Starting phenix.real_space_refine on Mon May 19 19:25:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8x2i_38011/05_2025/8x2i_38011.cif Found real_map, /net/cci-nas-00/data/ceres_data/8x2i_38011/05_2025/8x2i_38011.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8x2i_38011/05_2025/8x2i_38011.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8x2i_38011/05_2025/8x2i_38011.map" model { file = "/net/cci-nas-00/data/ceres_data/8x2i_38011/05_2025/8x2i_38011.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8x2i_38011/05_2025/8x2i_38011.cif" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.107 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 46 5.16 5 C 11942 2.51 5 N 2959 2.21 5 O 3697 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 315 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 18645 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 18644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2303, 18644 Classifications: {'peptide': 2303} Link IDs: {'PCIS': 1, 'PTRANS': 53, 'TRANS': 2248} Chain breaks: 3 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 5704 SG CYS A 698 63.049 86.639 163.551 1.00 8.69 S Time building chain proxies: 11.07, per 1000 atoms: 0.59 Number of scatterers: 18645 At special positions: 0 Unit cell: (144.571, 119.57, 247.836, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 1 29.99 S 46 16.00 O 3697 8.00 N 2959 7.00 C 11942 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 4.92 Conformation dependent library (CDL) restraints added in 2.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A3000 " pdb="ZN ZN A3000 " - pdb=" ND1 HIS A 653 " pdb="ZN ZN A3000 " - pdb=" SG CYS A 698 " pdb="ZN ZN A3000 " - pdb=" NE2 HIS A 757 " 4590 Ramachandran restraints generated. 2295 Oldfield, 0 Emsley, 2295 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4352 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 40 sheets defined 31.4% alpha, 23.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.75 Creating SS restraints... Processing helix chain 'A' and resid 5 through 13 Processing helix chain 'A' and resid 21 through 36 Processing helix chain 'A' and resid 41 through 63 Processing helix chain 'A' and resid 68 through 88 removed outlier: 3.502A pdb=" N ASN A 88 " --> pdb=" O LEU A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 122 removed outlier: 3.572A pdb=" N ILE A 112 " --> pdb=" O ASN A 108 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N GLN A 117 " --> pdb=" O ASN A 113 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N TRP A 118 " --> pdb=" O TYR A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 156 Processing helix chain 'A' and resid 167 through 197 Processing helix chain 'A' and resid 201 through 214 removed outlier: 3.577A pdb=" N ILE A 205 " --> pdb=" O ILE A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 234 Processing helix chain 'A' and resid 248 through 261 Processing helix chain 'A' and resid 264 through 281 removed outlier: 3.958A pdb=" N ILE A 274 " --> pdb=" O ASP A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 324 Processing helix chain 'A' and resid 339 through 353 removed outlier: 3.972A pdb=" N SER A 352 " --> pdb=" O SER A 348 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N LYS A 353 " --> pdb=" O ALA A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 358 Processing helix chain 'A' and resid 393 through 420 Proline residue: A 416 - end of helix Processing helix chain 'A' and resid 423 through 438 Processing helix chain 'A' and resid 443 through 450 Processing helix chain 'A' and resid 451 through 456 removed outlier: 4.682A pdb=" N LEU A 454 " --> pdb=" O THR A 451 " (cutoff:3.500A) Processing helix chain 'A' and resid 464 through 468 Processing helix chain 'A' and resid 470 through 484 removed outlier: 3.826A pdb=" N TYR A 474 " --> pdb=" O GLY A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 499 Processing helix chain 'A' and resid 500 through 502 No H-bonds generated for 'chain 'A' and resid 500 through 502' Processing helix chain 'A' and resid 504 through 506 No H-bonds generated for 'chain 'A' and resid 504 through 506' Processing helix chain 'A' and resid 512 through 519 Processing helix chain 'A' and resid 523 through 539 Processing helix chain 'A' and resid 558 through 568 Processing helix chain 'A' and resid 587 through 601 removed outlier: 3.750A pdb=" N ASP A 601 " --> pdb=" O LEU A 597 " (cutoff:3.500A) Processing helix chain 'A' and resid 639 through 643 removed outlier: 4.265A pdb=" N ASN A 642 " --> pdb=" O GLN A 639 " (cutoff:3.500A) Processing helix chain 'A' and resid 667 through 683 Processing helix chain 'A' and resid 706 through 709 Processing helix chain 'A' and resid 710 through 727 removed outlier: 4.891A pdb=" N ASP A 721 " --> pdb=" O LEU A 717 " (cutoff:3.500A) removed outlier: 5.246A pdb=" N ARG A 722 " --> pdb=" O LYS A 718 " (cutoff:3.500A) Processing helix chain 'A' and resid 731 through 733 No H-bonds generated for 'chain 'A' and resid 731 through 733' Processing helix chain 'A' and resid 764 through 774 Processing helix chain 'A' and resid 793 through 809 removed outlier: 3.821A pdb=" N LEU A 797 " --> pdb=" O TYR A 793 " (cutoff:3.500A) Processing helix chain 'A' and resid 814 through 839 Processing helix chain 'A' and resid 850 through 876 removed outlier: 3.527A pdb=" N ASN A 876 " --> pdb=" O LEU A 872 " (cutoff:3.500A) Processing helix chain 'A' and resid 916 through 934 Processing helix chain 'A' and resid 954 through 971 removed outlier: 3.992A pdb=" N THR A 958 " --> pdb=" O HIS A 954 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N PHE A 964 " --> pdb=" O ASN A 960 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N TYR A 971 " --> pdb=" O SER A 967 " (cutoff:3.500A) Processing helix chain 'A' and resid 978 through 995 removed outlier: 3.592A pdb=" N SER A 995 " --> pdb=" O ALA A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 997 through 1001 Processing helix chain 'A' and resid 1003 through 1017 Processing helix chain 'A' and resid 1073 through 1090 Processing helix chain 'A' and resid 1116 through 1129 Processing helix chain 'A' and resid 1129 through 1134 Processing helix chain 'A' and resid 1245 through 1258 removed outlier: 3.594A pdb=" N TYR A1258 " --> pdb=" O ILE A1254 " (cutoff:3.500A) Processing helix chain 'A' and resid 1305 through 1311 Processing helix chain 'A' and resid 1348 through 1352 Processing helix chain 'A' and resid 1370 through 1374 removed outlier: 3.721A pdb=" N SER A1373 " --> pdb=" O ASN A1370 " (cutoff:3.500A) Processing helix chain 'A' and resid 1432 through 1448 removed outlier: 5.639A pdb=" N SER A1441 " --> pdb=" O ILE A1437 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N ASP A1442 " --> pdb=" O GLU A1438 " (cutoff:3.500A) Processing helix chain 'A' and resid 1558 through 1572 Processing helix chain 'A' and resid 1580 through 1589 Processing helix chain 'A' and resid 1651 through 1653 No H-bonds generated for 'chain 'A' and resid 1651 through 1653' Processing helix chain 'A' and resid 1680 through 1683 Processing helix chain 'A' and resid 1685 through 1689 Processing helix chain 'A' and resid 1737 through 1739 No H-bonds generated for 'chain 'A' and resid 1737 through 1739' Processing helix chain 'A' and resid 1776 through 1779 removed outlier: 3.532A pdb=" N ASP A1779 " --> pdb=" O THR A1776 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1776 through 1779' Processing helix chain 'A' and resid 1792 through 1800 removed outlier: 3.805A pdb=" N ILE A1797 " --> pdb=" O VAL A1793 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N SER A1798 " --> pdb=" O SER A1794 " (cutoff:3.500A) Processing helix chain 'A' and resid 1868 through 1872 Processing sheet with id=AA1, first strand: chain 'A' and resid 92 through 93 Processing sheet with id=AA2, first strand: chain 'A' and resid 237 through 239 removed outlier: 7.195A pdb=" N ASN A 238 " --> pdb=" O VAL A 127 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N VAL A 129 " --> pdb=" O ASN A 238 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N LEU A 98 " --> pdb=" O LYS A 128 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N PHE A 130 " --> pdb=" O LEU A 98 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N PHE A 100 " --> pdb=" O PHE A 130 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N ILE A 101 " --> pdb=" O LEU A 285 " (cutoff:3.500A) removed outlier: 8.092A pdb=" N GLN A 385 " --> pdb=" O LYS A 374 " (cutoff:3.500A) removed outlier: 11.200A pdb=" N LYS A 374 " --> pdb=" O GLN A 385 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 360 through 361 removed outlier: 4.313A pdb=" N GLY A 292 " --> pdb=" O LEU A 361 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 627 through 632 removed outlier: 7.434A pdb=" N THR A 617 " --> pdb=" O GLN A 609 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N GLN A 609 " --> pdb=" O THR A 617 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N TYR A 621 " --> pdb=" O SER A 605 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N SER A 605 " --> pdb=" O TYR A 621 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N ILE A 578 " --> pdb=" O LYS A 647 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N THR A 649 " --> pdb=" O ILE A 578 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N TYR A 580 " --> pdb=" O THR A 649 " (cutoff:3.500A) removed outlier: 7.958A pdb=" N ILE A 651 " --> pdb=" O TYR A 580 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N VAL A 582 " --> pdb=" O ILE A 651 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 744 through 746 Processing sheet with id=AA6, first strand: chain 'A' and resid 777 through 781 removed outlier: 4.710A pdb=" N TYR A 777 " --> pdb=" O LYS A 790 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 882 through 884 Processing sheet with id=AA8, first strand: chain 'A' and resid 882 through 884 Processing sheet with id=AA9, first strand: chain 'A' and resid 1105 through 1107 Processing sheet with id=AB1, first strand: chain 'A' and resid 1136 through 1139 removed outlier: 6.644A pdb=" N ILE A1144 " --> pdb=" O VAL A1221 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N MET A1220 " --> pdb=" O SER A1297 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ILE A1299 " --> pdb=" O MET A1220 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N ARG A1296 " --> pdb=" O SER A1324 " (cutoff:3.500A) removed outlier: 8.164A pdb=" N SER A1326 " --> pdb=" O ARG A1296 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N PHE A1298 " --> pdb=" O SER A1326 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU A1325 " --> pdb=" O VAL A1345 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N TRP A1344 " --> pdb=" O SER A1403 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N THR A1405 " --> pdb=" O TRP A1344 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N ILE A1346 " --> pdb=" O THR A1405 " (cutoff:3.500A) removed outlier: 8.742A pdb=" N SER A1407 " --> pdb=" O ILE A1346 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 1161 through 1164 removed outlier: 6.834A pdb=" N SER A1161 " --> pdb=" O ILE A1155 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N ILE A1155 " --> pdb=" O SER A1161 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N THR A1163 " --> pdb=" O SER A1153 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N SER A1153 " --> pdb=" O ARG A1288 " (cutoff:3.500A) removed outlier: 8.266A pdb=" N ASN A1290 " --> pdb=" O SER A1153 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N ILE A1155 " --> pdb=" O ASN A1290 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N THR A1285 " --> pdb=" O SER A1313 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N SER A1315 " --> pdb=" O THR A1285 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N VAL A1287 " --> pdb=" O SER A1315 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N TYR A1317 " --> pdb=" O VAL A1287 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N ILE A1289 " --> pdb=" O TYR A1317 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N ILE A1334 " --> pdb=" O THR A1388 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU A1336 " --> pdb=" O ASN A1390 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1171 through 1173 Processing sheet with id=AB4, first strand: chain 'A' and resid 1179 through 1181 removed outlier: 6.737A pdb=" N ASP A1185 " --> pdb=" O PHE A1267 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N ILE A1275 " --> pdb=" O GLY A1235 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N GLY A1235 " --> pdb=" O ILE A1275 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ASN A1227 " --> pdb=" O GLU A1283 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1353 through 1358 removed outlier: 4.354A pdb=" N GLU A1366 " --> pdb=" O ASN A1354 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N THR A1356 " --> pdb=" O LYS A1364 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N LYS A1364 " --> pdb=" O THR A1356 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N GLU A1358 " --> pdb=" O ILE A1362 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N ILE A1362 " --> pdb=" O GLU A1358 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1460 through 1464 Processing sheet with id=AB7, first strand: chain 'A' and resid 1514 through 1521 removed outlier: 4.022A pdb=" N ILE A1516 " --> pdb=" O ILE A1528 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ILE A1528 " --> pdb=" O ILE A1516 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N ILE A1518 " --> pdb=" O LEU A1526 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N LEU A1526 " --> pdb=" O ILE A1518 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N ASN A1520 " --> pdb=" O VAL A1524 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N VAL A1524 " --> pdb=" O ASN A1520 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N LYS A1525 " --> pdb=" O ILE A1544 " (cutoff:3.500A) removed outlier: 5.144A pdb=" N ILE A1544 " --> pdb=" O LYS A1525 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N LYS A1537 " --> pdb=" O LEU A1557 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N LEU A1557 " --> pdb=" O LYS A1537 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N SER A1539 " --> pdb=" O VAL A1555 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N VAL A1555 " --> pdb=" O SER A1539 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N SER A1541 " --> pdb=" O ASN A1553 " (cutoff:3.500A) removed outlier: 14.824A pdb=" N THR A1549 " --> pdb=" O ASP A1608 " (cutoff:3.500A) removed outlier: 15.698A pdb=" N ASN A1610 " --> pdb=" O THR A1549 " (cutoff:3.500A) removed outlier: 12.095A pdb=" N LYS A1551 " --> pdb=" O ASN A1610 " (cutoff:3.500A) removed outlier: 10.284A pdb=" N ILE A1612 " --> pdb=" O LYS A1551 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ASN A1553 " --> pdb=" O ILE A1612 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N SER A1614 " --> pdb=" O ASN A1553 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N VAL A1555 " --> pdb=" O SER A1614 " (cutoff:3.500A) removed outlier: 8.062A pdb=" N SER A1616 " --> pdb=" O VAL A1555 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N LEU A1557 " --> pdb=" O SER A1616 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N PHE A1611 " --> pdb=" O CYS A1626 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N CYS A1626 " --> pdb=" O PHE A1611 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N GLN A1621 " --> pdb=" O ILE A1637 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N ILE A1637 " --> pdb=" O GLN A1621 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N GLU A1623 " --> pdb=" O TYR A1635 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N TYR A1649 " --> pdb=" O ASN A1655 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N ASN A1655 " --> pdb=" O TYR A1649 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N VAL A1692 " --> pdb=" O ILE A1719 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N VAL A1718 " --> pdb=" O ARG A1767 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1674 through 1678 removed outlier: 6.610A pdb=" N ILE A1675 " --> pdb=" O ASN A1704 " (cutoff:3.500A) removed outlier: 7.863A pdb=" N THR A1706 " --> pdb=" O ILE A1675 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N PHE A1677 " --> pdb=" O THR A1706 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N PHE A1785 " --> pdb=" O GLN A1789 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N GLN A1789 " --> pdb=" O PHE A1785 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 1815 through 1819 Processing sheet with id=AC1, first strand: chain 'A' and resid 1835 through 1839 removed outlier: 3.642A pdb=" N ASN A1852 " --> pdb=" O LYS A1847 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 1856 through 1860 Processing sheet with id=AC3, first strand: chain 'A' and resid 1878 through 1882 Processing sheet with id=AC4, first strand: chain 'A' and resid 1898 through 1902 removed outlier: 3.766A pdb=" N GLU A1922 " --> pdb=" O ALA A1910 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 1928 through 1932 Processing sheet with id=AC6, first strand: chain 'A' and resid 1969 through 1973 removed outlier: 4.567A pdb=" N TYR A1979 " --> pdb=" O GLN A1987 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 1991 through 1992 Processing sheet with id=AC8, first strand: chain 'A' and resid 2009 through 2013 Processing sheet with id=AC9, first strand: chain 'A' and resid 2029 through 2033 Processing sheet with id=AD1, first strand: chain 'A' and resid 2059 through 2063 Processing sheet with id=AD2, first strand: chain 'A' and resid 2079 through 2082 Processing sheet with id=AD3, first strand: chain 'A' and resid 2101 through 2105 Processing sheet with id=AD4, first strand: chain 'A' and resid 2143 through 2145 Processing sheet with id=AD5, first strand: chain 'A' and resid 2161 through 2165 removed outlier: 4.696A pdb=" N TYR A2171 " --> pdb=" O VAL A2187 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLN A2185 " --> pdb=" O ALA A2173 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'A' and resid 2191 through 2194 Processing sheet with id=AD7, first strand: chain 'A' and resid 2211 through 2215 Processing sheet with id=AD8, first strand: chain 'A' and resid 2232 through 2236 Processing sheet with id=AD9, first strand: chain 'A' and resid 2252 through 2256 Processing sheet with id=AE1, first strand: chain 'A' and resid 2272 through 2276 Processing sheet with id=AE2, first strand: chain 'A' and resid 2292 through 2296 removed outlier: 4.544A pdb=" N TYR A2302 " --> pdb=" O ILE A2318 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'A' and resid 2322 through 2326 Processing sheet with id=AE4, first strand: chain 'A' and resid 2343 through 2346 803 hydrogen bonds defined for protein. 2154 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: 13.57 Time building geometry restraints manager: 5.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 3588 1.32 - 1.44: 4798 1.44 - 1.57: 10554 1.57 - 1.69: 1 1.69 - 1.81: 82 Bond restraints: 19023 Sorted by residual: bond pdb=" N VAL A1924 " pdb=" CA VAL A1924 " ideal model delta sigma weight residual 1.456 1.493 -0.037 1.11e-02 8.12e+03 1.11e+01 bond pdb=" CA ARG A 499 " pdb=" C ARG A 499 " ideal model delta sigma weight residual 1.523 1.465 0.058 1.80e-02 3.09e+03 1.04e+01 bond pdb=" N GLN A1633 " pdb=" CA GLN A1633 " ideal model delta sigma weight residual 1.457 1.417 0.040 1.41e-02 5.03e+03 7.91e+00 bond pdb=" N TYR A1957 " pdb=" CA TYR A1957 " ideal model delta sigma weight residual 1.455 1.488 -0.033 1.18e-02 7.18e+03 7.67e+00 bond pdb=" N ASN A1925 " pdb=" CA ASN A1925 " ideal model delta sigma weight residual 1.458 1.491 -0.034 1.24e-02 6.50e+03 7.49e+00 ... (remaining 19018 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.64: 25195 2.64 - 5.29: 484 5.29 - 7.93: 45 7.93 - 10.58: 7 10.58 - 13.22: 3 Bond angle restraints: 25734 Sorted by residual: angle pdb=" C VAL A1947 " pdb=" N GLU A1948 " pdb=" CA GLU A1948 " ideal model delta sigma weight residual 121.54 132.75 -11.21 1.91e+00 2.74e-01 3.44e+01 angle pdb=" N GLN A1763 " pdb=" CA GLN A1763 " pdb=" C GLN A1763 " ideal model delta sigma weight residual 111.37 118.96 -7.59 1.64e+00 3.72e-01 2.14e+01 angle pdb=" C LEU A 91 " pdb=" N THR A 92 " pdb=" CA THR A 92 " ideal model delta sigma weight residual 122.36 133.55 -11.19 2.42e+00 1.71e-01 2.14e+01 angle pdb=" C PRO A1762 " pdb=" N GLN A1763 " pdb=" CA GLN A1763 " ideal model delta sigma weight residual 121.19 128.02 -6.83 1.59e+00 3.96e-01 1.85e+01 angle pdb=" C LEU A1015 " pdb=" N ASP A1016 " pdb=" CA ASP A1016 " ideal model delta sigma weight residual 121.92 114.64 7.28 1.73e+00 3.34e-01 1.77e+01 ... (remaining 25729 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.10: 9561 18.10 - 36.20: 1272 36.20 - 54.29: 410 54.29 - 72.39: 90 72.39 - 90.49: 37 Dihedral angle restraints: 11370 sinusoidal: 4574 harmonic: 6796 Sorted by residual: dihedral pdb=" CA LYS A1511 " pdb=" C LYS A1511 " pdb=" N ASP A1512 " pdb=" CA ASP A1512 " ideal model delta harmonic sigma weight residual 180.00 -128.34 -51.66 0 5.00e+00 4.00e-02 1.07e+02 dihedral pdb=" CA ASP A 364 " pdb=" C ASP A 364 " pdb=" N ASP A 365 " pdb=" CA ASP A 365 " ideal model delta harmonic sigma weight residual -180.00 -147.84 -32.16 0 5.00e+00 4.00e-02 4.14e+01 dihedral pdb=" CA LEU A 243 " pdb=" C LEU A 243 " pdb=" N GLU A 244 " pdb=" CA GLU A 244 " ideal model delta harmonic sigma weight residual 180.00 150.94 29.06 0 5.00e+00 4.00e-02 3.38e+01 ... (remaining 11367 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 2055 0.061 - 0.122: 655 0.122 - 0.184: 108 0.184 - 0.245: 9 0.245 - 0.306: 4 Chirality restraints: 2831 Sorted by residual: chirality pdb=" CB ILE A 508 " pdb=" CA ILE A 508 " pdb=" CG1 ILE A 508 " pdb=" CG2 ILE A 508 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.31 2.00e-01 2.50e+01 2.34e+00 chirality pdb=" CB ILE A 969 " pdb=" CA ILE A 969 " pdb=" CG1 ILE A 969 " pdb=" CG2 ILE A 969 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.26 2.00e-01 2.50e+01 1.68e+00 chirality pdb=" CA ASN A1925 " pdb=" N ASN A1925 " pdb=" C ASN A1925 " pdb=" CB ASN A1925 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.56e+00 ... (remaining 2828 not shown) Planarity restraints: 3324 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY A2342 " -0.022 2.00e-02 2.50e+03 4.41e-02 1.95e+01 pdb=" C GLY A2342 " 0.076 2.00e-02 2.50e+03 pdb=" O GLY A2342 " -0.029 2.00e-02 2.50e+03 pdb=" N SER A2343 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 186 " 0.043 2.00e-02 2.50e+03 2.77e-02 1.35e+01 pdb=" CG PHE A 186 " -0.043 2.00e-02 2.50e+03 pdb=" CD1 PHE A 186 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 PHE A 186 " -0.029 2.00e-02 2.50e+03 pdb=" CE1 PHE A 186 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE A 186 " 0.021 2.00e-02 2.50e+03 pdb=" CZ PHE A 186 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN A1761 " 0.055 5.00e-02 4.00e+02 8.32e-02 1.11e+01 pdb=" N PRO A1762 " -0.144 5.00e-02 4.00e+02 pdb=" CA PRO A1762 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO A1762 " 0.045 5.00e-02 4.00e+02 ... (remaining 3321 not shown) Histogram of nonbonded interaction distances: 1.06 - 1.83: 6 1.83 - 2.59: 176 2.59 - 3.36: 23219 3.36 - 4.13: 46762 4.13 - 4.90: 83046 Nonbonded interactions: 153209 Sorted by model distance: nonbonded pdb=" OD1 ASN A1925 " pdb=" CD1 TYR A1943 " model vdw 1.057 3.340 nonbonded pdb=" ND2 ASN A1925 " pdb=" CE1 TYR A1943 " model vdw 1.091 3.420 nonbonded pdb=" ND2 ASN A1925 " pdb=" CZ TYR A1943 " model vdw 1.196 3.340 nonbonded pdb=" OD1 ASN A1925 " pdb=" CG TYR A1943 " model vdw 1.353 3.260 nonbonded pdb=" CG ASN A1925 " pdb=" CD1 TYR A1943 " model vdw 1.499 3.570 ... (remaining 153204 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.720 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: 0.010 Extract box with map and model: 0.730 Check model and map are aligned: 0.130 Set scattering table: 0.180 Process input model: 55.740 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.090 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:13.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 74.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6539 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 : 0.010 0.431 19027 Z= 0.507 Angle : 0.931 13.219 25734 Z= 0.532 Chirality : 0.060 0.306 2831 Planarity : 0.006 0.083 3324 Dihedral : 19.082 90.491 7018 Min Nonbonded Distance : 1.057 Molprobity Statistics. All-atom Clashscore : 14.15 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.58 % Favored : 94.25 % Rotamer: Outliers : 8.96 % Allowed : 21.41 % Favored : 69.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.37 (0.15), residues: 2295 helix: -1.04 (0.18), residues: 625 sheet: -1.56 (0.22), residues: 457 loop : -1.84 (0.15), residues: 1213 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP A 102 HIS 0.010 0.002 HIS A 35 PHE 0.043 0.003 PHE A 186 TYR 0.047 0.003 TYR A 46 ARG 0.010 0.001 ARG A1296 Details of bonding type rmsd hydrogen bonds : bond 0.15096 ( 801) hydrogen bonds : angle 6.92540 ( 2154) metal coordination : bond 0.25301 ( 3) covalent geometry : bond 0.00873 (19023) covalent geometry : angle 0.93074 (25734) Misc. bond : bond 0.43105 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4590 Ramachandran restraints generated. 2295 Oldfield, 0 Emsley, 2295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4590 Ramachandran restraints generated. 2295 Oldfield, 0 Emsley, 2295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 187 poor density : 145 time to evaluate : 1.891 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 157 PHE cc_start: 0.6756 (m-10) cc_final: 0.6343 (m-10) REVERT: A 166 PHE cc_start: 0.5349 (t80) cc_final: 0.4689 (t80) REVERT: A 195 GLU cc_start: 0.6054 (OUTLIER) cc_final: 0.5765 (mp0) REVERT: A 314 MET cc_start: 0.7776 (mtp) cc_final: 0.7529 (mtp) REVERT: A 439 SER cc_start: 0.8697 (OUTLIER) cc_final: 0.8346 (t) REVERT: A 450 ILE cc_start: 0.9077 (OUTLIER) cc_final: 0.8771 (pp) REVERT: A 526 ARG cc_start: 0.7692 (ttm-80) cc_final: 0.7391 (tpm170) REVERT: A 800 LEU cc_start: 0.8171 (OUTLIER) cc_final: 0.7931 (mt) REVERT: A 980 ASN cc_start: 0.4512 (OUTLIER) cc_final: 0.4019 (p0) REVERT: A 1116 LYS cc_start: 0.2422 (OUTLIER) cc_final: 0.1080 (ttmt) REVERT: A 1129 LEU cc_start: 0.3554 (OUTLIER) cc_final: 0.3283 (tt) REVERT: A 1270 ILE cc_start: 0.0581 (OUTLIER) cc_final: 0.0139 (pp) REVERT: A 1310 LYS cc_start: 0.3785 (OUTLIER) cc_final: 0.3541 (tppt) REVERT: A 1409 LEU cc_start: 0.2026 (OUTLIER) cc_final: 0.1682 (mp) REVERT: A 1434 MET cc_start: 0.1535 (OUTLIER) cc_final: 0.1204 (mtp) REVERT: A 1465 ILE cc_start: 0.4517 (OUTLIER) cc_final: 0.4273 (tt) REVERT: A 1512 ASP cc_start: 0.5732 (OUTLIER) cc_final: 0.5502 (m-30) REVERT: A 1647 THR cc_start: 0.8172 (OUTLIER) cc_final: 0.7849 (m) REVERT: A 1779 ASP cc_start: 0.6717 (OUTLIER) cc_final: 0.6455 (m-30) REVERT: A 1857 PHE cc_start: 0.5182 (OUTLIER) cc_final: 0.3996 (m-80) REVERT: A 1952 LEU cc_start: 0.0542 (OUTLIER) cc_final: 0.0239 (mm) outliers start: 187 outliers final: 90 residues processed: 313 average time/residue: 0.9835 time to fit residues: 361.3745 Evaluate side-chains 229 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 122 time to evaluate : 1.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 40 SER Chi-restraints excluded: chain A residue 41 SER Chi-restraints excluded: chain A residue 74 LYS Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 106 GLN Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 195 GLU Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 223 LYS Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 325 GLU Chi-restraints excluded: chain A residue 332 SER Chi-restraints excluded: chain A residue 333 LYS Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 366 ILE Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 422 THR Chi-restraints excluded: chain A residue 439 SER Chi-restraints excluded: chain A residue 444 MET Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 489 THR Chi-restraints excluded: chain A residue 508 ILE Chi-restraints excluded: chain A residue 517 THR Chi-restraints excluded: chain A residue 518 SER Chi-restraints excluded: chain A residue 529 SER Chi-restraints excluded: chain A residue 532 GLU Chi-restraints excluded: chain A residue 576 GLU Chi-restraints excluded: chain A residue 590 SER Chi-restraints excluded: chain A residue 622 SER Chi-restraints excluded: chain A residue 640 ILE Chi-restraints excluded: chain A residue 667 ASP Chi-restraints excluded: chain A residue 670 SER Chi-restraints excluded: chain A residue 738 SER Chi-restraints excluded: chain A residue 774 SER Chi-restraints excluded: chain A residue 800 LEU Chi-restraints excluded: chain A residue 825 GLU Chi-restraints excluded: chain A residue 826 ILE Chi-restraints excluded: chain A residue 830 SER Chi-restraints excluded: chain A residue 836 ILE Chi-restraints excluded: chain A residue 849 SER Chi-restraints excluded: chain A residue 852 ILE Chi-restraints excluded: chain A residue 865 ILE Chi-restraints excluded: chain A residue 890 SER Chi-restraints excluded: chain A residue 920 GLU Chi-restraints excluded: chain A residue 937 PHE Chi-restraints excluded: chain A residue 945 VAL Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 950 LEU Chi-restraints excluded: chain A residue 968 LEU Chi-restraints excluded: chain A residue 979 SER Chi-restraints excluded: chain A residue 980 ASN Chi-restraints excluded: chain A residue 1002 THR Chi-restraints excluded: chain A residue 1007 VAL Chi-restraints excluded: chain A residue 1072 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1116 LYS Chi-restraints excluded: chain A residue 1129 LEU Chi-restraints excluded: chain A residue 1161 SER Chi-restraints excluded: chain A residue 1169 ILE Chi-restraints excluded: chain A residue 1181 THR Chi-restraints excluded: chain A residue 1197 LYS Chi-restraints excluded: chain A residue 1214 ASP Chi-restraints excluded: chain A residue 1228 ARG Chi-restraints excluded: chain A residue 1270 ILE Chi-restraints excluded: chain A residue 1310 LYS Chi-restraints excluded: chain A residue 1345 VAL Chi-restraints excluded: chain A residue 1409 LEU Chi-restraints excluded: chain A residue 1434 MET Chi-restraints excluded: chain A residue 1435 LYS Chi-restraints excluded: chain A residue 1465 ILE Chi-restraints excluded: chain A residue 1478 SER Chi-restraints excluded: chain A residue 1512 ASP Chi-restraints excluded: chain A residue 1516 ILE Chi-restraints excluded: chain A residue 1524 VAL Chi-restraints excluded: chain A residue 1539 SER Chi-restraints excluded: chain A residue 1541 SER Chi-restraints excluded: chain A residue 1547 THR Chi-restraints excluded: chain A residue 1588 SER Chi-restraints excluded: chain A residue 1591 ILE Chi-restraints excluded: chain A residue 1610 ASN Chi-restraints excluded: chain A residue 1614 SER Chi-restraints excluded: chain A residue 1616 SER Chi-restraints excluded: chain A residue 1618 SER Chi-restraints excluded: chain A residue 1641 ILE Chi-restraints excluded: chain A residue 1645 SER Chi-restraints excluded: chain A residue 1647 THR Chi-restraints excluded: chain A residue 1662 TYR Chi-restraints excluded: chain A residue 1682 LEU Chi-restraints excluded: chain A residue 1698 LEU Chi-restraints excluded: chain A residue 1714 ILE Chi-restraints excluded: chain A residue 1722 ASP Chi-restraints excluded: chain A residue 1748 SER Chi-restraints excluded: chain A residue 1779 ASP Chi-restraints excluded: chain A residue 1782 SER Chi-restraints excluded: chain A residue 1801 SER Chi-restraints excluded: chain A residue 1841 ASP Chi-restraints excluded: chain A residue 1842 SER Chi-restraints excluded: chain A residue 1857 PHE Chi-restraints excluded: chain A residue 1914 THR Chi-restraints excluded: chain A residue 1952 LEU Chi-restraints excluded: chain A residue 1955 GLU Chi-restraints excluded: chain A residue 2235 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 194 optimal weight: 0.9980 chunk 174 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 59 optimal weight: 0.6980 chunk 117 optimal weight: 9.9990 chunk 93 optimal weight: 1.9990 chunk 180 optimal weight: 2.9990 chunk 69 optimal weight: 0.8980 chunk 109 optimal weight: 5.9990 chunk 134 optimal weight: 7.9990 chunk 208 optimal weight: 7.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 2 ASN A 106 GLN A 379 ASN ** A 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 419 ASN A 579 HIS A 639 GLN A 694 ASN A 741 GLN ** A 795 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 827 ASN A 876 ASN A 924 HIS A 988 GLN A1114 GLN A1178 HIS A1207 ASN A1257 HIS A1333 ASN ** A1350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1385 ASN A1444 GLN A1449 HIS A1530 ASN A1548 ASN A1580 ASN A1598 ASN A1654 GLN A1663 HIS A1690 ASN A1727 ASN A1763 GLN A2058 ASN A2143 GLN ** A2260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2319 ASN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4830 r_free = 0.4830 target = 0.271724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4361 r_free = 0.4361 target = 0.222203 restraints weight = 19572.263| |-----------------------------------------------------------------------------| r_work (start): 0.4323 rms_B_bonded: 4.10 r_work: 0.3912 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3864 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.3864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7122 moved from start: 0.1305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 19027 Z= 0.210 Angle : 0.706 10.248 25734 Z= 0.382 Chirality : 0.050 0.190 2831 Planarity : 0.005 0.051 3324 Dihedral : 10.451 87.130 2681 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.49 % Favored : 95.47 % Rotamer: Outliers : 6.23 % Allowed : 23.99 % Favored : 69.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.16), residues: 2295 helix: 0.38 (0.19), residues: 635 sheet: -1.17 (0.23), residues: 445 loop : -1.37 (0.16), residues: 1215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 102 HIS 0.005 0.002 HIS A1456 PHE 0.027 0.002 PHE A 186 TYR 0.033 0.002 TYR A 46 ARG 0.004 0.001 ARG A 253 Details of bonding type rmsd hydrogen bonds : bond 0.07086 ( 801) hydrogen bonds : angle 5.60778 ( 2154) metal coordination : bond 0.00556 ( 3) covalent geometry : bond 0.00478 (19023) covalent geometry : angle 0.70585 (25734) Misc. bond : bond 0.00697 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4590 Ramachandran restraints generated. 2295 Oldfield, 0 Emsley, 2295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4590 Ramachandran restraints generated. 2295 Oldfield, 0 Emsley, 2295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 130 time to evaluate : 1.975 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 157 PHE cc_start: 0.6926 (m-80) cc_final: 0.6319 (m-10) REVERT: A 166 PHE cc_start: 0.5805 (t80) cc_final: 0.5178 (t80) REVERT: A 314 MET cc_start: 0.8449 (mtp) cc_final: 0.8245 (mtp) REVERT: A 485 LYS cc_start: 0.8582 (OUTLIER) cc_final: 0.8380 (tppp) REVERT: A 526 ARG cc_start: 0.7949 (ttm-80) cc_final: 0.7492 (tpm170) REVERT: A 560 ASP cc_start: 0.6278 (OUTLIER) cc_final: 0.5820 (t0) REVERT: A 570 MET cc_start: 0.6072 (tmt) cc_final: 0.5758 (mpt) REVERT: A 705 ILE cc_start: 0.7874 (OUTLIER) cc_final: 0.7417 (pt) REVERT: A 800 LEU cc_start: 0.8195 (OUTLIER) cc_final: 0.7945 (mt) REVERT: A 1114 GLN cc_start: 0.3041 (OUTLIER) cc_final: 0.2411 (mp-120) REVERT: A 1116 LYS cc_start: 0.1521 (OUTLIER) cc_final: 0.0368 (ttmt) REVERT: A 1214 ASP cc_start: 0.1116 (OUTLIER) cc_final: 0.0643 (t70) REVERT: A 1327 LEU cc_start: 0.3359 (OUTLIER) cc_final: 0.3094 (pt) REVERT: A 1397 GLU cc_start: 0.2551 (OUTLIER) cc_final: 0.2293 (tp30) REVERT: A 1409 LEU cc_start: 0.2108 (OUTLIER) cc_final: 0.1888 (mp) REVERT: A 1610 ASN cc_start: 0.6844 (OUTLIER) cc_final: 0.6581 (p0) REVERT: A 1647 THR cc_start: 0.8292 (OUTLIER) cc_final: 0.8009 (m) REVERT: A 1857 PHE cc_start: 0.5357 (OUTLIER) cc_final: 0.5064 (m-80) REVERT: A 1986 MET cc_start: 0.1956 (mmt) cc_final: -0.0034 (ttp) REVERT: A 2143 GLN cc_start: 0.0431 (OUTLIER) cc_final: 0.0146 (mp-120) REVERT: A 2212 TRP cc_start: 0.0275 (OUTLIER) cc_final: -0.0333 (t60) outliers start: 130 outliers final: 73 residues processed: 245 average time/residue: 0.9983 time to fit residues: 286.2714 Evaluate side-chains 211 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 123 time to evaluate : 2.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 41 SER Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 74 LYS Chi-restraints excluded: chain A residue 90 SER Chi-restraints excluded: chain A residue 106 GLN Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 195 GLU Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 325 GLU Chi-restraints excluded: chain A residue 332 SER Chi-restraints excluded: chain A residue 333 LYS Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 366 ILE Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 423 ASP Chi-restraints excluded: chain A residue 444 MET Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 485 LYS Chi-restraints excluded: chain A residue 508 ILE Chi-restraints excluded: chain A residue 518 SER Chi-restraints excluded: chain A residue 532 GLU Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 560 ASP Chi-restraints excluded: chain A residue 640 ILE Chi-restraints excluded: chain A residue 667 ASP Chi-restraints excluded: chain A residue 670 SER Chi-restraints excluded: chain A residue 705 ILE Chi-restraints excluded: chain A residue 756 ASP Chi-restraints excluded: chain A residue 800 LEU Chi-restraints excluded: chain A residue 826 ILE Chi-restraints excluded: chain A residue 865 ILE Chi-restraints excluded: chain A residue 937 PHE Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 950 LEU Chi-restraints excluded: chain A residue 968 LEU Chi-restraints excluded: chain A residue 979 SER Chi-restraints excluded: chain A residue 1005 SER Chi-restraints excluded: chain A residue 1072 THR Chi-restraints excluded: chain A residue 1114 GLN Chi-restraints excluded: chain A residue 1116 LYS Chi-restraints excluded: chain A residue 1143 ILE Chi-restraints excluded: chain A residue 1169 ILE Chi-restraints excluded: chain A residue 1178 HIS Chi-restraints excluded: chain A residue 1181 THR Chi-restraints excluded: chain A residue 1214 ASP Chi-restraints excluded: chain A residue 1228 ARG Chi-restraints excluded: chain A residue 1304 THR Chi-restraints excluded: chain A residue 1327 LEU Chi-restraints excluded: chain A residue 1343 THR Chi-restraints excluded: chain A residue 1345 VAL Chi-restraints excluded: chain A residue 1380 ASN Chi-restraints excluded: chain A residue 1385 ASN Chi-restraints excluded: chain A residue 1397 GLU Chi-restraints excluded: chain A residue 1402 ILE Chi-restraints excluded: chain A residue 1403 SER Chi-restraints excluded: chain A residue 1409 LEU Chi-restraints excluded: chain A residue 1509 SER Chi-restraints excluded: chain A residue 1516 ILE Chi-restraints excluded: chain A residue 1539 SER Chi-restraints excluded: chain A residue 1547 THR Chi-restraints excluded: chain A residue 1582 LEU Chi-restraints excluded: chain A residue 1588 SER Chi-restraints excluded: chain A residue 1591 ILE Chi-restraints excluded: chain A residue 1609 THR Chi-restraints excluded: chain A residue 1610 ASN Chi-restraints excluded: chain A residue 1614 SER Chi-restraints excluded: chain A residue 1641 ILE Chi-restraints excluded: chain A residue 1645 SER Chi-restraints excluded: chain A residue 1647 THR Chi-restraints excluded: chain A residue 1662 TYR Chi-restraints excluded: chain A residue 1682 LEU Chi-restraints excluded: chain A residue 1698 LEU Chi-restraints excluded: chain A residue 1714 ILE Chi-restraints excluded: chain A residue 1837 ILE Chi-restraints excluded: chain A residue 1841 ASP Chi-restraints excluded: chain A residue 1842 SER Chi-restraints excluded: chain A residue 1857 PHE Chi-restraints excluded: chain A residue 1894 ILE Chi-restraints excluded: chain A residue 1978 TYR Chi-restraints excluded: chain A residue 2005 VAL Chi-restraints excluded: chain A residue 2088 THR Chi-restraints excluded: chain A residue 2125 ILE Chi-restraints excluded: chain A residue 2143 GLN Chi-restraints excluded: chain A residue 2212 TRP Chi-restraints excluded: chain A residue 2235 VAL Chi-restraints excluded: chain A residue 2323 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 27 optimal weight: 0.3980 chunk 201 optimal weight: 6.9990 chunk 7 optimal weight: 0.5980 chunk 119 optimal weight: 30.0000 chunk 142 optimal weight: 4.9990 chunk 16 optimal weight: 0.0050 chunk 93 optimal weight: 0.4980 chunk 204 optimal weight: 5.9990 chunk 171 optimal weight: 3.9990 chunk 170 optimal weight: 0.9990 chunk 140 optimal weight: 0.0970 overall best weight: 0.3192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 379 ASN A 405 ASN A 763 ASN ** A 795 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 835 GLN A1114 GLN A1178 HIS A1350 ASN A2058 ASN ** A2260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4856 r_free = 0.4856 target = 0.274067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4690 r_free = 0.4690 target = 0.254428 restraints weight = 19983.457| |-----------------------------------------------------------------------------| r_work (start): 0.4689 rms_B_bonded: 0.94 r_work: 0.4217 rms_B_bonded: 1.28 restraints_weight: 0.5000 r_work: 0.4008 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.4008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6928 moved from start: 0.2012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 19027 Z= 0.113 Angle : 0.563 8.883 25734 Z= 0.302 Chirality : 0.045 0.174 2831 Planarity : 0.004 0.051 3324 Dihedral : 8.166 83.508 2596 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 4.50 % Allowed : 24.76 % Favored : 70.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.17), residues: 2295 helix: 1.48 (0.21), residues: 639 sheet: -0.93 (0.23), residues: 451 loop : -1.08 (0.17), residues: 1205 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 102 HIS 0.013 0.001 HIS A1178 PHE 0.018 0.001 PHE A 246 TYR 0.020 0.001 TYR A1978 ARG 0.005 0.000 ARG A1265 Details of bonding type rmsd hydrogen bonds : bond 0.04650 ( 801) hydrogen bonds : angle 5.04570 ( 2154) metal coordination : bond 0.00114 ( 3) covalent geometry : bond 0.00231 (19023) covalent geometry : angle 0.56261 (25734) Misc. bond : bond 0.00668 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4590 Ramachandran restraints generated. 2295 Oldfield, 0 Emsley, 2295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4590 Ramachandran restraints generated. 2295 Oldfield, 0 Emsley, 2295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 140 time to evaluate : 2.094 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 ASN cc_start: 0.7657 (m-40) cc_final: 0.7064 (t0) REVERT: A 106 GLN cc_start: 0.8750 (OUTLIER) cc_final: 0.7436 (tp-100) REVERT: A 157 PHE cc_start: 0.6669 (m-80) cc_final: 0.6136 (m-80) REVERT: A 166 PHE cc_start: 0.5690 (t80) cc_final: 0.5085 (t80) REVERT: A 314 MET cc_start: 0.8390 (mtp) cc_final: 0.8162 (mtp) REVERT: A 419 ASN cc_start: 0.8071 (m-40) cc_final: 0.7628 (t0) REVERT: A 422 THR cc_start: 0.7005 (p) cc_final: 0.6714 (p) REVERT: A 526 ARG cc_start: 0.7851 (ttm-80) cc_final: 0.7529 (tpm170) REVERT: A 560 ASP cc_start: 0.6462 (t70) cc_final: 0.6091 (t0) REVERT: A 570 MET cc_start: 0.6039 (tmt) cc_final: 0.5745 (mpt) REVERT: A 754 ILE cc_start: 0.7458 (OUTLIER) cc_final: 0.7036 (pp) REVERT: A 1145 MET cc_start: 0.2269 (mmp) cc_final: 0.1775 (mmt) REVERT: A 1214 ASP cc_start: 0.1182 (OUTLIER) cc_final: 0.0657 (t70) REVERT: A 1327 LEU cc_start: 0.2475 (OUTLIER) cc_final: 0.2106 (pt) REVERT: A 1499 MET cc_start: 0.3528 (mpt) cc_final: 0.2890 (mmm) REVERT: A 1609 THR cc_start: 0.7435 (p) cc_final: 0.7057 (t) REVERT: A 1857 PHE cc_start: 0.5244 (OUTLIER) cc_final: 0.4928 (m-80) REVERT: A 1986 MET cc_start: 0.1944 (mmt) cc_final: 0.0057 (ttp) outliers start: 94 outliers final: 43 residues processed: 221 average time/residue: 1.0497 time to fit residues: 270.4157 Evaluate side-chains 172 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 124 time to evaluate : 1.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 SER Chi-restraints excluded: chain A residue 106 GLN Chi-restraints excluded: chain A residue 195 GLU Chi-restraints excluded: chain A residue 325 GLU Chi-restraints excluded: chain A residue 366 ILE Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 423 ASP Chi-restraints excluded: chain A residue 532 GLU Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 640 ILE Chi-restraints excluded: chain A residue 667 ASP Chi-restraints excluded: chain A residue 721 ASP Chi-restraints excluded: chain A residue 754 ILE Chi-restraints excluded: chain A residue 757 HIS Chi-restraints excluded: chain A residue 774 SER Chi-restraints excluded: chain A residue 812 ASP Chi-restraints excluded: chain A residue 826 ILE Chi-restraints excluded: chain A residue 937 PHE Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 950 LEU Chi-restraints excluded: chain A residue 956 VAL Chi-restraints excluded: chain A residue 1007 VAL Chi-restraints excluded: chain A residue 1072 THR Chi-restraints excluded: chain A residue 1116 LYS Chi-restraints excluded: chain A residue 1143 ILE Chi-restraints excluded: chain A residue 1169 ILE Chi-restraints excluded: chain A residue 1176 SER Chi-restraints excluded: chain A residue 1181 THR Chi-restraints excluded: chain A residue 1194 THR Chi-restraints excluded: chain A residue 1214 ASP Chi-restraints excluded: chain A residue 1228 ARG Chi-restraints excluded: chain A residue 1251 LEU Chi-restraints excluded: chain A residue 1327 LEU Chi-restraints excluded: chain A residue 1343 THR Chi-restraints excluded: chain A residue 1345 VAL Chi-restraints excluded: chain A residue 1380 ASN Chi-restraints excluded: chain A residue 1403 SER Chi-restraints excluded: chain A residue 1547 THR Chi-restraints excluded: chain A residue 1582 LEU Chi-restraints excluded: chain A residue 1588 SER Chi-restraints excluded: chain A residue 1591 ILE Chi-restraints excluded: chain A residue 1614 SER Chi-restraints excluded: chain A residue 1662 TYR Chi-restraints excluded: chain A residue 1667 SER Chi-restraints excluded: chain A residue 1782 SER Chi-restraints excluded: chain A residue 1857 PHE Chi-restraints excluded: chain A residue 2005 VAL Chi-restraints excluded: chain A residue 2235 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 0 optimal weight: 3.9990 chunk 213 optimal weight: 0.4980 chunk 220 optimal weight: 20.0000 chunk 104 optimal weight: 40.0000 chunk 20 optimal weight: 0.7980 chunk 111 optimal weight: 40.0000 chunk 216 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 212 optimal weight: 20.0000 chunk 98 optimal weight: 6.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 405 ASN A 785 ASN ** A 795 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1633 GLN A2143 GLN ** A2260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4894 r_free = 0.4894 target = 0.277763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4721 r_free = 0.4721 target = 0.257098 restraints weight = 19759.299| |-----------------------------------------------------------------------------| r_work (start): 0.4724 rms_B_bonded: 0.96 r_work: 0.4569 rms_B_bonded: 1.62 restraints_weight: 0.5000 r_work: 0.4539 rms_B_bonded: 2.06 restraints_weight: 0.2500 r_work (final): 0.4539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6216 moved from start: 0.2181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 19027 Z= 0.158 Angle : 0.601 8.334 25734 Z= 0.325 Chirality : 0.047 0.167 2831 Planarity : 0.004 0.050 3324 Dihedral : 7.250 83.377 2543 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 4.93 % Allowed : 24.62 % Favored : 70.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.17), residues: 2295 helix: 1.43 (0.20), residues: 639 sheet: -0.78 (0.23), residues: 451 loop : -0.92 (0.17), residues: 1205 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 102 HIS 0.005 0.001 HIS A 757 PHE 0.023 0.002 PHE A 186 TYR 0.025 0.002 TYR A 46 ARG 0.005 0.001 ARG A 262 Details of bonding type rmsd hydrogen bonds : bond 0.05972 ( 801) hydrogen bonds : angle 5.08129 ( 2154) metal coordination : bond 0.00383 ( 3) covalent geometry : bond 0.00352 (19023) covalent geometry : angle 0.60107 (25734) Misc. bond : bond 0.00632 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4590 Ramachandran restraints generated. 2295 Oldfield, 0 Emsley, 2295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4590 Ramachandran restraints generated. 2295 Oldfield, 0 Emsley, 2295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 127 time to evaluate : 2.059 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 GLN cc_start: 0.8603 (OUTLIER) cc_final: 0.7209 (tp-100) REVERT: A 157 PHE cc_start: 0.6304 (m-80) cc_final: 0.5962 (m-80) REVERT: A 166 PHE cc_start: 0.5668 (t80) cc_final: 0.5069 (t80) REVERT: A 314 MET cc_start: 0.8049 (mtp) cc_final: 0.7822 (mtp) REVERT: A 337 MET cc_start: 0.7435 (OUTLIER) cc_final: 0.6925 (mtp) REVERT: A 419 ASN cc_start: 0.7766 (m-40) cc_final: 0.7447 (t0) REVERT: A 526 ARG cc_start: 0.7711 (ttm-80) cc_final: 0.7506 (tpm170) REVERT: A 1145 MET cc_start: 0.2041 (mmp) cc_final: 0.1385 (mtm) REVERT: A 1214 ASP cc_start: 0.2106 (OUTLIER) cc_final: 0.1863 (t70) REVERT: A 1249 LYS cc_start: 0.3270 (OUTLIER) cc_final: 0.2974 (mttt) REVERT: A 1533 LYS cc_start: 0.5139 (OUTLIER) cc_final: 0.4637 (tmtt) REVERT: A 1647 THR cc_start: 0.8034 (OUTLIER) cc_final: 0.7729 (m) REVERT: A 1857 PHE cc_start: 0.5130 (OUTLIER) cc_final: 0.4766 (m-80) REVERT: A 1986 MET cc_start: 0.1943 (mmt) cc_final: 0.0593 (ttp) REVERT: A 2212 TRP cc_start: 0.0202 (OUTLIER) cc_final: -0.0593 (t60) outliers start: 103 outliers final: 53 residues processed: 216 average time/residue: 1.0386 time to fit residues: 260.6354 Evaluate side-chains 174 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 113 time to evaluate : 1.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 SER Chi-restraints excluded: chain A residue 106 GLN Chi-restraints excluded: chain A residue 143 LYS Chi-restraints excluded: chain A residue 195 GLU Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 325 GLU Chi-restraints excluded: chain A residue 337 MET Chi-restraints excluded: chain A residue 366 ILE Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 532 GLU Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 667 ASP Chi-restraints excluded: chain A residue 721 ASP Chi-restraints excluded: chain A residue 774 SER Chi-restraints excluded: chain A residue 812 ASP Chi-restraints excluded: chain A residue 826 ILE Chi-restraints excluded: chain A residue 881 SER Chi-restraints excluded: chain A residue 903 LYS Chi-restraints excluded: chain A residue 937 PHE Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 950 LEU Chi-restraints excluded: chain A residue 956 VAL Chi-restraints excluded: chain A residue 978 LEU Chi-restraints excluded: chain A residue 981 LEU Chi-restraints excluded: chain A residue 1005 SER Chi-restraints excluded: chain A residue 1007 VAL Chi-restraints excluded: chain A residue 1072 THR Chi-restraints excluded: chain A residue 1116 LYS Chi-restraints excluded: chain A residue 1143 ILE Chi-restraints excluded: chain A residue 1169 ILE Chi-restraints excluded: chain A residue 1176 SER Chi-restraints excluded: chain A residue 1181 THR Chi-restraints excluded: chain A residue 1194 THR Chi-restraints excluded: chain A residue 1214 ASP Chi-restraints excluded: chain A residue 1228 ARG Chi-restraints excluded: chain A residue 1249 LYS Chi-restraints excluded: chain A residue 1251 LEU Chi-restraints excluded: chain A residue 1279 LYS Chi-restraints excluded: chain A residue 1343 THR Chi-restraints excluded: chain A residue 1374 LYS Chi-restraints excluded: chain A residue 1402 ILE Chi-restraints excluded: chain A residue 1533 LYS Chi-restraints excluded: chain A residue 1541 SER Chi-restraints excluded: chain A residue 1547 THR Chi-restraints excluded: chain A residue 1582 LEU Chi-restraints excluded: chain A residue 1588 SER Chi-restraints excluded: chain A residue 1591 ILE Chi-restraints excluded: chain A residue 1614 SER Chi-restraints excluded: chain A residue 1647 THR Chi-restraints excluded: chain A residue 1662 TYR Chi-restraints excluded: chain A residue 1667 SER Chi-restraints excluded: chain A residue 1698 LEU Chi-restraints excluded: chain A residue 1782 SER Chi-restraints excluded: chain A residue 1837 ILE Chi-restraints excluded: chain A residue 1857 PHE Chi-restraints excluded: chain A residue 1978 TYR Chi-restraints excluded: chain A residue 2125 ILE Chi-restraints excluded: chain A residue 2212 TRP Chi-restraints excluded: chain A residue 2235 VAL Chi-restraints excluded: chain A residue 2323 TRP Chi-restraints excluded: chain A residue 2361 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 148 optimal weight: 4.9990 chunk 205 optimal weight: 0.0020 chunk 12 optimal weight: 0.9980 chunk 131 optimal weight: 9.9990 chunk 162 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 216 optimal weight: 8.9990 chunk 65 optimal weight: 1.9990 chunk 146 optimal weight: 5.9990 chunk 100 optimal weight: 0.0980 chunk 130 optimal weight: 10.0000 overall best weight: 1.0192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 795 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 931 ASN A1633 GLN ** A2001 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2058 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4840 r_free = 0.4840 target = 0.272059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.213103 restraints weight = 19715.075| |-----------------------------------------------------------------------------| r_work (start): 0.4228 rms_B_bonded: 5.92 r_work: 0.3699 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work: 0.3650 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7322 moved from start: 0.2429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 19027 Z= 0.153 Angle : 0.583 7.910 25734 Z= 0.315 Chirality : 0.047 0.165 2831 Planarity : 0.004 0.054 3324 Dihedral : 7.042 82.450 2540 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 4.84 % Allowed : 24.86 % Favored : 70.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.17), residues: 2295 helix: 1.53 (0.20), residues: 639 sheet: -0.66 (0.24), residues: 453 loop : -0.80 (0.17), residues: 1203 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 102 HIS 0.005 0.001 HIS A 757 PHE 0.023 0.002 PHE A 186 TYR 0.023 0.002 TYR A 46 ARG 0.003 0.000 ARG A 68 Details of bonding type rmsd hydrogen bonds : bond 0.05648 ( 801) hydrogen bonds : angle 4.96312 ( 2154) metal coordination : bond 0.00564 ( 3) covalent geometry : bond 0.00340 (19023) covalent geometry : angle 0.58302 (25734) Misc. bond : bond 0.00613 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4590 Ramachandran restraints generated. 2295 Oldfield, 0 Emsley, 2295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4590 Ramachandran restraints generated. 2295 Oldfield, 0 Emsley, 2295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 124 time to evaluate : 2.079 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 GLN cc_start: 0.9064 (OUTLIER) cc_final: 0.7727 (tp-100) REVERT: A 157 PHE cc_start: 0.6737 (m-80) cc_final: 0.6129 (m-80) REVERT: A 166 PHE cc_start: 0.6075 (t80) cc_final: 0.5322 (t80) REVERT: A 337 MET cc_start: 0.7890 (OUTLIER) cc_final: 0.7332 (mtp) REVERT: A 419 ASN cc_start: 0.8312 (m-40) cc_final: 0.7888 (t0) REVERT: A 526 ARG cc_start: 0.8004 (ttm-80) cc_final: 0.7595 (tpm170) REVERT: A 689 LYS cc_start: 0.7287 (mmtp) cc_final: 0.7035 (ptpt) REVERT: A 705 ILE cc_start: 0.7827 (OUTLIER) cc_final: 0.7321 (pp) REVERT: A 1145 MET cc_start: 0.0858 (mmp) cc_final: 0.0285 (mtm) REVERT: A 1164 LEU cc_start: 0.2125 (OUTLIER) cc_final: 0.1659 (tm) REVERT: A 1214 ASP cc_start: 0.1170 (OUTLIER) cc_final: 0.0664 (t70) REVERT: A 1332 MET cc_start: 0.2074 (mtm) cc_final: 0.1284 (ppp) REVERT: A 1499 MET cc_start: 0.2996 (mpt) cc_final: 0.2221 (ttp) REVERT: A 1533 LYS cc_start: 0.5916 (OUTLIER) cc_final: 0.5200 (tmtt) REVERT: A 1647 THR cc_start: 0.8365 (OUTLIER) cc_final: 0.8141 (m) REVERT: A 1857 PHE cc_start: 0.5376 (OUTLIER) cc_final: 0.5009 (m-80) REVERT: A 1986 MET cc_start: 0.1986 (mmt) cc_final: -0.0104 (ttp) REVERT: A 2212 TRP cc_start: 0.0268 (OUTLIER) cc_final: -0.0541 (t60) outliers start: 101 outliers final: 56 residues processed: 214 average time/residue: 0.9769 time to fit residues: 245.7184 Evaluate side-chains 179 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 114 time to evaluate : 1.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 90 SER Chi-restraints excluded: chain A residue 106 GLN Chi-restraints excluded: chain A residue 143 LYS Chi-restraints excluded: chain A residue 195 GLU Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 245 LYS Chi-restraints excluded: chain A residue 325 GLU Chi-restraints excluded: chain A residue 337 MET Chi-restraints excluded: chain A residue 366 ILE Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 532 GLU Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 667 ASP Chi-restraints excluded: chain A residue 705 ILE Chi-restraints excluded: chain A residue 757 HIS Chi-restraints excluded: chain A residue 774 SER Chi-restraints excluded: chain A residue 812 ASP Chi-restraints excluded: chain A residue 826 ILE Chi-restraints excluded: chain A residue 881 SER Chi-restraints excluded: chain A residue 903 LYS Chi-restraints excluded: chain A residue 937 PHE Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 950 LEU Chi-restraints excluded: chain A residue 956 VAL Chi-restraints excluded: chain A residue 969 ILE Chi-restraints excluded: chain A residue 981 LEU Chi-restraints excluded: chain A residue 1005 SER Chi-restraints excluded: chain A residue 1007 VAL Chi-restraints excluded: chain A residue 1072 THR Chi-restraints excluded: chain A residue 1116 LYS Chi-restraints excluded: chain A residue 1143 ILE Chi-restraints excluded: chain A residue 1164 LEU Chi-restraints excluded: chain A residue 1169 ILE Chi-restraints excluded: chain A residue 1176 SER Chi-restraints excluded: chain A residue 1181 THR Chi-restraints excluded: chain A residue 1194 THR Chi-restraints excluded: chain A residue 1214 ASP Chi-restraints excluded: chain A residue 1228 ARG Chi-restraints excluded: chain A residue 1251 LEU Chi-restraints excluded: chain A residue 1343 THR Chi-restraints excluded: chain A residue 1402 ILE Chi-restraints excluded: chain A residue 1403 SER Chi-restraints excluded: chain A residue 1533 LYS Chi-restraints excluded: chain A residue 1541 SER Chi-restraints excluded: chain A residue 1547 THR Chi-restraints excluded: chain A residue 1582 LEU Chi-restraints excluded: chain A residue 1591 ILE Chi-restraints excluded: chain A residue 1614 SER Chi-restraints excluded: chain A residue 1647 THR Chi-restraints excluded: chain A residue 1662 TYR Chi-restraints excluded: chain A residue 1667 SER Chi-restraints excluded: chain A residue 1698 LEU Chi-restraints excluded: chain A residue 1782 SER Chi-restraints excluded: chain A residue 1837 ILE Chi-restraints excluded: chain A residue 1857 PHE Chi-restraints excluded: chain A residue 1978 TYR Chi-restraints excluded: chain A residue 2088 THR Chi-restraints excluded: chain A residue 2125 ILE Chi-restraints excluded: chain A residue 2212 TRP Chi-restraints excluded: chain A residue 2235 VAL Chi-restraints excluded: chain A residue 2253 LEU Chi-restraints excluded: chain A residue 2289 MET Chi-restraints excluded: chain A residue 2323 TRP Chi-restraints excluded: chain A residue 2361 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 71 optimal weight: 1.9990 chunk 208 optimal weight: 8.9990 chunk 165 optimal weight: 0.6980 chunk 206 optimal weight: 4.9990 chunk 150 optimal weight: 0.7980 chunk 156 optimal weight: 1.9990 chunk 108 optimal weight: 10.0000 chunk 80 optimal weight: 1.9990 chunk 109 optimal weight: 10.0000 chunk 76 optimal weight: 2.9990 chunk 193 optimal weight: 7.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 ASN A 385 GLN ** A 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 795 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1290 ASN A1633 GLN A2001 ASN ** A2058 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4989 r_free = 0.4989 target = 0.283826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4784 r_free = 0.4784 target = 0.258569 restraints weight = 20420.532| |-----------------------------------------------------------------------------| r_work (start): 0.4772 rms_B_bonded: 1.21 r_work: 0.4606 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.4573 rms_B_bonded: 2.53 restraints_weight: 0.2500 r_work (final): 0.4573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6401 moved from start: 0.2494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 19027 Z= 0.196 Angle : 0.634 8.748 25734 Z= 0.343 Chirality : 0.049 0.201 2831 Planarity : 0.004 0.053 3324 Dihedral : 7.158 87.014 2539 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 4.60 % Allowed : 25.57 % Favored : 69.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.17), residues: 2295 helix: 1.28 (0.20), residues: 641 sheet: -0.64 (0.24), residues: 451 loop : -0.81 (0.17), residues: 1203 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 102 HIS 0.005 0.001 HIS A 757 PHE 0.029 0.002 PHE A 186 TYR 0.028 0.002 TYR A 46 ARG 0.005 0.001 ARG A1653 Details of bonding type rmsd hydrogen bonds : bond 0.06570 ( 801) hydrogen bonds : angle 5.10438 ( 2154) metal coordination : bond 0.00533 ( 3) covalent geometry : bond 0.00450 (19023) covalent geometry : angle 0.63368 (25734) Misc. bond : bond 0.00606 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4590 Ramachandran restraints generated. 2295 Oldfield, 0 Emsley, 2295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4590 Ramachandran restraints generated. 2295 Oldfield, 0 Emsley, 2295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 118 time to evaluate : 1.876 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 GLN cc_start: 0.8681 (OUTLIER) cc_final: 0.7199 (tp-100) REVERT: A 166 PHE cc_start: 0.5713 (t80) cc_final: 0.5032 (t80) REVERT: A 337 MET cc_start: 0.7483 (OUTLIER) cc_final: 0.6946 (mtp) REVERT: A 526 ARG cc_start: 0.7778 (ttm-80) cc_final: 0.7476 (tpm170) REVERT: A 705 ILE cc_start: 0.7603 (OUTLIER) cc_final: 0.7151 (pp) REVERT: A 1145 MET cc_start: 0.0997 (mmp) cc_final: -0.0314 (mtp) REVERT: A 1164 LEU cc_start: 0.3300 (OUTLIER) cc_final: 0.2974 (tm) REVERT: A 1214 ASP cc_start: 0.2350 (OUTLIER) cc_final: 0.2063 (t70) REVERT: A 1332 MET cc_start: 0.1844 (mtm) cc_final: 0.0620 (ppp) REVERT: A 1647 THR cc_start: 0.8115 (OUTLIER) cc_final: 0.7862 (m) REVERT: A 1857 PHE cc_start: 0.5555 (OUTLIER) cc_final: 0.4692 (m-80) REVERT: A 1986 MET cc_start: 0.1947 (mmt) cc_final: 0.0428 (ttp) REVERT: A 2212 TRP cc_start: 0.0296 (OUTLIER) cc_final: -0.0909 (t60) REVERT: A 2245 GLU cc_start: -0.1720 (OUTLIER) cc_final: -0.1941 (tt0) REVERT: A 2320 TYR cc_start: 0.1351 (OUTLIER) cc_final: 0.0918 (t80) outliers start: 96 outliers final: 64 residues processed: 203 average time/residue: 0.9971 time to fit residues: 236.6949 Evaluate side-chains 188 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 114 time to evaluate : 1.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 90 SER Chi-restraints excluded: chain A residue 106 GLN Chi-restraints excluded: chain A residue 143 LYS Chi-restraints excluded: chain A residue 195 GLU Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 245 LYS Chi-restraints excluded: chain A residue 296 ASP Chi-restraints excluded: chain A residue 325 GLU Chi-restraints excluded: chain A residue 337 MET Chi-restraints excluded: chain A residue 366 ILE Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 529 SER Chi-restraints excluded: chain A residue 532 GLU Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 640 ILE Chi-restraints excluded: chain A residue 667 ASP Chi-restraints excluded: chain A residue 705 ILE Chi-restraints excluded: chain A residue 721 ASP Chi-restraints excluded: chain A residue 756 ASP Chi-restraints excluded: chain A residue 757 HIS Chi-restraints excluded: chain A residue 774 SER Chi-restraints excluded: chain A residue 812 ASP Chi-restraints excluded: chain A residue 825 GLU Chi-restraints excluded: chain A residue 881 SER Chi-restraints excluded: chain A residue 903 LYS Chi-restraints excluded: chain A residue 937 PHE Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 950 LEU Chi-restraints excluded: chain A residue 969 ILE Chi-restraints excluded: chain A residue 978 LEU Chi-restraints excluded: chain A residue 981 LEU Chi-restraints excluded: chain A residue 1005 SER Chi-restraints excluded: chain A residue 1007 VAL Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1116 LYS Chi-restraints excluded: chain A residue 1143 ILE Chi-restraints excluded: chain A residue 1164 LEU Chi-restraints excluded: chain A residue 1169 ILE Chi-restraints excluded: chain A residue 1176 SER Chi-restraints excluded: chain A residue 1181 THR Chi-restraints excluded: chain A residue 1194 THR Chi-restraints excluded: chain A residue 1214 ASP Chi-restraints excluded: chain A residue 1221 VAL Chi-restraints excluded: chain A residue 1228 ARG Chi-restraints excluded: chain A residue 1251 LEU Chi-restraints excluded: chain A residue 1343 THR Chi-restraints excluded: chain A residue 1391 PHE Chi-restraints excluded: chain A residue 1402 ILE Chi-restraints excluded: chain A residue 1403 SER Chi-restraints excluded: chain A residue 1436 LEU Chi-restraints excluded: chain A residue 1541 SER Chi-restraints excluded: chain A residue 1547 THR Chi-restraints excluded: chain A residue 1582 LEU Chi-restraints excluded: chain A residue 1591 ILE Chi-restraints excluded: chain A residue 1614 SER Chi-restraints excluded: chain A residue 1647 THR Chi-restraints excluded: chain A residue 1662 TYR Chi-restraints excluded: chain A residue 1667 SER Chi-restraints excluded: chain A residue 1714 ILE Chi-restraints excluded: chain A residue 1748 SER Chi-restraints excluded: chain A residue 1782 SER Chi-restraints excluded: chain A residue 1837 ILE Chi-restraints excluded: chain A residue 1857 PHE Chi-restraints excluded: chain A residue 1978 TYR Chi-restraints excluded: chain A residue 2125 ILE Chi-restraints excluded: chain A residue 2212 TRP Chi-restraints excluded: chain A residue 2235 VAL Chi-restraints excluded: chain A residue 2245 GLU Chi-restraints excluded: chain A residue 2253 LEU Chi-restraints excluded: chain A residue 2289 MET Chi-restraints excluded: chain A residue 2320 TYR Chi-restraints excluded: chain A residue 2323 TRP Chi-restraints excluded: chain A residue 2361 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 116 optimal weight: 0.5980 chunk 160 optimal weight: 0.9980 chunk 189 optimal weight: 10.0000 chunk 167 optimal weight: 0.9990 chunk 57 optimal weight: 0.9980 chunk 203 optimal weight: 10.0000 chunk 80 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 59 optimal weight: 4.9990 chunk 28 optimal weight: 0.9980 chunk 89 optimal weight: 4.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 795 HIS A1633 GLN ** A2058 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4839 r_free = 0.4839 target = 0.272212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.218026 restraints weight = 19599.460| |-----------------------------------------------------------------------------| r_work (start): 0.4283 rms_B_bonded: 5.13 r_work: 0.3795 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work: 0.3750 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7221 moved from start: 0.2749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 19027 Z= 0.143 Angle : 0.574 9.601 25734 Z= 0.308 Chirality : 0.046 0.156 2831 Planarity : 0.004 0.059 3324 Dihedral : 6.859 82.997 2536 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 4.17 % Allowed : 26.25 % Favored : 69.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.17), residues: 2295 helix: 1.57 (0.20), residues: 641 sheet: -0.54 (0.24), residues: 457 loop : -0.70 (0.18), residues: 1197 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 102 HIS 0.005 0.001 HIS A 757 PHE 0.022 0.001 PHE A 186 TYR 0.022 0.001 TYR A 46 ARG 0.003 0.000 ARG A 262 Details of bonding type rmsd hydrogen bonds : bond 0.05453 ( 801) hydrogen bonds : angle 4.88687 ( 2154) metal coordination : bond 0.00338 ( 3) covalent geometry : bond 0.00315 (19023) covalent geometry : angle 0.57442 (25734) Misc. bond : bond 0.00585 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4590 Ramachandran restraints generated. 2295 Oldfield, 0 Emsley, 2295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4590 Ramachandran restraints generated. 2295 Oldfield, 0 Emsley, 2295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 123 time to evaluate : 1.861 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 GLN cc_start: 0.9002 (OUTLIER) cc_final: 0.7653 (tp-100) REVERT: A 157 PHE cc_start: 0.6638 (m-80) cc_final: 0.6064 (m-80) REVERT: A 166 PHE cc_start: 0.5786 (t80) cc_final: 0.4988 (t80) REVERT: A 337 MET cc_start: 0.7854 (OUTLIER) cc_final: 0.7304 (mtp) REVERT: A 419 ASN cc_start: 0.8287 (m-40) cc_final: 0.7872 (t0) REVERT: A 526 ARG cc_start: 0.7958 (ttm-80) cc_final: 0.7590 (tpm170) REVERT: A 597 LEU cc_start: 0.7915 (OUTLIER) cc_final: 0.7605 (tt) REVERT: A 689 LYS cc_start: 0.7026 (ptpt) cc_final: 0.6702 (mmtp) REVERT: A 754 ILE cc_start: 0.7513 (OUTLIER) cc_final: 0.7002 (pp) REVERT: A 927 LYS cc_start: 0.7340 (OUTLIER) cc_final: 0.6959 (ttpp) REVERT: A 1015 LEU cc_start: 0.7354 (OUTLIER) cc_final: 0.6990 (mp) REVERT: A 1145 MET cc_start: 0.0626 (mmp) cc_final: -0.0609 (mtp) REVERT: A 1164 LEU cc_start: 0.2287 (OUTLIER) cc_final: 0.1817 (tm) REVERT: A 1213 ILE cc_start: 0.0847 (OUTLIER) cc_final: 0.0364 (pp) REVERT: A 1214 ASP cc_start: 0.1562 (OUTLIER) cc_final: 0.1005 (t70) REVERT: A 1647 THR cc_start: 0.8303 (OUTLIER) cc_final: 0.8079 (m) REVERT: A 1751 ILE cc_start: 0.8396 (OUTLIER) cc_final: 0.8125 (mm) REVERT: A 1857 PHE cc_start: 0.5483 (OUTLIER) cc_final: 0.4761 (m-80) REVERT: A 1986 MET cc_start: 0.2252 (mmt) cc_final: 0.0233 (ttp) REVERT: A 2212 TRP cc_start: 0.0241 (OUTLIER) cc_final: -0.0696 (t60) REVERT: A 2320 TYR cc_start: 0.0665 (OUTLIER) cc_final: 0.0461 (t80) outliers start: 87 outliers final: 50 residues processed: 202 average time/residue: 1.0616 time to fit residues: 251.6001 Evaluate side-chains 181 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 117 time to evaluate : 1.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 SER Chi-restraints excluded: chain A residue 106 GLN Chi-restraints excluded: chain A residue 143 LYS Chi-restraints excluded: chain A residue 195 GLU Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 296 ASP Chi-restraints excluded: chain A residue 325 GLU Chi-restraints excluded: chain A residue 337 MET Chi-restraints excluded: chain A residue 366 ILE Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 529 SER Chi-restraints excluded: chain A residue 532 GLU Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 667 ASP Chi-restraints excluded: chain A residue 754 ILE Chi-restraints excluded: chain A residue 756 ASP Chi-restraints excluded: chain A residue 757 HIS Chi-restraints excluded: chain A residue 774 SER Chi-restraints excluded: chain A residue 881 SER Chi-restraints excluded: chain A residue 903 LYS Chi-restraints excluded: chain A residue 927 LYS Chi-restraints excluded: chain A residue 937 PHE Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 950 LEU Chi-restraints excluded: chain A residue 969 ILE Chi-restraints excluded: chain A residue 981 LEU Chi-restraints excluded: chain A residue 1005 SER Chi-restraints excluded: chain A residue 1007 VAL Chi-restraints excluded: chain A residue 1015 LEU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1116 LYS Chi-restraints excluded: chain A residue 1143 ILE Chi-restraints excluded: chain A residue 1164 LEU Chi-restraints excluded: chain A residue 1169 ILE Chi-restraints excluded: chain A residue 1181 THR Chi-restraints excluded: chain A residue 1194 THR Chi-restraints excluded: chain A residue 1213 ILE Chi-restraints excluded: chain A residue 1214 ASP Chi-restraints excluded: chain A residue 1228 ARG Chi-restraints excluded: chain A residue 1251 LEU Chi-restraints excluded: chain A residue 1391 PHE Chi-restraints excluded: chain A residue 1403 SER Chi-restraints excluded: chain A residue 1436 LEU Chi-restraints excluded: chain A residue 1541 SER Chi-restraints excluded: chain A residue 1547 THR Chi-restraints excluded: chain A residue 1582 LEU Chi-restraints excluded: chain A residue 1588 SER Chi-restraints excluded: chain A residue 1591 ILE Chi-restraints excluded: chain A residue 1614 SER Chi-restraints excluded: chain A residue 1647 THR Chi-restraints excluded: chain A residue 1662 TYR Chi-restraints excluded: chain A residue 1667 SER Chi-restraints excluded: chain A residue 1698 LEU Chi-restraints excluded: chain A residue 1751 ILE Chi-restraints excluded: chain A residue 1782 SER Chi-restraints excluded: chain A residue 1837 ILE Chi-restraints excluded: chain A residue 1857 PHE Chi-restraints excluded: chain A residue 1978 TYR Chi-restraints excluded: chain A residue 2212 TRP Chi-restraints excluded: chain A residue 2235 VAL Chi-restraints excluded: chain A residue 2253 LEU Chi-restraints excluded: chain A residue 2320 TYR Chi-restraints excluded: chain A residue 2361 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 124 optimal weight: 6.9990 chunk 135 optimal weight: 0.4980 chunk 14 optimal weight: 0.9990 chunk 112 optimal weight: 7.9990 chunk 16 optimal weight: 0.2980 chunk 125 optimal weight: 6.9990 chunk 196 optimal weight: 7.9990 chunk 156 optimal weight: 1.9990 chunk 153 optimal weight: 4.9990 chunk 104 optimal weight: 10.0000 chunk 181 optimal weight: 8.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 795 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1633 GLN ** A2058 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4883 r_free = 0.4883 target = 0.277263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4738 r_free = 0.4738 target = 0.260205 restraints weight = 19568.647| |-----------------------------------------------------------------------------| r_work (start): 0.4741 rms_B_bonded: 0.78 r_work: 0.4601 rms_B_bonded: 1.14 restraints_weight: 0.5000 r_work: 0.4572 rms_B_bonded: 1.52 restraints_weight: 0.2500 r_work (final): 0.4572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6167 moved from start: 0.2737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 19027 Z= 0.222 Angle : 0.669 10.216 25734 Z= 0.360 Chirality : 0.050 0.199 2831 Planarity : 0.004 0.056 3324 Dihedral : 7.170 87.605 2536 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 4.26 % Allowed : 26.44 % Favored : 69.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.17), residues: 2295 helix: 1.16 (0.20), residues: 641 sheet: -0.52 (0.24), residues: 466 loop : -0.79 (0.17), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 102 HIS 0.005 0.001 HIS A 757 PHE 0.032 0.002 PHE A 186 TYR 0.030 0.002 TYR A 46 ARG 0.005 0.001 ARG A1653 Details of bonding type rmsd hydrogen bonds : bond 0.06918 ( 801) hydrogen bonds : angle 5.11996 ( 2154) metal coordination : bond 0.00616 ( 3) covalent geometry : bond 0.00514 (19023) covalent geometry : angle 0.66873 (25734) Misc. bond : bond 0.00598 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4590 Ramachandran restraints generated. 2295 Oldfield, 0 Emsley, 2295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4590 Ramachandran restraints generated. 2295 Oldfield, 0 Emsley, 2295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 114 time to evaluate : 2.185 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: A 106 GLN cc_start: 0.8641 (OUTLIER) cc_final: 0.7134 (tp-100) REVERT: A 166 PHE cc_start: 0.5564 (t80) cc_final: 0.4933 (t80) REVERT: A 337 MET cc_start: 0.7393 (OUTLIER) cc_final: 0.6876 (mtp) REVERT: A 526 ARG cc_start: 0.7764 (ttm-80) cc_final: 0.7465 (tpm170) REVERT: A 927 LYS cc_start: 0.7250 (OUTLIER) cc_final: 0.7001 (ttpp) REVERT: A 1145 MET cc_start: 0.1148 (mmp) cc_final: -0.0210 (mtp) REVERT: A 1164 LEU cc_start: 0.3435 (OUTLIER) cc_final: 0.3144 (tm) REVERT: A 1213 ILE cc_start: 0.1537 (OUTLIER) cc_final: 0.1134 (pp) REVERT: A 1436 LEU cc_start: 0.2611 (OUTLIER) cc_final: 0.2384 (tt) REVERT: A 1647 THR cc_start: 0.8052 (OUTLIER) cc_final: 0.7804 (m) REVERT: A 1986 MET cc_start: 0.2431 (mmt) cc_final: 0.0958 (ttp) REVERT: A 2212 TRP cc_start: 0.0502 (OUTLIER) cc_final: -0.0824 (t60) REVERT: A 2320 TYR cc_start: 0.1456 (OUTLIER) cc_final: 0.1045 (t80) outliers start: 89 outliers final: 59 residues processed: 193 average time/residue: 1.0782 time to fit residues: 241.5034 Evaluate side-chains 179 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 111 time to evaluate : 2.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 90 SER Chi-restraints excluded: chain A residue 106 GLN Chi-restraints excluded: chain A residue 143 LYS Chi-restraints excluded: chain A residue 195 GLU Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 296 ASP Chi-restraints excluded: chain A residue 325 GLU Chi-restraints excluded: chain A residue 337 MET Chi-restraints excluded: chain A residue 366 ILE Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 379 ASN Chi-restraints excluded: chain A residue 529 SER Chi-restraints excluded: chain A residue 532 GLU Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 667 ASP Chi-restraints excluded: chain A residue 721 ASP Chi-restraints excluded: chain A residue 756 ASP Chi-restraints excluded: chain A residue 757 HIS Chi-restraints excluded: chain A residue 774 SER Chi-restraints excluded: chain A residue 825 GLU Chi-restraints excluded: chain A residue 881 SER Chi-restraints excluded: chain A residue 903 LYS Chi-restraints excluded: chain A residue 927 LYS Chi-restraints excluded: chain A residue 937 PHE Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 950 LEU Chi-restraints excluded: chain A residue 969 ILE Chi-restraints excluded: chain A residue 978 LEU Chi-restraints excluded: chain A residue 981 LEU Chi-restraints excluded: chain A residue 1005 SER Chi-restraints excluded: chain A residue 1007 VAL Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1116 LYS Chi-restraints excluded: chain A residue 1164 LEU Chi-restraints excluded: chain A residue 1169 ILE Chi-restraints excluded: chain A residue 1181 THR Chi-restraints excluded: chain A residue 1194 THR Chi-restraints excluded: chain A residue 1213 ILE Chi-restraints excluded: chain A residue 1221 VAL Chi-restraints excluded: chain A residue 1228 ARG Chi-restraints excluded: chain A residue 1251 LEU Chi-restraints excluded: chain A residue 1304 THR Chi-restraints excluded: chain A residue 1391 PHE Chi-restraints excluded: chain A residue 1403 SER Chi-restraints excluded: chain A residue 1436 LEU Chi-restraints excluded: chain A residue 1541 SER Chi-restraints excluded: chain A residue 1547 THR Chi-restraints excluded: chain A residue 1582 LEU Chi-restraints excluded: chain A residue 1588 SER Chi-restraints excluded: chain A residue 1591 ILE Chi-restraints excluded: chain A residue 1614 SER Chi-restraints excluded: chain A residue 1647 THR Chi-restraints excluded: chain A residue 1662 TYR Chi-restraints excluded: chain A residue 1667 SER Chi-restraints excluded: chain A residue 1698 LEU Chi-restraints excluded: chain A residue 1748 SER Chi-restraints excluded: chain A residue 1782 SER Chi-restraints excluded: chain A residue 1837 ILE Chi-restraints excluded: chain A residue 1857 PHE Chi-restraints excluded: chain A residue 1978 TYR Chi-restraints excluded: chain A residue 2125 ILE Chi-restraints excluded: chain A residue 2212 TRP Chi-restraints excluded: chain A residue 2235 VAL Chi-restraints excluded: chain A residue 2253 LEU Chi-restraints excluded: chain A residue 2289 MET Chi-restraints excluded: chain A residue 2320 TYR Chi-restraints excluded: chain A residue 2361 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 18 optimal weight: 0.6980 chunk 47 optimal weight: 0.6980 chunk 35 optimal weight: 0.9990 chunk 189 optimal weight: 10.0000 chunk 169 optimal weight: 2.9990 chunk 221 optimal weight: 0.9990 chunk 88 optimal weight: 1.9990 chunk 226 optimal weight: 0.2980 chunk 65 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 487 ASN A 574 ASN ** A 639 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 795 HIS A1633 GLN ** A2058 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4973 r_free = 0.4973 target = 0.283135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.4766 r_free = 0.4766 target = 0.257408 restraints weight = 20732.382| |-----------------------------------------------------------------------------| r_work (start): 0.4784 rms_B_bonded: 1.33 r_work: 0.4597 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.4565 rms_B_bonded: 2.70 restraints_weight: 0.2500 r_work (final): 0.4565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6417 moved from start: 0.3038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 19027 Z= 0.129 Angle : 0.565 9.252 25734 Z= 0.301 Chirality : 0.046 0.152 2831 Planarity : 0.004 0.075 3324 Dihedral : 6.738 83.347 2534 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 3.35 % Allowed : 27.49 % Favored : 69.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.18), residues: 2295 helix: 1.67 (0.21), residues: 640 sheet: -0.44 (0.24), residues: 463 loop : -0.65 (0.18), residues: 1192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 102 HIS 0.004 0.001 HIS A 757 PHE 0.019 0.001 PHE A 186 TYR 0.020 0.001 TYR A 284 ARG 0.010 0.000 ARG A1653 Details of bonding type rmsd hydrogen bonds : bond 0.05089 ( 801) hydrogen bonds : angle 4.82253 ( 2154) metal coordination : bond 0.00274 ( 3) covalent geometry : bond 0.00277 (19023) covalent geometry : angle 0.56525 (25734) Misc. bond : bond 0.00574 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4590 Ramachandran restraints generated. 2295 Oldfield, 0 Emsley, 2295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4590 Ramachandran restraints generated. 2295 Oldfield, 0 Emsley, 2295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 120 time to evaluate : 2.006 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 157 PHE cc_start: 0.6372 (m-80) cc_final: 0.5997 (m-80) REVERT: A 166 PHE cc_start: 0.5556 (t80) cc_final: 0.4930 (t80) REVERT: A 337 MET cc_start: 0.7571 (OUTLIER) cc_final: 0.7091 (mtp) REVERT: A 419 ASN cc_start: 0.7864 (m-40) cc_final: 0.7538 (t0) REVERT: A 526 ARG cc_start: 0.7796 (ttm-80) cc_final: 0.7522 (tpm170) REVERT: A 705 ILE cc_start: 0.7589 (OUTLIER) cc_final: 0.7143 (pp) REVERT: A 981 LEU cc_start: 0.7211 (OUTLIER) cc_final: 0.6866 (tp) REVERT: A 1145 MET cc_start: 0.0984 (mmp) cc_final: -0.0311 (mtp) REVERT: A 1164 LEU cc_start: 0.3166 (OUTLIER) cc_final: 0.2819 (tm) REVERT: A 1234 MET cc_start: 0.2526 (tpp) cc_final: -0.1070 (mmm) REVERT: A 1332 MET cc_start: 0.1092 (mpt) cc_final: 0.0527 (ptm) REVERT: A 1436 LEU cc_start: 0.2745 (OUTLIER) cc_final: 0.2518 (tt) REVERT: A 1647 THR cc_start: 0.8108 (OUTLIER) cc_final: 0.7811 (m) REVERT: A 1857 PHE cc_start: 0.5530 (OUTLIER) cc_final: 0.4577 (m-80) REVERT: A 1986 MET cc_start: 0.2624 (mmt) cc_final: 0.0962 (ttp) REVERT: A 2212 TRP cc_start: 0.0393 (OUTLIER) cc_final: -0.0772 (t60) REVERT: A 2320 TYR cc_start: 0.1348 (OUTLIER) cc_final: 0.0987 (t80) outliers start: 70 outliers final: 52 residues processed: 184 average time/residue: 1.0274 time to fit residues: 222.1874 Evaluate side-chains 176 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 115 time to evaluate : 1.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 90 SER Chi-restraints excluded: chain A residue 143 LYS Chi-restraints excluded: chain A residue 195 GLU Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 296 ASP Chi-restraints excluded: chain A residue 325 GLU Chi-restraints excluded: chain A residue 337 MET Chi-restraints excluded: chain A residue 366 ILE Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 532 GLU Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 667 ASP Chi-restraints excluded: chain A residue 705 ILE Chi-restraints excluded: chain A residue 730 ILE Chi-restraints excluded: chain A residue 757 HIS Chi-restraints excluded: chain A residue 762 ILE Chi-restraints excluded: chain A residue 774 SER Chi-restraints excluded: chain A residue 881 SER Chi-restraints excluded: chain A residue 903 LYS Chi-restraints excluded: chain A residue 937 PHE Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 950 LEU Chi-restraints excluded: chain A residue 969 ILE Chi-restraints excluded: chain A residue 981 LEU Chi-restraints excluded: chain A residue 1005 SER Chi-restraints excluded: chain A residue 1007 VAL Chi-restraints excluded: chain A residue 1091 ILE Chi-restraints excluded: chain A residue 1116 LYS Chi-restraints excluded: chain A residue 1143 ILE Chi-restraints excluded: chain A residue 1164 LEU Chi-restraints excluded: chain A residue 1169 ILE Chi-restraints excluded: chain A residue 1181 THR Chi-restraints excluded: chain A residue 1194 THR Chi-restraints excluded: chain A residue 1221 VAL Chi-restraints excluded: chain A residue 1228 ARG Chi-restraints excluded: chain A residue 1251 LEU Chi-restraints excluded: chain A residue 1279 LYS Chi-restraints excluded: chain A residue 1391 PHE Chi-restraints excluded: chain A residue 1403 SER Chi-restraints excluded: chain A residue 1436 LEU Chi-restraints excluded: chain A residue 1541 SER Chi-restraints excluded: chain A residue 1547 THR Chi-restraints excluded: chain A residue 1582 LEU Chi-restraints excluded: chain A residue 1588 SER Chi-restraints excluded: chain A residue 1591 ILE Chi-restraints excluded: chain A residue 1614 SER Chi-restraints excluded: chain A residue 1647 THR Chi-restraints excluded: chain A residue 1662 TYR Chi-restraints excluded: chain A residue 1667 SER Chi-restraints excluded: chain A residue 1714 ILE Chi-restraints excluded: chain A residue 1748 SER Chi-restraints excluded: chain A residue 1782 SER Chi-restraints excluded: chain A residue 1837 ILE Chi-restraints excluded: chain A residue 1857 PHE Chi-restraints excluded: chain A residue 1978 TYR Chi-restraints excluded: chain A residue 2125 ILE Chi-restraints excluded: chain A residue 2212 TRP Chi-restraints excluded: chain A residue 2235 VAL Chi-restraints excluded: chain A residue 2253 LEU Chi-restraints excluded: chain A residue 2320 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 18 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 chunk 101 optimal weight: 6.9990 chunk 130 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 chunk 32 optimal weight: 0.6980 chunk 175 optimal weight: 0.9980 chunk 162 optimal weight: 0.0470 chunk 5 optimal weight: 0.5980 chunk 59 optimal weight: 5.9990 chunk 36 optimal weight: 0.7980 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 639 GLN ** A 781 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 795 HIS A1633 GLN ** A2058 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4976 r_free = 0.4976 target = 0.283669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4753 r_free = 0.4753 target = 0.255554 restraints weight = 20708.724| |-----------------------------------------------------------------------------| r_work (start): 0.4768 rms_B_bonded: 1.41 r_work: 0.4593 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.4555 rms_B_bonded: 2.92 restraints_weight: 0.2500 r_work (final): 0.4555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6425 moved from start: 0.3201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 19027 Z= 0.118 Angle : 0.550 9.334 25734 Z= 0.292 Chirality : 0.045 0.150 2831 Planarity : 0.004 0.057 3324 Dihedral : 6.321 82.978 2531 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 2.73 % Allowed : 28.07 % Favored : 69.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.18), residues: 2295 helix: 1.83 (0.21), residues: 639 sheet: -0.36 (0.24), residues: 460 loop : -0.57 (0.18), residues: 1196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 102 HIS 0.004 0.001 HIS A 757 PHE 0.017 0.001 PHE A 186 TYR 0.017 0.001 TYR A 46 ARG 0.007 0.000 ARG A1653 Details of bonding type rmsd hydrogen bonds : bond 0.04821 ( 801) hydrogen bonds : angle 4.71988 ( 2154) metal coordination : bond 0.00236 ( 3) covalent geometry : bond 0.00252 (19023) covalent geometry : angle 0.54989 (25734) Misc. bond : bond 0.00556 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4590 Ramachandran restraints generated. 2295 Oldfield, 0 Emsley, 2295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4590 Ramachandran restraints generated. 2295 Oldfield, 0 Emsley, 2295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 124 time to evaluate : 1.818 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 ASN cc_start: 0.7539 (m-40) cc_final: 0.7250 (t0) REVERT: A 157 PHE cc_start: 0.6414 (m-80) cc_final: 0.6031 (m-80) REVERT: A 166 PHE cc_start: 0.5527 (t80) cc_final: 0.4855 (t80) REVERT: A 195 GLU cc_start: 0.6197 (OUTLIER) cc_final: 0.5954 (mp0) REVERT: A 337 MET cc_start: 0.7543 (OUTLIER) cc_final: 0.7088 (mtp) REVERT: A 526 ARG cc_start: 0.7785 (ttm-80) cc_final: 0.7546 (tpm170) REVERT: A 667 ASP cc_start: 0.7683 (OUTLIER) cc_final: 0.7399 (m-30) REVERT: A 727 MET cc_start: 0.6285 (mtp) cc_final: 0.6057 (mtp) REVERT: A 981 LEU cc_start: 0.7095 (OUTLIER) cc_final: 0.6794 (tp) REVERT: A 1145 MET cc_start: 0.1054 (mmp) cc_final: -0.0249 (mtp) REVERT: A 1164 LEU cc_start: 0.3227 (OUTLIER) cc_final: 0.2871 (tm) REVERT: A 1234 MET cc_start: 0.2377 (tpp) cc_final: -0.0357 (mmm) REVERT: A 1332 MET cc_start: 0.0918 (mpt) cc_final: 0.0406 (ptm) REVERT: A 1436 LEU cc_start: 0.2691 (OUTLIER) cc_final: 0.2459 (tt) REVERT: A 1647 THR cc_start: 0.8166 (OUTLIER) cc_final: 0.7889 (m) REVERT: A 1857 PHE cc_start: 0.5462 (OUTLIER) cc_final: 0.4534 (m-80) REVERT: A 1986 MET cc_start: 0.2472 (mmt) cc_final: 0.0888 (ttp) REVERT: A 2212 TRP cc_start: 0.0283 (OUTLIER) cc_final: -0.0724 (t60) REVERT: A 2320 TYR cc_start: 0.1426 (OUTLIER) cc_final: 0.1074 (t80) outliers start: 57 outliers final: 40 residues processed: 177 average time/residue: 1.0931 time to fit residues: 224.8621 Evaluate side-chains 169 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 119 time to evaluate : 2.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 90 SER Chi-restraints excluded: chain A residue 143 LYS Chi-restraints excluded: chain A residue 195 GLU Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 325 GLU Chi-restraints excluded: chain A residue 337 MET Chi-restraints excluded: chain A residue 366 ILE Chi-restraints excluded: chain A residue 532 GLU Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 667 ASP Chi-restraints excluded: chain A residue 757 HIS Chi-restraints excluded: chain A residue 774 SER Chi-restraints excluded: chain A residue 881 SER Chi-restraints excluded: chain A residue 903 LYS Chi-restraints excluded: chain A residue 937 PHE Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 950 LEU Chi-restraints excluded: chain A residue 969 ILE Chi-restraints excluded: chain A residue 981 LEU Chi-restraints excluded: chain A residue 1005 SER Chi-restraints excluded: chain A residue 1007 VAL Chi-restraints excluded: chain A residue 1091 ILE Chi-restraints excluded: chain A residue 1116 LYS Chi-restraints excluded: chain A residue 1143 ILE Chi-restraints excluded: chain A residue 1164 LEU Chi-restraints excluded: chain A residue 1181 THR Chi-restraints excluded: chain A residue 1194 THR Chi-restraints excluded: chain A residue 1228 ARG Chi-restraints excluded: chain A residue 1304 THR Chi-restraints excluded: chain A residue 1391 PHE Chi-restraints excluded: chain A residue 1403 SER Chi-restraints excluded: chain A residue 1436 LEU Chi-restraints excluded: chain A residue 1541 SER Chi-restraints excluded: chain A residue 1547 THR Chi-restraints excluded: chain A residue 1582 LEU Chi-restraints excluded: chain A residue 1588 SER Chi-restraints excluded: chain A residue 1591 ILE Chi-restraints excluded: chain A residue 1614 SER Chi-restraints excluded: chain A residue 1647 THR Chi-restraints excluded: chain A residue 1667 SER Chi-restraints excluded: chain A residue 1748 SER Chi-restraints excluded: chain A residue 1782 SER Chi-restraints excluded: chain A residue 1837 ILE Chi-restraints excluded: chain A residue 1857 PHE Chi-restraints excluded: chain A residue 1978 TYR Chi-restraints excluded: chain A residue 2212 TRP Chi-restraints excluded: chain A residue 2235 VAL Chi-restraints excluded: chain A residue 2253 LEU Chi-restraints excluded: chain A residue 2320 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 49 optimal weight: 0.6980 chunk 188 optimal weight: 8.9990 chunk 2 optimal weight: 0.8980 chunk 178 optimal weight: 0.9980 chunk 225 optimal weight: 20.0000 chunk 7 optimal weight: 0.4980 chunk 99 optimal weight: 0.9990 chunk 83 optimal weight: 2.9990 chunk 18 optimal weight: 0.5980 chunk 23 optimal weight: 2.9990 chunk 168 optimal weight: 4.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 781 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 795 HIS A 835 GLN A1633 GLN ** A2058 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5002 r_free = 0.5002 target = 0.285439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4789 r_free = 0.4789 target = 0.258693 restraints weight = 20494.912| |-----------------------------------------------------------------------------| r_work (start): 0.4777 rms_B_bonded: 1.25 r_work: 0.4625 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.4593 rms_B_bonded: 2.56 restraints_weight: 0.2500 r_work (final): 0.4593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6358 moved from start: 0.3214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 19027 Z= 0.130 Angle : 0.564 9.307 25734 Z= 0.300 Chirality : 0.046 0.153 2831 Planarity : 0.004 0.072 3324 Dihedral : 6.232 81.981 2526 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 2.97 % Allowed : 27.92 % Favored : 69.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.18), residues: 2295 helix: 1.80 (0.21), residues: 639 sheet: -0.42 (0.24), residues: 478 loop : -0.52 (0.18), residues: 1178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 102 HIS 0.004 0.001 HIS A 757 PHE 0.019 0.001 PHE A 186 TYR 0.020 0.001 TYR A 46 ARG 0.021 0.001 ARG A1653 Details of bonding type rmsd hydrogen bonds : bond 0.05150 ( 801) hydrogen bonds : angle 4.75085 ( 2154) metal coordination : bond 0.00270 ( 3) covalent geometry : bond 0.00282 (19023) covalent geometry : angle 0.56371 (25734) Misc. bond : bond 0.00545 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16151.74 seconds wall clock time: 280 minutes 37.16 seconds (16837.16 seconds total)