cc_start: 0.8053 (m) cc_final: 0.7641 (p) REVERT: C 1776 GLU cc_start: 0.6497 (mm-30) cc_final: 0.6126 (mp0) REVERT: C 1827 LEU cc_start: 0.8047 (mt) cc_final: 0.7622 (mt) REVERT: C 2028 GLN cc_start: 0.7700 (mt0) cc_final: 0.7161 (mt0) REVERT: C 2058 SER cc_start: 0.7539 (OUTLIER) cc_final: 0.7251 (m) REVERT: C 2315 MET cc_start: 0.7993 (mtp) cc_final: 0.7736 (mtp) REVERT: C 2332 LEU cc_start: 0.7866 (OUTLIER) cc_final: 0.7464 (mp) REVERT: C 2418 LYS cc_start: 0.6110 (mmtt) cc_final: 0.5585 (mmtp) REVERT: C 2453 ARG cc_start: 0.7003 (mtm110) cc_final: 0.6739 (mtm110) REVERT: C 2457 GLU cc_start: 0.7585 (mm-30) cc_final: 0.7280 (mp0) REVERT: C 2458 ASP cc_start: 0.8361 (OUTLIER) cc_final: 0.7799 (t0) REVERT: C 2519 LEU cc_start: 0.8757 (OUTLIER) cc_final: 0.8540 (pp) REVERT: C 2531 MET cc_start: 0.6429 (mtp) cc_final: 0.5781 (mtp) REVERT: C 2596 GLU cc_start: 0.7601 (OUTLIER) cc_final: 0.7267 (mm-30) REVERT: C 2612 ARG cc_start: 0.6991 (ttm170) cc_final: 0.6612 (ttp-170) REVERT: C 2638 TRP cc_start: 0.6660 (m-90) cc_final: 0.6368 (m-90) REVERT: C 2667 MET cc_start: 0.7998 (mtm) cc_final: 0.7780 (mtp) REVERT: C 2763 ARG cc_start: 0.7282 (mtp-110) cc_final: 0.6918 (ttm170) REVERT: C 2799 PHE cc_start: 0.7848 (t80) cc_final: 0.7453 (t80) outliers start: 84 outliers final: 32 residues processed: 393 average time/residue: 0.4936 time to fit residues: 236.6591 Evaluate side-chains 369 residues out of total 5058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 321 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 MET Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 433 SER Chi-restraints excluded: chain A residue 767 THR Chi-restraints excluded: chain A residue 1256 ILE Chi-restraints excluded: chain A residue 1313 GLU Chi-restraints excluded: chain A residue 1448 LEU Chi-restraints excluded: chain A residue 1563 ASP Chi-restraints excluded: chain A residue 1623 LEU Chi-restraints excluded: chain A residue 1678 VAL Chi-restraints excluded: chain A residue 1836 ASP Chi-restraints excluded: chain A residue 2057 SER Chi-restraints excluded: chain A residue 2058 SER Chi-restraints excluded: chain A residue 2332 LEU Chi-restraints excluded: chain A residue 2447 LEU Chi-restraints excluded: chain A residue 2458 ASP Chi-restraints excluded: chain A residue 2519 LEU Chi-restraints excluded: chain A residue 2596 GLU Chi-restraints excluded: chain A residue 2670 LYS Chi-restraints excluded: chain A residue 2742 ASN Chi-restraints excluded: chain A residue 2946 LEU Chi-restraints excluded: chain A residue 3043 LYS Chi-restraints excluded: chain C residue 94 MET Chi-restraints excluded: chain C residue 97 ILE Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain C residue 433 SER Chi-restraints excluded: chain C residue 487 ILE Chi-restraints excluded: chain C residue 767 THR Chi-restraints excluded: chain C residue 1256 ILE Chi-restraints excluded: chain C residue 1313 GLU Chi-restraints excluded: chain C residue 1448 LEU Chi-restraints excluded: chain C residue 1563 ASP Chi-restraints excluded: chain C residue 1623 LEU Chi-restraints excluded: chain C residue 1678 VAL Chi-restraints excluded: chain C residue 1836 ASP Chi-restraints excluded: chain C residue 2057 SER Chi-restraints excluded: chain C residue 2058 SER Chi-restraints excluded: chain C residue 2193 VAL Chi-restraints excluded: chain C residue 2332 LEU Chi-restraints excluded: chain C residue 2447 LEU Chi-restraints excluded: chain C residue 2458 ASP Chi-restraints excluded: chain C residue 2519 LEU Chi-restraints excluded: chain C residue 2596 GLU Chi-restraints excluded: chain C residue 2670 LYS Chi-restraints excluded: chain C residue 2742 ASN Chi-restraints excluded: chain C residue 2946 LEU Chi-restraints excluded: chain C residue 3043 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 69.6768 > 50: distance: 45 - 62: 25.833 distance: 49 - 69: 32.940 distance: 53 - 77: 35.398 distance: 56 - 62: 27.441 distance: 57 - 88: 29.175 distance: 62 - 63: 7.614 distance: 63 - 64: 25.311 distance: 63 - 66: 25.080 distance: 64 - 65: 48.204 distance: 64 - 69: 16.365 distance: 65 - 96: 17.013 distance: 66 - 67: 14.313 distance: 66 - 68: 11.419 distance: 69 - 70: 18.207 distance: 70 - 71: 40.889 distance: 70 - 73: 21.404 distance: 71 - 72: 47.002 distance: 71 - 77: 25.253 distance: 72 - 105: 12.127 distance: 73 - 74: 22.046 distance: 73 - 75: 31.652 distance: 74 - 76: 35.660 distance: 77 - 78: 28.679 distance: 78 - 79: 22.381 distance: 78 - 81: 14.747 distance: 79 - 80: 41.805 distance: 79 - 88: 28.721 distance: 80 - 112: 47.170 distance: 81 - 82: 38.069 distance: 82 - 83: 16.421 distance: 82 - 84: 19.885 distance: 83 - 85: 27.625 distance: 84 - 86: 23.544 distance: 85 - 87: 4.804 distance: 88 - 89: 24.790 distance: 89 - 90: 40.262 distance: 89 - 92: 44.987 distance: 90 - 91: 41.085 distance: 90 - 96: 14.159 distance: 91 - 120: 17.559 distance: 92 - 93: 9.336 distance: 93 - 94: 34.717 distance: 93 - 95: 40.232 distance: 96 - 97: 21.880 distance: 97 - 98: 44.183 distance: 97 - 100: 22.719 distance: 98 - 99: 45.953 distance: 98 - 105: 29.677 distance: 100 - 101: 16.301 distance: 101 - 102: 11.355 distance: 102 - 103: 26.679 distance: 103 - 104: 9.530 distance: 105 - 106: 28.905 distance: 106 - 107: 31.494 distance: 106 - 109: 21.940 distance: 107 - 108: 42.413 distance: 107 - 112: 16.797 distance: 109 - 110: 14.360 distance: 109 - 111: 28.975 distance: 112 - 113: 45.814 distance: 113 - 114: 42.110 distance: 113 - 116: 14.304 distance: 114 - 115: 42.162 distance: 114 - 120: 47.534 distance: 116 - 117: 38.175 distance: 117 - 118: 22.024 distance: 117 - 119: 43.506 distance: 120 - 121: 23.129 distance: 121 - 122: 40.466 distance: 121 - 124: 36.802 distance: 122 - 123: 69.677 distance: 122 - 125: 5.472 distance: 125 - 126: 38.588 distance: 126 - 127: 58.108 distance: 126 - 129: 42.643 distance: 127 - 128: 65.001 distance: 127 - 132: 45.857 distance: 129 - 130: 36.324 distance: 129 - 131: 32.819 distance: 132 - 133: 29.650 distance: 133 - 134: 19.056 distance: 133 - 136: 50.130 distance: 134 - 135: 33.378 distance: 134 - 140: 23.747 distance: 136 - 137: 6.654 distance: 137 - 138: 50.025 distance: 137 - 139: 44.390