Starting phenix.real_space_refine on Sat Oct 11 23:28:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8x2i_38011/10_2025/8x2i_38011.cif Found real_map, /net/cci-nas-00/data/ceres_data/8x2i_38011/10_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_38011/10_2025/8x2i_38011.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8x2i_38011/10_2025/8x2i_38011.map" model { file = "/net/cci-nas-00/data/ceres_data/8x2i_38011/10_2025/8x2i_38011.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8x2i_38011/10_2025/8x2i_38011.cif" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.107 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/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: 3.66, per 1000 atoms: 0.20 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: 1.76 Conformation dependent library (CDL) restraints added in 800.6 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 1.28 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: 6.05 Time building geometry restraints manager: 2.23 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: 3.830 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: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 22.220 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 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:5.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.420 ------------------------------------------------------------------------------- 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 : 14.23 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.37 (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 ARG 0.010 0.001 ARG A1296 TYR 0.047 0.003 TYR A 46 PHE 0.043 0.003 PHE A 186 TRP 0.030 0.003 TRP A 102 HIS 0.010 0.002 HIS A 35 Details of bonding type rmsd covalent geometry : bond 0.00873 (19023) covalent geometry : angle 0.93074 (25734) hydrogen bonds : bond 0.15096 ( 801) hydrogen bonds : angle 6.92540 ( 2154) metal coordination : bond 0.25301 ( 3) 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 : 0.698 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: 0.4708 time to fit residues: 171.6252 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 : 0.739 ------------------------------------------------------------------------------- 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 216 optimal weight: 0.5980 chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 0.9980 chunk 227 optimal weight: 7.9990 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 0.0970 chunk 66 optimal weight: 0.0470 chunk 130 optimal weight: 8.9990 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 6.9990 chunk 200 optimal weight: 7.9990 overall best weight: 0.9478 ------------------------------------------------------------------------------- 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 A 419 ASN A 579 HIS 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 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: 31 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4842 r_free = 0.4842 target = 0.273029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4660 r_free = 0.4660 target = 0.251637 restraints weight = 19710.404| |-----------------------------------------------------------------------------| r_work (start): 0.4658 rms_B_bonded: 0.99 r_work: 0.4194 rms_B_bonded: 1.28 restraints_weight: 0.5000 r_work: 0.3869 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7063 moved from start: 0.1470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 19027 Z= 0.162 Angle : 0.652 10.207 25734 Z= 0.351 Chirality : 0.048 0.199 2831 Planarity : 0.004 0.053 3324 Dihedral : 9.896 84.312 2681 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.40 % Favored : 95.56 % Rotamer: Outliers : 5.60 % Allowed : 24.23 % Favored : 70.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.05 (0.16), residues: 2295 helix: 0.73 (0.20), residues: 635 sheet: -1.10 (0.23), residues: 440 loop : -1.31 (0.16), residues: 1220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A1517 TYR 0.030 0.002 TYR A1978 PHE 0.022 0.002 PHE A 186 TRP 0.014 0.002 TRP A 102 HIS 0.004 0.001 HIS A 757 Details of bonding type rmsd covalent geometry : bond 0.00355 (19023) covalent geometry : angle 0.65176 (25734) hydrogen bonds : bond 0.06082 ( 801) hydrogen bonds : angle 5.40110 ( 2154) metal coordination : bond 0.00707 ( 3) Misc. bond : bond 0.00708 ( 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 252 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 135 time to evaluate : 0.754 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 VAL cc_start: 0.8406 (OUTLIER) cc_final: 0.8200 (p) REVERT: A 157 PHE cc_start: 0.6928 (m-80) cc_final: 0.6336 (m-10) REVERT: A 166 PHE cc_start: 0.5751 (t80) cc_final: 0.5157 (t80) REVERT: A 276 MET cc_start: 0.8589 (mmt) cc_final: 0.8303 (mmm) REVERT: A 314 MET cc_start: 0.8482 (mtp) cc_final: 0.8259 (mtp) REVERT: A 331 THR cc_start: 0.8153 (p) cc_final: 0.7886 (t) REVERT: A 526 ARG cc_start: 0.7964 (ttm-80) cc_final: 0.7462 (tpm170) REVERT: A 540 GLU cc_start: 0.6474 (pm20) cc_final: 0.6252 (pm20) REVERT: A 560 ASP cc_start: 0.6523 (OUTLIER) cc_final: 0.6123 (t0) REVERT: A 570 MET cc_start: 0.6205 (tmt) cc_final: 0.5808 (mpt) REVERT: A 592 GLU cc_start: 0.6973 (OUTLIER) cc_final: 0.6740 (mm-30) REVERT: A 800 LEU cc_start: 0.7844 (OUTLIER) cc_final: 0.7608 (mt) REVERT: A 1114 GLN cc_start: 0.2935 (OUTLIER) cc_final: 0.2293 (mp-120) REVERT: A 1116 LYS cc_start: 0.1420 (OUTLIER) cc_final: 0.0276 (ttmt) REVERT: A 1214 ASP cc_start: 0.0987 (OUTLIER) cc_final: 0.0464 (t70) REVERT: A 1327 LEU cc_start: 0.3200 (OUTLIER) cc_final: 0.2931 (pt) REVERT: A 1610 ASN cc_start: 0.6642 (OUTLIER) cc_final: 0.6407 (p0) REVERT: A 1647 THR cc_start: 0.8326 (OUTLIER) cc_final: 0.8053 (m) REVERT: A 1857 PHE cc_start: 0.5159 (OUTLIER) cc_final: 0.4879 (m-80) REVERT: A 1986 MET cc_start: 0.1918 (mmt) cc_final: -0.0065 (ttp) REVERT: A 2143 GLN cc_start: 0.0448 (OUTLIER) cc_final: 0.0142 (mp-120) outliers start: 117 outliers final: 55 residues processed: 238 average time/residue: 0.5144 time to fit residues: 142.4002 Evaluate side-chains 189 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 122 time to evaluate : 0.710 ------------------------------------------------------------------------------- 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 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 325 GLU Chi-restraints excluded: chain A residue 332 SER Chi-restraints excluded: chain A residue 333 LYS Chi-restraints excluded: chain A residue 366 ILE Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 508 ILE 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 592 GLU Chi-restraints excluded: chain A residue 640 ILE Chi-restraints excluded: chain A residue 667 ASP 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 937 PHE Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 950 LEU 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 1509 SER 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 1647 THR Chi-restraints excluded: chain A residue 1662 TYR Chi-restraints excluded: chain A residue 1682 LEU Chi-restraints excluded: chain A residue 1714 ILE Chi-restraints excluded: chain A residue 1837 ILE 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 2125 ILE Chi-restraints excluded: chain A residue 2143 GLN Chi-restraints excluded: chain A residue 2235 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 104 optimal weight: 50.0000 chunk 170 optimal weight: 0.9990 chunk 151 optimal weight: 7.9990 chunk 15 optimal weight: 0.9990 chunk 159 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 86 optimal weight: 0.9980 chunk 56 optimal weight: 0.8980 chunk 82 optimal weight: 2.9990 chunk 186 optimal weight: 9.9990 chunk 130 optimal weight: 5.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 379 ASN A 785 ASN ** A 795 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 835 GLN A 931 ASN ** A1114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1178 HIS A1350 ASN A2058 ASN ** A2260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4893 r_free = 0.4893 target = 0.277596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4764 r_free = 0.4764 target = 0.262181 restraints weight = 19892.745| |-----------------------------------------------------------------------------| r_work (start): 0.4766 rms_B_bonded: 0.75 r_work: 0.4618 rms_B_bonded: 1.09 restraints_weight: 0.5000 r_work: 0.4592 rms_B_bonded: 1.44 restraints_weight: 0.2500 r_work (final): 0.4592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6121 moved from start: 0.1795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 19027 Z= 0.174 Angle : 0.637 9.276 25734 Z= 0.344 Chirality : 0.048 0.171 2831 Planarity : 0.004 0.055 3324 Dihedral : 8.275 83.954 2574 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 5.65 % Allowed : 24.09 % Favored : 70.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.71 (0.17), residues: 2295 helix: 1.10 (0.20), residues: 640 sheet: -0.98 (0.23), residues: 453 loop : -1.11 (0.17), residues: 1202 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A1265 TYR 0.026 0.002 TYR A 46 PHE 0.025 0.002 PHE A 186 TRP 0.014 0.001 TRP A 102 HIS 0.010 0.001 HIS A1178 Details of bonding type rmsd covalent geometry : bond 0.00390 (19023) covalent geometry : angle 0.63679 (25734) hydrogen bonds : bond 0.06274 ( 801) hydrogen bonds : angle 5.24503 ( 2154) metal coordination : bond 0.00262 ( 3) Misc. bond : bond 0.00676 ( 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 248 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 130 time to evaluate : 0.854 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 LYS cc_start: 0.8392 (OUTLIER) cc_final: 0.8065 (mptt) REVERT: A 106 GLN cc_start: 0.8632 (OUTLIER) cc_final: 0.7227 (tp-100) REVERT: A 157 PHE cc_start: 0.6459 (m-80) cc_final: 0.6146 (m-10) REVERT: A 166 PHE cc_start: 0.5446 (t80) cc_final: 0.4945 (t80) REVERT: A 276 MET cc_start: 0.8388 (mmt) cc_final: 0.8048 (mmm) REVERT: A 314 MET cc_start: 0.7983 (mtp) cc_final: 0.7744 (mtp) REVERT: A 337 MET cc_start: 0.7361 (OUTLIER) cc_final: 0.6856 (mtp) REVERT: A 526 ARG cc_start: 0.7721 (ttm-80) cc_final: 0.7439 (tpm170) REVERT: A 1145 MET cc_start: 0.2689 (mmp) cc_final: 0.1711 (mtm) REVERT: A 1327 LEU cc_start: 0.2082 (OUTLIER) cc_final: 0.1870 (pt) REVERT: A 1332 MET cc_start: 0.0832 (ppp) cc_final: 0.0516 (mmm) REVERT: A 1609 THR cc_start: 0.7169 (OUTLIER) cc_final: 0.6965 (t) REVERT: A 1647 THR cc_start: 0.8099 (OUTLIER) cc_final: 0.7794 (m) REVERT: A 1857 PHE cc_start: 0.5080 (OUTLIER) cc_final: 0.4764 (m-80) REVERT: A 1986 MET cc_start: 0.2017 (mmt) cc_final: 0.0715 (ttp) REVERT: A 2212 TRP cc_start: 0.0142 (OUTLIER) cc_final: -0.0564 (t60) outliers start: 118 outliers final: 65 residues processed: 228 average time/residue: 0.5105 time to fit residues: 134.4884 Evaluate side-chains 195 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 122 time to evaluate : 0.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL 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 143 LYS 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 333 LYS 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 469 SER Chi-restraints excluded: chain A residue 508 ILE 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 756 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 969 ILE 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 1178 HIS 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 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 1402 ILE Chi-restraints excluded: chain A residue 1403 SER 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 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 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 1857 PHE 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 2212 TRP Chi-restraints excluded: chain A residue 2235 VAL Chi-restraints excluded: chain A residue 2323 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 89 optimal weight: 3.9990 chunk 182 optimal weight: 4.9990 chunk 71 optimal weight: 3.9990 chunk 159 optimal weight: 0.5980 chunk 29 optimal weight: 1.9990 chunk 156 optimal weight: 0.9980 chunk 206 optimal weight: 0.7980 chunk 93 optimal weight: 4.9990 chunk 48 optimal weight: 0.5980 chunk 58 optimal weight: 0.5980 chunk 191 optimal weight: 9.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 379 ASN A 405 ASN A 763 ASN A 781 ASN ** A 795 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1114 GLN A1178 HIS A2143 GLN ** A2260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4845 r_free = 0.4845 target = 0.272587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.216715 restraints weight = 19916.555| |-----------------------------------------------------------------------------| r_work (start): 0.4271 rms_B_bonded: 5.36 r_work: 0.3781 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work: 0.3735 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7236 moved from start: 0.2193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 19027 Z= 0.131 Angle : 0.573 8.705 25734 Z= 0.308 Chirality : 0.046 0.172 2831 Planarity : 0.004 0.055 3324 Dihedral : 7.572 82.417 2562 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 4.79 % Allowed : 24.81 % Favored : 70.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.30 (0.17), residues: 2295 helix: 1.55 (0.20), residues: 639 sheet: -0.83 (0.23), residues: 454 loop : -0.89 (0.17), residues: 1202 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 644 TYR 0.019 0.001 TYR A 46 PHE 0.021 0.001 PHE A2000 TRP 0.012 0.001 TRP A 102 HIS 0.014 0.001 HIS A1178 Details of bonding type rmsd covalent geometry : bond 0.00282 (19023) covalent geometry : angle 0.57278 (25734) hydrogen bonds : bond 0.05264 ( 801) hydrogen bonds : angle 4.98485 ( 2154) metal coordination : bond 0.00142 ( 3) Misc. bond : bond 0.00631 ( 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 234 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 134 time to evaluate : 0.661 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: 0.8986 (OUTLIER) cc_final: 0.7659 (tp-100) REVERT: A 157 PHE cc_start: 0.6750 (m-80) cc_final: 0.6164 (m-80) REVERT: A 166 PHE cc_start: 0.5926 (t80) cc_final: 0.5285 (t80) REVERT: A 276 MET cc_start: 0.8693 (mmt) cc_final: 0.8428 (mmm) REVERT: A 314 MET cc_start: 0.8472 (mtp) cc_final: 0.8266 (mtp) REVERT: A 419 ASN cc_start: 0.8214 (m-40) cc_final: 0.7811 (t0) REVERT: A 423 ASP cc_start: 0.7624 (OUTLIER) cc_final: 0.7337 (p0) REVERT: A 526 ARG cc_start: 0.7931 (ttm-80) cc_final: 0.7543 (tpm170) REVERT: A 689 LYS cc_start: 0.7021 (ptpt) cc_final: 0.6806 (mmtp) REVERT: A 705 ILE cc_start: 0.7850 (OUTLIER) cc_final: 0.7297 (pp) REVERT: A 754 ILE cc_start: 0.7411 (OUTLIER) cc_final: 0.6922 (pp) REVERT: A 981 LEU cc_start: 0.7197 (OUTLIER) cc_final: 0.6814 (tp) REVERT: A 1145 MET cc_start: 0.1682 (mmp) cc_final: 0.0644 (mtm) REVERT: A 1228 ARG cc_start: 0.2057 (OUTLIER) cc_final: 0.1095 (ptm160) REVERT: A 1327 LEU cc_start: 0.1335 (OUTLIER) cc_final: 0.1020 (pt) REVERT: A 1533 LYS cc_start: 0.5832 (OUTLIER) cc_final: 0.5161 (tmtt) REVERT: A 1587 GLU cc_start: 0.6185 (pp20) cc_final: 0.5708 (pp20) REVERT: A 1609 THR cc_start: 0.7369 (OUTLIER) cc_final: 0.7025 (t) REVERT: A 1647 THR cc_start: 0.8328 (OUTLIER) cc_final: 0.8082 (m) REVERT: A 1841 ASP cc_start: 0.6925 (OUTLIER) cc_final: 0.6459 (t0) REVERT: A 1857 PHE cc_start: 0.5357 (OUTLIER) cc_final: 0.5055 (m-80) REVERT: A 1986 MET cc_start: 0.2207 (mmt) cc_final: 0.0204 (ttp) REVERT: A 2212 TRP cc_start: 0.0283 (OUTLIER) cc_final: -0.0506 (t60) outliers start: 100 outliers final: 51 residues processed: 218 average time/residue: 0.5283 time to fit residues: 132.8232 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 : 0.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 SER 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 366 ILE Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 423 ASP Chi-restraints excluded: chain A residue 469 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 705 ILE Chi-restraints excluded: chain A residue 721 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 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 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 1228 ARG Chi-restraints excluded: chain A residue 1251 LEU Chi-restraints excluded: chain A residue 1279 LYS 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 1374 LYS Chi-restraints excluded: chain A residue 1402 ILE Chi-restraints excluded: chain A residue 1436 LEU Chi-restraints excluded: chain A residue 1533 LYS 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 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 1837 ILE Chi-restraints excluded: chain A residue 1841 ASP 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 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 183 optimal weight: 6.9990 chunk 222 optimal weight: 8.9990 chunk 91 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 60 optimal weight: 4.9990 chunk 137 optimal weight: 5.9990 chunk 9 optimal weight: 0.9980 chunk 153 optimal weight: 7.9990 chunk 75 optimal weight: 0.0980 chunk 101 optimal weight: 3.9990 chunk 79 optimal weight: 5.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 385 GLN A 405 ASN ** A 795 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1633 GLN A1654 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 = 0.4887 r_free = 0.4887 target = 0.277603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4766 r_free = 0.4766 target = 0.263297 restraints weight = 19567.774| |-----------------------------------------------------------------------------| r_work (start): 0.4767 rms_B_bonded: 0.62 r_work: 0.4615 rms_B_bonded: 0.91 restraints_weight: 0.5000 r_work: 0.4585 rms_B_bonded: 1.34 restraints_weight: 0.2500 r_work (final): 0.4585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6147 moved from start: 0.2249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 19027 Z= 0.208 Angle : 0.651 8.847 25734 Z= 0.353 Chirality : 0.050 0.252 2831 Planarity : 0.004 0.055 3324 Dihedral : 7.582 87.646 2543 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 4.84 % Allowed : 25.10 % Favored : 70.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.40 (0.17), residues: 2295 helix: 1.22 (0.20), residues: 641 sheet: -0.80 (0.24), residues: 457 loop : -0.84 (0.17), residues: 1197 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 406 TYR 0.029 0.002 TYR A 46 PHE 0.030 0.002 PHE A 186 TRP 0.017 0.002 TRP A 102 HIS 0.006 0.001 HIS A 757 Details of bonding type rmsd covalent geometry : bond 0.00478 (19023) covalent geometry : angle 0.65086 (25734) hydrogen bonds : bond 0.06798 ( 801) hydrogen bonds : angle 5.19000 ( 2154) metal coordination : bond 0.00509 ( 3) Misc. bond : bond 0.00620 ( 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 221 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 120 time to evaluate : 0.728 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 GLN cc_start: 0.8637 (OUTLIER) cc_final: 0.7182 (tp-100) REVERT: A 166 PHE cc_start: 0.5619 (t80) cc_final: 0.5003 (t80) REVERT: A 337 MET cc_start: 0.7389 (OUTLIER) cc_final: 0.6884 (mtp) REVERT: A 526 ARG cc_start: 0.7710 (ttm-80) cc_final: 0.7438 (tpm170) REVERT: A 705 ILE cc_start: 0.7502 (OUTLIER) cc_final: 0.7039 (pp) REVERT: A 1164 LEU cc_start: 0.3338 (OUTLIER) cc_final: 0.3069 (tm) REVERT: A 1647 THR cc_start: 0.8075 (OUTLIER) cc_final: 0.7793 (m) REVERT: A 1857 PHE cc_start: 0.5409 (OUTLIER) cc_final: 0.4694 (m-80) REVERT: A 1986 MET cc_start: 0.2063 (mmt) cc_final: 0.0653 (ttp) REVERT: A 2212 TRP cc_start: 0.0300 (OUTLIER) cc_final: -0.0949 (t60) outliers start: 101 outliers final: 62 residues processed: 207 average time/residue: 0.5059 time to fit residues: 122.1555 Evaluate side-chains 183 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 114 time to evaluate : 0.756 ------------------------------------------------------------------------------- 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 90 SER Chi-restraints excluded: chain A residue 106 GLN Chi-restraints excluded: chain A residue 143 LYS 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 337 MET Chi-restraints excluded: chain A residue 366 ILE Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 469 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 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 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 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 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 1228 ARG Chi-restraints excluded: chain A residue 1251 LEU Chi-restraints excluded: chain A residue 1279 LYS Chi-restraints excluded: chain A residue 1304 THR 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 1440 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 1837 ILE Chi-restraints excluded: chain A residue 1841 ASP 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 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 216 optimal weight: 9.9990 chunk 100 optimal weight: 0.1980 chunk 182 optimal weight: 4.9990 chunk 45 optimal weight: 0.6980 chunk 16 optimal weight: 0.7980 chunk 121 optimal weight: 10.0000 chunk 152 optimal weight: 0.0570 chunk 212 optimal weight: 7.9990 chunk 83 optimal weight: 0.5980 chunk 50 optimal weight: 0.9990 chunk 179 optimal weight: 3.9990 overall best weight: 0.4698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 ASN A 795 HIS 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 = 0.4851 r_free = 0.4851 target = 0.273527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.217624 restraints weight = 19748.110| |-----------------------------------------------------------------------------| r_work (start): 0.4279 rms_B_bonded: 5.51 r_work: 0.3774 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work: 0.3715 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7243 moved from start: 0.2674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 19027 Z= 0.113 Angle : 0.533 8.191 25734 Z= 0.287 Chirality : 0.045 0.244 2831 Planarity : 0.004 0.058 3324 Dihedral : 6.963 83.579 2543 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 3.83 % Allowed : 26.34 % Favored : 69.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.03 (0.18), residues: 2295 helix: 1.76 (0.21), residues: 639 sheet: -0.56 (0.24), residues: 450 loop : -0.68 (0.18), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1653 TYR 0.015 0.001 TYR A 284 PHE 0.015 0.001 PHE A 186 TRP 0.009 0.001 TRP A 102 HIS 0.004 0.001 HIS A 757 Details of bonding type rmsd covalent geometry : bond 0.00237 (19023) covalent geometry : angle 0.53321 (25734) hydrogen bonds : bond 0.04648 ( 801) hydrogen bonds : angle 4.80053 ( 2154) metal coordination : bond 0.00240 ( 3) Misc. bond : bond 0.00600 ( 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 211 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 131 time to evaluate : 0.714 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 2 ASN cc_start: 0.7757 (m-40) cc_final: 0.7077 (t0) REVERT: A 157 PHE cc_start: 0.6695 (m-80) cc_final: 0.6131 (m-80) REVERT: A 166 PHE cc_start: 0.5999 (t80) cc_final: 0.5298 (t80) REVERT: A 276 MET cc_start: 0.8678 (mmt) cc_final: 0.8475 (mmm) REVERT: A 337 MET cc_start: 0.7818 (OUTLIER) cc_final: 0.7321 (mtp) REVERT: A 419 ASN cc_start: 0.8202 (m-40) cc_final: 0.7777 (t0) REVERT: A 423 ASP cc_start: 0.7626 (p0) cc_final: 0.7309 (p0) REVERT: A 526 ARG cc_start: 0.7941 (ttm-80) cc_final: 0.7568 (tpm170) REVERT: A 689 LYS cc_start: 0.7349 (mmtp) cc_final: 0.7139 (ptpt) REVERT: A 754 ILE cc_start: 0.7371 (OUTLIER) cc_final: 0.6878 (pp) REVERT: A 981 LEU cc_start: 0.7233 (OUTLIER) cc_final: 0.6898 (tp) REVERT: A 1164 LEU cc_start: 0.2182 (OUTLIER) cc_final: 0.1734 (tm) REVERT: A 1213 ILE cc_start: 0.0713 (OUTLIER) cc_final: 0.0288 (pp) REVERT: A 1332 MET cc_start: 0.1825 (mtm) cc_final: 0.1085 (ppp) REVERT: A 1533 LYS cc_start: 0.5774 (OUTLIER) cc_final: 0.5139 (tmtt) REVERT: A 1647 THR cc_start: 0.8400 (OUTLIER) cc_final: 0.8190 (m) REVERT: A 1841 ASP cc_start: 0.6954 (OUTLIER) cc_final: 0.6462 (t0) REVERT: A 1857 PHE cc_start: 0.5641 (OUTLIER) cc_final: 0.5256 (m-80) REVERT: A 1986 MET cc_start: 0.1987 (mmt) cc_final: -0.0070 (ttp) REVERT: A 2212 TRP cc_start: 0.0210 (OUTLIER) cc_final: -0.0740 (t60) outliers start: 80 outliers final: 41 residues processed: 200 average time/residue: 0.5450 time to fit residues: 125.8064 Evaluate side-chains 167 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 116 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 SER Chi-restraints excluded: chain A residue 143 LYS 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 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 754 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 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 981 LEU Chi-restraints excluded: chain A residue 1005 SER Chi-restraints excluded: chain A residue 1007 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 1228 ARG Chi-restraints excluded: chain A residue 1251 LEU Chi-restraints excluded: chain A residue 1279 LYS Chi-restraints excluded: chain A residue 1304 THR Chi-restraints excluded: chain A residue 1403 SER Chi-restraints excluded: chain A residue 1440 SER Chi-restraints excluded: chain A residue 1533 LYS 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 1837 ILE Chi-restraints excluded: chain A residue 1841 ASP 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 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 208 optimal weight: 0.8980 chunk 9 optimal weight: 0.9990 chunk 126 optimal weight: 10.0000 chunk 117 optimal weight: 0.2980 chunk 168 optimal weight: 4.9990 chunk 92 optimal weight: 0.6980 chunk 198 optimal weight: 0.9980 chunk 116 optimal weight: 0.7980 chunk 188 optimal weight: 1.9990 chunk 195 optimal weight: 0.0970 chunk 20 optimal weight: 1.9990 overall best weight: 0.5578 ------------------------------------------------------------------------------- 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 = 0.4848 r_free = 0.4848 target = 0.273214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4327 r_free = 0.4327 target = 0.218692 restraints weight = 19894.460| |-----------------------------------------------------------------------------| r_work (start): 0.4289 rms_B_bonded: 5.29 r_work: 0.3793 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work: 0.3748 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7212 moved from start: 0.2818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 19027 Z= 0.117 Angle : 0.543 9.328 25734 Z= 0.288 Chirality : 0.045 0.154 2831 Planarity : 0.004 0.055 3324 Dihedral : 6.470 82.531 2535 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 3.35 % Allowed : 27.11 % Favored : 69.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.18 (0.18), residues: 2295 helix: 1.87 (0.21), residues: 640 sheet: -0.39 (0.25), residues: 442 loop : -0.61 (0.18), residues: 1213 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 175 TYR 0.017 0.001 TYR A 284 PHE 0.017 0.001 PHE A 186 TRP 0.010 0.001 TRP A 102 HIS 0.004 0.001 HIS A 757 Details of bonding type rmsd covalent geometry : bond 0.00246 (19023) covalent geometry : angle 0.54257 (25734) hydrogen bonds : bond 0.04857 ( 801) hydrogen bonds : angle 4.74888 ( 2154) metal coordination : bond 0.00251 ( 3) Misc. bond : bond 0.00582 ( 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 194 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 124 time to evaluate : 0.734 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 2 ASN cc_start: 0.7742 (m-40) cc_final: 0.7119 (t0) REVERT: A 157 PHE cc_start: 0.6796 (m-80) cc_final: 0.6221 (m-80) REVERT: A 166 PHE cc_start: 0.5846 (t80) cc_final: 0.5097 (t80) REVERT: A 195 GLU cc_start: 0.6523 (OUTLIER) cc_final: 0.6247 (mp0) REVERT: A 276 MET cc_start: 0.8701 (mmt) cc_final: 0.8450 (mmm) REVERT: A 337 MET cc_start: 0.7813 (OUTLIER) cc_final: 0.7313 (mtp) REVERT: A 348 SER cc_start: 0.8370 (OUTLIER) cc_final: 0.8129 (p) REVERT: A 367 LYS cc_start: 0.8738 (mttt) cc_final: 0.8503 (mtpt) REVERT: A 419 ASN cc_start: 0.8159 (m-40) cc_final: 0.7847 (t0) REVERT: A 423 ASP cc_start: 0.7614 (p0) cc_final: 0.7346 (p0) REVERT: A 526 ARG cc_start: 0.7948 (ttm-80) cc_final: 0.7559 (tpm170) REVERT: A 981 LEU cc_start: 0.7103 (OUTLIER) cc_final: 0.6793 (tp) REVERT: A 1145 MET cc_start: 0.0201 (mmm) cc_final: -0.0972 (mtp) REVERT: A 1164 LEU cc_start: 0.2229 (OUTLIER) cc_final: 0.1777 (tm) REVERT: A 1332 MET cc_start: 0.2340 (mtm) cc_final: 0.1115 (ppp) REVERT: A 1587 GLU cc_start: 0.6369 (pp20) cc_final: 0.5869 (pp20) REVERT: A 1647 THR cc_start: 0.8376 (OUTLIER) cc_final: 0.8154 (m) REVERT: A 1841 ASP cc_start: 0.6905 (OUTLIER) cc_final: 0.6425 (t0) REVERT: A 1857 PHE cc_start: 0.5504 (OUTLIER) cc_final: 0.5098 (m-80) REVERT: A 1986 MET cc_start: 0.2142 (mmt) cc_final: 0.0064 (ttp) REVERT: A 2212 TRP cc_start: 0.0144 (OUTLIER) cc_final: -0.0783 (t60) outliers start: 70 outliers final: 40 residues processed: 187 average time/residue: 0.5332 time to fit residues: 114.7382 Evaluate side-chains 169 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 120 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 SER Chi-restraints excluded: chain A residue 90 SER Chi-restraints excluded: chain A residue 143 LYS Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 195 GLU Chi-restraints excluded: chain A residue 325 GLU Chi-restraints excluded: chain A residue 337 MET Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 366 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 667 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 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 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 1228 ARG Chi-restraints excluded: chain A residue 1251 LEU Chi-restraints excluded: chain A residue 1304 THR Chi-restraints excluded: chain A residue 1374 LYS Chi-restraints excluded: chain A residue 1403 SER Chi-restraints excluded: chain A residue 1440 SER Chi-restraints excluded: chain A residue 1447 ILE 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 1667 SER Chi-restraints excluded: chain A residue 1841 ASP 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 2289 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 105 optimal weight: 4.9990 chunk 202 optimal weight: 0.0030 chunk 145 optimal weight: 0.6980 chunk 172 optimal weight: 0.9980 chunk 28 optimal weight: 0.0270 chunk 81 optimal weight: 0.8980 chunk 149 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 143 optimal weight: 1.9990 chunk 108 optimal weight: 7.9990 chunk 25 optimal weight: 0.6980 overall best weight: 0.4648 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1570 ASN A1633 GLN A1654 GLN ** 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 = 0.4852 r_free = 0.4852 target = 0.273932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.217179 restraints weight = 19928.334| |-----------------------------------------------------------------------------| r_work (start): 0.4264 rms_B_bonded: 5.77 r_work: 0.3734 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work: 0.3681 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7264 moved from start: 0.3024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 19027 Z= 0.107 Angle : 0.522 9.733 25734 Z= 0.277 Chirality : 0.045 0.154 2831 Planarity : 0.003 0.056 3324 Dihedral : 6.142 82.098 2531 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 3.26 % Allowed : 27.44 % Favored : 69.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.35 (0.18), residues: 2295 helix: 2.01 (0.21), residues: 640 sheet: -0.30 (0.25), residues: 442 loop : -0.51 (0.18), residues: 1213 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 722 TYR 0.018 0.001 TYR A 284 PHE 0.015 0.001 PHE A 186 TRP 0.009 0.001 TRP A 102 HIS 0.004 0.001 HIS A 757 Details of bonding type rmsd covalent geometry : bond 0.00224 (19023) covalent geometry : angle 0.52236 (25734) hydrogen bonds : bond 0.04456 ( 801) hydrogen bonds : angle 4.61679 ( 2154) metal coordination : bond 0.00214 ( 3) Misc. bond : bond 0.00566 ( 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 195 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 127 time to evaluate : 0.751 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 ASN cc_start: 0.7806 (m-40) cc_final: 0.7154 (t0) REVERT: A 157 PHE cc_start: 0.6768 (m-80) cc_final: 0.6129 (m-80) REVERT: A 166 PHE cc_start: 0.5879 (t80) cc_final: 0.5098 (t80) REVERT: A 276 MET cc_start: 0.8694 (mmt) cc_final: 0.8477 (mmm) REVERT: A 337 MET cc_start: 0.7823 (OUTLIER) cc_final: 0.7350 (mtp) REVERT: A 419 ASN cc_start: 0.8256 (m-40) cc_final: 0.7878 (t0) REVERT: A 423 ASP cc_start: 0.7666 (p0) cc_final: 0.7313 (p0) REVERT: A 526 ARG cc_start: 0.8040 (ttm-80) cc_final: 0.7643 (tpm170) REVERT: A 667 ASP cc_start: 0.8029 (OUTLIER) cc_final: 0.7819 (m-30) REVERT: A 754 ILE cc_start: 0.7301 (OUTLIER) cc_final: 0.6787 (pp) REVERT: A 786 LYS cc_start: 0.6934 (mmmt) cc_final: 0.6441 (mmtm) REVERT: A 788 ILE cc_start: 0.8413 (OUTLIER) cc_final: 0.8181 (pp) REVERT: A 981 LEU cc_start: 0.6970 (OUTLIER) cc_final: 0.6738 (tp) REVERT: A 1145 MET cc_start: -0.0023 (mmm) cc_final: -0.1078 (mtp) REVERT: A 1164 LEU cc_start: 0.2192 (OUTLIER) cc_final: 0.1728 (tm) REVERT: A 1213 ILE cc_start: 0.0542 (OUTLIER) cc_final: 0.0260 (pp) REVERT: A 1332 MET cc_start: 0.1971 (mtm) cc_final: 0.1076 (ppp) REVERT: A 1533 LYS cc_start: 0.5803 (OUTLIER) cc_final: 0.5212 (tmtt) REVERT: A 1583 MET cc_start: 0.7853 (tpp) cc_final: 0.7527 (mmt) REVERT: A 1587 GLU cc_start: 0.6315 (pp20) cc_final: 0.5819 (pp20) REVERT: A 1751 ILE cc_start: 0.8404 (OUTLIER) cc_final: 0.8168 (mm) REVERT: A 1841 ASP cc_start: 0.6971 (OUTLIER) cc_final: 0.6458 (t0) REVERT: A 1857 PHE cc_start: 0.5390 (OUTLIER) cc_final: 0.4860 (m-80) REVERT: A 1986 MET cc_start: 0.2045 (mmt) cc_final: 0.0153 (ttp) REVERT: A 2212 TRP cc_start: 0.0263 (OUTLIER) cc_final: -0.0598 (t60) outliers start: 68 outliers final: 38 residues processed: 188 average time/residue: 0.5513 time to fit residues: 119.4263 Evaluate side-chains 170 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 120 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 SER Chi-restraints excluded: chain A residue 143 LYS 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 485 LYS 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 640 ILE Chi-restraints excluded: chain A residue 667 ASP Chi-restraints excluded: chain A residue 670 SER 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 788 ILE 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 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 1228 ARG Chi-restraints excluded: chain A residue 1304 THR Chi-restraints excluded: chain A residue 1374 LYS Chi-restraints excluded: chain A residue 1440 SER Chi-restraints excluded: chain A residue 1447 ILE Chi-restraints excluded: chain A residue 1533 LYS 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 1667 SER Chi-restraints excluded: chain A residue 1751 ILE Chi-restraints excluded: chain A residue 1841 ASP Chi-restraints excluded: chain A residue 1857 PHE Chi-restraints excluded: chain A residue 2088 THR Chi-restraints excluded: chain A residue 2212 TRP Chi-restraints excluded: chain A residue 2235 VAL Chi-restraints excluded: chain A residue 2253 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 163 optimal weight: 1.9990 chunk 103 optimal weight: 10.0000 chunk 159 optimal weight: 0.6980 chunk 115 optimal weight: 8.9990 chunk 87 optimal weight: 0.5980 chunk 138 optimal weight: 7.9990 chunk 11 optimal weight: 0.2980 chunk 25 optimal weight: 0.8980 chunk 155 optimal weight: 0.5980 chunk 108 optimal weight: 0.9980 chunk 68 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 405 ASN A 732 GLN A1570 ASN A1633 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 = 0.4848 r_free = 0.4848 target = 0.273078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.215375 restraints weight = 19715.541| |-----------------------------------------------------------------------------| r_work (start): 0.4247 rms_B_bonded: 5.91 r_work: 0.3721 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work: 0.3663 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7287 moved from start: 0.3075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 19027 Z= 0.119 Angle : 0.538 8.649 25734 Z= 0.286 Chirality : 0.045 0.178 2831 Planarity : 0.004 0.053 3324 Dihedral : 5.746 81.537 2525 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 3.02 % Allowed : 27.63 % Favored : 69.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.36 (0.18), residues: 2295 helix: 1.97 (0.21), residues: 639 sheet: -0.30 (0.25), residues: 449 loop : -0.46 (0.18), residues: 1207 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A1653 TYR 0.018 0.001 TYR A 284 PHE 0.019 0.001 PHE A 186 TRP 0.010 0.001 TRP A 102 HIS 0.004 0.001 HIS A 757 Details of bonding type rmsd covalent geometry : bond 0.00254 (19023) covalent geometry : angle 0.53766 (25734) hydrogen bonds : bond 0.04879 ( 801) hydrogen bonds : angle 4.66260 ( 2154) metal coordination : bond 0.00273 ( 3) Misc. bond : bond 0.00560 ( 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 183 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 120 time to evaluate : 0.730 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 2 ASN cc_start: 0.7829 (m-40) cc_final: 0.7213 (t0) REVERT: A 106 GLN cc_start: 0.9016 (OUTLIER) cc_final: 0.7696 (tp-100) REVERT: A 157 PHE cc_start: 0.6840 (m-80) cc_final: 0.6202 (m-80) REVERT: A 166 PHE cc_start: 0.5908 (t80) cc_final: 0.5119 (t80) REVERT: A 195 GLU cc_start: 0.6854 (OUTLIER) cc_final: 0.6643 (tp30) REVERT: A 276 MET cc_start: 0.8732 (mmt) cc_final: 0.8480 (mmm) REVERT: A 337 MET cc_start: 0.7871 (OUTLIER) cc_final: 0.7372 (mtp) REVERT: A 419 ASN cc_start: 0.8206 (m-40) cc_final: 0.7879 (t0) REVERT: A 423 ASP cc_start: 0.7656 (p0) cc_final: 0.7374 (p0) REVERT: A 526 ARG cc_start: 0.8020 (ttm-80) cc_final: 0.7603 (tpm170) REVERT: A 667 ASP cc_start: 0.7997 (OUTLIER) cc_final: 0.7776 (m-30) REVERT: A 722 ARG cc_start: 0.6996 (mtm180) cc_final: 0.6719 (mtm180) REVERT: A 727 MET cc_start: 0.6475 (mtp) cc_final: 0.6245 (mtt) REVERT: A 754 ILE cc_start: 0.7409 (OUTLIER) cc_final: 0.6906 (pp) REVERT: A 788 ILE cc_start: 0.8433 (OUTLIER) cc_final: 0.8199 (pp) REVERT: A 981 LEU cc_start: 0.6973 (OUTLIER) cc_final: 0.6711 (tp) REVERT: A 1145 MET cc_start: 0.0056 (mmm) cc_final: -0.0256 (mmt) REVERT: A 1164 LEU cc_start: 0.2181 (OUTLIER) cc_final: 0.1712 (tm) REVERT: A 1332 MET cc_start: 0.2164 (mtm) cc_final: 0.1136 (ppp) REVERT: A 1583 MET cc_start: 0.7873 (tpp) cc_final: 0.7532 (mmt) REVERT: A 1587 GLU cc_start: 0.6295 (pp20) cc_final: 0.5877 (pp20) REVERT: A 1751 ILE cc_start: 0.8419 (OUTLIER) cc_final: 0.8167 (mm) REVERT: A 1841 ASP cc_start: 0.6961 (OUTLIER) cc_final: 0.6438 (t0) REVERT: A 1857 PHE cc_start: 0.5259 (OUTLIER) cc_final: 0.4738 (m-80) REVERT: A 1986 MET cc_start: 0.2244 (mmt) cc_final: 0.0382 (ttp) REVERT: A 2212 TRP cc_start: 0.0246 (OUTLIER) cc_final: -0.0716 (t60) outliers start: 63 outliers final: 39 residues processed: 179 average time/residue: 0.5478 time to fit residues: 113.0677 Evaluate side-chains 170 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 119 time to evaluate : 0.705 ------------------------------------------------------------------------------- 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 325 GLU Chi-restraints excluded: chain A residue 337 MET Chi-restraints excluded: chain A residue 366 ILE Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 485 LYS 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 667 ASP Chi-restraints excluded: chain A residue 670 SER Chi-restraints excluded: chain A residue 730 ILE 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 788 ILE 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 1116 LYS 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 1374 LYS Chi-restraints excluded: chain A residue 1440 SER Chi-restraints excluded: chain A residue 1447 ILE 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 1667 SER Chi-restraints excluded: chain A residue 1751 ILE Chi-restraints excluded: chain A residue 1841 ASP Chi-restraints excluded: chain A residue 1857 PHE Chi-restraints excluded: chain A residue 2088 THR Chi-restraints excluded: chain A residue 2212 TRP Chi-restraints excluded: chain A residue 2253 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 32 optimal weight: 0.4980 chunk 160 optimal weight: 0.9990 chunk 220 optimal weight: 9.9990 chunk 148 optimal weight: 1.9990 chunk 139 optimal weight: 9.9990 chunk 161 optimal weight: 0.9990 chunk 101 optimal weight: 5.9990 chunk 37 optimal weight: 0.9990 chunk 127 optimal weight: 6.9990 chunk 94 optimal weight: 0.9980 chunk 197 optimal weight: 5.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 835 GLN A1633 GLN ** 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 = 0.4891 r_free = 0.4891 target = 0.278503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4757 r_free = 0.4757 target = 0.262602 restraints weight = 19553.857| |-----------------------------------------------------------------------------| r_work (start): 0.4759 rms_B_bonded: 0.72 r_work: 0.4615 rms_B_bonded: 1.06 restraints_weight: 0.5000 r_work: 0.4586 rms_B_bonded: 1.47 restraints_weight: 0.2500 r_work (final): 0.4586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6110 moved from start: 0.3058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 19027 Z= 0.140 Angle : 0.564 8.698 25734 Z= 0.302 Chirality : 0.046 0.172 2831 Planarity : 0.004 0.054 3324 Dihedral : 5.831 81.258 2522 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.73 % Allowed : 27.87 % Favored : 69.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.28 (0.18), residues: 2295 helix: 1.83 (0.20), residues: 640 sheet: -0.30 (0.24), residues: 470 loop : -0.49 (0.18), residues: 1185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 722 TYR 0.021 0.001 TYR A 46 PHE 0.021 0.001 PHE A 186 TRP 0.013 0.001 TRP A 102 HIS 0.005 0.001 HIS A 757 Details of bonding type rmsd covalent geometry : bond 0.00310 (19023) covalent geometry : angle 0.56415 (25734) hydrogen bonds : bond 0.05465 ( 801) hydrogen bonds : angle 4.75913 ( 2154) metal coordination : bond 0.00318 ( 3) Misc. bond : bond 0.00559 ( 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 179 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 122 time to evaluate : 0.727 Fit side-chains 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: 0.7145 (tp-100) REVERT: A 157 PHE cc_start: 0.6117 (m-80) cc_final: 0.5811 (m-80) REVERT: A 166 PHE cc_start: 0.5384 (t80) cc_final: 0.4800 (t80) REVERT: A 276 MET cc_start: 0.8395 (mmt) cc_final: 0.8091 (mmm) REVERT: A 337 MET cc_start: 0.7345 (OUTLIER) cc_final: 0.6849 (mtp) REVERT: A 419 ASN cc_start: 0.7745 (m-40) cc_final: 0.7407 (t0) REVERT: A 667 ASP cc_start: 0.7465 (OUTLIER) cc_final: 0.7210 (m-30) REVERT: A 981 LEU cc_start: 0.7048 (OUTLIER) cc_final: 0.6690 (tp) REVERT: A 1164 LEU cc_start: 0.3413 (OUTLIER) cc_final: 0.3144 (tm) REVERT: A 1234 MET cc_start: 0.2571 (tpp) cc_final: -0.0181 (mmm) REVERT: A 1751 ILE cc_start: 0.7890 (OUTLIER) cc_final: 0.7543 (mm) REVERT: A 1857 PHE cc_start: 0.4963 (OUTLIER) cc_final: 0.4290 (m-80) REVERT: A 1986 MET cc_start: 0.2542 (mmt) cc_final: 0.1094 (ttp) REVERT: A 2212 TRP cc_start: 0.0183 (OUTLIER) cc_final: -0.1079 (t60) outliers start: 57 outliers final: 40 residues processed: 173 average time/residue: 0.5324 time to fit residues: 106.3601 Evaluate side-chains 168 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 120 time to evaluate : 0.711 ------------------------------------------------------------------------------- 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 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 469 SER 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 667 ASP Chi-restraints excluded: chain A residue 670 SER Chi-restraints excluded: chain A residue 730 ILE Chi-restraints excluded: chain A residue 757 HIS Chi-restraints excluded: chain A residue 774 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 1015 LEU Chi-restraints excluded: chain A residue 1116 LYS 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 1403 SER Chi-restraints excluded: chain A residue 1440 SER Chi-restraints excluded: chain A residue 1447 ILE 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 1667 SER Chi-restraints excluded: chain A residue 1751 ILE Chi-restraints excluded: chain A residue 1837 ILE Chi-restraints excluded: chain A residue 1857 PHE 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 2253 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 8 optimal weight: 0.6980 chunk 6 optimal weight: 1.9990 chunk 226 optimal weight: 10.0000 chunk 132 optimal weight: 8.9990 chunk 210 optimal weight: 0.8980 chunk 172 optimal weight: 2.9990 chunk 215 optimal weight: 0.0370 chunk 193 optimal weight: 9.9990 chunk 59 optimal weight: 1.9990 chunk 67 optimal weight: 0.7980 chunk 31 optimal weight: 2.9990 overall best weight: 0.8860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1633 GLN ** 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 = 0.4893 r_free = 0.4893 target = 0.278797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4763 r_free = 0.4763 target = 0.263341 restraints weight = 19761.024| |-----------------------------------------------------------------------------| r_work (start): 0.4765 rms_B_bonded: 0.72 r_work: 0.4623 rms_B_bonded: 1.06 restraints_weight: 0.5000 r_work: 0.4594 rms_B_bonded: 1.46 restraints_weight: 0.2500 r_work (final): 0.4594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6091 moved from start: 0.3149 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= 0.139 Angle : 0.563 8.596 25734 Z= 0.301 Chirality : 0.046 0.226 2831 Planarity : 0.004 0.054 3324 Dihedral : 5.815 82.061 2522 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 2.87 % Allowed : 27.73 % Favored : 69.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.30 (0.18), residues: 2295 helix: 1.82 (0.20), residues: 639 sheet: -0.35 (0.24), residues: 473 loop : -0.43 (0.18), residues: 1183 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 463 TYR 0.021 0.001 TYR A 46 PHE 0.022 0.001 PHE A 186 TRP 0.012 0.001 TRP A 102 HIS 0.005 0.001 HIS A 757 Details of bonding type rmsd covalent geometry : bond 0.00307 (19023) covalent geometry : angle 0.56293 (25734) hydrogen bonds : bond 0.05321 ( 801) hydrogen bonds : angle 4.73210 ( 2154) metal coordination : bond 0.00315 ( 3) Misc. bond : bond 0.00555 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8851.19 seconds wall clock time: 151 minutes 7.89 seconds (9067.89 seconds total)