Starting phenix.real_space_refine on Sun Jun 7 07:15:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9rsq_54222/06_2026/9rsq_54222.cif Found real_map, /net/cci-nas-00/data/ceres_data/9rsq_54222/06_2026/9rsq_54222.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.07 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9rsq_54222/06_2026/9rsq_54222.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9rsq_54222/06_2026/9rsq_54222.map" model { file = "/net/cci-nas-00/data/ceres_data/9rsq_54222/06_2026/9rsq_54222.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9rsq_54222/06_2026/9rsq_54222.cif" } resolution = 3.07 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.032 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 6 5.49 5 S 173 5.16 5 C 21854 2.51 5 N 5848 2.21 5 O 6271 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 34152 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 18184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2268, 18184 Classifications: {'peptide': 2268} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 94, 'TRANS': 2173} Chain breaks: 12 Chain: "B" Number of atoms: 2386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2386 Classifications: {'peptide': 302} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 292} Chain: "C" Number of atoms: 8314 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1020, 8314 Classifications: {'peptide': 1020} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 24, 'TRANS': 995} Chain breaks: 4 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "D" Number of atoms: 1518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1518 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 6, 'TRANS': 182} Chain breaks: 1 Chain: "E" Number of atoms: 1776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1776 Classifications: {'peptide': 215} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 209} Chain breaks: 4 Chain: "G" Number of atoms: 1625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1625 Classifications: {'peptide': 196} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 185} Chain breaks: 4 Chain: "H" Number of atoms: 313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 313 Classifications: {'peptide': 39} Link IDs: {'PTRANS': 1, 'TRANS': 37} Chain: "A" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'IHP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.34, per 1000 atoms: 0.21 Number of scatterers: 34152 At special positions: 0 Unit cell: (204.3, 188.864, 160.716, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 173 16.00 P 6 15.00 O 6271 8.00 N 5848 7.00 C 21854 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.54 Conformation dependent library (CDL) restraints added in 1.7 seconds 8330 Ramachandran restraints generated. 4165 Oldfield, 0 Emsley, 4165 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8118 Finding SS restraints... Secondary structure from input PDB file: 245 helices and 13 sheets defined 72.0% alpha, 4.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.55 Creating SS restraints... Processing helix chain 'A' and resid 75 through 94 Processing helix chain 'A' and resid 97 through 119 Processing helix chain 'A' and resid 120 through 141 Processing helix chain 'A' and resid 143 through 164 removed outlier: 3.685A pdb=" N LYS A 147 " --> pdb=" O THR A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 181 removed outlier: 3.776A pdb=" N VAL A 180 " --> pdb=" O ASN A 176 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N LEU A 181 " --> pdb=" O TYR A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 200 Processing helix chain 'A' and resid 207 through 224 Processing helix chain 'A' and resid 232 through 254 Processing helix chain 'A' and resid 254 through 259 removed outlier: 3.636A pdb=" N LEU A 258 " --> pdb=" O SER A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 268 removed outlier: 3.548A pdb=" N ASN A 268 " --> pdb=" O SER A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 274 Processing helix chain 'A' and resid 277 through 299 Processing helix chain 'A' and resid 299 through 317 Processing helix chain 'A' and resid 322 through 340 Processing helix chain 'A' and resid 343 through 358 removed outlier: 4.449A pdb=" N LYS A 347 " --> pdb=" O TYR A 343 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N ASP A 349 " --> pdb=" O ARG A 345 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N ASP A 350 " --> pdb=" O ASP A 346 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N TYR A 358 " --> pdb=" O SER A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 381 removed outlier: 3.616A pdb=" N ARG A 367 " --> pdb=" O PHE A 363 " (cutoff:3.500A) Proline residue: A 375 - end of helix removed outlier: 3.848A pdb=" N ASP A 381 " --> pdb=" O LEU A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 389 removed outlier: 3.685A pdb=" N PHE A 385 " --> pdb=" O ASP A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 402 Processing helix chain 'A' and resid 407 through 412 removed outlier: 3.783A pdb=" N ASN A 411 " --> pdb=" O ALA A 408 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N SER A 412 " --> pdb=" O ALA A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 428 Processing helix chain 'A' and resid 432 through 448 removed outlier: 4.114A pdb=" N THR A 437 " --> pdb=" O SER A 433 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N LEU A 438 " --> pdb=" O PRO A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 454 through 456 No H-bonds generated for 'chain 'A' and resid 454 through 456' Processing helix chain 'A' and resid 457 through 473 removed outlier: 3.996A pdb=" N PHE A 462 " --> pdb=" O GLU A 458 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N TYR A 463 " --> pdb=" O LYS A 459 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N CYS A 464 " --> pdb=" O ASP A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 483 removed outlier: 3.730A pdb=" N LEU A 480 " --> pdb=" O PHE A 476 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LYS A 482 " --> pdb=" O LYS A 478 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 489 removed outlier: 3.628A pdb=" N LEU A 487 " --> pdb=" O ASP A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 508 Processing helix chain 'A' and resid 511 through 529 Processing helix chain 'A' and resid 545 through 559 Processing helix chain 'A' and resid 566 through 582 removed outlier: 3.874A pdb=" N ALA A 571 " --> pdb=" O ASP A 567 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLN A 572 " --> pdb=" O ILE A 568 " (cutoff:3.500A) Processing helix chain 'A' and resid 590 through 597 removed outlier: 3.892A pdb=" N LEU A 596 " --> pdb=" O GLU A 592 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 604 removed outlier: 3.981A pdb=" N GLU A 603 " --> pdb=" O SER A 600 " (cutoff:3.500A) Processing helix chain 'A' and resid 606 through 623 removed outlier: 3.881A pdb=" N LYS A 623 " --> pdb=" O ASP A 619 " (cutoff:3.500A) Processing helix chain 'A' and resid 624 through 628 removed outlier: 3.898A pdb=" N CYS A 627 " --> pdb=" O ASP A 624 " (cutoff:3.500A) Processing helix chain 'A' and resid 631 through 649 removed outlier: 3.566A pdb=" N ILE A 648 " --> pdb=" O LYS A 644 " (cutoff:3.500A) Processing helix chain 'A' and resid 654 through 664 Processing helix chain 'A' and resid 665 through 668 removed outlier: 6.754A pdb=" N ASN A 668 " --> pdb=" O LEU A 665 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 665 through 668' Processing helix chain 'A' and resid 669 through 674 Processing helix chain 'A' and resid 675 through 687 removed outlier: 3.681A pdb=" N LEU A 681 " --> pdb=" O ASP A 677 " (cutoff:3.500A) Processing helix chain 'A' and resid 690 through 704 removed outlier: 3.800A pdb=" N ILE A 700 " --> pdb=" O GLU A 696 " (cutoff:3.500A) Processing helix chain 'A' and resid 705 through 707 No H-bonds generated for 'chain 'A' and resid 705 through 707' Processing helix chain 'A' and resid 711 through 729 Processing helix chain 'A' and resid 732 through 750 Processing helix chain 'A' and resid 757 through 769 Proline residue: A 767 - end of helix Processing helix chain 'A' and resid 773 through 792 removed outlier: 3.535A pdb=" N LEU A 781 " --> pdb=" O ALA A 777 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N LYS A 782 " --> pdb=" O SER A 778 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU A 784 " --> pdb=" O ALA A 780 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL A 790 " --> pdb=" O GLU A 786 " (cutoff:3.500A) Processing helix chain 'A' and resid 793 through 797 removed outlier: 4.012A pdb=" N ARG A 797 " --> pdb=" O GLU A 794 " (cutoff:3.500A) Processing helix chain 'A' and resid 798 through 811 Proline residue: A 804 - end of helix Processing helix chain 'A' and resid 816 through 834 removed outlier: 3.931A pdb=" N ALA A 822 " --> pdb=" O LYS A 818 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N THR A 824 " --> pdb=" O ASP A 820 " (cutoff:3.500A) Processing helix chain 'A' and resid 837 through 843 Processing helix chain 'A' and resid 845 through 857 removed outlier: 3.588A pdb=" N LEU A 854 " --> pdb=" O LEU A 850 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LYS A 855 " --> pdb=" O ILE A 851 " (cutoff:3.500A) Processing helix chain 'A' and resid 859 through 874 removed outlier: 3.565A pdb=" N VAL A 867 " --> pdb=" O ARG A 863 " (cutoff:3.500A) Processing helix chain 'A' and resid 900 through 908 removed outlier: 3.768A pdb=" N LEU A 906 " --> pdb=" O ASP A 902 " (cutoff:3.500A) Processing helix chain 'A' and resid 916 through 932 removed outlier: 3.759A pdb=" N THR A 920 " --> pdb=" O GLU A 916 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ILE A 929 " --> pdb=" O ASN A 925 " (cutoff:3.500A) Processing helix chain 'A' and resid 933 through 937 removed outlier: 4.796A pdb=" N ILE A 937 " --> pdb=" O SER A 934 " (cutoff:3.500A) Processing helix chain 'A' and resid 938 through 954 Processing helix chain 'A' and resid 955 through 959 removed outlier: 4.822A pdb=" N SER A 959 " --> pdb=" O ARG A 956 " (cutoff:3.500A) Processing helix chain 'A' and resid 960 through 973 Proline residue: A 966 - end of helix Processing helix chain 'A' and resid 974 through 975 No H-bonds generated for 'chain 'A' and resid 974 through 975' Processing helix chain 'A' and resid 976 through 978 No H-bonds generated for 'chain 'A' and resid 976 through 978' Processing helix chain 'A' and resid 979 through 994 Processing helix chain 'A' and resid 998 through 1000 No H-bonds generated for 'chain 'A' and resid 998 through 1000' Processing helix chain 'A' and resid 1001 through 1013 removed outlier: 3.537A pdb=" N VAL A1008 " --> pdb=" O LYS A1004 " (cutoff:3.500A) Processing helix chain 'A' and resid 1021 through 1033 Processing helix chain 'A' and resid 1035 through 1039 removed outlier: 3.724A pdb=" N LYS A1038 " --> pdb=" O GLY A1035 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ARG A1039 " --> pdb=" O GLU A1036 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1035 through 1039' Processing helix chain 'A' and resid 1040 through 1051 Processing helix chain 'A' and resid 1061 through 1073 removed outlier: 3.628A pdb=" N LYS A1068 " --> pdb=" O ILE A1064 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N VAL A1071 " --> pdb=" O LEU A1067 " (cutoff:3.500A) Processing helix chain 'A' and resid 1074 through 1078 Processing helix chain 'A' and resid 1084 through 1095 removed outlier: 4.507A pdb=" N GLU A1093 " --> pdb=" O VAL A1089 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N SER A1095 " --> pdb=" O MET A1091 " (cutoff:3.500A) Processing helix chain 'A' and resid 1098 through 1111 removed outlier: 3.539A pdb=" N ILE A1104 " --> pdb=" O LYS A1100 " (cutoff:3.500A) Processing helix chain 'A' and resid 1119 through 1133 removed outlier: 3.680A pdb=" N ASN A1133 " --> pdb=" O ARG A1129 " (cutoff:3.500A) Processing helix chain 'A' and resid 1135 through 1154 removed outlier: 4.236A pdb=" N LYS A1140 " --> pdb=" O ARG A1136 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N ALA A1141 " --> pdb=" O GLU A1137 " (cutoff:3.500A) Processing helix chain 'A' and resid 1155 through 1159 removed outlier: 3.934A pdb=" N VAL A1159 " --> pdb=" O ASP A1156 " (cutoff:3.500A) Processing helix chain 'A' and resid 1160 through 1171 Processing helix chain 'A' and resid 1175 through 1187 Processing helix chain 'A' and resid 1221 through 1230 removed outlier: 3.904A pdb=" N ASN A1227 " --> pdb=" O ASN A1223 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ALA A1228 " --> pdb=" O ILE A1224 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N TRP A1229 " --> pdb=" O LEU A1225 " (cutoff:3.500A) Processing helix chain 'A' and resid 1236 through 1254 removed outlier: 3.530A pdb=" N GLN A1241 " --> pdb=" O LYS A1237 " (cutoff:3.500A) Processing helix chain 'A' and resid 1257 through 1262 Processing helix chain 'A' and resid 1263 through 1268 removed outlier: 3.541A pdb=" N SER A1268 " --> pdb=" O SER A1264 " (cutoff:3.500A) Processing helix chain 'A' and resid 1271 through 1277 Processing helix chain 'A' and resid 1277 through 1289 removed outlier: 3.956A pdb=" N VAL A1287 " --> pdb=" O SER A1283 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N GLU A1288 " --> pdb=" O SER A1284 " (cutoff:3.500A) Processing helix chain 'A' and resid 1290 through 1307 removed outlier: 3.596A pdb=" N GLU A1295 " --> pdb=" O THR A1291 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ASP A1296 " --> pdb=" O SER A1292 " (cutoff:3.500A) Processing helix chain 'A' and resid 1311 through 1328 Processing helix chain 'A' and resid 1335 through 1346 Processing helix chain 'A' and resid 1348 through 1363 Processing helix chain 'A' and resid 1365 through 1379 Processing helix chain 'A' and resid 1381 through 1394 removed outlier: 3.526A pdb=" N GLY A1387 " --> pdb=" O ASP A1383 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA A1392 " --> pdb=" O ILE A1388 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLN A1393 " --> pdb=" O LEU A1389 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLN A1394 " --> pdb=" O LYS A1390 " (cutoff:3.500A) Processing helix chain 'A' and resid 1403 through 1408 Processing helix chain 'A' and resid 1410 through 1424 removed outlier: 3.729A pdb=" N ALA A1424 " --> pdb=" O GLU A1420 " (cutoff:3.500A) Processing helix chain 'A' and resid 1428 through 1443 Processing helix chain 'A' and resid 1444 through 1455 removed outlier: 3.626A pdb=" N LYS A1450 " --> pdb=" O GLU A1446 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLU A1454 " --> pdb=" O LYS A1450 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LYS A1455 " --> pdb=" O LEU A1451 " (cutoff:3.500A) Processing helix chain 'A' and resid 1460 through 1478 Proline residue: A1469 - end of helix removed outlier: 3.564A pdb=" N ALA A1474 " --> pdb=" O LEU A1470 " (cutoff:3.500A) Processing helix chain 'A' and resid 1480 through 1490 removed outlier: 3.756A pdb=" N ILE A1484 " --> pdb=" O GLN A1480 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ALA A1485 " --> pdb=" O TRP A1481 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLN A1486 " --> pdb=" O ASP A1482 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N VAL A1490 " --> pdb=" O GLN A1486 " (cutoff:3.500A) Processing helix chain 'A' and resid 1495 through 1509 Processing helix chain 'A' and resid 1511 through 1533 removed outlier: 3.649A pdb=" N VAL A1517 " --> pdb=" O LYS A1513 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N THR A1528 " --> pdb=" O ASP A1524 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA A1532 " --> pdb=" O THR A1528 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LEU A1533 " --> pdb=" O GLU A1529 " (cutoff:3.500A) Processing helix chain 'A' and resid 1541 through 1563 removed outlier: 3.545A pdb=" N ILE A1558 " --> pdb=" O LEU A1554 " (cutoff:3.500A) Processing helix chain 'A' and resid 1568 through 1583 removed outlier: 3.751A pdb=" N THR A1572 " --> pdb=" O ASP A1568 " (cutoff:3.500A) Processing helix chain 'A' and resid 1587 through 1599 removed outlier: 3.508A pdb=" N VAL A1597 " --> pdb=" O ARG A1593 " (cutoff:3.500A) Processing helix chain 'A' and resid 1603 through 1606 Processing helix chain 'A' and resid 1607 through 1621 removed outlier: 3.713A pdb=" N LYS A1613 " --> pdb=" O GLN A1609 " (cutoff:3.500A) Processing helix chain 'A' and resid 1623 through 1633 removed outlier: 3.720A pdb=" N LYS A1629 " --> pdb=" O ALA A1625 " (cutoff:3.500A) Processing helix chain 'A' and resid 1650 through 1665 removed outlier: 3.908A pdb=" N GLY A1665 " --> pdb=" O LEU A1661 " (cutoff:3.500A) Processing helix chain 'A' and resid 1666 through 1685 removed outlier: 3.503A pdb=" N SER A1679 " --> pdb=" O ILE A1675 " (cutoff:3.500A) Processing helix chain 'A' and resid 1707 through 1730 Processing helix chain 'A' and resid 1738 through 1752 Processing helix chain 'A' and resid 1755 through 1774 removed outlier: 3.501A pdb=" N TRP A1759 " --> pdb=" O TRP A1755 " (cutoff:3.500A) Processing helix chain 'A' and resid 1813 through 1818 removed outlier: 3.622A pdb=" N HIS A1818 " --> pdb=" O SER A1814 " (cutoff:3.500A) Processing helix chain 'A' and resid 1820 through 1835 Processing helix chain 'A' and resid 1839 through 1853 Processing helix chain 'A' and resid 1856 through 1867 Processing helix chain 'A' and resid 1871 through 1878 removed outlier: 3.538A pdb=" N TRP A1875 " --> pdb=" O ILE A1872 " (cutoff:3.500A) Processing helix chain 'A' and resid 1879 through 1884 removed outlier: 3.632A pdb=" N SER A1884 " --> pdb=" O PRO A1880 " (cutoff:3.500A) Processing helix chain 'A' and resid 1890 through 1908 removed outlier: 3.780A pdb=" N ALA A1907 " --> pdb=" O ASP A1903 " (cutoff:3.500A) Processing helix chain 'A' and resid 1908 through 1921 removed outlier: 3.766A pdb=" N LEU A1912 " --> pdb=" O HIS A1908 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N TYR A1914 " --> pdb=" O GLN A1910 " (cutoff:3.500A) Proline residue: A1915 - end of helix removed outlier: 3.573A pdb=" N VAL A1918 " --> pdb=" O TYR A1914 " (cutoff:3.500A) Processing helix chain 'A' and resid 1924 through 1942 removed outlier: 3.809A pdb=" N ILE A1934 " --> pdb=" O ALA A1930 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ILE A1940 " --> pdb=" O GLU A1936 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N HIS A1941 " --> pdb=" O LYS A1937 " (cutoff:3.500A) Processing helix chain 'A' and resid 1942 through 1961 Processing helix chain 'A' and resid 1962 through 1977 Processing helix chain 'A' and resid 1983 through 1998 Proline residue: A1993 - end of helix removed outlier: 3.534A pdb=" N MET A1997 " --> pdb=" O PRO A1993 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N LEU A1998 " --> pdb=" O LEU A1994 " (cutoff:3.500A) Processing helix chain 'A' and resid 2004 through 2031 removed outlier: 4.849A pdb=" N ARG A2016 " --> pdb=" O ASN A2012 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N ASP A2017 " --> pdb=" O SER A2013 " (cutoff:3.500A) Processing helix chain 'A' and resid 2033 through 2055 removed outlier: 4.076A pdb=" N LEU A2037 " --> pdb=" O ASP A2033 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASP A2042 " --> pdb=" O ASN A2038 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ILE A2043 " --> pdb=" O GLN A2039 " (cutoff:3.500A) Processing helix chain 'A' and resid 2063 through 2067 Processing helix chain 'A' and resid 2067 through 2073 removed outlier: 3.643A pdb=" N LEU A2071 " --> pdb=" O SER A2067 " (cutoff:3.500A) Processing helix chain 'A' and resid 2133 through 2153 removed outlier: 3.512A pdb=" N LEU A2145 " --> pdb=" O GLN A2141 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ASP A2153 " --> pdb=" O LEU A2149 " (cutoff:3.500A) Processing helix chain 'A' and resid 2153 through 2159 removed outlier: 3.945A pdb=" N ARG A2159 " --> pdb=" O GLU A2155 " (cutoff:3.500A) Processing helix chain 'A' and resid 2187 through 2198 Processing helix chain 'A' and resid 2203 through 2213 Processing helix chain 'A' and resid 2215 through 2219 removed outlier: 3.581A pdb=" N LEU A2219 " --> pdb=" O TYR A2216 " (cutoff:3.500A) Processing helix chain 'A' and resid 2220 through 2234 Processing helix chain 'A' and resid 2238 through 2247 removed outlier: 3.639A pdb=" N TRP A2245 " --> pdb=" O TYR A2241 " (cutoff:3.500A) Processing helix chain 'A' and resid 2250 through 2276 Processing helix chain 'A' and resid 2281 through 2283 No H-bonds generated for 'chain 'A' and resid 2281 through 2283' Processing helix chain 'A' and resid 2304 through 2309 Processing helix chain 'A' and resid 2321 through 2327 Processing helix chain 'A' and resid 2331 through 2334 removed outlier: 3.912A pdb=" N GLU A2334 " --> pdb=" O SER A2331 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2331 through 2334' Processing helix chain 'A' and resid 2335 through 2351 removed outlier: 3.704A pdb=" N ILE A2339 " --> pdb=" O GLY A2335 " (cutoff:3.500A) Processing helix chain 'A' and resid 2351 through 2364 Processing helix chain 'A' and resid 2411 through 2435 removed outlier: 3.658A pdb=" N ASN A2415 " --> pdb=" O ASN A2411 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA A2420 " --> pdb=" O ALA A2416 " (cutoff:3.500A) Processing helix chain 'A' and resid 2445 through 2458 Processing helix chain 'A' and resid 2459 through 2464 Processing helix chain 'A' and resid 2465 through 2466 No H-bonds generated for 'chain 'A' and resid 2465 through 2466' Processing helix chain 'A' and resid 2467 through 2471 Processing helix chain 'C' and resid 300 through 315 removed outlier: 3.615A pdb=" N GLN C 315 " --> pdb=" O MET C 311 " (cutoff:3.500A) Processing helix chain 'C' and resid 320 through 338 Processing helix chain 'C' and resid 339 through 345 removed outlier: 3.822A pdb=" N ARG C 342 " --> pdb=" O SER C 339 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ASP C 344 " --> pdb=" O ILE C 341 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LEU C 345 " --> pdb=" O ARG C 342 " (cutoff:3.500A) Processing helix chain 'C' and resid 347 through 359 removed outlier: 4.213A pdb=" N SER C 352 " --> pdb=" O THR C 348 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N SER C 353 " --> pdb=" O SER C 349 " (cutoff:3.500A) Processing helix chain 'C' and resid 362 through 376 Processing helix chain 'C' and resid 379 through 388 removed outlier: 3.603A pdb=" N ILE C 383 " --> pdb=" O SER C 379 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU C 388 " --> pdb=" O ASP C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 390 through 400 Processing helix chain 'C' and resid 401 through 404 removed outlier: 6.297A pdb=" N SER C 404 " --> pdb=" O LYS C 401 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 401 through 404' Processing helix chain 'C' and resid 405 through 422 Processing helix chain 'C' and resid 427 through 440 Processing helix chain 'C' and resid 445 through 460 removed outlier: 3.611A pdb=" N PHE C 458 " --> pdb=" O LEU C 454 " (cutoff:3.500A) Processing helix chain 'C' and resid 460 through 467 removed outlier: 3.610A pdb=" N VAL C 464 " --> pdb=" O ALA C 460 " (cutoff:3.500A) Processing helix chain 'C' and resid 468 through 475 removed outlier: 4.002A pdb=" N VAL C 472 " --> pdb=" O ARG C 468 " (cutoff:3.500A) Processing helix chain 'C' and resid 482 through 496 removed outlier: 3.540A pdb=" N ALA C 486 " --> pdb=" O SER C 482 " (cutoff:3.500A) Processing helix chain 'C' and resid 499 through 504 removed outlier: 3.504A pdb=" N GLN C 504 " --> pdb=" O HIS C 500 " (cutoff:3.500A) Processing helix chain 'C' and resid 512 through 517 removed outlier: 3.796A pdb=" N THR C 516 " --> pdb=" O VAL C 512 " (cutoff:3.500A) Processing helix chain 'C' and resid 529 through 544 Processing helix chain 'C' and resid 546 through 554 Processing helix chain 'C' and resid 554 through 566 Proline residue: C 560 - end of helix Processing helix chain 'C' and resid 567 through 569 No H-bonds generated for 'chain 'C' and resid 567 through 569' Processing helix chain 'C' and resid 570 through 585 removed outlier: 3.962A pdb=" N TYR C 576 " --> pdb=" O ILE C 572 " (cutoff:3.500A) Processing helix chain 'C' and resid 608 through 612 Processing helix chain 'C' and resid 613 through 630 removed outlier: 3.592A pdb=" N ARG C 619 " --> pdb=" O SER C 615 " (cutoff:3.500A) Processing helix chain 'C' and resid 632 through 641 Processing helix chain 'C' and resid 646 through 668 Processing helix chain 'C' and resid 685 through 702 Processing helix chain 'C' and resid 713 through 733 Processing helix chain 'C' and resid 735 through 746 Processing helix chain 'C' and resid 753 through 757 Processing helix chain 'C' and resid 758 through 768 removed outlier: 3.682A pdb=" N ILE C 762 " --> pdb=" O ASN C 758 " (cutoff:3.500A) Processing helix chain 'C' and resid 769 through 771 No H-bonds generated for 'chain 'C' and resid 769 through 771' Processing helix chain 'C' and resid 772 through 783 Processing helix chain 'C' and resid 784 through 793 Processing helix chain 'C' and resid 809 through 825 removed outlier: 3.571A pdb=" N VAL C 814 " --> pdb=" O SER C 810 " (cutoff:3.500A) Processing helix chain 'C' and resid 827 through 837 Processing helix chain 'C' and resid 840 through 854 Processing helix chain 'C' and resid 862 through 869 removed outlier: 3.544A pdb=" N LEU C 866 " --> pdb=" O ASN C 862 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ARG C 867 " --> pdb=" O LYS C 863 " (cutoff:3.500A) Processing helix chain 'C' and resid 871 through 883 removed outlier: 3.865A pdb=" N PHE C 875 " --> pdb=" O ILE C 871 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LYS C 876 " --> pdb=" O PHE C 872 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N LEU C 881 " --> pdb=" O PHE C 877 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N THR C 882 " --> pdb=" O ILE C 878 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLN C 883 " --> pdb=" O GLY C 879 " (cutoff:3.500A) Processing helix chain 'C' and resid 884 through 895 removed outlier: 3.630A pdb=" N HIS C 889 " --> pdb=" O LYS C 885 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ILE C 890 " --> pdb=" O ASN C 886 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU C 891 " --> pdb=" O GLY C 887 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ARG C 893 " --> pdb=" O HIS C 889 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N TRP C 894 " --> pdb=" O ILE C 890 " (cutoff:3.500A) Processing helix chain 'C' and resid 896 through 903 removed outlier: 4.159A pdb=" N ILE C 900 " --> pdb=" O PHE C 896 " (cutoff:3.500A) Processing helix chain 'C' and resid 908 through 917 removed outlier: 3.628A pdb=" N LEU C 912 " --> pdb=" O SER C 908 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU C 916 " --> pdb=" O LEU C 912 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU C 917 " --> pdb=" O GLU C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 928 through 940 removed outlier: 3.717A pdb=" N VAL C 932 " --> pdb=" O SER C 928 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 962 removed outlier: 3.639A pdb=" N GLU C 948 " --> pdb=" O LYS C 944 " (cutoff:3.500A) Processing helix chain 'C' and resid 968 through 988 Processing helix chain 'C' and resid 989 through 991 No H-bonds generated for 'chain 'C' and resid 989 through 991' Processing helix chain 'C' and resid 993 through 1012 removed outlier: 3.526A pdb=" N VAL C 997 " --> pdb=" O SER C 993 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ASN C1012 " --> pdb=" O ILE C1008 " (cutoff:3.500A) Processing helix chain 'C' and resid 1014 through 1020 removed outlier: 4.071A pdb=" N GLY C1018 " --> pdb=" O SER C1014 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N SER C1020 " --> pdb=" O GLU C1016 " (cutoff:3.500A) Processing helix chain 'C' and resid 1021 through 1023 No H-bonds generated for 'chain 'C' and resid 1021 through 1023' Processing helix chain 'C' and resid 1024 through 1031 Processing helix chain 'C' and resid 1034 through 1041 removed outlier: 3.527A pdb=" N SER C1041 " --> pdb=" O PHE C1037 " (cutoff:3.500A) Processing helix chain 'C' and resid 1042 through 1052 removed outlier: 3.927A pdb=" N GLN C1047 " --> pdb=" O PRO C1043 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU C1048 " --> pdb=" O TYR C1044 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ILE C1052 " --> pdb=" O LEU C1048 " (cutoff:3.500A) Processing helix chain 'C' and resid 1053 through 1065 removed outlier: 3.891A pdb=" N ARG C1059 " --> pdb=" O VAL C1055 " (cutoff:3.500A) Processing helix chain 'C' and resid 1065 through 1081 removed outlier: 3.994A pdb=" N VAL C1071 " --> pdb=" O ASN C1067 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N HIS C1072 " --> pdb=" O ILE C1068 " (cutoff:3.500A) Processing helix chain 'C' and resid 1100 through 1106 removed outlier: 3.526A pdb=" N SER C1104 " --> pdb=" O HIS C1100 " (cutoff:3.500A) Processing helix chain 'C' and resid 1108 through 1118 removed outlier: 3.554A pdb=" N LEU C1113 " --> pdb=" O GLU C1109 " (cutoff:3.500A) Processing helix chain 'C' and resid 1119 through 1133 Processing helix chain 'C' and resid 1134 through 1138 removed outlier: 4.420A pdb=" N MET C1137 " --> pdb=" O GLY C1134 " (cutoff:3.500A) Processing helix chain 'C' and resid 1142 through 1160 Processing helix chain 'C' and resid 1165 through 1172 removed outlier: 3.664A pdb=" N LEU C1169 " --> pdb=" O GLY C1165 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N TYR C1172 " --> pdb=" O LEU C1168 " (cutoff:3.500A) Processing helix chain 'C' and resid 1173 through 1185 removed outlier: 3.722A pdb=" N ASP C1177 " --> pdb=" O SER C1173 " (cutoff:3.500A) Processing helix chain 'C' and resid 1187 through 1202 Processing helix chain 'C' and resid 1204 through 1214 Processing helix chain 'C' and resid 1234 through 1239 removed outlier: 3.626A pdb=" N PHE C1238 " --> pdb=" O ARG C1234 " (cutoff:3.500A) Processing helix chain 'C' and resid 1339 through 1349 removed outlier: 3.516A pdb=" N ILE C1346 " --> pdb=" O LYS C1342 " (cutoff:3.500A) Processing helix chain 'C' and resid 1350 through 1352 No H-bonds generated for 'chain 'C' and resid 1350 through 1352' Processing helix chain 'C' and resid 1355 through 1371 removed outlier: 3.757A pdb=" N LYS C1361 " --> pdb=" O ASN C1357 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASN C1368 " --> pdb=" O THR C1364 " (cutoff:3.500A) Processing helix chain 'C' and resid 1371 through 1376 removed outlier: 3.513A pdb=" N PHE C1375 " --> pdb=" O GLY C1371 " (cutoff:3.500A) Processing helix chain 'C' and resid 1377 through 1392 Processing helix chain 'C' and resid 1394 through 1403 Processing helix chain 'C' and resid 1407 through 1421 removed outlier: 3.547A pdb=" N ASN C1413 " --> pdb=" O ARG C1409 " (cutoff:3.500A) Processing helix chain 'D' and resid 4 through 16 Processing helix chain 'D' and resid 17 through 28 Processing helix chain 'D' and resid 29 through 32 removed outlier: 3.956A pdb=" N LEU D 32 " --> pdb=" O PRO D 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 29 through 32' Processing helix chain 'D' and resid 42 through 50 Processing helix chain 'D' and resid 52 through 63 Processing helix chain 'D' and resid 77 through 86 removed outlier: 3.524A pdb=" N MET D 84 " --> pdb=" O HIS D 80 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N LYS D 85 " --> pdb=" O LEU D 81 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 98 Processing helix chain 'D' and resid 99 through 102 removed outlier: 3.910A pdb=" N ILE D 102 " --> pdb=" O PRO D 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 99 through 102' Processing helix chain 'D' and resid 106 through 110 Processing helix chain 'D' and resid 111 through 120 Processing helix chain 'D' and resid 121 through 132 Processing helix chain 'D' and resid 144 through 153 Processing helix chain 'D' and resid 155 through 162 Processing helix chain 'D' and resid 187 through 198 Processing helix chain 'E' and resid 289 through 299 Processing helix chain 'E' and resid 299 through 307 Processing helix chain 'E' and resid 308 through 310 No H-bonds generated for 'chain 'E' and resid 308 through 310' Processing helix chain 'E' and resid 311 through 331 Processing helix chain 'E' and resid 332 through 335 Processing helix chain 'E' and resid 338 through 342 removed outlier: 3.841A pdb=" N LEU E 342 " --> pdb=" O ILE E 339 " (cutoff:3.500A) Processing helix chain 'E' and resid 345 through 362 Processing helix chain 'E' and resid 369 through 393 removed outlier: 3.731A pdb=" N ILE E 373 " --> pdb=" O GLY E 369 " (cutoff:3.500A) Processing helix chain 'E' and resid 404 through 420 Processing helix chain 'E' and resid 420 through 428 removed outlier: 3.537A pdb=" N ALA E 426 " --> pdb=" O TYR E 422 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL E 427 " --> pdb=" O ASP E 423 " (cutoff:3.500A) Processing helix chain 'E' and resid 428 through 435 Processing helix chain 'E' and resid 459 through 472 removed outlier: 3.517A pdb=" N LEU E 465 " --> pdb=" O GLY E 461 " (cutoff:3.500A) Processing helix chain 'E' and resid 472 through 478 removed outlier: 3.545A pdb=" N CYS E 476 " --> pdb=" O ILE E 472 " (cutoff:3.500A) Processing helix chain 'E' and resid 488 through 499 removed outlier: 3.587A pdb=" N GLU E 499 " --> pdb=" O ILE E 495 " (cutoff:3.500A) Processing helix chain 'E' and resid 505 through 520 Processing helix chain 'E' and resid 526 through 543 Processing helix chain 'G' and resid 2 through 18 Processing helix chain 'G' and resid 20 through 28 Processing helix chain 'G' and resid 44 through 51 Processing helix chain 'G' and resid 638 through 644 Processing helix chain 'G' and resid 1153 through 1175 Processing helix chain 'H' and resid 1276 through 1288 Processing sheet with id=AA1, first strand: chain 'A' and resid 1646 through 1649 Processing sheet with id=AA2, first strand: chain 'A' and resid 2060 through 2062 removed outlier: 6.956A pdb=" N VAL A2100 " --> pdb=" O CYS A2114 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N CYS A2114 " --> pdb=" O VAL A2100 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 2060 through 2062 removed outlier: 6.956A pdb=" N VAL A2100 " --> pdb=" O CYS A2114 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N CYS A2114 " --> pdb=" O VAL A2100 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N SER A2175 " --> pdb=" O LEU A2171 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 2184 through 2186 Processing sheet with id=AA5, first strand: chain 'B' and resid 24 through 29 removed outlier: 3.948A pdb=" N ARG B 26 " --> pdb=" O PHE B 16 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N LEU B 5 " --> pdb=" O TRP B 17 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 38 through 40 Processing sheet with id=AA7, first strand: chain 'B' and resid 78 through 83 removed outlier: 3.687A pdb=" N SER B 80 " --> pdb=" O SER B 93 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 119 through 124 removed outlier: 3.673A pdb=" N GLU B 121 " --> pdb=" O CYS B 134 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N ILE B 140 " --> pdb=" O GLN B 153 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N GLN B 153 " --> pdb=" O ILE B 140 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N ILE B 142 " --> pdb=" O THR B 151 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 164 through 167 removed outlier: 3.601A pdb=" N THR B 201 " --> pdb=" O VAL B 185 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N GLU B 187 " --> pdb=" O PRO B 199 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 210 through 215 removed outlier: 4.284A pdb=" N THR B 230 " --> pdb=" O SER B 226 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N ALA B 231 " --> pdb=" O THR B 245 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N THR B 245 " --> pdb=" O ALA B 231 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N VAL B 233 " --> pdb=" O GLU B 243 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 253 through 258 removed outlier: 6.618A pdb=" N ALA B 268 " --> pdb=" O TRP B 254 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N CYS B 256 " --> pdb=" O VAL B 266 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N VAL B 266 " --> pdb=" O CYS B 256 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N SER B 269 " --> pdb=" O TYR B 273 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N TYR B 273 " --> pdb=" O SER B 269 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ARG B 286 " --> pdb=" O LEU B 276 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 1216 through 1220 removed outlier: 5.022A pdb=" N ILE C1229 " --> pdb=" O CYS C1219 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 1112 through 1115 removed outlier: 3.630A pdb=" N LYS G1112 " --> pdb=" O ILE G1096 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N HIS G1067 " --> pdb=" O ILE G1089 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N HIS G1131 " --> pdb=" O LYS G1124 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N LYS G1124 " --> pdb=" O HIS G1131 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N LYS G1133 " --> pdb=" O VAL G1122 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N VAL G1122 " --> pdb=" O LYS G1133 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N PHE G1135 " --> pdb=" O VAL G1120 " (cutoff:3.500A) 2008 hydrogen bonds defined for protein. 5913 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: 8.00 Time building geometry restraints manager: 4.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 11061 1.34 - 1.46: 7495 1.46 - 1.58: 15982 1.58 - 1.69: 6 1.69 - 1.81: 279 Bond restraints: 34823 Sorted by residual: bond pdb=" N PHE A 142 " pdb=" CA PHE A 142 " ideal model delta sigma weight residual 1.459 1.490 -0.031 1.21e-02 6.83e+03 6.51e+00 bond pdb=" N HIS A 140 " pdb=" CA HIS A 140 " ideal model delta sigma weight residual 1.457 1.488 -0.031 1.33e-02 5.65e+03 5.37e+00 bond pdb=" N SER A 144 " pdb=" CA SER A 144 " ideal model delta sigma weight residual 1.459 1.487 -0.028 1.23e-02 6.61e+03 5.21e+00 bond pdb=" N SER A 145 " pdb=" CA SER A 145 " ideal model delta sigma weight residual 1.459 1.485 -0.026 1.23e-02 6.61e+03 4.55e+00 bond pdb=" N THR A 143 " pdb=" CA THR A 143 " ideal model delta sigma weight residual 1.456 1.481 -0.024 1.28e-02 6.10e+03 3.60e+00 ... (remaining 34818 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.27: 46397 1.27 - 2.53: 517 2.53 - 3.80: 129 3.80 - 5.07: 29 5.07 - 6.33: 26 Bond angle restraints: 47098 Sorted by residual: angle pdb=" N HIS A 140 " pdb=" CA HIS A 140 " pdb=" C HIS A 140 " ideal model delta sigma weight residual 112.89 108.84 4.05 1.24e+00 6.50e-01 1.07e+01 angle pdb=" C THR G 627 " pdb=" N THR G 628 " pdb=" CA THR G 628 " ideal model delta sigma weight residual 121.54 127.09 -5.55 1.91e+00 2.74e-01 8.44e+00 angle pdb=" CA THR A 143 " pdb=" CB THR A 143 " pdb=" OG1 THR A 143 " ideal model delta sigma weight residual 109.60 105.35 4.25 1.50e+00 4.44e-01 8.02e+00 angle pdb=" N VAL C 512 " pdb=" CA VAL C 512 " pdb=" C VAL C 512 " ideal model delta sigma weight residual 112.98 109.56 3.42 1.25e+00 6.40e-01 7.51e+00 angle pdb=" C VAL A 836 " pdb=" N VAL A 837 " pdb=" CA VAL A 837 " ideal model delta sigma weight residual 121.97 126.85 -4.88 1.80e+00 3.09e-01 7.35e+00 ... (remaining 47093 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.56: 18522 17.56 - 35.12: 2232 35.12 - 52.68: 347 52.68 - 70.24: 63 70.24 - 87.80: 20 Dihedral angle restraints: 21184 sinusoidal: 8728 harmonic: 12456 Sorted by residual: dihedral pdb=" CA ASP D 134 " pdb=" CB ASP D 134 " pdb=" CG ASP D 134 " pdb=" OD1 ASP D 134 " ideal model delta sinusoidal sigma weight residual -30.00 -89.70 59.70 1 2.00e+01 2.50e-03 1.19e+01 dihedral pdb=" CA ASP C 392 " pdb=" CB ASP C 392 " pdb=" CG ASP C 392 " pdb=" OD1 ASP C 392 " ideal model delta sinusoidal sigma weight residual -30.00 -89.46 59.46 1 2.00e+01 2.50e-03 1.18e+01 dihedral pdb=" CA ASP A 652 " pdb=" CB ASP A 652 " pdb=" CG ASP A 652 " pdb=" OD1 ASP A 652 " ideal model delta sinusoidal sigma weight residual -30.00 -88.42 58.42 1 2.00e+01 2.50e-03 1.14e+01 ... (remaining 21181 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 3359 0.028 - 0.056: 1330 0.056 - 0.084: 472 0.084 - 0.113: 185 0.113 - 0.141: 37 Chirality restraints: 5383 Sorted by residual: chirality pdb=" CA VAL A2080 " pdb=" N VAL A2080 " pdb=" C VAL A2080 " pdb=" CB VAL A2080 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.94e-01 chirality pdb=" CB ILE B 109 " pdb=" CA ILE B 109 " pdb=" CG1 ILE B 109 " pdb=" CG2 ILE B 109 " both_signs ideal model delta sigma weight residual False 2.64 2.51 0.13 2.00e-01 2.50e+01 4.37e-01 chirality pdb=" CA ILE B 14 " pdb=" N ILE B 14 " pdb=" C ILE B 14 " pdb=" CB ILE B 14 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.32e-01 ... (remaining 5380 not shown) Planarity restraints: 5944 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A2172 " -0.031 5.00e-02 4.00e+02 4.71e-02 3.55e+00 pdb=" N PRO A2173 " 0.081 5.00e-02 4.00e+02 pdb=" CA PRO A2173 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A2173 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A1013 " -0.031 5.00e-02 4.00e+02 4.67e-02 3.49e+00 pdb=" N PRO A1014 " 0.081 5.00e-02 4.00e+02 pdb=" CA PRO A1014 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO A1014 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 838 " -0.030 5.00e-02 4.00e+02 4.51e-02 3.26e+00 pdb=" N PRO A 839 " 0.078 5.00e-02 4.00e+02 pdb=" CA PRO A 839 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 839 " -0.025 5.00e-02 4.00e+02 ... (remaining 5941 not shown) Histogram of nonbonded interaction distances: 2.58 - 3.05: 19501 3.05 - 3.51: 35150 3.51 - 3.97: 54606 3.97 - 4.44: 64762 4.44 - 4.90: 99704 Nonbonded interactions: 273723 Sorted by model distance: nonbonded pdb=" O LYS A 94 " pdb=" OG SER A 145 " model vdw 2.582 3.040 nonbonded pdb=" N VAL C 512 " pdb=" N SER C 513 " model vdw 2.615 2.560 nonbonded pdb=" N ILE C1052 " pdb=" N ASN C1053 " model vdw 2.617 2.560 nonbonded pdb=" N SER A2172 " pdb=" O SER A2172 " model vdw 2.621 2.496 nonbonded pdb=" N GLY B 248 " pdb=" N HIS B 249 " model vdw 2.626 2.560 ... (remaining 273718 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 13.280 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: 0.030 Extract box with map and model: 0.660 Check model and map are aligned: 0.110 Set scattering table: 0.090 Process input model: 33.600 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 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 : 0.002 0.039 34823 Z= 0.098 Angle : 0.408 6.331 47098 Z= 0.220 Chirality : 0.037 0.141 5383 Planarity : 0.003 0.047 5944 Dihedral : 14.722 87.798 13066 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.97 % Favored : 98.01 % Rotamer: Outliers : 0.16 % Allowed : 3.27 % Favored : 96.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.12), residues: 4165 helix: -0.10 (0.09), residues: 2729 sheet: -0.31 (0.35), residues: 223 loop : -0.39 (0.18), residues: 1213 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1623 TYR 0.008 0.001 TYR C 655 PHE 0.012 0.001 PHE B 83 TRP 0.019 0.001 TRP A1229 HIS 0.004 0.000 HIS B 272 Details of bonding type rmsd/Z covalent geometry : bond 0.00201 / 0.10 (34823) covalent geometry : angle 0.40834 / 0.22 (47098) hydrogen bonds : bond 0.23473 / 15.78 ( 2004) hydrogen bonds : angle 6.78803 / 4.95 ( 5913) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8330 Ramachandran restraints generated. 4165 Oldfield, 0 Emsley, 4165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8330 Ramachandran restraints generated. 4165 Oldfield, 0 Emsley, 4165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1195 residues out of total 3824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 1189 time to evaluate : 1.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 324 ASP cc_start: 0.7109 (m-30) cc_final: 0.6717 (m-30) REVERT: A 508 ILE cc_start: 0.7376 (mt) cc_final: 0.7140 (mt) REVERT: A 557 PHE cc_start: 0.6604 (t80) cc_final: 0.6345 (t80) REVERT: A 594 VAL cc_start: 0.9152 (m) cc_final: 0.8932 (p) REVERT: A 647 MET cc_start: 0.7577 (ttm) cc_final: 0.7361 (tmm) REVERT: A 684 MET cc_start: 0.8626 (mtt) cc_final: 0.8242 (mmp) REVERT: A 763 ASP cc_start: 0.8544 (m-30) cc_final: 0.8179 (m-30) REVERT: A 794 GLU cc_start: 0.8479 (mt-10) cc_final: 0.8202 (mt-10) REVERT: A 808 ASN cc_start: 0.8259 (m-40) cc_final: 0.8009 (m-40) REVERT: A 832 SER cc_start: 0.8653 (m) cc_final: 0.8432 (p) REVERT: A 852 ASN cc_start: 0.8491 (m-40) cc_final: 0.8283 (m-40) REVERT: A 902 ASP cc_start: 0.8413 (m-30) cc_final: 0.8025 (t0) REVERT: A 947 MET cc_start: 0.8058 (tpt) cc_final: 0.7463 (tmm) REVERT: A 951 GLN cc_start: 0.8640 (mm110) cc_final: 0.8410 (mm110) REVERT: A 1065 ARG cc_start: 0.8366 (tpt170) cc_final: 0.7803 (tpt170) REVERT: A 1068 LYS cc_start: 0.8454 (tttp) cc_final: 0.8183 (ttpp) REVERT: A 1140 LYS cc_start: 0.8601 (mttt) cc_final: 0.8327 (tmtt) REVERT: A 1166 LYS cc_start: 0.8370 (mtmt) cc_final: 0.8140 (mmtt) REVERT: A 1179 ASP cc_start: 0.8491 (m-30) cc_final: 0.7631 (m-30) REVERT: A 1184 LYS cc_start: 0.8426 (mttt) cc_final: 0.8099 (mttp) REVERT: A 1250 GLN cc_start: 0.8495 (tp-100) cc_final: 0.7279 (tp-100) REVERT: A 1254 GLU cc_start: 0.8042 (mm-30) cc_final: 0.7439 (mm-30) REVERT: A 1301 LEU cc_start: 0.9010 (mt) cc_final: 0.8807 (mt) REVERT: A 1328 ASP cc_start: 0.8630 (t0) cc_final: 0.8069 (t0) REVERT: A 1336 ILE cc_start: 0.8612 (pt) cc_final: 0.8378 (mt) REVERT: A 1341 LYS cc_start: 0.8748 (tttt) cc_final: 0.8538 (tttt) REVERT: A 1357 GLU cc_start: 0.8221 (mt-10) cc_final: 0.8018 (mt-10) REVERT: A 1406 GLU cc_start: 0.7211 (tt0) cc_final: 0.6735 (tt0) REVERT: A 1432 MET cc_start: 0.7583 (ttp) cc_final: 0.6626 (ttp) REVERT: A 1437 ARG cc_start: 0.8070 (mtm-85) cc_final: 0.7817 (mtm110) REVERT: A 1451 LEU cc_start: 0.9079 (tp) cc_final: 0.8766 (tp) REVERT: A 1514 LYS cc_start: 0.8484 (tttt) cc_final: 0.8083 (tttp) REVERT: A 1605 LYS cc_start: 0.9127 (mttt) cc_final: 0.8906 (mttm) REVERT: A 1650 SER cc_start: 0.9049 (t) cc_final: 0.8668 (m) REVERT: A 1676 ASN cc_start: 0.8377 (t0) cc_final: 0.8041 (t0) REVERT: A 1691 ASN cc_start: 0.7717 (t0) cc_final: 0.7458 (t0) REVERT: A 1734 ARG cc_start: 0.8289 (ptt-90) cc_final: 0.7296 (ptp-170) REVERT: A 1818 HIS cc_start: 0.7607 (m90) cc_final: 0.7323 (m90) REVERT: A 1826 LYS cc_start: 0.8799 (mttt) cc_final: 0.8540 (mttp) REVERT: A 1864 HIS cc_start: 0.8352 (m90) cc_final: 0.7927 (m-70) REVERT: A 1903 ASP cc_start: 0.7655 (m-30) cc_final: 0.7419 (m-30) REVERT: A 1944 VAL cc_start: 0.8596 (t) cc_final: 0.8362 (p) REVERT: A 1972 ASP cc_start: 0.8697 (t0) cc_final: 0.8492 (t0) REVERT: A 2112 LYS cc_start: 0.8836 (tttt) cc_final: 0.8507 (tttm) REVERT: A 2124 LYS cc_start: 0.8664 (mttt) cc_final: 0.8235 (mtpp) REVERT: A 2131 GLU cc_start: 0.7809 (tt0) cc_final: 0.7529 (mt-10) REVERT: A 2136 ASP cc_start: 0.8298 (m-30) cc_final: 0.8076 (m-30) REVERT: A 2183 ASN cc_start: 0.8263 (m-40) cc_final: 0.8062 (m-40) REVERT: A 2185 ASP cc_start: 0.8223 (m-30) cc_final: 0.7952 (p0) REVERT: A 2211 GLN cc_start: 0.8130 (tt0) cc_final: 0.7865 (tm-30) REVERT: A 2216 TYR cc_start: 0.8292 (t80) cc_final: 0.7870 (t80) REVERT: A 2268 MET cc_start: 0.8737 (tpt) cc_final: 0.8487 (tpp) REVERT: A 2439 ARG cc_start: 0.8044 (ttm170) cc_final: 0.7724 (mtm110) REVERT: A 2440 ARG cc_start: 0.8277 (ptp90) cc_final: 0.8039 (ptp90) REVERT: A 2444 LEU cc_start: 0.8812 (mt) cc_final: 0.8561 (mt) REVERT: B 151 THR cc_start: 0.6019 (p) cc_final: 0.5801 (p) REVERT: B 162 LEU cc_start: 0.6993 (mt) cc_final: 0.6558 (tt) REVERT: B 203 PHE cc_start: 0.5960 (p90) cc_final: 0.5473 (p90) REVERT: B 265 LEU cc_start: 0.6240 (tp) cc_final: 0.6014 (tp) REVERT: C 351 MET cc_start: 0.8075 (mmm) cc_final: 0.7853 (mmm) REVERT: C 356 ASN cc_start: 0.9064 (m110) cc_final: 0.8770 (m-40) REVERT: C 357 LEU cc_start: 0.8722 (mt) cc_final: 0.8228 (mt) REVERT: C 403 ASN cc_start: 0.8314 (m-40) cc_final: 0.8108 (m-40) REVERT: C 440 LYS cc_start: 0.8458 (tttt) cc_final: 0.8212 (tttt) REVERT: C 465 LYS cc_start: 0.8727 (tttt) cc_final: 0.8435 (tttm) REVERT: C 497 MET cc_start: 0.8562 (mmt) cc_final: 0.7145 (mmm) REVERT: C 512 VAL cc_start: 0.9017 (m) cc_final: 0.8806 (p) REVERT: C 631 GLU cc_start: 0.8203 (mt-10) cc_final: 0.7920 (mm-30) REVERT: C 642 GLU cc_start: 0.8042 (mm-30) cc_final: 0.7650 (mm-30) REVERT: C 666 ASN cc_start: 0.8140 (m110) cc_final: 0.7866 (m110) REVERT: C 716 GLN cc_start: 0.8370 (tp40) cc_final: 0.8160 (tp-100) REVERT: C 721 PHE cc_start: 0.8498 (t80) cc_final: 0.8115 (t80) REVERT: C 725 ILE cc_start: 0.8213 (mt) cc_final: 0.7833 (mt) REVERT: C 742 MET cc_start: 0.8024 (mtm) cc_final: 0.7610 (mtt) REVERT: C 831 MET cc_start: 0.7509 (tpt) cc_final: 0.7300 (tpt) REVERT: C 848 MET cc_start: 0.8358 (mtp) cc_final: 0.7186 (mmt) REVERT: C 864 ASN cc_start: 0.9091 (m-40) cc_final: 0.8644 (t0) REVERT: C 894 TRP cc_start: 0.5481 (m100) cc_final: 0.5168 (m100) REVERT: C 904 PHE cc_start: 0.6925 (m-80) cc_final: 0.6602 (m-80) REVERT: C 923 ASP cc_start: 0.7792 (t0) cc_final: 0.7269 (t70) REVERT: C 948 GLU cc_start: 0.8027 (mm-30) cc_final: 0.7719 (tm-30) REVERT: C 952 HIS cc_start: 0.7430 (t70) cc_final: 0.7172 (t70) REVERT: C 958 LYS cc_start: 0.8961 (mtmt) cc_final: 0.8702 (mtmm) REVERT: C 980 PHE cc_start: 0.8195 (t80) cc_final: 0.7435 (t80) REVERT: C 991 ASP cc_start: 0.7703 (t70) cc_final: 0.7347 (t70) REVERT: C 1006 GLU cc_start: 0.8796 (mt-10) cc_final: 0.8343 (mm-30) REVERT: C 1038 GLU cc_start: 0.8316 (tm-30) cc_final: 0.7915 (tp30) REVERT: C 1059 ARG cc_start: 0.8139 (ttt-90) cc_final: 0.7910 (ttt-90) REVERT: C 1080 LYS cc_start: 0.8933 (tttt) cc_final: 0.8677 (tttm) REVERT: C 1096 ARG cc_start: 0.8213 (ptm160) cc_final: 0.7928 (ptm160) REVERT: C 1118 THR cc_start: 0.8736 (p) cc_final: 0.8442 (p) REVERT: C 1122 VAL cc_start: 0.8110 (t) cc_final: 0.7901 (p) REVERT: C 1125 MET cc_start: 0.7975 (ttp) cc_final: 0.7754 (ttp) REVERT: C 1342 LYS cc_start: 0.8550 (mmtt) cc_final: 0.8151 (mtmt) REVERT: C 1346 ILE cc_start: 0.9030 (mt) cc_final: 0.8601 (tp) REVERT: C 1364 THR cc_start: 0.8666 (t) cc_final: 0.8465 (t) REVERT: C 1377 ASN cc_start: 0.7657 (t0) cc_final: 0.7427 (t0) REVERT: C 1383 LYS cc_start: 0.7159 (mttt) cc_final: 0.6635 (mtmm) REVERT: C 1387 MET cc_start: 0.7868 (mtp) cc_final: 0.7155 (mmp) REVERT: D 24 LEU cc_start: 0.7298 (mt) cc_final: 0.6611 (mt) REVERT: D 34 ASN cc_start: 0.8509 (t0) cc_final: 0.8286 (t0) REVERT: D 65 ASP cc_start: 0.7773 (m-30) cc_final: 0.7567 (m-30) REVERT: D 71 LYS cc_start: 0.8495 (mtmt) cc_final: 0.8286 (mtmt) REVERT: D 96 GLN cc_start: 0.8591 (tm-30) cc_final: 0.8272 (tm-30) REVERT: D 107 GLU cc_start: 0.7749 (tt0) cc_final: 0.7488 (tt0) REVERT: D 110 ARG cc_start: 0.8113 (mtt180) cc_final: 0.7595 (ttm110) REVERT: D 119 ASN cc_start: 0.8691 (m-40) cc_final: 0.8478 (m-40) REVERT: D 121 TYR cc_start: 0.8011 (m-10) cc_final: 0.7688 (m-10) REVERT: D 125 LEU cc_start: 0.8148 (tp) cc_final: 0.7830 (mt) REVERT: D 136 TRP cc_start: 0.7256 (m-90) cc_final: 0.7014 (m-90) REVERT: D 160 MET cc_start: 0.8081 (mmm) cc_final: 0.7244 (mpp) REVERT: D 178 ASN cc_start: 0.6711 (t0) cc_final: 0.6392 (t0) REVERT: E 296 LEU cc_start: 0.8086 (tp) cc_final: 0.7843 (pp) REVERT: E 415 ILE cc_start: 0.8293 (mt) cc_final: 0.8062 (mm) REVERT: E 493 LEU cc_start: 0.8403 (mt) cc_final: 0.7836 (mm) REVERT: E 510 LEU cc_start: 0.8529 (mt) cc_final: 0.8318 (mt) REVERT: E 529 GLN cc_start: 0.7020 (tp40) cc_final: 0.6577 (mm110) REVERT: E 532 ILE cc_start: 0.8180 (mm) cc_final: 0.7896 (tp) REVERT: E 533 GLU cc_start: 0.7995 (mt-10) cc_final: 0.7485 (mt-10) REVERT: G 21 LYS cc_start: 0.7854 (mmtm) cc_final: 0.7391 (mmmt) REVERT: G 24 MET cc_start: 0.7479 (mtm) cc_final: 0.7175 (mtp) REVERT: G 25 LYS cc_start: 0.8123 (mttt) cc_final: 0.7832 (mttt) REVERT: G 28 ILE cc_start: 0.8872 (mt) cc_final: 0.8630 (mm) REVERT: G 1072 TRP cc_start: 0.8017 (m-90) cc_final: 0.7432 (m-90) REVERT: G 1074 ARG cc_start: 0.8065 (ttp80) cc_final: 0.7359 (ttp80) REVERT: G 1083 HIS cc_start: 0.8181 (m90) cc_final: 0.7770 (m-70) REVERT: G 1094 ILE cc_start: 0.8276 (mt) cc_final: 0.8056 (mt) REVERT: G 1114 LEU cc_start: 0.8614 (mt) cc_final: 0.8383 (mt) REVERT: G 1123 LYS cc_start: 0.7871 (tttt) cc_final: 0.7592 (tttt) REVERT: G 1156 GLU cc_start: 0.8616 (mt-10) cc_final: 0.8261 (mt-10) REVERT: G 1159 GLU cc_start: 0.8974 (tt0) cc_final: 0.8761 (tt0) REVERT: G 1165 GLN cc_start: 0.8923 (mt0) cc_final: 0.8529 (mt0) REVERT: G 1166 ASN cc_start: 0.9047 (m-40) cc_final: 0.8824 (m-40) REVERT: G 1172 ARG cc_start: 0.9103 (mtt180) cc_final: 0.8884 (ttm110) REVERT: H 1256 MET cc_start: 0.7678 (mmt) cc_final: 0.7003 (mmt) REVERT: H 1282 LYS cc_start: 0.8062 (mtpt) cc_final: 0.7817 (mtpt) outliers start: 6 outliers final: 3 residues processed: 1193 average time/residue: 0.2426 time to fit residues: 455.0064 Evaluate side-chains 968 residues out of total 3824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 965 time to evaluate : 1.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 1961 VAL Chi-restraints excluded: chain G residue 628 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 419 random chunks: chunk 197 optimal weight: 0.9990 chunk 388 optimal weight: 0.7980 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 0.0030 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 1.9990 chunk 401 optimal weight: 3.9990 chunk 155 optimal weight: 0.0070 chunk 244 optimal weight: 5.9990 overall best weight: 0.5410 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 308 GLN A 403 ASN A 410 ASN A 687 ASN A1001 HIS A1344 GLN A1480 GLN A1510 ASN A1539 ASN A1766 ASN A1928 GLN A2036 ASN A2351 ASN B 30 HIS B 85 GLN B 148 ASN ** B 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 569 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 804 ASN C 855 ASN ** C 979 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1117 GLN C1345 HIS G 23 GLN G1076 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.148156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.117272 restraints weight = 73627.961| |-----------------------------------------------------------------------------| r_work (start): 0.3684 rms_B_bonded: 2.85 r_work: 0.3546 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.2482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 34823 Z= 0.149 Angle : 0.581 9.152 47098 Z= 0.306 Chirality : 0.041 0.196 5383 Planarity : 0.004 0.053 5944 Dihedral : 4.279 75.769 4603 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.35 % Favored : 97.62 % Rotamer: Outliers : 2.17 % Allowed : 12.22 % Favored : 85.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.05 (0.13), residues: 4165 helix: 1.23 (0.10), residues: 2740 sheet: -0.20 (0.35), residues: 233 loop : -0.21 (0.19), residues: 1192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 448 TYR 0.030 0.001 TYR E 386 PHE 0.025 0.001 PHE C 323 TRP 0.018 0.001 TRP D 41 HIS 0.008 0.001 HIS C 338 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.15 (34823) covalent geometry : angle 0.58147 / 0.31 (47098) hydrogen bonds : bond 0.05253 / 3.49 ( 2004) hydrogen bonds : angle 4.47356 / 3.27 ( 5913) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8330 Ramachandran restraints generated. 4165 Oldfield, 0 Emsley, 4165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8330 Ramachandran restraints generated. 4165 Oldfield, 0 Emsley, 4165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1089 residues out of total 3824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 1006 time to evaluate : 1.438 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 324 ASP cc_start: 0.7379 (m-30) cc_final: 0.6876 (m-30) REVERT: A 349 ASP cc_start: 0.8484 (OUTLIER) cc_final: 0.8159 (m-30) REVERT: A 394 MET cc_start: 0.8219 (mmm) cc_final: 0.7934 (mmm) REVERT: A 414 LYS cc_start: 0.7930 (tttt) cc_final: 0.7576 (ttpp) REVERT: A 442 ASN cc_start: 0.7461 (m-40) cc_final: 0.7103 (m-40) REVERT: A 456 GLN cc_start: 0.5485 (pm20) cc_final: 0.5169 (pm20) REVERT: A 507 LYS cc_start: 0.8306 (mmmm) cc_final: 0.8084 (mmmt) REVERT: A 555 GLN cc_start: 0.7180 (pp30) cc_final: 0.6519 (tp-100) REVERT: A 563 GLU cc_start: 0.6970 (mt-10) cc_final: 0.6103 (tm-30) REVERT: A 581 LEU cc_start: 0.8291 (OUTLIER) cc_final: 0.8090 (tt) REVERT: A 759 ASP cc_start: 0.8624 (t0) cc_final: 0.8181 (t0) REVERT: A 794 GLU cc_start: 0.8345 (mt-10) cc_final: 0.8119 (mt-10) REVERT: A 803 MET cc_start: 0.8866 (mmm) cc_final: 0.8624 (tpp) REVERT: A 820 ASP cc_start: 0.8395 (t70) cc_final: 0.8180 (t0) REVERT: A 880 LYS cc_start: 0.8786 (mttt) cc_final: 0.8450 (ptpp) REVERT: A 973 ARG cc_start: 0.7650 (mtp85) cc_final: 0.7428 (mtp85) REVERT: A 1068 LYS cc_start: 0.8513 (tttp) cc_final: 0.8257 (ttpp) REVERT: A 1142 THR cc_start: 0.8320 (m) cc_final: 0.8040 (p) REVERT: A 1179 ASP cc_start: 0.8502 (m-30) cc_final: 0.7965 (m-30) REVERT: A 1184 LYS cc_start: 0.8525 (mttt) cc_final: 0.8002 (mtmm) REVERT: A 1243 TRP cc_start: 0.8338 (t60) cc_final: 0.7904 (t60) REVERT: A 1245 ARG cc_start: 0.8020 (mtt-85) cc_final: 0.7716 (mtt90) REVERT: A 1250 GLN cc_start: 0.8379 (tp-100) cc_final: 0.7040 (tp-100) REVERT: A 1254 GLU cc_start: 0.8135 (mm-30) cc_final: 0.7077 (mm-30) REVERT: A 1275 ARG cc_start: 0.8242 (ttp-110) cc_final: 0.7949 (ttp-110) REVERT: A 1328 ASP cc_start: 0.8655 (t0) cc_final: 0.8113 (t0) REVERT: A 1377 ASN cc_start: 0.8496 (m-40) cc_final: 0.8249 (m-40) REVERT: A 1390 LYS cc_start: 0.8616 (tttm) cc_final: 0.8135 (tptm) REVERT: A 1393 GLN cc_start: 0.7619 (mp10) cc_final: 0.6956 (mp10) REVERT: A 1406 GLU cc_start: 0.7267 (tt0) cc_final: 0.6925 (tt0) REVERT: A 1455 LYS cc_start: 0.8945 (mttt) cc_final: 0.8629 (mttp) REVERT: A 1480 GLN cc_start: 0.8315 (OUTLIER) cc_final: 0.7665 (mp10) REVERT: A 1514 LYS cc_start: 0.8534 (tttt) cc_final: 0.8252 (tttp) REVERT: A 1555 GLU cc_start: 0.8230 (mt-10) cc_final: 0.8019 (mt-10) REVERT: A 1605 LYS cc_start: 0.9095 (mttt) cc_final: 0.8893 (mttm) REVERT: A 1734 ARG cc_start: 0.8339 (ptt-90) cc_final: 0.7790 (ptp-170) REVERT: A 1768 GLU cc_start: 0.8499 (tt0) cc_final: 0.8294 (tp30) REVERT: A 1818 HIS cc_start: 0.7525 (m90) cc_final: 0.7297 (m90) REVERT: A 1826 LYS cc_start: 0.8881 (mttt) cc_final: 0.8661 (mttp) REVERT: A 1864 HIS cc_start: 0.8165 (m90) cc_final: 0.7749 (m-70) REVERT: A 1903 ASP cc_start: 0.7901 (m-30) cc_final: 0.7690 (m-30) REVERT: A 1925 LEU cc_start: 0.8284 (mt) cc_final: 0.7344 (mp) REVERT: A 1929 LYS cc_start: 0.8175 (mttt) cc_final: 0.7949 (mttt) REVERT: A 1944 VAL cc_start: 0.8739 (t) cc_final: 0.8521 (p) REVERT: A 1985 GLU cc_start: 0.7867 (tp30) cc_final: 0.7639 (tp30) REVERT: A 2023 GLU cc_start: 0.7897 (tm-30) cc_final: 0.7571 (tm-30) REVERT: A 2095 SER cc_start: 0.8598 (t) cc_final: 0.8215 (p) REVERT: A 2098 GLU cc_start: 0.8418 (mm-30) cc_final: 0.8196 (mm-30) REVERT: A 2121 LYS cc_start: 0.8701 (mttt) cc_final: 0.8303 (mttt) REVERT: A 2124 LYS cc_start: 0.8645 (mttt) cc_final: 0.8432 (mtpp) REVERT: A 2131 GLU cc_start: 0.7898 (tt0) cc_final: 0.7679 (mt-10) REVERT: A 2157 PHE cc_start: 0.8685 (t80) cc_final: 0.8368 (t80) REVERT: A 2218 ASN cc_start: 0.8318 (m-40) cc_final: 0.7990 (t0) REVERT: A 2418 ARG cc_start: 0.7697 (ttp-170) cc_final: 0.7339 (ttp-170) REVERT: A 2440 ARG cc_start: 0.8364 (ptp90) cc_final: 0.8124 (ptp90) REVERT: A 2444 LEU cc_start: 0.8808 (mt) cc_final: 0.8572 (mt) REVERT: B 44 LYS cc_start: 0.8067 (mmtp) cc_final: 0.7542 (mmtp) REVERT: B 112 ASN cc_start: 0.8176 (p0) cc_final: 0.7949 (p0) REVERT: B 149 GLN cc_start: 0.8800 (mt0) cc_final: 0.8520 (mp10) REVERT: B 162 LEU cc_start: 0.7270 (mt) cc_final: 0.6527 (tt) REVERT: B 232 ARG cc_start: 0.6844 (mtt180) cc_final: 0.6527 (mtm-85) REVERT: B 242 LEU cc_start: 0.7712 (OUTLIER) cc_final: 0.7211 (tp) REVERT: B 258 PHE cc_start: 0.7055 (m-10) cc_final: 0.6757 (m-10) REVERT: B 265 LEU cc_start: 0.6831 (tp) cc_final: 0.6627 (tp) REVERT: C 351 MET cc_start: 0.7982 (mmm) cc_final: 0.7760 (mmm) REVERT: C 356 ASN cc_start: 0.8926 (m110) cc_final: 0.8613 (m-40) REVERT: C 397 ILE cc_start: 0.8460 (mt) cc_final: 0.8249 (mp) REVERT: C 462 GLU cc_start: 0.8160 (tt0) cc_final: 0.7865 (tt0) REVERT: C 465 LYS cc_start: 0.8629 (tttt) cc_final: 0.8306 (tttm) REVERT: C 497 MET cc_start: 0.8707 (mmt) cc_final: 0.7125 (mmm) REVERT: C 512 VAL cc_start: 0.8994 (m) cc_final: 0.8744 (p) REVERT: C 532 LYS cc_start: 0.8227 (ttpt) cc_final: 0.7881 (ttpp) REVERT: C 642 GLU cc_start: 0.8233 (mm-30) cc_final: 0.7824 (mm-30) REVERT: C 689 GLU cc_start: 0.8291 (tt0) cc_final: 0.7866 (tt0) REVERT: C 759 TRP cc_start: 0.6532 (m-10) cc_final: 0.5933 (m-10) REVERT: C 813 TYR cc_start: 0.7808 (OUTLIER) cc_final: 0.7300 (m-10) REVERT: C 864 ASN cc_start: 0.8961 (m-40) cc_final: 0.8653 (t0) REVERT: C 875 PHE cc_start: 0.8862 (m-80) cc_final: 0.8550 (m-80) REVERT: C 893 ARG cc_start: 0.8182 (ptm-80) cc_final: 0.7827 (ptm-80) REVERT: C 894 TRP cc_start: 0.5575 (m100) cc_final: 0.4520 (m100) REVERT: C 923 ASP cc_start: 0.7742 (t0) cc_final: 0.7104 (t70) REVERT: C 931 ARG cc_start: 0.8283 (mtm180) cc_final: 0.7962 (mtm180) REVERT: C 980 PHE cc_start: 0.8425 (t80) cc_final: 0.8037 (t80) REVERT: C 1006 GLU cc_start: 0.8896 (mt-10) cc_final: 0.8434 (mm-30) REVERT: C 1009 VAL cc_start: 0.8887 (p) cc_final: 0.8650 (t) REVERT: C 1024 PHE cc_start: 0.7742 (m-80) cc_final: 0.6339 (m-80) REVERT: C 1080 LYS cc_start: 0.8874 (tttt) cc_final: 0.8547 (tttp) REVERT: C 1342 LYS cc_start: 0.8255 (mmtt) cc_final: 0.8047 (mtmt) REVERT: C 1349 GLN cc_start: 0.8209 (mt0) cc_final: 0.7916 (mt0) REVERT: C 1364 THR cc_start: 0.8707 (t) cc_final: 0.8460 (t) REVERT: C 1383 LYS cc_start: 0.6971 (mttt) cc_final: 0.6455 (mtmm) REVERT: C 1387 MET cc_start: 0.7769 (mtp) cc_final: 0.7231 (mmp) REVERT: D 96 GLN cc_start: 0.8511 (tm-30) cc_final: 0.8128 (tm-30) REVERT: D 110 ARG cc_start: 0.7956 (mtt180) cc_final: 0.7573 (ttm110) REVERT: D 119 ASN cc_start: 0.8670 (m-40) cc_final: 0.8410 (t0) REVERT: D 125 LEU cc_start: 0.8127 (tp) cc_final: 0.7901 (mt) REVERT: D 136 TRP cc_start: 0.7455 (m-90) cc_final: 0.7208 (m-90) REVERT: D 160 MET cc_start: 0.8174 (mmm) cc_final: 0.7642 (mpp) REVERT: D 178 ASN cc_start: 0.7174 (t0) cc_final: 0.6825 (t0) REVERT: E 329 ASN cc_start: 0.8478 (m-40) cc_final: 0.8269 (m-40) REVERT: E 354 GLU cc_start: 0.8615 (pt0) cc_final: 0.8106 (pp20) REVERT: E 407 LYS cc_start: 0.8095 (ptpp) cc_final: 0.7854 (ptpp) REVERT: E 415 ILE cc_start: 0.8501 (mt) cc_final: 0.8107 (mm) REVERT: E 424 LEU cc_start: 0.7700 (mt) cc_final: 0.7443 (tt) REVERT: E 493 LEU cc_start: 0.8481 (mt) cc_final: 0.8180 (mm) REVERT: E 510 LEU cc_start: 0.8367 (mt) cc_final: 0.8034 (mm) REVERT: E 518 ILE cc_start: 0.8181 (mt) cc_final: 0.7923 (mt) REVERT: E 529 GLN cc_start: 0.7137 (tp40) cc_final: 0.6749 (mm110) REVERT: E 532 ILE cc_start: 0.8617 (mm) cc_final: 0.8307 (tp) REVERT: E 533 GLU cc_start: 0.8307 (mt-10) cc_final: 0.7737 (mt-10) REVERT: G 7 LEU cc_start: 0.7941 (mp) cc_final: 0.7258 (mt) REVERT: G 21 LYS cc_start: 0.7853 (mmtm) cc_final: 0.7186 (mmmt) REVERT: G 24 MET cc_start: 0.7487 (mtm) cc_final: 0.7017 (mtm) REVERT: G 25 LYS cc_start: 0.8241 (mttt) cc_final: 0.7911 (mttt) REVERT: G 52 MET cc_start: 0.7295 (ttp) cc_final: 0.6572 (tmm) REVERT: G 626 LYS cc_start: 0.7920 (ttpp) cc_final: 0.7513 (ttpp) REVERT: G 1068 LYS cc_start: 0.8404 (OUTLIER) cc_final: 0.8043 (ptmm) REVERT: G 1072 TRP cc_start: 0.8233 (m-90) cc_final: 0.7772 (m-90) REVERT: G 1073 ARG cc_start: 0.7590 (ttt180) cc_final: 0.7310 (ttt-90) REVERT: G 1074 ARG cc_start: 0.8239 (ttp80) cc_final: 0.7703 (ttp-170) REVERT: G 1083 HIS cc_start: 0.8182 (m90) cc_final: 0.7801 (m-70) REVERT: G 1123 LYS cc_start: 0.7878 (tttt) cc_final: 0.7637 (tttt) REVERT: G 1124 LYS cc_start: 0.7558 (ttmm) cc_final: 0.7235 (ttmm) REVERT: G 1156 GLU cc_start: 0.8436 (mt-10) cc_final: 0.8151 (mt-10) REVERT: G 1159 GLU cc_start: 0.8722 (tt0) cc_final: 0.8482 (tt0) REVERT: G 1165 GLN cc_start: 0.9007 (mt0) cc_final: 0.8633 (mt0) REVERT: G 1166 ASN cc_start: 0.9007 (m-40) cc_final: 0.8783 (m-40) REVERT: H 1256 MET cc_start: 0.7636 (mmt) cc_final: 0.7434 (tpp) REVERT: H 1282 LYS cc_start: 0.8301 (mtpt) cc_final: 0.8021 (mtpt) outliers start: 83 outliers final: 38 residues processed: 1039 average time/residue: 0.2397 time to fit residues: 389.9894 Evaluate side-chains 991 residues out of total 3824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 947 time to evaluate : 1.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 349 ASP Chi-restraints excluded: chain A residue 435 TYR Chi-restraints excluded: chain A residue 457 PHE Chi-restraints excluded: chain A residue 479 HIS Chi-restraints excluded: chain A residue 503 ILE Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 635 LEU Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain A residue 905 LEU Chi-restraints excluded: chain A residue 1030 SER Chi-restraints excluded: chain A residue 1100 LYS Chi-restraints excluded: chain A residue 1185 LEU Chi-restraints excluded: chain A residue 1191 LEU Chi-restraints excluded: chain A residue 1290 GLN Chi-restraints excluded: chain A residue 1302 CYS Chi-restraints excluded: chain A residue 1314 ILE Chi-restraints excluded: chain A residue 1334 ILE Chi-restraints excluded: chain A residue 1480 GLN Chi-restraints excluded: chain A residue 1922 SER Chi-restraints excluded: chain A residue 1961 VAL Chi-restraints excluded: chain A residue 1973 ASP Chi-restraints excluded: chain A residue 1975 SER Chi-restraints excluded: chain A residue 2025 LEU Chi-restraints excluded: chain B residue 14 ILE Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain C residue 384 ASP Chi-restraints excluded: chain C residue 727 GLU Chi-restraints excluded: chain C residue 813 TYR Chi-restraints excluded: chain C residue 903 MET Chi-restraints excluded: chain C residue 928 SER Chi-restraints excluded: chain C residue 995 SER Chi-restraints excluded: chain C residue 1063 LEU Chi-restraints excluded: chain C residue 1345 HIS Chi-restraints excluded: chain D residue 11 GLU Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain E residue 393 VAL Chi-restraints excluded: chain E residue 466 MET Chi-restraints excluded: chain G residue 628 THR Chi-restraints excluded: chain G residue 1067 HIS Chi-restraints excluded: chain G residue 1068 LYS Chi-restraints excluded: chain G residue 1069 TYR Chi-restraints excluded: chain G residue 1126 LYS Chi-restraints excluded: chain G residue 1174 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 419 random chunks: chunk 313 optimal weight: 5.9990 chunk 171 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 349 optimal weight: 0.0980 chunk 12 optimal weight: 10.0000 chunk 260 optimal weight: 1.9990 chunk 363 optimal weight: 2.9990 chunk 302 optimal weight: 6.9990 chunk 328 optimal weight: 0.9990 chunk 309 optimal weight: 5.9990 chunk 18 optimal weight: 0.5980 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 481 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 554 ASN A 672 GLN A 687 ASN A1174 GLN A1480 GLN A1539 ASN A1982 HIS A2036 ASN A2064 GLN A2065 HIS A2194 HIS B 287 GLN C 569 GLN C 716 GLN C1117 GLN ** E 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 523 GLN G 23 GLN G 639 GLN G 642 ASN G1115 HIS G1174 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.145769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.114806 restraints weight = 73173.435| |-----------------------------------------------------------------------------| r_work (start): 0.3659 rms_B_bonded: 2.80 r_work: 0.3521 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.3160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 34823 Z= 0.215 Angle : 0.602 14.596 47098 Z= 0.312 Chirality : 0.043 0.285 5383 Planarity : 0.004 0.071 5944 Dihedral : 4.398 73.187 4602 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.69 % Favored : 97.26 % Rotamer: Outliers : 2.90 % Allowed : 14.81 % Favored : 82.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.16 (0.13), residues: 4165 helix: 1.34 (0.10), residues: 2760 sheet: 0.01 (0.36), residues: 224 loop : -0.28 (0.19), residues: 1181 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 444 TYR 0.046 0.002 TYR E 386 PHE 0.050 0.002 PHE E 496 TRP 0.016 0.002 TRP A1229 HIS 0.006 0.001 HIS A 636 Details of bonding type rmsd/Z covalent geometry : bond 0.00496 / 0.21 (34823) covalent geometry : angle 0.60248 / 0.31 (47098) hydrogen bonds : bond 0.04821 / 3.20 ( 2004) hydrogen bonds : angle 4.36250 / 3.17 ( 5913) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8330 Ramachandran restraints generated. 4165 Oldfield, 0 Emsley, 4165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8330 Ramachandran restraints generated. 4165 Oldfield, 0 Emsley, 4165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1117 residues out of total 3824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 1006 time to evaluate : 1.325 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 324 ASP cc_start: 0.7379 (m-30) cc_final: 0.6895 (m-30) REVERT: A 349 ASP cc_start: 0.8391 (OUTLIER) cc_final: 0.7946 (p0) REVERT: A 394 MET cc_start: 0.8113 (mmm) cc_final: 0.7823 (tmm) REVERT: A 414 LYS cc_start: 0.7948 (tttt) cc_final: 0.7500 (ttpp) REVERT: A 442 ASN cc_start: 0.7425 (m-40) cc_final: 0.7158 (m-40) REVERT: A 444 ARG cc_start: 0.8475 (ttp80) cc_final: 0.8053 (ttp80) REVERT: A 502 MET cc_start: 0.6916 (tmm) cc_final: 0.6192 (tmm) REVERT: A 548 LYS cc_start: 0.8555 (tttt) cc_final: 0.8265 (tptt) REVERT: A 555 GLN cc_start: 0.7124 (pp30) cc_final: 0.6431 (tp-100) REVERT: A 737 GLU cc_start: 0.7168 (mm-30) cc_final: 0.6931 (mm-30) REVERT: A 797 ARG cc_start: 0.8698 (ttp-110) cc_final: 0.8454 (ttp-110) REVERT: A 808 ASN cc_start: 0.8291 (m-40) cc_final: 0.8047 (m-40) REVERT: A 820 ASP cc_start: 0.8486 (t70) cc_final: 0.8227 (t0) REVERT: A 879 TYR cc_start: 0.8509 (t80) cc_final: 0.7942 (t80) REVERT: A 973 ARG cc_start: 0.7646 (mtp85) cc_final: 0.7390 (mtp85) REVERT: A 1068 LYS cc_start: 0.8491 (tttp) cc_final: 0.8221 (ttpp) REVERT: A 1143 MET cc_start: 0.8091 (mmm) cc_final: 0.7591 (mmt) REVERT: A 1179 ASP cc_start: 0.8540 (m-30) cc_final: 0.8090 (m-30) REVERT: A 1184 LYS cc_start: 0.8487 (mttt) cc_final: 0.7961 (mtmm) REVERT: A 1237 LYS cc_start: 0.8481 (tttt) cc_final: 0.8249 (tttt) REVERT: A 1245 ARG cc_start: 0.7987 (mtt-85) cc_final: 0.7730 (mtt90) REVERT: A 1250 GLN cc_start: 0.8414 (tp-100) cc_final: 0.7024 (tp-100) REVERT: A 1253 LYS cc_start: 0.8838 (mttt) cc_final: 0.8401 (mttm) REVERT: A 1254 GLU cc_start: 0.8176 (mm-30) cc_final: 0.7196 (mm-30) REVERT: A 1275 ARG cc_start: 0.8421 (ttp-110) cc_final: 0.8136 (ttp-110) REVERT: A 1328 ASP cc_start: 0.8737 (t0) cc_final: 0.8222 (t0) REVERT: A 1377 ASN cc_start: 0.8504 (m-40) cc_final: 0.8273 (m-40) REVERT: A 1390 LYS cc_start: 0.8641 (tttm) cc_final: 0.7992 (tptm) REVERT: A 1393 GLN cc_start: 0.7559 (mp10) cc_final: 0.6857 (mp10) REVERT: A 1406 GLU cc_start: 0.7239 (tt0) cc_final: 0.6974 (tt0) REVERT: A 1455 LYS cc_start: 0.8895 (mttt) cc_final: 0.8597 (mttp) REVERT: A 1465 LYS cc_start: 0.8761 (mttt) cc_final: 0.8490 (mttm) REVERT: A 1480 GLN cc_start: 0.8483 (mt0) cc_final: 0.8247 (mp10) REVERT: A 1484 ILE cc_start: 0.8823 (mt) cc_final: 0.8546 (tt) REVERT: A 1734 ARG cc_start: 0.8343 (ptt-90) cc_final: 0.7949 (ptp-170) REVERT: A 1864 HIS cc_start: 0.8205 (m90) cc_final: 0.7661 (m-70) REVERT: A 1925 LEU cc_start: 0.8357 (mt) cc_final: 0.8156 (mt) REVERT: A 1959 MET cc_start: 0.8631 (mtp) cc_final: 0.8350 (mtp) REVERT: A 1976 ARG cc_start: 0.8414 (tpp80) cc_final: 0.8097 (tpp80) REVERT: A 2023 GLU cc_start: 0.7964 (tm-30) cc_final: 0.7538 (tm-30) REVERT: A 2121 LYS cc_start: 0.8734 (mttt) cc_final: 0.8351 (mttt) REVERT: A 2218 ASN cc_start: 0.8324 (m-40) cc_final: 0.7920 (t0) REVERT: A 2253 THR cc_start: 0.8861 (OUTLIER) cc_final: 0.8589 (p) REVERT: A 2440 ARG cc_start: 0.8415 (ptp90) cc_final: 0.8184 (ptp90) REVERT: A 2444 LEU cc_start: 0.8932 (mt) cc_final: 0.8709 (mt) REVERT: B 26 ARG cc_start: 0.6495 (tpp80) cc_final: 0.6249 (tpp80) REVERT: B 44 LYS cc_start: 0.8394 (mmtp) cc_final: 0.8084 (mmtp) REVERT: B 242 LEU cc_start: 0.7670 (OUTLIER) cc_final: 0.7134 (tt) REVERT: B 275 ARG cc_start: 0.7120 (mpp80) cc_final: 0.6597 (mtt180) REVERT: B 286 ARG cc_start: 0.8409 (mmm160) cc_final: 0.7840 (mmm-85) REVERT: C 351 MET cc_start: 0.7969 (mmm) cc_final: 0.7716 (mmm) REVERT: C 356 ASN cc_start: 0.9010 (m110) cc_final: 0.8594 (m-40) REVERT: C 373 CYS cc_start: 0.8740 (t) cc_final: 0.8309 (t) REVERT: C 388 GLU cc_start: 0.8223 (tp30) cc_final: 0.7885 (tm-30) REVERT: C 397 ILE cc_start: 0.8618 (mt) cc_final: 0.8389 (mp) REVERT: C 440 LYS cc_start: 0.8465 (tttt) cc_final: 0.8209 (tttt) REVERT: C 462 GLU cc_start: 0.8405 (tt0) cc_final: 0.8141 (tt0) REVERT: C 465 LYS cc_start: 0.8717 (tttt) cc_final: 0.8370 (tttm) REVERT: C 497 MET cc_start: 0.8816 (mmt) cc_final: 0.7006 (mmm) REVERT: C 512 VAL cc_start: 0.9082 (m) cc_final: 0.8804 (p) REVERT: C 532 LYS cc_start: 0.8393 (ttpt) cc_final: 0.8019 (ttpp) REVERT: C 642 GLU cc_start: 0.8254 (mm-30) cc_final: 0.7862 (mm-30) REVERT: C 689 GLU cc_start: 0.8343 (tt0) cc_final: 0.7962 (tt0) REVERT: C 709 MET cc_start: 0.8541 (mtp) cc_final: 0.8205 (mtp) REVERT: C 713 ASP cc_start: 0.7914 (m-30) cc_final: 0.7443 (t70) REVERT: C 742 MET cc_start: 0.8046 (mtm) cc_final: 0.7740 (mtm) REVERT: C 759 TRP cc_start: 0.6623 (m-10) cc_final: 0.5896 (m-10) REVERT: C 813 TYR cc_start: 0.7956 (OUTLIER) cc_final: 0.7449 (m-10) REVERT: C 864 ASN cc_start: 0.8970 (m-40) cc_final: 0.8644 (t0) REVERT: C 875 PHE cc_start: 0.8883 (m-80) cc_final: 0.8531 (m-80) REVERT: C 893 ARG cc_start: 0.8271 (ptm-80) cc_final: 0.7759 (ptm-80) REVERT: C 923 ASP cc_start: 0.7848 (t0) cc_final: 0.7230 (t70) REVERT: C 1006 GLU cc_start: 0.8937 (mt-10) cc_final: 0.8358 (mm-30) REVERT: C 1080 LYS cc_start: 0.8921 (tttt) cc_final: 0.8644 (tttm) REVERT: C 1096 ARG cc_start: 0.7955 (ptm160) cc_final: 0.7611 (ptm160) REVERT: C 1103 GLU cc_start: 0.7779 (tt0) cc_final: 0.7250 (tt0) REVERT: C 1142 ASN cc_start: 0.8032 (t0) cc_final: 0.7657 (t0) REVERT: C 1342 LYS cc_start: 0.8439 (mmtt) cc_final: 0.8080 (mtmt) REVERT: C 1349 GLN cc_start: 0.8343 (mt0) cc_final: 0.8041 (mt0) REVERT: C 1364 THR cc_start: 0.8727 (t) cc_final: 0.8501 (t) REVERT: C 1383 LYS cc_start: 0.7056 (mttt) cc_final: 0.6761 (mtmm) REVERT: D 65 ASP cc_start: 0.7848 (m-30) cc_final: 0.7645 (m-30) REVERT: D 85 LYS cc_start: 0.8803 (mtmt) cc_final: 0.8599 (mtpt) REVERT: D 96 GLN cc_start: 0.8562 (tm-30) cc_final: 0.8156 (tm-30) REVERT: D 110 ARG cc_start: 0.8005 (mtt180) cc_final: 0.7664 (ttm110) REVERT: D 136 TRP cc_start: 0.7530 (m-90) cc_final: 0.7220 (m-90) REVERT: D 148 VAL cc_start: 0.7990 (OUTLIER) cc_final: 0.7693 (p) REVERT: D 160 MET cc_start: 0.8242 (mmm) cc_final: 0.7780 (mpp) REVERT: D 178 ASN cc_start: 0.7198 (t0) cc_final: 0.6826 (t0) REVERT: E 326 PHE cc_start: 0.7429 (t80) cc_final: 0.7184 (t80) REVERT: E 354 GLU cc_start: 0.8614 (OUTLIER) cc_final: 0.8026 (pp20) REVERT: E 407 LYS cc_start: 0.8056 (ptpp) cc_final: 0.7665 (ptpp) REVERT: E 493 LEU cc_start: 0.8574 (mt) cc_final: 0.8313 (mm) REVERT: E 510 LEU cc_start: 0.8429 (mt) cc_final: 0.8095 (mm) REVERT: E 519 LEU cc_start: 0.8427 (mt) cc_final: 0.7993 (pp) REVERT: E 529 GLN cc_start: 0.7187 (tp40) cc_final: 0.6767 (mm-40) REVERT: E 530 ARG cc_start: 0.8573 (ptp-170) cc_final: 0.8167 (ptp-170) REVERT: E 533 GLU cc_start: 0.8322 (mt-10) cc_final: 0.7823 (mt-10) REVERT: G 7 LEU cc_start: 0.7961 (mp) cc_final: 0.7546 (mt) REVERT: G 9 GLU cc_start: 0.7997 (mt-10) cc_final: 0.7553 (mt-10) REVERT: G 21 LYS cc_start: 0.7987 (mmtm) cc_final: 0.7353 (mmmt) REVERT: G 24 MET cc_start: 0.7655 (mtm) cc_final: 0.7338 (mtm) REVERT: G 25 LYS cc_start: 0.8398 (mttt) cc_final: 0.8063 (mttt) REVERT: G 52 MET cc_start: 0.7365 (ttp) cc_final: 0.6597 (tmm) REVERT: G 626 LYS cc_start: 0.7961 (ttpp) cc_final: 0.7553 (ttpp) REVERT: G 634 LYS cc_start: 0.5810 (ttpp) cc_final: 0.5243 (tptp) REVERT: G 638 SER cc_start: 0.7630 (p) cc_final: 0.7391 (p) REVERT: G 643 MET cc_start: 0.7654 (mtt) cc_final: 0.7412 (ptp) REVERT: G 1068 LYS cc_start: 0.8562 (OUTLIER) cc_final: 0.8207 (ptmm) REVERT: G 1073 ARG cc_start: 0.7776 (ttt180) cc_final: 0.7417 (ttt-90) REVERT: G 1074 ARG cc_start: 0.8288 (ttp80) cc_final: 0.7801 (ttp-170) REVERT: G 1083 HIS cc_start: 0.8408 (m90) cc_final: 0.7995 (m-70) REVERT: G 1123 LYS cc_start: 0.7861 (tttt) cc_final: 0.7591 (tttt) REVERT: G 1148 TYR cc_start: 0.7951 (m-80) cc_final: 0.7304 (m-80) REVERT: G 1156 GLU cc_start: 0.8434 (mt-10) cc_final: 0.8148 (mt-10) REVERT: G 1165 GLN cc_start: 0.8985 (mt0) cc_final: 0.8595 (mt0) REVERT: G 1166 ASN cc_start: 0.8996 (m-40) cc_final: 0.8794 (m-40) REVERT: H 1282 LYS cc_start: 0.8340 (mtpt) cc_final: 0.8042 (mtpt) REVERT: H 1283 GLU cc_start: 0.8166 (tp30) cc_final: 0.7820 (mp0) outliers start: 111 outliers final: 61 residues processed: 1045 average time/residue: 0.2482 time to fit residues: 402.9087 Evaluate side-chains 1035 residues out of total 3824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 967 time to evaluate : 1.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 349 ASP Chi-restraints excluded: chain A residue 389 TYR Chi-restraints excluded: chain A residue 435 TYR Chi-restraints excluded: chain A residue 457 PHE Chi-restraints excluded: chain A residue 479 HIS Chi-restraints excluded: chain A residue 503 ILE Chi-restraints excluded: chain A residue 546 ILE Chi-restraints excluded: chain A residue 589 SER Chi-restraints excluded: chain A residue 624 ASP Chi-restraints excluded: chain A residue 635 LEU Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain A residue 721 LEU Chi-restraints excluded: chain A residue 746 LEU Chi-restraints excluded: chain A residue 854 LEU Chi-restraints excluded: chain A residue 905 LEU Chi-restraints excluded: chain A residue 962 ASP Chi-restraints excluded: chain A residue 1030 SER Chi-restraints excluded: chain A residue 1100 LYS Chi-restraints excluded: chain A residue 1171 ASN Chi-restraints excluded: chain A residue 1191 LEU Chi-restraints excluded: chain A residue 1290 GLN Chi-restraints excluded: chain A residue 1314 ILE Chi-restraints excluded: chain A residue 1517 VAL Chi-restraints excluded: chain A residue 1544 VAL Chi-restraints excluded: chain A residue 1816 LEU Chi-restraints excluded: chain A residue 1922 SER Chi-restraints excluded: chain A residue 1961 VAL Chi-restraints excluded: chain A residue 1973 ASP Chi-restraints excluded: chain A residue 1975 SER Chi-restraints excluded: chain A residue 2025 LEU Chi-restraints excluded: chain A residue 2160 HIS Chi-restraints excluded: chain A residue 2253 THR Chi-restraints excluded: chain A residue 2331 SER Chi-restraints excluded: chain B residue 14 ILE Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 269 SER Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain C residue 384 ASP Chi-restraints excluded: chain C residue 482 SER Chi-restraints excluded: chain C residue 712 ILE Chi-restraints excluded: chain C residue 725 ILE Chi-restraints excluded: chain C residue 727 GLU Chi-restraints excluded: chain C residue 813 TYR Chi-restraints excluded: chain C residue 924 LEU Chi-restraints excluded: chain C residue 995 SER Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1345 HIS Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 113 ILE Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain E residue 354 GLU Chi-restraints excluded: chain E residue 382 VAL Chi-restraints excluded: chain E residue 466 MET Chi-restraints excluded: chain E residue 474 LEU Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain G residue 57 VAL Chi-restraints excluded: chain G residue 628 THR Chi-restraints excluded: chain G residue 1067 HIS Chi-restraints excluded: chain G residue 1068 LYS Chi-restraints excluded: chain G residue 1069 TYR Chi-restraints excluded: chain G residue 1110 LYS Chi-restraints excluded: chain G residue 1120 VAL Chi-restraints excluded: chain G residue 1126 LYS Chi-restraints excluded: chain G residue 1174 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 419 random chunks: chunk 323 optimal weight: 5.9990 chunk 100 optimal weight: 0.2980 chunk 32 optimal weight: 0.9980 chunk 108 optimal weight: 3.9990 chunk 194 optimal weight: 0.5980 chunk 142 optimal weight: 0.9980 chunk 317 optimal weight: 6.9990 chunk 183 optimal weight: 4.9990 chunk 89 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 481 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 687 ASN A1174 GLN A1180 GLN ** A1691 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 87 ASN B 287 GLN C 666 ASN ** C 952 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1117 GLN ** D 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 299 ASN ** E 391 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 498 GLN G 23 GLN ** G1067 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.146745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.116279 restraints weight = 73205.062| |-----------------------------------------------------------------------------| r_work (start): 0.3666 rms_B_bonded: 2.81 r_work: 0.3531 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.3544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 34823 Z= 0.150 Angle : 0.572 13.679 47098 Z= 0.294 Chirality : 0.041 0.259 5383 Planarity : 0.004 0.086 5944 Dihedral : 4.393 71.966 4602 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.64 % Favored : 97.31 % Rotamer: Outliers : 2.72 % Allowed : 16.32 % Favored : 80.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.35 (0.13), residues: 4165 helix: 1.51 (0.10), residues: 2754 sheet: 0.09 (0.36), residues: 215 loop : -0.29 (0.19), residues: 1196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 664 TYR 0.052 0.001 TYR E 386 PHE 0.026 0.001 PHE E 468 TRP 0.015 0.001 TRP A1229 HIS 0.012 0.001 HIS C 952 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.15 (34823) covalent geometry : angle 0.57152 / 0.29 (47098) hydrogen bonds : bond 0.04131 / 2.76 ( 2004) hydrogen bonds : angle 4.18368 / 3.04 ( 5913) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8330 Ramachandran restraints generated. 4165 Oldfield, 0 Emsley, 4165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8330 Ramachandran restraints generated. 4165 Oldfield, 0 Emsley, 4165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1095 residues out of total 3824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 991 time to evaluate : 1.467 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 324 ASP cc_start: 0.7310 (m-30) cc_final: 0.6802 (m-30) REVERT: A 394 MET cc_start: 0.8159 (mmm) cc_final: 0.7848 (tmm) REVERT: A 414 LYS cc_start: 0.7938 (tttt) cc_final: 0.7557 (ttpt) REVERT: A 442 ASN cc_start: 0.7374 (m-40) cc_final: 0.7060 (m-40) REVERT: A 444 ARG cc_start: 0.8414 (ttp80) cc_final: 0.8160 (ttp80) REVERT: A 507 LYS cc_start: 0.8360 (mmmm) cc_final: 0.7983 (mmmm) REVERT: A 512 GLU cc_start: 0.8048 (pm20) cc_final: 0.7672 (pm20) REVERT: A 548 LYS cc_start: 0.8546 (tttt) cc_final: 0.8227 (tptt) REVERT: A 555 GLN cc_start: 0.7102 (pp30) cc_final: 0.6383 (tp-100) REVERT: A 670 ASP cc_start: 0.7617 (m-30) cc_final: 0.7339 (t0) REVERT: A 672 GLN cc_start: 0.7982 (mp10) cc_final: 0.7610 (mt0) REVERT: A 708 ASN cc_start: 0.8536 (t0) cc_final: 0.8179 (t0) REVERT: A 737 GLU cc_start: 0.7195 (mm-30) cc_final: 0.6935 (mm-30) REVERT: A 763 ASP cc_start: 0.7865 (m-30) cc_final: 0.7656 (m-30) REVERT: A 804 PRO cc_start: 0.8006 (Cg_exo) cc_final: 0.7658 (Cg_endo) REVERT: A 808 ASN cc_start: 0.8264 (m-40) cc_final: 0.8025 (m-40) REVERT: A 820 ASP cc_start: 0.8384 (t70) cc_final: 0.8129 (t0) REVERT: A 846 LEU cc_start: 0.8441 (tp) cc_final: 0.8197 (tt) REVERT: A 880 LYS cc_start: 0.8879 (mtmm) cc_final: 0.8677 (ptpp) REVERT: A 973 ARG cc_start: 0.7620 (mtp85) cc_final: 0.7410 (mtp85) REVERT: A 1068 LYS cc_start: 0.8494 (tttp) cc_final: 0.8178 (ttmm) REVERT: A 1179 ASP cc_start: 0.8504 (m-30) cc_final: 0.8043 (m-30) REVERT: A 1222 GLN cc_start: 0.7775 (pm20) cc_final: 0.7468 (pm20) REVERT: A 1237 LYS cc_start: 0.8332 (tttt) cc_final: 0.8071 (tttt) REVERT: A 1245 ARG cc_start: 0.7945 (mtt-85) cc_final: 0.7673 (mtt90) REVERT: A 1250 GLN cc_start: 0.8396 (tp-100) cc_final: 0.7866 (tp-100) REVERT: A 1275 ARG cc_start: 0.8429 (ttp-110) cc_final: 0.8133 (ttp-110) REVERT: A 1328 ASP cc_start: 0.8726 (t0) cc_final: 0.8204 (t0) REVERT: A 1377 ASN cc_start: 0.8452 (m-40) cc_final: 0.8204 (m-40) REVERT: A 1390 LYS cc_start: 0.8615 (tttm) cc_final: 0.8045 (tptm) REVERT: A 1393 GLN cc_start: 0.7557 (mp10) cc_final: 0.6966 (mp10) REVERT: A 1406 GLU cc_start: 0.7247 (tt0) cc_final: 0.6937 (tt0) REVERT: A 1465 LYS cc_start: 0.8712 (mttt) cc_final: 0.8450 (mttm) REVERT: A 1480 GLN cc_start: 0.8437 (mt0) cc_final: 0.8214 (mp10) REVERT: A 1484 ILE cc_start: 0.8794 (mt) cc_final: 0.8521 (tt) REVERT: A 1513 LYS cc_start: 0.8769 (mttt) cc_final: 0.8488 (mmmm) REVERT: A 1514 LYS cc_start: 0.8425 (tttt) cc_final: 0.8023 (ttpp) REVERT: A 1609 GLN cc_start: 0.8684 (tp-100) cc_final: 0.8335 (tp40) REVERT: A 1734 ARG cc_start: 0.8301 (ptt-90) cc_final: 0.7987 (ptp-170) REVERT: A 1766 ASN cc_start: 0.8521 (m110) cc_final: 0.8035 (m-40) REVERT: A 1818 HIS cc_start: 0.7693 (m90) cc_final: 0.7420 (m90) REVERT: A 1864 HIS cc_start: 0.8284 (m90) cc_final: 0.7722 (m-70) REVERT: A 1917 MET cc_start: 0.8251 (mtm) cc_final: 0.8039 (mtt) REVERT: A 1925 LEU cc_start: 0.8267 (mt) cc_final: 0.8018 (mt) REVERT: A 1929 LYS cc_start: 0.8156 (mttt) cc_final: 0.7955 (mtmt) REVERT: A 1959 MET cc_start: 0.8599 (mtp) cc_final: 0.8315 (mtp) REVERT: A 1996 GLU cc_start: 0.8092 (mt-10) cc_final: 0.7745 (mt-10) REVERT: A 2023 GLU cc_start: 0.8018 (tm-30) cc_final: 0.7550 (tm-30) REVERT: A 2121 LYS cc_start: 0.8729 (mttt) cc_final: 0.8355 (mttt) REVERT: A 2124 LYS cc_start: 0.8691 (mttt) cc_final: 0.8487 (mtmt) REVERT: A 2218 ASN cc_start: 0.8324 (m-40) cc_final: 0.7961 (t0) REVERT: A 2253 THR cc_start: 0.8756 (OUTLIER) cc_final: 0.8542 (p) REVERT: A 2418 ARG cc_start: 0.7644 (ttp-170) cc_final: 0.7299 (ttp-170) REVERT: A 2440 ARG cc_start: 0.8389 (ptp90) cc_final: 0.8167 (ptp90) REVERT: A 2444 LEU cc_start: 0.8911 (mt) cc_final: 0.8637 (mt) REVERT: B 182 ASN cc_start: 0.6874 (t0) cc_final: 0.6436 (t0) REVERT: B 206 HIS cc_start: 0.6750 (m90) cc_final: 0.6305 (m90) REVERT: B 232 ARG cc_start: 0.6965 (ttm170) cc_final: 0.6307 (ttm-80) REVERT: B 275 ARG cc_start: 0.7068 (mpp80) cc_final: 0.6592 (mtt180) REVERT: B 286 ARG cc_start: 0.8347 (mmm160) cc_final: 0.7737 (mmm-85) REVERT: C 338 HIS cc_start: 0.7456 (t70) cc_final: 0.7208 (p-80) REVERT: C 339 SER cc_start: 0.8463 (OUTLIER) cc_final: 0.8125 (p) REVERT: C 340 GLU cc_start: 0.8241 (mp0) cc_final: 0.8039 (pm20) REVERT: C 351 MET cc_start: 0.7969 (mmm) cc_final: 0.7707 (mmm) REVERT: C 356 ASN cc_start: 0.9015 (m110) cc_final: 0.8528 (m110) REVERT: C 373 CYS cc_start: 0.8697 (t) cc_final: 0.8324 (t) REVERT: C 388 GLU cc_start: 0.8197 (tp30) cc_final: 0.7833 (tm-30) REVERT: C 421 GLU cc_start: 0.8337 (mt-10) cc_final: 0.8135 (mt-10) REVERT: C 462 GLU cc_start: 0.8436 (tt0) cc_final: 0.8180 (tt0) REVERT: C 465 LYS cc_start: 0.8711 (tttt) cc_final: 0.8350 (tttm) REVERT: C 497 MET cc_start: 0.8839 (mmt) cc_final: 0.7427 (mmt) REVERT: C 512 VAL cc_start: 0.9084 (m) cc_final: 0.8863 (p) REVERT: C 642 GLU cc_start: 0.8243 (mm-30) cc_final: 0.7857 (mm-30) REVERT: C 689 GLU cc_start: 0.8302 (tt0) cc_final: 0.7946 (tt0) REVERT: C 742 MET cc_start: 0.8044 (mtm) cc_final: 0.7678 (mtm) REVERT: C 759 TRP cc_start: 0.6704 (m-10) cc_final: 0.6007 (m-10) REVERT: C 765 LEU cc_start: 0.8321 (tp) cc_final: 0.8083 (mm) REVERT: C 813 TYR cc_start: 0.7914 (OUTLIER) cc_final: 0.7377 (m-10) REVERT: C 848 MET cc_start: 0.8390 (mtp) cc_final: 0.7520 (mmp) REVERT: C 864 ASN cc_start: 0.9017 (m-40) cc_final: 0.8657 (t0) REVERT: C 875 PHE cc_start: 0.8844 (m-80) cc_final: 0.8474 (m-80) REVERT: C 893 ARG cc_start: 0.8356 (ptm-80) cc_final: 0.7868 (ptm-80) REVERT: C 923 ASP cc_start: 0.7903 (t0) cc_final: 0.7224 (t70) REVERT: C 931 ARG cc_start: 0.8264 (mtm180) cc_final: 0.7730 (mtm110) REVERT: C 987 ARG cc_start: 0.7659 (OUTLIER) cc_final: 0.7293 (mmp80) REVERT: C 996 VAL cc_start: 0.7621 (OUTLIER) cc_final: 0.7380 (t) REVERT: C 1006 GLU cc_start: 0.8931 (mt-10) cc_final: 0.8329 (mm-30) REVERT: C 1076 GLU cc_start: 0.8433 (tt0) cc_final: 0.8159 (tt0) REVERT: C 1080 LYS cc_start: 0.8942 (tttt) cc_final: 0.8660 (tttm) REVERT: C 1096 ARG cc_start: 0.7885 (ptm160) cc_final: 0.7510 (ptm160) REVERT: C 1103 GLU cc_start: 0.7815 (tt0) cc_final: 0.7258 (tt0) REVERT: C 1342 LYS cc_start: 0.8415 (mmtt) cc_final: 0.8048 (mtmt) REVERT: C 1349 GLN cc_start: 0.8279 (mt0) cc_final: 0.8032 (mt0) REVERT: C 1364 THR cc_start: 0.8674 (t) cc_final: 0.8424 (t) REVERT: C 1383 LYS cc_start: 0.7061 (mttt) cc_final: 0.6758 (mtmm) REVERT: C 1409 ARG cc_start: 0.8574 (ttm110) cc_final: 0.8303 (mtm110) REVERT: D 96 GLN cc_start: 0.8567 (tm-30) cc_final: 0.8178 (tm-30) REVERT: D 110 ARG cc_start: 0.7973 (mtt180) cc_final: 0.7611 (ttm110) REVERT: D 119 ASN cc_start: 0.8669 (OUTLIER) cc_final: 0.7661 (t0) REVERT: D 148 VAL cc_start: 0.7936 (m) cc_final: 0.7674 (p) REVERT: D 160 MET cc_start: 0.8255 (mmm) cc_final: 0.7714 (mpp) REVERT: D 178 ASN cc_start: 0.7246 (t0) cc_final: 0.6794 (t0) REVERT: E 326 PHE cc_start: 0.7531 (t80) cc_final: 0.7248 (t80) REVERT: E 329 ASN cc_start: 0.8447 (m-40) cc_final: 0.8237 (m-40) REVERT: E 354 GLU cc_start: 0.8583 (OUTLIER) cc_final: 0.8017 (pp20) REVERT: E 407 LYS cc_start: 0.7951 (ptpp) cc_final: 0.7532 (ptpp) REVERT: E 493 LEU cc_start: 0.8586 (mt) cc_final: 0.8379 (mm) REVERT: E 510 LEU cc_start: 0.8425 (mt) cc_final: 0.8168 (mt) REVERT: E 529 GLN cc_start: 0.7152 (tp40) cc_final: 0.6673 (mm-40) REVERT: E 530 ARG cc_start: 0.8545 (ptp-170) cc_final: 0.8295 (ptp-170) REVERT: E 532 ILE cc_start: 0.8778 (mm) cc_final: 0.8302 (tp) REVERT: E 533 GLU cc_start: 0.8349 (mt-10) cc_final: 0.7768 (mt-10) REVERT: G 21 LYS cc_start: 0.8002 (mmtm) cc_final: 0.7320 (mmmt) REVERT: G 24 MET cc_start: 0.7567 (mtm) cc_final: 0.7165 (mtm) REVERT: G 25 LYS cc_start: 0.8389 (mttt) cc_final: 0.8025 (mttt) REVERT: G 52 MET cc_start: 0.7249 (ttp) cc_final: 0.6490 (tmm) REVERT: G 626 LYS cc_start: 0.7904 (ttpp) cc_final: 0.7462 (ttpp) REVERT: G 634 LYS cc_start: 0.5873 (ttpp) cc_final: 0.5192 (tptm) REVERT: G 638 SER cc_start: 0.7478 (p) cc_final: 0.7248 (p) REVERT: G 643 MET cc_start: 0.7698 (mtt) cc_final: 0.7474 (ptp) REVERT: G 1068 LYS cc_start: 0.8531 (OUTLIER) cc_final: 0.8192 (ptmm) REVERT: G 1073 ARG cc_start: 0.7741 (ttt180) cc_final: 0.7422 (ttt-90) REVERT: G 1074 ARG cc_start: 0.8330 (ttp80) cc_final: 0.7820 (ttp-170) REVERT: G 1082 LYS cc_start: 0.8675 (mttt) cc_final: 0.8307 (mttt) REVERT: G 1083 HIS cc_start: 0.8463 (m90) cc_final: 0.8036 (m-70) REVERT: G 1123 LYS cc_start: 0.7863 (tttt) cc_final: 0.7539 (tttt) REVERT: G 1148 TYR cc_start: 0.7951 (m-80) cc_final: 0.7285 (m-80) REVERT: G 1156 GLU cc_start: 0.8486 (mt-10) cc_final: 0.8185 (mt-10) REVERT: G 1159 GLU cc_start: 0.8793 (tt0) cc_final: 0.8468 (tt0) REVERT: G 1163 ARG cc_start: 0.8797 (tpp80) cc_final: 0.8586 (tpp80) REVERT: G 1165 GLN cc_start: 0.8990 (mt0) cc_final: 0.8546 (mt0) REVERT: G 1166 ASN cc_start: 0.9035 (m-40) cc_final: 0.8793 (m-40) REVERT: G 1173 MET cc_start: 0.8697 (mtm) cc_final: 0.8487 (mtm) REVERT: H 1256 MET cc_start: 0.7856 (mpp) cc_final: 0.7574 (tpp) REVERT: H 1282 LYS cc_start: 0.8339 (mtpt) cc_final: 0.8039 (mtpt) REVERT: H 1283 GLU cc_start: 0.8172 (tp30) cc_final: 0.7823 (mp0) outliers start: 104 outliers final: 62 residues processed: 1031 average time/residue: 0.2477 time to fit residues: 398.6232 Evaluate side-chains 1025 residues out of total 3824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 955 time to evaluate : 1.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 389 TYR Chi-restraints excluded: chain A residue 435 TYR Chi-restraints excluded: chain A residue 457 PHE Chi-restraints excluded: chain A residue 479 HIS Chi-restraints excluded: chain A residue 503 ILE Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 563 GLU Chi-restraints excluded: chain A residue 624 ASP Chi-restraints excluded: chain A residue 635 LEU Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain A residue 721 LEU Chi-restraints excluded: chain A residue 905 LEU Chi-restraints excluded: chain A residue 1100 LYS Chi-restraints excluded: chain A residue 1191 LEU Chi-restraints excluded: chain A residue 1290 GLN Chi-restraints excluded: chain A residue 1314 ILE Chi-restraints excluded: chain A residue 1382 THR Chi-restraints excluded: chain A residue 1502 ASP Chi-restraints excluded: chain A residue 1544 VAL Chi-restraints excluded: chain A residue 1816 LEU Chi-restraints excluded: chain A residue 1922 SER Chi-restraints excluded: chain A residue 1944 VAL Chi-restraints excluded: chain A residue 1961 VAL Chi-restraints excluded: chain A residue 1973 ASP Chi-restraints excluded: chain A residue 1975 SER Chi-restraints excluded: chain A residue 2155 GLU Chi-restraints excluded: chain A residue 2253 THR Chi-restraints excluded: chain A residue 2331 SER Chi-restraints excluded: chain B residue 14 ILE Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 287 GLN Chi-restraints excluded: chain C residue 309 ASP Chi-restraints excluded: chain C residue 339 SER Chi-restraints excluded: chain C residue 364 LEU Chi-restraints excluded: chain C residue 384 ASP Chi-restraints excluded: chain C residue 687 VAL Chi-restraints excluded: chain C residue 712 ILE Chi-restraints excluded: chain C residue 725 ILE Chi-restraints excluded: chain C residue 727 GLU Chi-restraints excluded: chain C residue 813 TYR Chi-restraints excluded: chain C residue 825 THR Chi-restraints excluded: chain C residue 891 LEU Chi-restraints excluded: chain C residue 987 ARG Chi-restraints excluded: chain C residue 995 SER Chi-restraints excluded: chain C residue 996 VAL Chi-restraints excluded: chain C residue 1022 ARG Chi-restraints excluded: chain C residue 1024 PHE Chi-restraints excluded: chain C residue 1083 SER Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1345 HIS Chi-restraints excluded: chain D residue 14 ILE Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 119 ASN Chi-restraints excluded: chain E residue 354 GLU Chi-restraints excluded: chain E residue 382 VAL Chi-restraints excluded: chain E residue 419 GLU Chi-restraints excluded: chain E residue 474 LEU Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain G residue 628 THR Chi-restraints excluded: chain G residue 1067 HIS Chi-restraints excluded: chain G residue 1068 LYS Chi-restraints excluded: chain G residue 1096 ILE Chi-restraints excluded: chain G residue 1113 SER Chi-restraints excluded: chain G residue 1120 VAL Chi-restraints excluded: chain G residue 1126 LYS Chi-restraints excluded: chain G residue 1174 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 419 random chunks: chunk 210 optimal weight: 0.9980 chunk 278 optimal weight: 1.9990 chunk 179 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 188 optimal weight: 0.7980 chunk 117 optimal weight: 1.9990 chunk 416 optimal weight: 7.9990 chunk 401 optimal weight: 0.8980 chunk 70 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 301 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 327 HIS A 481 ASN A 687 ASN A1227 ASN A1539 ASN ** A1691 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2419 ASN B 148 ASN B 287 GLN ** C 952 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1100 HIS C1396 HIS ** D 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 498 GLN G 23 GLN G1174 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.145860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.115367 restraints weight = 73205.186| |-----------------------------------------------------------------------------| r_work (start): 0.3657 rms_B_bonded: 2.80 r_work: 0.3516 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.3783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 34823 Z= 0.190 Angle : 0.591 13.044 47098 Z= 0.304 Chirality : 0.042 0.254 5383 Planarity : 0.004 0.072 5944 Dihedral : 4.446 72.071 4602 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.95 % Favored : 97.00 % Rotamer: Outliers : 3.01 % Allowed : 17.71 % Favored : 79.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.33 (0.13), residues: 4165 helix: 1.50 (0.10), residues: 2771 sheet: 0.15 (0.36), residues: 215 loop : -0.35 (0.19), residues: 1179 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 664 TYR 0.056 0.002 TYR E 386 PHE 0.026 0.002 PHE A 532 TRP 0.017 0.001 TRP A1229 HIS 0.012 0.001 HIS C 952 Details of bonding type rmsd/Z covalent geometry : bond 0.00445 / 0.19 (34823) covalent geometry : angle 0.59129 / 0.30 (47098) hydrogen bonds : bond 0.04130 / 2.76 ( 2004) hydrogen bonds : angle 4.21180 / 3.05 ( 5913) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8330 Ramachandran restraints generated. 4165 Oldfield, 0 Emsley, 4165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8330 Ramachandran restraints generated. 4165 Oldfield, 0 Emsley, 4165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1082 residues out of total 3824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 967 time to evaluate : 1.468 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 324 ASP cc_start: 0.7355 (m-30) cc_final: 0.6877 (m-30) REVERT: A 349 ASP cc_start: 0.8418 (OUTLIER) cc_final: 0.8148 (p0) REVERT: A 414 LYS cc_start: 0.7968 (tttt) cc_final: 0.7497 (ttpp) REVERT: A 442 ASN cc_start: 0.7352 (m-40) cc_final: 0.6988 (m-40) REVERT: A 502 MET cc_start: 0.6875 (tmm) cc_final: 0.5657 (tmm) REVERT: A 507 LYS cc_start: 0.8395 (mmmm) cc_final: 0.8121 (mmmm) REVERT: A 512 GLU cc_start: 0.8040 (pm20) cc_final: 0.7682 (pm20) REVERT: A 548 LYS cc_start: 0.8544 (tttt) cc_final: 0.8256 (tptt) REVERT: A 555 GLN cc_start: 0.7114 (pp30) cc_final: 0.6388 (tp-100) REVERT: A 595 ARG cc_start: 0.8404 (ttp80) cc_final: 0.8104 (ttp80) REVERT: A 670 ASP cc_start: 0.7693 (m-30) cc_final: 0.7421 (t0) REVERT: A 672 GLN cc_start: 0.8119 (mp10) cc_final: 0.7753 (mt0) REVERT: A 708 ASN cc_start: 0.8558 (t0) cc_final: 0.8203 (t0) REVERT: A 737 GLU cc_start: 0.7145 (mm-30) cc_final: 0.6899 (mm-30) REVERT: A 763 ASP cc_start: 0.7881 (m-30) cc_final: 0.7651 (m-30) REVERT: A 794 GLU cc_start: 0.7921 (tm-30) cc_final: 0.7708 (tm-30) REVERT: A 803 MET cc_start: 0.8763 (mmm) cc_final: 0.8500 (mmp) REVERT: A 804 PRO cc_start: 0.8007 (Cg_exo) cc_final: 0.7657 (Cg_endo) REVERT: A 808 ASN cc_start: 0.8266 (m-40) cc_final: 0.8017 (m-40) REVERT: A 820 ASP cc_start: 0.8407 (t70) cc_final: 0.8160 (t0) REVERT: A 879 TYR cc_start: 0.8647 (t80) cc_final: 0.8078 (t80) REVERT: A 880 LYS cc_start: 0.8927 (mtmm) cc_final: 0.8669 (ptpp) REVERT: A 951 GLN cc_start: 0.8708 (mt0) cc_final: 0.8384 (mt0) REVERT: A 973 ARG cc_start: 0.7670 (mtp85) cc_final: 0.7420 (mtp85) REVERT: A 1068 LYS cc_start: 0.8502 (tttp) cc_final: 0.8196 (ttmm) REVERT: A 1087 ILE cc_start: 0.8349 (tp) cc_final: 0.8085 (pt) REVERT: A 1179 ASP cc_start: 0.8507 (m-30) cc_final: 0.8071 (m-30) REVERT: A 1222 GLN cc_start: 0.7854 (pm20) cc_final: 0.7576 (pm20) REVERT: A 1237 LYS cc_start: 0.8338 (tttt) cc_final: 0.8117 (tttt) REVERT: A 1245 ARG cc_start: 0.7962 (mtt-85) cc_final: 0.7693 (mtt90) REVERT: A 1250 GLN cc_start: 0.8405 (tp-100) cc_final: 0.7986 (tp40) REVERT: A 1275 ARG cc_start: 0.8490 (ttp-110) cc_final: 0.8219 (ttp-110) REVERT: A 1328 ASP cc_start: 0.8767 (t0) cc_final: 0.8219 (t0) REVERT: A 1390 LYS cc_start: 0.8630 (tttm) cc_final: 0.8038 (tptm) REVERT: A 1393 GLN cc_start: 0.7515 (mp10) cc_final: 0.6931 (mp10) REVERT: A 1406 GLU cc_start: 0.7279 (tt0) cc_final: 0.6966 (tt0) REVERT: A 1465 LYS cc_start: 0.8733 (mttt) cc_final: 0.8462 (mttm) REVERT: A 1480 GLN cc_start: 0.8414 (mt0) cc_final: 0.8198 (mp10) REVERT: A 1484 ILE cc_start: 0.8813 (mt) cc_final: 0.8552 (tt) REVERT: A 1513 LYS cc_start: 0.8810 (mttt) cc_final: 0.8533 (mmmm) REVERT: A 1514 LYS cc_start: 0.8447 (tttt) cc_final: 0.8041 (ttpp) REVERT: A 1609 GLN cc_start: 0.8693 (tp-100) cc_final: 0.8338 (tp40) REVERT: A 1681 MET cc_start: 0.9077 (mmm) cc_final: 0.8869 (mmm) REVERT: A 1734 ARG cc_start: 0.8290 (ptt-90) cc_final: 0.7917 (ptp-170) REVERT: A 1818 HIS cc_start: 0.7694 (m90) cc_final: 0.7407 (m90) REVERT: A 1864 HIS cc_start: 0.8335 (m90) cc_final: 0.7790 (m-70) REVERT: A 1917 MET cc_start: 0.8276 (mtm) cc_final: 0.8033 (mtt) REVERT: A 1925 LEU cc_start: 0.8423 (mt) cc_final: 0.8127 (mt) REVERT: A 1959 MET cc_start: 0.8592 (mtp) cc_final: 0.8261 (mtp) REVERT: A 1996 GLU cc_start: 0.8089 (mt-10) cc_final: 0.7766 (mt-10) REVERT: A 2023 GLU cc_start: 0.8036 (tm-30) cc_final: 0.7544 (tm-30) REVERT: A 2121 LYS cc_start: 0.8731 (mttt) cc_final: 0.8397 (mttt) REVERT: A 2124 LYS cc_start: 0.8733 (mttt) cc_final: 0.8529 (mtmt) REVERT: A 2218 ASN cc_start: 0.8322 (m-40) cc_final: 0.7926 (t0) REVERT: A 2253 THR cc_start: 0.8767 (OUTLIER) cc_final: 0.8534 (p) REVERT: A 2329 GLU cc_start: 0.8747 (OUTLIER) cc_final: 0.8493 (mp0) REVERT: A 2440 ARG cc_start: 0.8446 (ptp90) cc_final: 0.8223 (ptp90) REVERT: A 2444 LEU cc_start: 0.8933 (mt) cc_final: 0.8679 (mt) REVERT: B 90 MET cc_start: 0.6912 (OUTLIER) cc_final: 0.6697 (ptm) REVERT: B 182 ASN cc_start: 0.7050 (t0) cc_final: 0.6594 (t0) REVERT: B 232 ARG cc_start: 0.6998 (ttm170) cc_final: 0.6406 (ttm110) REVERT: B 275 ARG cc_start: 0.7015 (mpp80) cc_final: 0.6380 (mtt180) REVERT: B 286 ARG cc_start: 0.8419 (mmm160) cc_final: 0.8068 (tpp-160) REVERT: C 351 MET cc_start: 0.7986 (mmm) cc_final: 0.7771 (mmm) REVERT: C 359 LEU cc_start: 0.8560 (mt) cc_final: 0.8201 (mt) REVERT: C 373 CYS cc_start: 0.8718 (t) cc_final: 0.8350 (t) REVERT: C 388 GLU cc_start: 0.8259 (tp30) cc_final: 0.7807 (tp30) REVERT: C 462 GLU cc_start: 0.8486 (tt0) cc_final: 0.8249 (tt0) REVERT: C 465 LYS cc_start: 0.8725 (tttt) cc_final: 0.8367 (tttm) REVERT: C 642 GLU cc_start: 0.8217 (mm-30) cc_final: 0.7812 (mm-30) REVERT: C 689 GLU cc_start: 0.8336 (tt0) cc_final: 0.7983 (tt0) REVERT: C 713 ASP cc_start: 0.7894 (m-30) cc_final: 0.7437 (t70) REVERT: C 742 MET cc_start: 0.8072 (mtm) cc_final: 0.7657 (mtm) REVERT: C 759 TRP cc_start: 0.6652 (m-10) cc_final: 0.5945 (m-10) REVERT: C 765 LEU cc_start: 0.8362 (tp) cc_final: 0.8124 (mm) REVERT: C 813 TYR cc_start: 0.7953 (OUTLIER) cc_final: 0.7408 (m-10) REVERT: C 848 MET cc_start: 0.8370 (mtp) cc_final: 0.7502 (mmp) REVERT: C 864 ASN cc_start: 0.9039 (m-40) cc_final: 0.8689 (t0) REVERT: C 875 PHE cc_start: 0.8858 (m-80) cc_final: 0.8539 (m-80) REVERT: C 893 ARG cc_start: 0.8447 (ptm-80) cc_final: 0.7956 (ptm-80) REVERT: C 923 ASP cc_start: 0.7861 (t0) cc_final: 0.7206 (t70) REVERT: C 982 MET cc_start: 0.7514 (tpp) cc_final: 0.6837 (tpp) REVERT: C 996 VAL cc_start: 0.7660 (OUTLIER) cc_final: 0.7454 (t) REVERT: C 1006 GLU cc_start: 0.8925 (mt-10) cc_final: 0.8370 (mm-30) REVERT: C 1076 GLU cc_start: 0.8398 (tt0) cc_final: 0.8129 (tt0) REVERT: C 1096 ARG cc_start: 0.7967 (ptm160) cc_final: 0.7698 (ptm160) REVERT: C 1342 LYS cc_start: 0.8501 (mmtt) cc_final: 0.8126 (mtmt) REVERT: C 1349 GLN cc_start: 0.8309 (mt0) cc_final: 0.8060 (mt0) REVERT: C 1364 THR cc_start: 0.8692 (t) cc_final: 0.8435 (t) REVERT: C 1383 LYS cc_start: 0.7065 (mttt) cc_final: 0.6757 (mtmm) REVERT: D 85 LYS cc_start: 0.8772 (mtpt) cc_final: 0.8433 (mtmt) REVERT: D 96 GLN cc_start: 0.8551 (tm-30) cc_final: 0.8140 (tm-30) REVERT: D 110 ARG cc_start: 0.8019 (mtt180) cc_final: 0.7653 (ttm110) REVERT: D 119 ASN cc_start: 0.8744 (OUTLIER) cc_final: 0.7678 (t0) REVERT: D 123 GLN cc_start: 0.8644 (mp10) cc_final: 0.8228 (mp10) REVERT: D 144 THR cc_start: 0.8840 (p) cc_final: 0.8195 (t) REVERT: D 148 VAL cc_start: 0.7977 (m) cc_final: 0.7743 (p) REVERT: D 160 MET cc_start: 0.8289 (mmm) cc_final: 0.7729 (mpp) REVERT: D 178 ASN cc_start: 0.7316 (t0) cc_final: 0.6858 (t0) REVERT: E 326 PHE cc_start: 0.7496 (t80) cc_final: 0.7252 (t80) REVERT: E 347 GLU cc_start: 0.8178 (mp0) cc_final: 0.7951 (mp0) REVERT: E 354 GLU cc_start: 0.8634 (OUTLIER) cc_final: 0.8076 (pp20) REVERT: E 379 GLU cc_start: 0.8920 (mm-30) cc_final: 0.8690 (mm-30) REVERT: E 407 LYS cc_start: 0.7963 (ptpp) cc_final: 0.7564 (ptpp) REVERT: E 510 LEU cc_start: 0.8429 (mt) cc_final: 0.8206 (mp) REVERT: E 529 GLN cc_start: 0.7140 (tp40) cc_final: 0.6617 (mm-40) REVERT: E 530 ARG cc_start: 0.8581 (ptp-170) cc_final: 0.8322 (ptp-170) REVERT: E 532 ILE cc_start: 0.8839 (mm) cc_final: 0.8431 (tp) REVERT: E 533 GLU cc_start: 0.8364 (mt-10) cc_final: 0.7781 (mt-10) REVERT: G 9 GLU cc_start: 0.7990 (mt-10) cc_final: 0.7494 (mt-10) REVERT: G 21 LYS cc_start: 0.8103 (mmtm) cc_final: 0.7480 (mmmt) REVERT: G 24 MET cc_start: 0.7681 (mtm) cc_final: 0.7475 (mtp) REVERT: G 25 LYS cc_start: 0.8488 (mttt) cc_final: 0.8134 (mttt) REVERT: G 52 MET cc_start: 0.7311 (ttp) cc_final: 0.6553 (tmm) REVERT: G 626 LYS cc_start: 0.7844 (ttpp) cc_final: 0.7433 (ttpp) REVERT: G 634 LYS cc_start: 0.5995 (ttpp) cc_final: 0.5326 (tptm) REVERT: G 638 SER cc_start: 0.7675 (p) cc_final: 0.7434 (p) REVERT: G 1068 LYS cc_start: 0.8647 (OUTLIER) cc_final: 0.8303 (ptmm) REVERT: G 1073 ARG cc_start: 0.7842 (ttt180) cc_final: 0.7487 (ttt-90) REVERT: G 1074 ARG cc_start: 0.8314 (ttp80) cc_final: 0.7808 (ttp-170) REVERT: G 1082 LYS cc_start: 0.8750 (mttt) cc_final: 0.8345 (mttt) REVERT: G 1083 HIS cc_start: 0.8567 (m90) cc_final: 0.8137 (m-70) REVERT: G 1123 LYS cc_start: 0.7889 (tttt) cc_final: 0.7564 (tttt) REVERT: G 1148 TYR cc_start: 0.7930 (m-80) cc_final: 0.7310 (m-80) REVERT: G 1156 GLU cc_start: 0.8449 (mt-10) cc_final: 0.8159 (mt-10) REVERT: G 1159 GLU cc_start: 0.8746 (tt0) cc_final: 0.8408 (tt0) REVERT: G 1163 ARG cc_start: 0.8848 (tpp80) cc_final: 0.8379 (ttt180) REVERT: G 1165 GLN cc_start: 0.8997 (mt0) cc_final: 0.8566 (mt0) REVERT: G 1166 ASN cc_start: 0.9017 (m-40) cc_final: 0.8758 (m-40) REVERT: G 1173 MET cc_start: 0.8706 (mtm) cc_final: 0.8416 (mtm) REVERT: H 1256 MET cc_start: 0.7884 (mpp) cc_final: 0.7599 (tpp) REVERT: H 1282 LYS cc_start: 0.8352 (mtpt) cc_final: 0.8060 (mtpt) REVERT: H 1283 GLU cc_start: 0.8172 (tp30) cc_final: 0.7809 (mp0) outliers start: 115 outliers final: 76 residues processed: 1025 average time/residue: 0.2474 time to fit residues: 396.2390 Evaluate side-chains 1029 residues out of total 3824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 944 time to evaluate : 1.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 349 ASP Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 389 TYR Chi-restraints excluded: chain A residue 435 TYR Chi-restraints excluded: chain A residue 457 PHE Chi-restraints excluded: chain A residue 503 ILE Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 624 ASP Chi-restraints excluded: chain A residue 635 LEU Chi-restraints excluded: chain A residue 661 ILE Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain A residue 698 ILE Chi-restraints excluded: chain A residue 721 LEU Chi-restraints excluded: chain A residue 905 LEU Chi-restraints excluded: chain A residue 962 ASP Chi-restraints excluded: chain A residue 1030 SER Chi-restraints excluded: chain A residue 1100 LYS Chi-restraints excluded: chain A residue 1171 ASN Chi-restraints excluded: chain A residue 1191 LEU Chi-restraints excluded: chain A residue 1314 ILE Chi-restraints excluded: chain A residue 1382 THR Chi-restraints excluded: chain A residue 1502 ASP Chi-restraints excluded: chain A residue 1544 VAL Chi-restraints excluded: chain A residue 1635 LEU Chi-restraints excluded: chain A residue 1696 SER Chi-restraints excluded: chain A residue 1816 LEU Chi-restraints excluded: chain A residue 1912 LEU Chi-restraints excluded: chain A residue 1922 SER Chi-restraints excluded: chain A residue 1944 VAL Chi-restraints excluded: chain A residue 1961 VAL Chi-restraints excluded: chain A residue 1973 ASP Chi-restraints excluded: chain A residue 1975 SER Chi-restraints excluded: chain A residue 2025 LEU Chi-restraints excluded: chain A residue 2155 GLU Chi-restraints excluded: chain A residue 2253 THR Chi-restraints excluded: chain A residue 2329 GLU Chi-restraints excluded: chain A residue 2331 SER Chi-restraints excluded: chain B residue 14 ILE Chi-restraints excluded: chain B residue 90 MET Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 269 SER Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 287 GLN Chi-restraints excluded: chain C residue 309 ASP Chi-restraints excluded: chain C residue 364 LEU Chi-restraints excluded: chain C residue 384 ASP Chi-restraints excluded: chain C residue 482 SER Chi-restraints excluded: chain C residue 687 VAL Chi-restraints excluded: chain C residue 712 ILE Chi-restraints excluded: chain C residue 725 ILE Chi-restraints excluded: chain C residue 813 TYR Chi-restraints excluded: chain C residue 825 THR Chi-restraints excluded: chain C residue 891 LEU Chi-restraints excluded: chain C residue 995 SER Chi-restraints excluded: chain C residue 996 VAL Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain C residue 1022 ARG Chi-restraints excluded: chain C residue 1024 PHE Chi-restraints excluded: chain C residue 1083 SER Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1218 CYS Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 119 ASN Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain E residue 354 GLU Chi-restraints excluded: chain E residue 382 VAL Chi-restraints excluded: chain E residue 419 GLU Chi-restraints excluded: chain E residue 459 SER Chi-restraints excluded: chain E residue 466 MET Chi-restraints excluded: chain E residue 541 MET Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain G residue 628 THR Chi-restraints excluded: chain G residue 1067 HIS Chi-restraints excluded: chain G residue 1068 LYS Chi-restraints excluded: chain G residue 1096 ILE Chi-restraints excluded: chain G residue 1110 LYS Chi-restraints excluded: chain G residue 1113 SER Chi-restraints excluded: chain G residue 1120 VAL Chi-restraints excluded: chain G residue 1126 LYS Chi-restraints excluded: chain G residue 1174 ASN Chi-restraints excluded: chain G residue 1175 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 419 random chunks: chunk 412 optimal weight: 2.9990 chunk 101 optimal weight: 0.7980 chunk 92 optimal weight: 0.8980 chunk 111 optimal weight: 2.9990 chunk 87 optimal weight: 0.0030 chunk 277 optimal weight: 0.8980 chunk 371 optimal weight: 0.9980 chunk 346 optimal weight: 0.5980 chunk 268 optimal weight: 0.9990 chunk 263 optimal weight: 0.5980 chunk 104 optimal weight: 0.5980 overall best weight: 0.5190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 308 GLN ** A 481 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 687 ASN A1521 ASN ** A1691 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 355 GLN ** C 843 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 952 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 50 HIS E 387 ASN E 498 GLN G 23 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.146863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.116369 restraints weight = 73085.509| |-----------------------------------------------------------------------------| r_work (start): 0.3669 rms_B_bonded: 2.81 r_work: 0.3529 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.3948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 34823 Z= 0.131 Angle : 0.579 12.323 47098 Z= 0.296 Chirality : 0.041 0.233 5383 Planarity : 0.004 0.115 5944 Dihedral : 4.453 71.237 4602 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.59 % Favored : 97.36 % Rotamer: Outliers : 2.80 % Allowed : 19.15 % Favored : 78.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.50 (0.13), residues: 4165 helix: 1.65 (0.10), residues: 2762 sheet: 0.10 (0.36), residues: 223 loop : -0.30 (0.19), residues: 1180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 444 TYR 0.056 0.001 TYR E 386 PHE 0.028 0.001 PHE E 380 TRP 0.017 0.001 TRP C 757 HIS 0.013 0.001 HIS C 952 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 (34823) covalent geometry : angle 0.57851 / 0.30 (47098) hydrogen bonds : bond 0.03778 / 2.53 ( 2004) hydrogen bonds : angle 4.07568 / 2.95 ( 5913) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8330 Ramachandran restraints generated. 4165 Oldfield, 0 Emsley, 4165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8330 Ramachandran restraints generated. 4165 Oldfield, 0 Emsley, 4165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1066 residues out of total 3824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 959 time to evaluate : 1.565 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 324 ASP cc_start: 0.7289 (m-30) cc_final: 0.6781 (m-30) REVERT: A 414 LYS cc_start: 0.7961 (tttt) cc_final: 0.7479 (ttpp) REVERT: A 442 ASN cc_start: 0.7359 (m-40) cc_final: 0.7043 (m-40) REVERT: A 507 LYS cc_start: 0.8360 (mmmm) cc_final: 0.8030 (mmmm) REVERT: A 512 GLU cc_start: 0.8014 (pm20) cc_final: 0.7650 (pm20) REVERT: A 548 LYS cc_start: 0.8550 (tttt) cc_final: 0.8192 (tptp) REVERT: A 555 GLN cc_start: 0.7051 (pp30) cc_final: 0.6338 (tp-100) REVERT: A 595 ARG cc_start: 0.8417 (ttp80) cc_final: 0.8099 (ttp80) REVERT: A 670 ASP cc_start: 0.7620 (m-30) cc_final: 0.7379 (t0) REVERT: A 737 GLU cc_start: 0.7115 (mm-30) cc_final: 0.6854 (mm-30) REVERT: A 763 ASP cc_start: 0.7876 (m-30) cc_final: 0.7638 (m-30) REVERT: A 803 MET cc_start: 0.8754 (mmm) cc_final: 0.8499 (mmp) REVERT: A 804 PRO cc_start: 0.8025 (Cg_exo) cc_final: 0.7694 (Cg_endo) REVERT: A 808 ASN cc_start: 0.8254 (m-40) cc_final: 0.8004 (m-40) REVERT: A 880 LYS cc_start: 0.8930 (mtmm) cc_final: 0.8696 (ptpp) REVERT: A 927 MET cc_start: 0.8226 (mmm) cc_final: 0.7981 (tpp) REVERT: A 948 HIS cc_start: 0.8318 (t-90) cc_final: 0.7534 (t70) REVERT: A 951 GLN cc_start: 0.8693 (mt0) cc_final: 0.8381 (mp10) REVERT: A 973 ARG cc_start: 0.7600 (mtp85) cc_final: 0.7362 (mtp85) REVERT: A 1068 LYS cc_start: 0.8471 (tttp) cc_final: 0.8189 (ttmm) REVERT: A 1142 THR cc_start: 0.8239 (m) cc_final: 0.7921 (p) REVERT: A 1179 ASP cc_start: 0.8495 (m-30) cc_final: 0.8039 (m-30) REVERT: A 1222 GLN cc_start: 0.7893 (pm20) cc_final: 0.7638 (pm20) REVERT: A 1237 LYS cc_start: 0.8245 (tttt) cc_final: 0.8022 (tttt) REVERT: A 1245 ARG cc_start: 0.7917 (mtt-85) cc_final: 0.7642 (mtt90) REVERT: A 1250 GLN cc_start: 0.8403 (tp-100) cc_final: 0.7991 (tp40) REVERT: A 1275 ARG cc_start: 0.8459 (ttp-110) cc_final: 0.8209 (ttp-110) REVERT: A 1328 ASP cc_start: 0.8711 (t0) cc_final: 0.8167 (t0) REVERT: A 1390 LYS cc_start: 0.8599 (tttm) cc_final: 0.8030 (tptm) REVERT: A 1393 GLN cc_start: 0.7517 (mp10) cc_final: 0.6928 (mp10) REVERT: A 1406 GLU cc_start: 0.7261 (tt0) cc_final: 0.6939 (tt0) REVERT: A 1465 LYS cc_start: 0.8727 (mttt) cc_final: 0.8451 (mttm) REVERT: A 1484 ILE cc_start: 0.8789 (mt) cc_final: 0.8553 (tt) REVERT: A 1513 LYS cc_start: 0.8798 (mttt) cc_final: 0.8523 (mmmm) REVERT: A 1514 LYS cc_start: 0.8392 (tttt) cc_final: 0.8037 (ttpp) REVERT: A 1681 MET cc_start: 0.9100 (mmm) cc_final: 0.8861 (mmm) REVERT: A 1734 ARG cc_start: 0.8283 (ptt-90) cc_final: 0.7992 (ptp-170) REVERT: A 1766 ASN cc_start: 0.8598 (m110) cc_final: 0.8121 (m-40) REVERT: A 1818 HIS cc_start: 0.7673 (m90) cc_final: 0.7373 (m90) REVERT: A 1864 HIS cc_start: 0.8303 (m90) cc_final: 0.7746 (m-70) REVERT: A 1917 MET cc_start: 0.8227 (mtm) cc_final: 0.8014 (mtt) REVERT: A 1959 MET cc_start: 0.8590 (mtp) cc_final: 0.8254 (mtp) REVERT: A 1996 GLU cc_start: 0.8054 (mt-10) cc_final: 0.7739 (mt-10) REVERT: A 2023 GLU cc_start: 0.8064 (tm-30) cc_final: 0.7528 (tm-30) REVERT: A 2121 LYS cc_start: 0.8709 (mttt) cc_final: 0.8371 (mttt) REVERT: A 2124 LYS cc_start: 0.8725 (mttt) cc_final: 0.8521 (mtmt) REVERT: A 2218 ASN cc_start: 0.8286 (m-40) cc_final: 0.7913 (t0) REVERT: A 2418 ARG cc_start: 0.7654 (ttp-170) cc_final: 0.7399 (ttp-170) REVERT: A 2440 ARG cc_start: 0.8394 (ptp90) cc_final: 0.8160 (ptp90) REVERT: A 2444 LEU cc_start: 0.8916 (mt) cc_final: 0.8657 (mt) REVERT: B 141 ARG cc_start: 0.7300 (mtp85) cc_final: 0.7000 (mtp85) REVERT: B 182 ASN cc_start: 0.7025 (t0) cc_final: 0.6598 (t0) REVERT: B 188 MET cc_start: 0.2015 (mmm) cc_final: 0.1137 (mmm) REVERT: B 232 ARG cc_start: 0.6970 (ttm170) cc_final: 0.6368 (ttm110) REVERT: B 275 ARG cc_start: 0.6839 (mpp80) cc_final: 0.6393 (mtt180) REVERT: B 286 ARG cc_start: 0.8433 (mmm160) cc_final: 0.7995 (tpp-160) REVERT: C 351 MET cc_start: 0.8016 (mmm) cc_final: 0.7780 (mmm) REVERT: C 359 LEU cc_start: 0.8524 (mt) cc_final: 0.8181 (mt) REVERT: C 373 CYS cc_start: 0.8636 (t) cc_final: 0.8281 (t) REVERT: C 388 GLU cc_start: 0.8215 (tp30) cc_final: 0.7831 (tm-30) REVERT: C 451 GLU cc_start: 0.7458 (tm-30) cc_final: 0.7163 (tm-30) REVERT: C 462 GLU cc_start: 0.8474 (tt0) cc_final: 0.8249 (tt0) REVERT: C 465 LYS cc_start: 0.8703 (tttt) cc_final: 0.8324 (tttm) REVERT: C 497 MET cc_start: 0.8835 (mmt) cc_final: 0.7325 (mmt) REVERT: C 642 GLU cc_start: 0.8205 (mm-30) cc_final: 0.7790 (mm-30) REVERT: C 742 MET cc_start: 0.8062 (mtm) cc_final: 0.7596 (mtm) REVERT: C 759 TRP cc_start: 0.6604 (m-10) cc_final: 0.6027 (m-10) REVERT: C 765 LEU cc_start: 0.8326 (tp) cc_final: 0.8084 (mm) REVERT: C 813 TYR cc_start: 0.7881 (OUTLIER) cc_final: 0.7356 (m-10) REVERT: C 848 MET cc_start: 0.8357 (mtp) cc_final: 0.7514 (mmp) REVERT: C 864 ASN cc_start: 0.9058 (m-40) cc_final: 0.8701 (t0) REVERT: C 875 PHE cc_start: 0.8835 (m-80) cc_final: 0.8328 (m-80) REVERT: C 893 ARG cc_start: 0.8442 (ptm-80) cc_final: 0.7970 (ptm-80) REVERT: C 923 ASP cc_start: 0.7899 (t0) cc_final: 0.7237 (t70) REVERT: C 982 MET cc_start: 0.7426 (tpp) cc_final: 0.6872 (tpp) REVERT: C 987 ARG cc_start: 0.7750 (OUTLIER) cc_final: 0.7373 (mmp80) REVERT: C 988 GLN cc_start: 0.8662 (tp40) cc_final: 0.8017 (tp40) REVERT: C 1006 GLU cc_start: 0.8883 (mt-10) cc_final: 0.8353 (mm-30) REVERT: C 1076 GLU cc_start: 0.8417 (tt0) cc_final: 0.8133 (tt0) REVERT: C 1096 ARG cc_start: 0.7901 (ptm160) cc_final: 0.7499 (ptm160) REVERT: C 1103 GLU cc_start: 0.7824 (tt0) cc_final: 0.7230 (tt0) REVERT: C 1342 LYS cc_start: 0.8483 (mmtt) cc_final: 0.8129 (mtmt) REVERT: C 1349 GLN cc_start: 0.8287 (mt0) cc_final: 0.8061 (mt0) REVERT: C 1364 THR cc_start: 0.8610 (t) cc_final: 0.8364 (t) REVERT: C 1383 LYS cc_start: 0.7004 (mttt) cc_final: 0.6705 (mtmm) REVERT: D 53 TYR cc_start: 0.7918 (t80) cc_final: 0.7649 (t80) REVERT: D 85 LYS cc_start: 0.8769 (mtpt) cc_final: 0.8459 (mtmt) REVERT: D 93 LEU cc_start: 0.8686 (tp) cc_final: 0.8420 (tp) REVERT: D 96 GLN cc_start: 0.8553 (tm-30) cc_final: 0.8124 (tm-30) REVERT: D 110 ARG cc_start: 0.8039 (mtt180) cc_final: 0.7646 (ttm110) REVERT: D 119 ASN cc_start: 0.8728 (OUTLIER) cc_final: 0.7563 (t0) REVERT: D 123 GLN cc_start: 0.8668 (mp10) cc_final: 0.8304 (mp10) REVERT: D 160 MET cc_start: 0.8294 (mmm) cc_final: 0.7673 (mpp) REVERT: D 178 ASN cc_start: 0.7284 (t0) cc_final: 0.6787 (t0) REVERT: E 326 PHE cc_start: 0.7529 (t80) cc_final: 0.7284 (t80) REVERT: E 354 GLU cc_start: 0.8650 (OUTLIER) cc_final: 0.8075 (pp20) REVERT: E 379 GLU cc_start: 0.8953 (mm-30) cc_final: 0.8704 (mm-30) REVERT: E 510 LEU cc_start: 0.8427 (mt) cc_final: 0.8194 (mp) REVERT: E 529 GLN cc_start: 0.7135 (tp40) cc_final: 0.6681 (mm-40) REVERT: E 530 ARG cc_start: 0.8574 (ptp-170) cc_final: 0.8333 (ptp-170) REVERT: E 532 ILE cc_start: 0.8865 (mm) cc_final: 0.8476 (tp) REVERT: E 533 GLU cc_start: 0.8379 (mt-10) cc_final: 0.7800 (mt-10) REVERT: G 9 GLU cc_start: 0.7986 (mt-10) cc_final: 0.7503 (mt-10) REVERT: G 21 LYS cc_start: 0.8096 (mmtm) cc_final: 0.7419 (mmmt) REVERT: G 24 MET cc_start: 0.7572 (mtm) cc_final: 0.7203 (mtm) REVERT: G 25 LYS cc_start: 0.8437 (mttt) cc_final: 0.8080 (mttt) REVERT: G 51 TYR cc_start: 0.7461 (m-80) cc_final: 0.7031 (m-80) REVERT: G 52 MET cc_start: 0.7193 (ttp) cc_final: 0.6469 (tmm) REVERT: G 626 LYS cc_start: 0.7809 (ttpp) cc_final: 0.7401 (ttpp) REVERT: G 634 LYS cc_start: 0.5971 (ttpp) cc_final: 0.5362 (tptm) REVERT: G 638 SER cc_start: 0.7473 (p) cc_final: 0.7243 (p) REVERT: G 1068 LYS cc_start: 0.8587 (OUTLIER) cc_final: 0.8228 (ptmm) REVERT: G 1073 ARG cc_start: 0.7762 (ttt180) cc_final: 0.7440 (ttt-90) REVERT: G 1074 ARG cc_start: 0.8351 (ttp80) cc_final: 0.7803 (ttp-170) REVERT: G 1082 LYS cc_start: 0.8753 (mttt) cc_final: 0.8324 (mttt) REVERT: G 1083 HIS cc_start: 0.8566 (m90) cc_final: 0.8355 (m-70) REVERT: G 1084 GLU cc_start: 0.7893 (tp30) cc_final: 0.7291 (tp30) REVERT: G 1123 LYS cc_start: 0.7884 (tttt) cc_final: 0.7552 (tttt) REVERT: G 1156 GLU cc_start: 0.8457 (mt-10) cc_final: 0.8156 (mt-10) REVERT: G 1159 GLU cc_start: 0.8781 (tt0) cc_final: 0.8415 (tt0) REVERT: G 1163 ARG cc_start: 0.8825 (tpp80) cc_final: 0.8334 (ttt180) REVERT: G 1165 GLN cc_start: 0.8977 (mt0) cc_final: 0.8524 (mt0) REVERT: G 1166 ASN cc_start: 0.9003 (m-40) cc_final: 0.8746 (m-40) REVERT: G 1173 MET cc_start: 0.8668 (mtm) cc_final: 0.8340 (mtm) REVERT: H 1256 MET cc_start: 0.7906 (mpp) cc_final: 0.7615 (tpp) REVERT: H 1282 LYS cc_start: 0.8331 (mtpt) cc_final: 0.8034 (mtpt) REVERT: H 1283 GLU cc_start: 0.8176 (tp30) cc_final: 0.7792 (mp0) outliers start: 107 outliers final: 70 residues processed: 1011 average time/residue: 0.2521 time to fit residues: 396.5072 Evaluate side-chains 1017 residues out of total 3824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 942 time to evaluate : 1.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 389 TYR Chi-restraints excluded: chain A residue 435 TYR Chi-restraints excluded: chain A residue 457 PHE Chi-restraints excluded: chain A residue 491 CYS Chi-restraints excluded: chain A residue 503 ILE Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 546 ILE Chi-restraints excluded: chain A residue 563 GLU Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 590 LEU Chi-restraints excluded: chain A residue 635 LEU Chi-restraints excluded: chain A residue 661 ILE Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain A residue 721 LEU Chi-restraints excluded: chain A residue 905 LEU Chi-restraints excluded: chain A residue 1030 SER Chi-restraints excluded: chain A residue 1171 ASN Chi-restraints excluded: chain A residue 1185 LEU Chi-restraints excluded: chain A residue 1191 LEU Chi-restraints excluded: chain A residue 1502 ASP Chi-restraints excluded: chain A residue 1544 VAL Chi-restraints excluded: chain A residue 1816 LEU Chi-restraints excluded: chain A residue 1912 LEU Chi-restraints excluded: chain A residue 1922 SER Chi-restraints excluded: chain A residue 1944 VAL Chi-restraints excluded: chain A residue 1961 VAL Chi-restraints excluded: chain A residue 2025 LEU Chi-restraints excluded: chain A residue 2155 GLU Chi-restraints excluded: chain B residue 14 ILE Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 269 SER Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 287 GLN Chi-restraints excluded: chain B residue 292 HIS Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain C residue 309 ASP Chi-restraints excluded: chain C residue 364 LEU Chi-restraints excluded: chain C residue 384 ASP Chi-restraints excluded: chain C residue 482 SER Chi-restraints excluded: chain C residue 687 VAL Chi-restraints excluded: chain C residue 712 ILE Chi-restraints excluded: chain C residue 725 ILE Chi-restraints excluded: chain C residue 813 TYR Chi-restraints excluded: chain C residue 825 THR Chi-restraints excluded: chain C residue 831 MET Chi-restraints excluded: chain C residue 891 LEU Chi-restraints excluded: chain C residue 987 ARG Chi-restraints excluded: chain C residue 995 SER Chi-restraints excluded: chain C residue 996 VAL Chi-restraints excluded: chain C residue 1022 ARG Chi-restraints excluded: chain C residue 1024 PHE Chi-restraints excluded: chain C residue 1083 SER Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1218 CYS Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 119 ASN Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain E residue 354 GLU Chi-restraints excluded: chain E residue 382 VAL Chi-restraints excluded: chain E residue 419 GLU Chi-restraints excluded: chain E residue 541 MET Chi-restraints excluded: chain G residue 59 LEU Chi-restraints excluded: chain G residue 628 THR Chi-restraints excluded: chain G residue 1067 HIS Chi-restraints excluded: chain G residue 1068 LYS Chi-restraints excluded: chain G residue 1092 ASP Chi-restraints excluded: chain G residue 1096 ILE Chi-restraints excluded: chain G residue 1110 LYS Chi-restraints excluded: chain G residue 1113 SER Chi-restraints excluded: chain G residue 1120 VAL Chi-restraints excluded: chain G residue 1126 LYS Chi-restraints excluded: chain G residue 1174 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 419 random chunks: chunk 166 optimal weight: 0.5980 chunk 201 optimal weight: 0.8980 chunk 390 optimal weight: 0.8980 chunk 341 optimal weight: 0.0870 chunk 156 optimal weight: 0.9980 chunk 383 optimal weight: 3.9990 chunk 143 optimal weight: 0.4980 chunk 378 optimal weight: 1.9990 chunk 205 optimal weight: 0.8980 chunk 241 optimal weight: 0.8980 chunk 15 optimal weight: 30.0000 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 481 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 687 ASN A1378 GLN A1480 GLN ** A1691 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2419 ASN ** B 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 843 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 952 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 498 GLN G 23 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.146940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.116193 restraints weight = 73661.883| |-----------------------------------------------------------------------------| r_work (start): 0.3674 rms_B_bonded: 2.81 r_work: 0.3532 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.4100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 34823 Z= 0.134 Angle : 0.587 12.328 47098 Z= 0.299 Chirality : 0.041 0.208 5383 Planarity : 0.004 0.069 5944 Dihedral : 4.442 71.328 4602 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.67 % Favored : 97.29 % Rotamer: Outliers : 2.43 % Allowed : 20.38 % Favored : 77.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.56 (0.13), residues: 4165 helix: 1.70 (0.10), residues: 2762 sheet: 0.18 (0.36), residues: 223 loop : -0.32 (0.19), residues: 1180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 444 TYR 0.054 0.001 TYR E 386 PHE 0.032 0.002 PHE A 385 TRP 0.022 0.001 TRP C 757 HIS 0.012 0.001 HIS C 952 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.13 (34823) covalent geometry : angle 0.58732 / 0.30 (47098) hydrogen bonds : bond 0.03704 / 2.49 ( 2004) hydrogen bonds : angle 4.04568 / 2.93 ( 5913) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8330 Ramachandran restraints generated. 4165 Oldfield, 0 Emsley, 4165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8330 Ramachandran restraints generated. 4165 Oldfield, 0 Emsley, 4165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1053 residues out of total 3824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 960 time to evaluate : 1.473 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 324 ASP cc_start: 0.7402 (m-30) cc_final: 0.6977 (m-30) REVERT: A 414 LYS cc_start: 0.7937 (tttt) cc_final: 0.7458 (ttpp) REVERT: A 442 ASN cc_start: 0.7343 (m-40) cc_final: 0.7027 (m-40) REVERT: A 502 MET cc_start: 0.6485 (tmm) cc_final: 0.5542 (tmm) REVERT: A 507 LYS cc_start: 0.8335 (mmmm) cc_final: 0.8024 (mmmm) REVERT: A 512 GLU cc_start: 0.7964 (pm20) cc_final: 0.7603 (pm20) REVERT: A 548 LYS cc_start: 0.8522 (tttt) cc_final: 0.8254 (tptt) REVERT: A 555 GLN cc_start: 0.7067 (pp30) cc_final: 0.6384 (tp-100) REVERT: A 595 ARG cc_start: 0.8382 (ttp80) cc_final: 0.8087 (ttp80) REVERT: A 670 ASP cc_start: 0.7676 (m-30) cc_final: 0.7414 (t0) REVERT: A 737 GLU cc_start: 0.7116 (mm-30) cc_final: 0.6856 (mm-30) REVERT: A 801 GLU cc_start: 0.8537 (mp0) cc_final: 0.8189 (pm20) REVERT: A 804 PRO cc_start: 0.8015 (Cg_exo) cc_final: 0.7681 (Cg_endo) REVERT: A 808 ASN cc_start: 0.8232 (m-40) cc_final: 0.7981 (m-40) REVERT: A 879 TYR cc_start: 0.8625 (t80) cc_final: 0.8093 (t80) REVERT: A 880 LYS cc_start: 0.8946 (mtmm) cc_final: 0.8688 (ptpp) REVERT: A 927 MET cc_start: 0.8281 (mmm) cc_final: 0.8070 (tpp) REVERT: A 947 MET cc_start: 0.8057 (mmm) cc_final: 0.6879 (tmm) REVERT: A 948 HIS cc_start: 0.8312 (t-90) cc_final: 0.7885 (t70) REVERT: A 951 GLN cc_start: 0.8708 (mt0) cc_final: 0.8199 (mt0) REVERT: A 1068 LYS cc_start: 0.8474 (tttp) cc_final: 0.8185 (ttmm) REVERT: A 1142 THR cc_start: 0.8261 (m) cc_final: 0.7912 (p) REVERT: A 1179 ASP cc_start: 0.8504 (m-30) cc_final: 0.8078 (m-30) REVERT: A 1222 GLN cc_start: 0.7878 (pm20) cc_final: 0.7615 (pm20) REVERT: A 1245 ARG cc_start: 0.7930 (mtt-85) cc_final: 0.7662 (mtt90) REVERT: A 1250 GLN cc_start: 0.8458 (tp-100) cc_final: 0.8030 (tp40) REVERT: A 1275 ARG cc_start: 0.8499 (ttp-110) cc_final: 0.8235 (ttp-110) REVERT: A 1296 ASP cc_start: 0.8441 (m-30) cc_final: 0.8169 (p0) REVERT: A 1328 ASP cc_start: 0.8715 (t0) cc_final: 0.8174 (t0) REVERT: A 1390 LYS cc_start: 0.8609 (tttm) cc_final: 0.8020 (tptm) REVERT: A 1393 GLN cc_start: 0.7542 (mp10) cc_final: 0.6947 (mp10) REVERT: A 1432 MET cc_start: 0.7415 (ttm) cc_final: 0.6980 (ttt) REVERT: A 1438 SER cc_start: 0.8557 (m) cc_final: 0.8286 (p) REVERT: A 1465 LYS cc_start: 0.8728 (mttt) cc_final: 0.8449 (mttm) REVERT: A 1484 ILE cc_start: 0.8791 (mt) cc_final: 0.8555 (tt) REVERT: A 1513 LYS cc_start: 0.8783 (mttt) cc_final: 0.8571 (mmmm) REVERT: A 1514 LYS cc_start: 0.8348 (tttt) cc_final: 0.8000 (ttpp) REVERT: A 1575 GLU cc_start: 0.8111 (mm-30) cc_final: 0.7771 (mp0) REVERT: A 1681 MET cc_start: 0.9129 (mmm) cc_final: 0.8893 (mmm) REVERT: A 1734 ARG cc_start: 0.8299 (ptt-90) cc_final: 0.8038 (ptp-170) REVERT: A 1766 ASN cc_start: 0.8582 (m110) cc_final: 0.8140 (m-40) REVERT: A 1864 HIS cc_start: 0.8319 (m90) cc_final: 0.7775 (m-70) REVERT: A 1917 MET cc_start: 0.8245 (mtm) cc_final: 0.8045 (mtt) REVERT: A 1928 GLN cc_start: 0.8613 (tt0) cc_final: 0.8248 (tt0) REVERT: A 1959 MET cc_start: 0.8599 (mtp) cc_final: 0.8249 (mtp) REVERT: A 1992 GLU cc_start: 0.8379 (mm-30) cc_final: 0.8137 (mm-30) REVERT: A 1996 GLU cc_start: 0.8008 (mt-10) cc_final: 0.7715 (mt-10) REVERT: A 2023 GLU cc_start: 0.8093 (tm-30) cc_final: 0.7546 (tm-30) REVERT: A 2121 LYS cc_start: 0.8715 (mttt) cc_final: 0.8328 (mttt) REVERT: A 2124 LYS cc_start: 0.8719 (mttt) cc_final: 0.8515 (mtmt) REVERT: A 2218 ASN cc_start: 0.8302 (m-40) cc_final: 0.7928 (t0) REVERT: A 2329 GLU cc_start: 0.8743 (OUTLIER) cc_final: 0.8506 (mp0) REVERT: A 2418 ARG cc_start: 0.7696 (ttp-170) cc_final: 0.7382 (ttp-170) REVERT: A 2440 ARG cc_start: 0.8443 (ptp90) cc_final: 0.8213 (ptp90) REVERT: B 182 ASN cc_start: 0.7110 (t0) cc_final: 0.6616 (t0) REVERT: B 232 ARG cc_start: 0.6900 (ttm170) cc_final: 0.6349 (ttm-80) REVERT: B 275 ARG cc_start: 0.6788 (mpp80) cc_final: 0.6395 (mtt180) REVERT: B 286 ARG cc_start: 0.8414 (mmm160) cc_final: 0.8003 (tpp-160) REVERT: C 351 MET cc_start: 0.8063 (mmm) cc_final: 0.7816 (mmm) REVERT: C 359 LEU cc_start: 0.8527 (mt) cc_final: 0.8187 (mt) REVERT: C 373 CYS cc_start: 0.8622 (t) cc_final: 0.8226 (t) REVERT: C 388 GLU cc_start: 0.8233 (tp30) cc_final: 0.7851 (tm-30) REVERT: C 462 GLU cc_start: 0.8462 (tt0) cc_final: 0.8260 (tt0) REVERT: C 465 LYS cc_start: 0.8723 (tttt) cc_final: 0.8436 (tttm) REVERT: C 497 MET cc_start: 0.8836 (mmt) cc_final: 0.7339 (mmt) REVERT: C 642 GLU cc_start: 0.8186 (mm-30) cc_final: 0.7755 (mm-30) REVERT: C 742 MET cc_start: 0.8172 (mtm) cc_final: 0.7743 (mtm) REVERT: C 759 TRP cc_start: 0.6859 (m-10) cc_final: 0.6162 (m-10) REVERT: C 765 LEU cc_start: 0.8440 (tp) cc_final: 0.8197 (mm) REVERT: C 813 TYR cc_start: 0.8025 (OUTLIER) cc_final: 0.7504 (m-10) REVERT: C 848 MET cc_start: 0.8409 (mtp) cc_final: 0.7563 (mmp) REVERT: C 864 ASN cc_start: 0.9126 (m-40) cc_final: 0.8673 (t0) REVERT: C 893 ARG cc_start: 0.8485 (ptm-80) cc_final: 0.8023 (ptm-80) REVERT: C 923 ASP cc_start: 0.7963 (t0) cc_final: 0.7242 (t70) REVERT: C 979 GLN cc_start: 0.8097 (pp30) cc_final: 0.7893 (pp30) REVERT: C 982 MET cc_start: 0.7548 (tpp) cc_final: 0.6941 (tpp) REVERT: C 1072 HIS cc_start: 0.7273 (t70) cc_final: 0.7066 (t70) REVERT: C 1076 GLU cc_start: 0.8413 (tt0) cc_final: 0.8096 (tt0) REVERT: C 1096 ARG cc_start: 0.7944 (ptm160) cc_final: 0.7601 (ptm160) REVERT: C 1103 GLU cc_start: 0.7898 (tt0) cc_final: 0.7477 (tt0) REVERT: C 1342 LYS cc_start: 0.8512 (mmtt) cc_final: 0.8152 (mtmt) REVERT: C 1349 GLN cc_start: 0.8316 (mt0) cc_final: 0.8096 (mt0) REVERT: C 1364 THR cc_start: 0.8566 (t) cc_final: 0.8310 (t) REVERT: C 1380 MET cc_start: 0.8301 (tpp) cc_final: 0.8030 (tpp) REVERT: C 1383 LYS cc_start: 0.6990 (mttt) cc_final: 0.6681 (mtmm) REVERT: D 53 TYR cc_start: 0.7932 (t80) cc_final: 0.7621 (t80) REVERT: D 85 LYS cc_start: 0.8767 (mtpt) cc_final: 0.8488 (mtmt) REVERT: D 93 LEU cc_start: 0.8662 (tp) cc_final: 0.8433 (tp) REVERT: D 96 GLN cc_start: 0.8539 (tm-30) cc_final: 0.8118 (tm-30) REVERT: D 110 ARG cc_start: 0.8013 (mtt180) cc_final: 0.7625 (ttm110) REVERT: D 119 ASN cc_start: 0.8715 (OUTLIER) cc_final: 0.7548 (t0) REVERT: D 178 ASN cc_start: 0.7172 (t0) cc_final: 0.6714 (t0) REVERT: E 303 LEU cc_start: 0.7572 (mt) cc_final: 0.7246 (pp) REVERT: E 329 ASN cc_start: 0.8316 (m-40) cc_final: 0.8029 (m110) REVERT: E 354 GLU cc_start: 0.8664 (OUTLIER) cc_final: 0.8092 (pp20) REVERT: E 379 GLU cc_start: 0.8884 (mm-30) cc_final: 0.8637 (mm-30) REVERT: E 510 LEU cc_start: 0.8430 (mt) cc_final: 0.8201 (mp) REVERT: E 529 GLN cc_start: 0.7170 (tp40) cc_final: 0.6681 (mm-40) REVERT: E 530 ARG cc_start: 0.8581 (ptp-170) cc_final: 0.8351 (ptp-170) REVERT: E 532 ILE cc_start: 0.8921 (mm) cc_final: 0.8555 (tp) REVERT: E 533 GLU cc_start: 0.8404 (mt-10) cc_final: 0.7826 (mt-10) REVERT: G 9 GLU cc_start: 0.7980 (mt-10) cc_final: 0.7488 (mt-10) REVERT: G 21 LYS cc_start: 0.8110 (mmtm) cc_final: 0.7414 (mmmt) REVERT: G 24 MET cc_start: 0.7567 (mtm) cc_final: 0.7173 (mtm) REVERT: G 25 LYS cc_start: 0.8458 (mttt) cc_final: 0.8088 (mttt) REVERT: G 51 TYR cc_start: 0.7347 (m-80) cc_final: 0.6893 (m-80) REVERT: G 52 MET cc_start: 0.7133 (ttp) cc_final: 0.6417 (tmm) REVERT: G 626 LYS cc_start: 0.7702 (ttpp) cc_final: 0.7325 (ttpp) REVERT: G 634 LYS cc_start: 0.5951 (ttpp) cc_final: 0.5366 (tptp) REVERT: G 638 SER cc_start: 0.7398 (p) cc_final: 0.7156 (p) REVERT: G 643 MET cc_start: 0.7534 (ptp) cc_final: 0.7219 (ptp) REVERT: G 1068 LYS cc_start: 0.8649 (OUTLIER) cc_final: 0.8290 (ptmm) REVERT: G 1074 ARG cc_start: 0.8347 (ttp80) cc_final: 0.7792 (ttp-170) REVERT: G 1082 LYS cc_start: 0.8801 (mttt) cc_final: 0.8371 (mttt) REVERT: G 1083 HIS cc_start: 0.8563 (m90) cc_final: 0.8356 (m-70) REVERT: G 1084 GLU cc_start: 0.7919 (tp30) cc_final: 0.7263 (tp30) REVERT: G 1123 LYS cc_start: 0.7882 (tttt) cc_final: 0.7559 (tttt) REVERT: G 1156 GLU cc_start: 0.8462 (mt-10) cc_final: 0.8154 (mt-10) REVERT: G 1159 GLU cc_start: 0.8833 (tt0) cc_final: 0.8451 (tt0) REVERT: G 1163 ARG cc_start: 0.8872 (tpp80) cc_final: 0.8396 (ttt180) REVERT: G 1165 GLN cc_start: 0.8993 (mt0) cc_final: 0.8531 (mt0) REVERT: G 1166 ASN cc_start: 0.8999 (m-40) cc_final: 0.8740 (m-40) REVERT: G 1173 MET cc_start: 0.8664 (mtm) cc_final: 0.8327 (mtm) REVERT: H 1282 LYS cc_start: 0.8329 (mtpt) cc_final: 0.8032 (mtpt) REVERT: H 1283 GLU cc_start: 0.8161 (tp30) cc_final: 0.7771 (mp0) outliers start: 93 outliers final: 66 residues processed: 1008 average time/residue: 0.2455 time to fit residues: 387.7269 Evaluate side-chains 1022 residues out of total 3824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 951 time to evaluate : 1.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 435 TYR Chi-restraints excluded: chain A residue 457 PHE Chi-restraints excluded: chain A residue 491 CYS Chi-restraints excluded: chain A residue 503 ILE Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 546 ILE Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 590 LEU Chi-restraints excluded: chain A residue 624 ASP Chi-restraints excluded: chain A residue 635 LEU Chi-restraints excluded: chain A residue 661 ILE Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain A residue 721 LEU Chi-restraints excluded: chain A residue 905 LEU Chi-restraints excluded: chain A residue 1030 SER Chi-restraints excluded: chain A residue 1073 PHE Chi-restraints excluded: chain A residue 1171 ASN Chi-restraints excluded: chain A residue 1185 LEU Chi-restraints excluded: chain A residue 1191 LEU Chi-restraints excluded: chain A residue 1314 ILE Chi-restraints excluded: chain A residue 1382 THR Chi-restraints excluded: chain A residue 1502 ASP Chi-restraints excluded: chain A residue 1544 VAL Chi-restraints excluded: chain A residue 1696 SER Chi-restraints excluded: chain A residue 1816 LEU Chi-restraints excluded: chain A residue 1912 LEU Chi-restraints excluded: chain A residue 1922 SER Chi-restraints excluded: chain A residue 1961 VAL Chi-restraints excluded: chain A residue 2025 LEU Chi-restraints excluded: chain A residue 2155 GLU Chi-restraints excluded: chain A residue 2329 GLU Chi-restraints excluded: chain B residue 14 ILE Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 269 SER Chi-restraints excluded: chain B residue 284 ILE Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 292 HIS Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain C residue 309 ASP Chi-restraints excluded: chain C residue 364 LEU Chi-restraints excluded: chain C residue 482 SER Chi-restraints excluded: chain C residue 687 VAL Chi-restraints excluded: chain C residue 712 ILE Chi-restraints excluded: chain C residue 725 ILE Chi-restraints excluded: chain C residue 813 TYR Chi-restraints excluded: chain C residue 831 MET Chi-restraints excluded: chain C residue 995 SER Chi-restraints excluded: chain C residue 996 VAL Chi-restraints excluded: chain C residue 1022 ARG Chi-restraints excluded: chain C residue 1024 PHE Chi-restraints excluded: chain C residue 1083 SER Chi-restraints excluded: chain C residue 1218 CYS Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 119 ASN Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain E residue 354 GLU Chi-restraints excluded: chain E residue 541 MET Chi-restraints excluded: chain G residue 59 LEU Chi-restraints excluded: chain G residue 628 THR Chi-restraints excluded: chain G residue 1067 HIS Chi-restraints excluded: chain G residue 1068 LYS Chi-restraints excluded: chain G residue 1096 ILE Chi-restraints excluded: chain G residue 1110 LYS Chi-restraints excluded: chain G residue 1113 SER Chi-restraints excluded: chain G residue 1120 VAL Chi-restraints excluded: chain G residue 1126 LYS Chi-restraints excluded: chain G residue 1174 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 419 random chunks: chunk 48 optimal weight: 4.9990 chunk 377 optimal weight: 0.8980 chunk 205 optimal weight: 0.8980 chunk 103 optimal weight: 0.6980 chunk 16 optimal weight: 7.9990 chunk 395 optimal weight: 10.0000 chunk 178 optimal weight: 0.6980 chunk 102 optimal weight: 0.9990 chunk 331 optimal weight: 0.9980 chunk 143 optimal weight: 0.5980 chunk 42 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 481 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1480 GLN ** A1691 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2419 ASN ** B 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 843 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 952 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 498 GLN G 23 GLN G 639 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.146822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.116355 restraints weight = 73241.237| |-----------------------------------------------------------------------------| r_work (start): 0.3669 rms_B_bonded: 2.80 r_work: 0.3525 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.4250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 34823 Z= 0.151 Angle : 0.603 12.511 47098 Z= 0.308 Chirality : 0.042 0.229 5383 Planarity : 0.004 0.137 5944 Dihedral : 4.512 71.266 4602 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.74 % Favored : 97.21 % Rotamer: Outliers : 2.54 % Allowed : 20.53 % Favored : 76.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.54 (0.13), residues: 4165 helix: 1.69 (0.10), residues: 2763 sheet: 0.17 (0.35), residues: 228 loop : -0.32 (0.19), residues: 1174 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG A 444 TYR 0.053 0.001 TYR E 386 PHE 0.036 0.002 PHE A 385 TRP 0.030 0.001 TRP C 757 HIS 0.012 0.001 HIS C 952 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.15 (34823) covalent geometry : angle 0.60346 / 0.31 (47098) hydrogen bonds : bond 0.03748 / 2.50 ( 2004) hydrogen bonds : angle 4.05924 / 2.94 ( 5913) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8330 Ramachandran restraints generated. 4165 Oldfield, 0 Emsley, 4165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8330 Ramachandran restraints generated. 4165 Oldfield, 0 Emsley, 4165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1064 residues out of total 3824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 967 time to evaluate : 1.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 324 ASP cc_start: 0.7400 (m-30) cc_final: 0.6972 (m-30) REVERT: A 414 LYS cc_start: 0.7943 (tttt) cc_final: 0.7565 (ttpt) REVERT: A 442 ASN cc_start: 0.7351 (m-40) cc_final: 0.7037 (m-40) REVERT: A 502 MET cc_start: 0.6534 (tmm) cc_final: 0.5550 (tmm) REVERT: A 512 GLU cc_start: 0.7944 (pm20) cc_final: 0.7654 (pm20) REVERT: A 548 LYS cc_start: 0.8530 (tttt) cc_final: 0.8270 (tptt) REVERT: A 555 GLN cc_start: 0.7072 (pp30) cc_final: 0.6374 (tp-100) REVERT: A 670 ASP cc_start: 0.7669 (m-30) cc_final: 0.7446 (t0) REVERT: A 737 GLU cc_start: 0.7115 (mm-30) cc_final: 0.6906 (mm-30) REVERT: A 763 ASP cc_start: 0.7871 (m-30) cc_final: 0.7641 (m-30) REVERT: A 808 ASN cc_start: 0.8222 (m-40) cc_final: 0.7960 (m-40) REVERT: A 879 TYR cc_start: 0.8654 (t80) cc_final: 0.8194 (t80) REVERT: A 880 LYS cc_start: 0.8942 (mtmm) cc_final: 0.8693 (ptpp) REVERT: A 927 MET cc_start: 0.8337 (mmm) cc_final: 0.8103 (tpp) REVERT: A 947 MET cc_start: 0.8056 (mmm) cc_final: 0.6791 (tmm) REVERT: A 948 HIS cc_start: 0.8350 (t-90) cc_final: 0.7887 (t70) REVERT: A 951 GLN cc_start: 0.8731 (mt0) cc_final: 0.8187 (mt0) REVERT: A 962 ASP cc_start: 0.8556 (p0) cc_final: 0.8229 (p0) REVERT: A 985 GLN cc_start: 0.8284 (mt0) cc_final: 0.7724 (mp10) REVERT: A 1068 LYS cc_start: 0.8478 (tttp) cc_final: 0.8199 (ttmm) REVERT: A 1142 THR cc_start: 0.8225 (m) cc_final: 0.7893 (p) REVERT: A 1179 ASP cc_start: 0.8519 (m-30) cc_final: 0.8092 (m-30) REVERT: A 1222 GLN cc_start: 0.7919 (pm20) cc_final: 0.7630 (pm20) REVERT: A 1245 ARG cc_start: 0.7914 (mtt-85) cc_final: 0.7655 (mtt90) REVERT: A 1250 GLN cc_start: 0.8490 (tp-100) cc_final: 0.8053 (tp40) REVERT: A 1275 ARG cc_start: 0.8504 (ttp-110) cc_final: 0.8265 (ttp-110) REVERT: A 1296 ASP cc_start: 0.8462 (m-30) cc_final: 0.8194 (p0) REVERT: A 1328 ASP cc_start: 0.8719 (t0) cc_final: 0.8168 (t0) REVERT: A 1390 LYS cc_start: 0.8592 (tttm) cc_final: 0.8000 (tptm) REVERT: A 1393 GLN cc_start: 0.7511 (mp10) cc_final: 0.6922 (mp10) REVERT: A 1438 SER cc_start: 0.8561 (m) cc_final: 0.8269 (p) REVERT: A 1439 LEU cc_start: 0.8427 (mt) cc_final: 0.8091 (mt) REVERT: A 1465 LYS cc_start: 0.8749 (mttt) cc_final: 0.8474 (mttm) REVERT: A 1484 ILE cc_start: 0.8785 (mt) cc_final: 0.8567 (tt) REVERT: A 1513 LYS cc_start: 0.8803 (mttt) cc_final: 0.8594 (mmmm) REVERT: A 1514 LYS cc_start: 0.8339 (tttt) cc_final: 0.7977 (ttpp) REVERT: A 1575 GLU cc_start: 0.8107 (mm-30) cc_final: 0.7785 (mp0) REVERT: A 1605 LYS cc_start: 0.9059 (mttm) cc_final: 0.8838 (mttm) REVERT: A 1681 MET cc_start: 0.9129 (mmm) cc_final: 0.8919 (mmm) REVERT: A 1734 ARG cc_start: 0.8305 (ptt-90) cc_final: 0.8007 (ptp-170) REVERT: A 1766 ASN cc_start: 0.8575 (m110) cc_final: 0.8161 (m-40) REVERT: A 1818 HIS cc_start: 0.7768 (m90) cc_final: 0.7458 (m-70) REVERT: A 1864 HIS cc_start: 0.8346 (m90) cc_final: 0.7795 (m-70) REVERT: A 1917 MET cc_start: 0.8251 (mtm) cc_final: 0.8045 (mtt) REVERT: A 1928 GLN cc_start: 0.8636 (tt0) cc_final: 0.8303 (tt0) REVERT: A 1959 MET cc_start: 0.8607 (mtp) cc_final: 0.8248 (mtp) REVERT: A 1992 GLU cc_start: 0.8416 (mm-30) cc_final: 0.8176 (mm-30) REVERT: A 1996 GLU cc_start: 0.8043 (mt-10) cc_final: 0.7763 (mt-10) REVERT: A 2023 GLU cc_start: 0.8109 (tm-30) cc_final: 0.7555 (tm-30) REVERT: A 2121 LYS cc_start: 0.8717 (mttt) cc_final: 0.8408 (mttt) REVERT: A 2124 LYS cc_start: 0.8700 (mttt) cc_final: 0.8497 (mtmt) REVERT: A 2218 ASN cc_start: 0.8303 (m-40) cc_final: 0.7924 (t0) REVERT: A 2329 GLU cc_start: 0.8755 (OUTLIER) cc_final: 0.8505 (mp0) REVERT: A 2418 ARG cc_start: 0.7688 (ttp-170) cc_final: 0.7336 (ttp-170) REVERT: A 2440 ARG cc_start: 0.8429 (ptp90) cc_final: 0.8193 (ptp90) REVERT: B 141 ARG cc_start: 0.7258 (mtp85) cc_final: 0.7012 (mtp85) REVERT: B 182 ASN cc_start: 0.7145 (t0) cc_final: 0.6644 (t0) REVERT: B 232 ARG cc_start: 0.6894 (ttm170) cc_final: 0.6322 (ttm-80) REVERT: B 275 ARG cc_start: 0.6762 (mpp80) cc_final: 0.6463 (mtt180) REVERT: B 286 ARG cc_start: 0.8408 (mmm160) cc_final: 0.7983 (tpp-160) REVERT: C 351 MET cc_start: 0.8042 (mmm) cc_final: 0.7808 (mmm) REVERT: C 373 CYS cc_start: 0.8637 (t) cc_final: 0.8246 (t) REVERT: C 388 GLU cc_start: 0.8260 (tp30) cc_final: 0.7731 (tp30) REVERT: C 462 GLU cc_start: 0.8488 (tt0) cc_final: 0.8282 (tt0) REVERT: C 465 LYS cc_start: 0.8748 (tttt) cc_final: 0.8361 (tttm) REVERT: C 497 MET cc_start: 0.8833 (mmt) cc_final: 0.7329 (mmt) REVERT: C 642 GLU cc_start: 0.8174 (mm-30) cc_final: 0.7831 (mm-30) REVERT: C 713 ASP cc_start: 0.7844 (OUTLIER) cc_final: 0.7393 (t70) REVERT: C 742 MET cc_start: 0.8172 (mtm) cc_final: 0.7787 (mtt) REVERT: C 759 TRP cc_start: 0.6874 (m-10) cc_final: 0.6226 (m-10) REVERT: C 813 TYR cc_start: 0.8039 (OUTLIER) cc_final: 0.7532 (m-10) REVERT: C 848 MET cc_start: 0.8407 (mtp) cc_final: 0.7606 (mmp) REVERT: C 864 ASN cc_start: 0.9122 (m-40) cc_final: 0.8686 (t0) REVERT: C 893 ARG cc_start: 0.8550 (ptm-80) cc_final: 0.8109 (ptm-80) REVERT: C 923 ASP cc_start: 0.7979 (t0) cc_final: 0.7281 (t70) REVERT: C 982 MET cc_start: 0.7455 (tpp) cc_final: 0.6807 (tpp) REVERT: C 1072 HIS cc_start: 0.7235 (t70) cc_final: 0.7020 (t70) REVERT: C 1076 GLU cc_start: 0.8410 (tt0) cc_final: 0.8078 (tt0) REVERT: C 1096 ARG cc_start: 0.7953 (ptm160) cc_final: 0.7587 (ptm160) REVERT: C 1103 GLU cc_start: 0.7887 (tt0) cc_final: 0.7466 (tt0) REVERT: C 1342 LYS cc_start: 0.8531 (mmtt) cc_final: 0.8171 (mtmt) REVERT: C 1349 GLN cc_start: 0.8347 (mt0) cc_final: 0.8130 (mt0) REVERT: C 1364 THR cc_start: 0.8588 (t) cc_final: 0.8336 (t) REVERT: C 1380 MET cc_start: 0.8300 (tpp) cc_final: 0.8002 (tpp) REVERT: C 1383 LYS cc_start: 0.6997 (mttt) cc_final: 0.6701 (mtmm) REVERT: D 53 TYR cc_start: 0.7910 (t80) cc_final: 0.7637 (t80) REVERT: D 110 ARG cc_start: 0.8000 (mtt180) cc_final: 0.7626 (ttm110) REVERT: D 119 ASN cc_start: 0.8732 (OUTLIER) cc_final: 0.8025 (t0) REVERT: D 123 GLN cc_start: 0.8709 (mp10) cc_final: 0.8363 (mp10) REVERT: D 178 ASN cc_start: 0.7230 (t0) cc_final: 0.6747 (t0) REVERT: E 329 ASN cc_start: 0.8205 (m-40) cc_final: 0.7903 (m110) REVERT: E 354 GLU cc_start: 0.8665 (OUTLIER) cc_final: 0.8104 (pp20) REVERT: E 379 GLU cc_start: 0.8897 (mm-30) cc_final: 0.8640 (mm-30) REVERT: E 407 LYS cc_start: 0.7936 (ptpp) cc_final: 0.7587 (ptpp) REVERT: E 529 GLN cc_start: 0.7193 (tp40) cc_final: 0.6273 (mm-40) REVERT: E 530 ARG cc_start: 0.8573 (ptp-170) cc_final: 0.8343 (ptp-170) REVERT: E 532 ILE cc_start: 0.8929 (mm) cc_final: 0.8587 (tp) REVERT: E 533 GLU cc_start: 0.8403 (mt-10) cc_final: 0.7821 (mt-10) REVERT: G 9 GLU cc_start: 0.7982 (mt-10) cc_final: 0.7497 (mt-10) REVERT: G 21 LYS cc_start: 0.8180 (mmtm) cc_final: 0.7576 (mmmt) REVERT: G 24 MET cc_start: 0.7601 (mtm) cc_final: 0.7285 (mtm) REVERT: G 25 LYS cc_start: 0.8479 (mttt) cc_final: 0.8129 (mttt) REVERT: G 51 TYR cc_start: 0.7339 (m-80) cc_final: 0.6944 (m-80) REVERT: G 52 MET cc_start: 0.7173 (ttp) cc_final: 0.6451 (tmm) REVERT: G 634 LYS cc_start: 0.5937 (ttpp) cc_final: 0.5451 (tptp) REVERT: G 643 MET cc_start: 0.7526 (ptp) cc_final: 0.7226 (ptp) REVERT: G 1068 LYS cc_start: 0.8672 (ptmm) cc_final: 0.8306 (ptmm) REVERT: G 1074 ARG cc_start: 0.8337 (ttp80) cc_final: 0.7830 (ttp-170) REVERT: G 1079 PHE cc_start: 0.8953 (m-80) cc_final: 0.8566 (m-80) REVERT: G 1082 LYS cc_start: 0.8853 (mttt) cc_final: 0.8368 (mttt) REVERT: G 1083 HIS cc_start: 0.8566 (m90) cc_final: 0.8312 (m-70) REVERT: G 1084 GLU cc_start: 0.7924 (tp30) cc_final: 0.7252 (tp30) REVERT: G 1123 LYS cc_start: 0.7891 (tttt) cc_final: 0.7571 (tttt) REVERT: G 1148 TYR cc_start: 0.7931 (m-80) cc_final: 0.7293 (m-80) REVERT: G 1156 GLU cc_start: 0.8473 (mt-10) cc_final: 0.8160 (mt-10) REVERT: G 1159 GLU cc_start: 0.8833 (tt0) cc_final: 0.8445 (tt0) REVERT: G 1163 ARG cc_start: 0.8880 (tpp80) cc_final: 0.8263 (ttt180) REVERT: G 1165 GLN cc_start: 0.8970 (mt0) cc_final: 0.8516 (mt0) REVERT: G 1166 ASN cc_start: 0.8998 (m-40) cc_final: 0.8767 (m110) REVERT: G 1173 MET cc_start: 0.8694 (mtm) cc_final: 0.8337 (mtm) REVERT: H 1282 LYS cc_start: 0.8329 (mtpt) cc_final: 0.8025 (mtpt) REVERT: H 1283 GLU cc_start: 0.8179 (tp30) cc_final: 0.7780 (mp0) outliers start: 97 outliers final: 73 residues processed: 1013 average time/residue: 0.2503 time to fit residues: 395.2918 Evaluate side-chains 1030 residues out of total 3824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 952 time to evaluate : 1.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 435 TYR Chi-restraints excluded: chain A residue 457 PHE Chi-restraints excluded: chain A residue 491 CYS Chi-restraints excluded: chain A residue 503 ILE Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 546 ILE Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 590 LEU Chi-restraints excluded: chain A residue 635 LEU Chi-restraints excluded: chain A residue 661 ILE Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain A residue 721 LEU Chi-restraints excluded: chain A residue 854 LEU Chi-restraints excluded: chain A residue 905 LEU Chi-restraints excluded: chain A residue 935 LEU Chi-restraints excluded: chain A residue 958 VAL Chi-restraints excluded: chain A residue 1030 SER Chi-restraints excluded: chain A residue 1073 PHE Chi-restraints excluded: chain A residue 1171 ASN Chi-restraints excluded: chain A residue 1185 LEU Chi-restraints excluded: chain A residue 1191 LEU Chi-restraints excluded: chain A residue 1314 ILE Chi-restraints excluded: chain A residue 1382 THR Chi-restraints excluded: chain A residue 1502 ASP Chi-restraints excluded: chain A residue 1544 VAL Chi-restraints excluded: chain A residue 1696 SER Chi-restraints excluded: chain A residue 1816 LEU Chi-restraints excluded: chain A residue 1912 LEU Chi-restraints excluded: chain A residue 1922 SER Chi-restraints excluded: chain A residue 1944 VAL Chi-restraints excluded: chain A residue 1951 LEU Chi-restraints excluded: chain A residue 1961 VAL Chi-restraints excluded: chain A residue 1975 SER Chi-restraints excluded: chain A residue 2025 LEU Chi-restraints excluded: chain A residue 2155 GLU Chi-restraints excluded: chain A residue 2329 GLU Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 269 SER Chi-restraints excluded: chain B residue 284 ILE Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 292 HIS Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain C residue 309 ASP Chi-restraints excluded: chain C residue 364 LEU Chi-restraints excluded: chain C residue 384 ASP Chi-restraints excluded: chain C residue 482 SER Chi-restraints excluded: chain C residue 687 VAL Chi-restraints excluded: chain C residue 712 ILE Chi-restraints excluded: chain C residue 713 ASP Chi-restraints excluded: chain C residue 725 ILE Chi-restraints excluded: chain C residue 798 LEU Chi-restraints excluded: chain C residue 813 TYR Chi-restraints excluded: chain C residue 831 MET Chi-restraints excluded: chain C residue 891 LEU Chi-restraints excluded: chain C residue 995 SER Chi-restraints excluded: chain C residue 1022 ARG Chi-restraints excluded: chain C residue 1024 PHE Chi-restraints excluded: chain C residue 1083 SER Chi-restraints excluded: chain C residue 1218 CYS Chi-restraints excluded: chain C residue 1401 LEU Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 119 ASN Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain E residue 354 GLU Chi-restraints excluded: chain E residue 541 MET Chi-restraints excluded: chain G residue 59 LEU Chi-restraints excluded: chain G residue 628 THR Chi-restraints excluded: chain G residue 1067 HIS Chi-restraints excluded: chain G residue 1096 ILE Chi-restraints excluded: chain G residue 1110 LYS Chi-restraints excluded: chain G residue 1113 SER Chi-restraints excluded: chain G residue 1120 VAL Chi-restraints excluded: chain G residue 1126 LYS Chi-restraints excluded: chain G residue 1174 ASN Chi-restraints excluded: chain G residue 1175 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 419 random chunks: chunk 134 optimal weight: 2.9990 chunk 352 optimal weight: 0.0970 chunk 167 optimal weight: 2.9990 chunk 18 optimal weight: 0.0770 chunk 16 optimal weight: 5.9990 chunk 224 optimal weight: 0.0040 chunk 49 optimal weight: 5.9990 chunk 227 optimal weight: 2.9990 chunk 380 optimal weight: 7.9990 chunk 222 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 overall best weight: 0.6350 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 481 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1378 GLN ** A1691 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1977 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2419 ASN ** B 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 843 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 952 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 498 GLN G 23 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.146957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.116298 restraints weight = 73010.825| |-----------------------------------------------------------------------------| r_work (start): 0.3676 rms_B_bonded: 2.81 r_work: 0.3534 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.4362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 34823 Z= 0.141 Angle : 0.621 12.182 47098 Z= 0.315 Chirality : 0.042 0.215 5383 Planarity : 0.004 0.082 5944 Dihedral : 4.497 71.088 4602 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.86 % Favored : 97.09 % Rotamer: Outliers : 2.33 % Allowed : 20.85 % Favored : 76.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.57 (0.13), residues: 4165 helix: 1.69 (0.10), residues: 2769 sheet: 0.31 (0.36), residues: 224 loop : -0.30 (0.19), residues: 1172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG A 444 TYR 0.053 0.001 TYR E 386 PHE 0.036 0.001 PHE A 385 TRP 0.028 0.001 TRP C 757 HIS 0.012 0.001 HIS C 952 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.14 (34823) covalent geometry : angle 0.62089 / 0.32 (47098) hydrogen bonds : bond 0.03683 / 2.47 ( 2004) hydrogen bonds : angle 4.04653 / 2.92 ( 5913) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8330 Ramachandran restraints generated. 4165 Oldfield, 0 Emsley, 4165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8330 Ramachandran restraints generated. 4165 Oldfield, 0 Emsley, 4165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1060 residues out of total 3824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 971 time to evaluate : 1.459 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 324 ASP cc_start: 0.7401 (m-30) cc_final: 0.6973 (m-30) REVERT: A 414 LYS cc_start: 0.7900 (tttt) cc_final: 0.7434 (ttpp) REVERT: A 442 ASN cc_start: 0.7353 (m-40) cc_final: 0.7065 (m-40) REVERT: A 502 MET cc_start: 0.6556 (tmm) cc_final: 0.5562 (tmm) REVERT: A 512 GLU cc_start: 0.7919 (pm20) cc_final: 0.7563 (pm20) REVERT: A 548 LYS cc_start: 0.8511 (tttt) cc_final: 0.8184 (tptp) REVERT: A 555 GLN cc_start: 0.7058 (pp30) cc_final: 0.6369 (tp-100) REVERT: A 563 GLU cc_start: 0.6646 (mt-10) cc_final: 0.6008 (tm-30) REVERT: A 670 ASP cc_start: 0.7635 (m-30) cc_final: 0.7400 (t0) REVERT: A 801 GLU cc_start: 0.8568 (mp0) cc_final: 0.8212 (pm20) REVERT: A 808 ASN cc_start: 0.8229 (m-40) cc_final: 0.7950 (m-40) REVERT: A 879 TYR cc_start: 0.8663 (t80) cc_final: 0.8205 (t80) REVERT: A 880 LYS cc_start: 0.8948 (mtmm) cc_final: 0.8713 (ptpp) REVERT: A 927 MET cc_start: 0.8365 (mmm) cc_final: 0.8131 (tpp) REVERT: A 947 MET cc_start: 0.8050 (mmm) cc_final: 0.6734 (tmm) REVERT: A 948 HIS cc_start: 0.8324 (t-90) cc_final: 0.7855 (t70) REVERT: A 951 GLN cc_start: 0.8728 (mt0) cc_final: 0.8163 (mt0) REVERT: A 962 ASP cc_start: 0.8552 (p0) cc_final: 0.8227 (p0) REVERT: A 985 GLN cc_start: 0.8263 (mt0) cc_final: 0.7786 (mp10) REVERT: A 1030 SER cc_start: 0.9113 (OUTLIER) cc_final: 0.8790 (p) REVERT: A 1068 LYS cc_start: 0.8485 (tttp) cc_final: 0.8208 (ttmm) REVERT: A 1109 ARG cc_start: 0.8601 (mtm-85) cc_final: 0.8365 (mtm-85) REVERT: A 1172 ARG cc_start: 0.8716 (mpp80) cc_final: 0.8429 (mtt90) REVERT: A 1179 ASP cc_start: 0.8510 (m-30) cc_final: 0.8079 (m-30) REVERT: A 1221 ASN cc_start: 0.7906 (t0) cc_final: 0.7202 (p0) REVERT: A 1222 GLN cc_start: 0.7923 (pm20) cc_final: 0.7626 (pm20) REVERT: A 1245 ARG cc_start: 0.7907 (mtt-85) cc_final: 0.7655 (mtt90) REVERT: A 1250 GLN cc_start: 0.8489 (tp-100) cc_final: 0.8027 (tp-100) REVERT: A 1259 CYS cc_start: 0.8610 (m) cc_final: 0.8403 (t) REVERT: A 1328 ASP cc_start: 0.8701 (t0) cc_final: 0.8141 (t0) REVERT: A 1390 LYS cc_start: 0.8576 (tttm) cc_final: 0.7991 (tptm) REVERT: A 1393 GLN cc_start: 0.7525 (mp10) cc_final: 0.6930 (mp10) REVERT: A 1438 SER cc_start: 0.8582 (m) cc_final: 0.8267 (p) REVERT: A 1439 LEU cc_start: 0.8424 (mt) cc_final: 0.8051 (mt) REVERT: A 1444 GLU cc_start: 0.8319 (mm-30) cc_final: 0.8080 (mm-30) REVERT: A 1465 LYS cc_start: 0.8749 (mttt) cc_final: 0.8465 (mttm) REVERT: A 1514 LYS cc_start: 0.8334 (tttt) cc_final: 0.7960 (ttpp) REVERT: A 1575 GLU cc_start: 0.8085 (mm-30) cc_final: 0.7769 (mp0) REVERT: A 1605 LYS cc_start: 0.9107 (mttm) cc_final: 0.8846 (mttm) REVERT: A 1681 MET cc_start: 0.9139 (mmm) cc_final: 0.8884 (mmm) REVERT: A 1734 ARG cc_start: 0.8291 (ptt-90) cc_final: 0.8066 (ptp-170) REVERT: A 1766 ASN cc_start: 0.8586 (m110) cc_final: 0.8174 (m-40) REVERT: A 1817 ILE cc_start: 0.8695 (mm) cc_final: 0.8415 (tp) REVERT: A 1818 HIS cc_start: 0.7764 (m90) cc_final: 0.7335 (m-70) REVERT: A 1864 HIS cc_start: 0.8337 (m90) cc_final: 0.7817 (m-70) REVERT: A 1917 MET cc_start: 0.8243 (mtm) cc_final: 0.8039 (mtt) REVERT: A 1928 GLN cc_start: 0.8643 (tt0) cc_final: 0.8303 (tt0) REVERT: A 1959 MET cc_start: 0.8603 (mtp) cc_final: 0.8238 (mtp) REVERT: A 1977 GLN cc_start: 0.8472 (tt0) cc_final: 0.7920 (tm-30) REVERT: A 1983 ASN cc_start: 0.7974 (t0) cc_final: 0.7353 (t0) REVERT: A 1992 GLU cc_start: 0.8407 (mm-30) cc_final: 0.8187 (mm-30) REVERT: A 1996 GLU cc_start: 0.8034 (mt-10) cc_final: 0.7753 (mt-10) REVERT: A 2023 GLU cc_start: 0.8103 (tm-30) cc_final: 0.7541 (tm-30) REVERT: A 2049 ARG cc_start: 0.8264 (mmm-85) cc_final: 0.7748 (mmm-85) REVERT: A 2121 LYS cc_start: 0.8719 (mttt) cc_final: 0.8356 (mttt) REVERT: A 2124 LYS cc_start: 0.8696 (mttt) cc_final: 0.8491 (mtmt) REVERT: A 2218 ASN cc_start: 0.8287 (m-40) cc_final: 0.7910 (t0) REVERT: A 2268 MET cc_start: 0.9024 (tpt) cc_final: 0.8793 (tpt) REVERT: A 2329 GLU cc_start: 0.8758 (OUTLIER) cc_final: 0.8504 (mp0) REVERT: A 2440 ARG cc_start: 0.8427 (ptp90) cc_final: 0.8195 (ptp90) REVERT: B 141 ARG cc_start: 0.7213 (mtp85) cc_final: 0.6938 (mtp85) REVERT: B 182 ASN cc_start: 0.7141 (t0) cc_final: 0.6627 (t0) REVERT: B 188 MET cc_start: 0.1949 (mmm) cc_final: 0.1046 (mmm) REVERT: B 212 ARG cc_start: 0.6222 (tpm170) cc_final: 0.5768 (tpm170) REVERT: B 232 ARG cc_start: 0.6895 (ttm170) cc_final: 0.6213 (ttm110) REVERT: B 275 ARG cc_start: 0.6753 (mpp80) cc_final: 0.6474 (mtt180) REVERT: B 286 ARG cc_start: 0.8399 (mmm160) cc_final: 0.7977 (tpp-160) REVERT: C 351 MET cc_start: 0.8025 (mmm) cc_final: 0.7794 (mmm) REVERT: C 360 ASN cc_start: 0.8301 (p0) cc_final: 0.8036 (p0) REVERT: C 373 CYS cc_start: 0.8612 (t) cc_final: 0.8221 (t) REVERT: C 388 GLU cc_start: 0.8259 (tp30) cc_final: 0.7744 (tp30) REVERT: C 465 LYS cc_start: 0.8750 (tttt) cc_final: 0.8359 (tttm) REVERT: C 497 MET cc_start: 0.8824 (mmt) cc_final: 0.7332 (mmt) REVERT: C 642 GLU cc_start: 0.8189 (mm-30) cc_final: 0.7834 (mm-30) REVERT: C 713 ASP cc_start: 0.7837 (OUTLIER) cc_final: 0.7405 (t70) REVERT: C 742 MET cc_start: 0.8258 (mtm) cc_final: 0.7981 (mtt) REVERT: C 759 TRP cc_start: 0.6934 (m-10) cc_final: 0.6264 (m-10) REVERT: C 813 TYR cc_start: 0.8040 (OUTLIER) cc_final: 0.7549 (m-10) REVERT: C 848 MET cc_start: 0.8432 (mtp) cc_final: 0.7597 (mmp) REVERT: C 852 MET cc_start: 0.7223 (OUTLIER) cc_final: 0.7022 (ptm) REVERT: C 864 ASN cc_start: 0.9122 (m-40) cc_final: 0.8684 (t0) REVERT: C 893 ARG cc_start: 0.8591 (ptm-80) cc_final: 0.8099 (ptm-80) REVERT: C 923 ASP cc_start: 0.7947 (t0) cc_final: 0.7237 (t70) REVERT: C 982 MET cc_start: 0.7452 (tpp) cc_final: 0.6792 (tpp) REVERT: C 1072 HIS cc_start: 0.7252 (t70) cc_final: 0.7031 (t70) REVERT: C 1076 GLU cc_start: 0.8417 (tt0) cc_final: 0.8103 (tt0) REVERT: C 1096 ARG cc_start: 0.7920 (ptm160) cc_final: 0.7519 (ptm160) REVERT: C 1103 GLU cc_start: 0.7895 (tt0) cc_final: 0.7474 (tt0) REVERT: C 1342 LYS cc_start: 0.8526 (mmtt) cc_final: 0.8186 (mtmt) REVERT: C 1349 GLN cc_start: 0.8323 (mt0) cc_final: 0.8122 (mt0) REVERT: C 1364 THR cc_start: 0.8566 (t) cc_final: 0.8310 (t) REVERT: C 1380 MET cc_start: 0.8282 (tpp) cc_final: 0.7967 (tpp) REVERT: C 1383 LYS cc_start: 0.7007 (mttt) cc_final: 0.6706 (mtmm) REVERT: D 53 TYR cc_start: 0.7871 (t80) cc_final: 0.7603 (t80) REVERT: D 110 ARG cc_start: 0.8011 (mtt180) cc_final: 0.7623 (ttm110) REVERT: D 118 MET cc_start: 0.6754 (mtp) cc_final: 0.6493 (mtm) REVERT: D 119 ASN cc_start: 0.8704 (OUTLIER) cc_final: 0.7565 (t0) REVERT: D 123 GLN cc_start: 0.8676 (mp10) cc_final: 0.8333 (mp10) REVERT: D 178 ASN cc_start: 0.7245 (t0) cc_final: 0.6789 (t0) REVERT: E 329 ASN cc_start: 0.8175 (m-40) cc_final: 0.7884 (m110) REVERT: E 354 GLU cc_start: 0.8656 (OUTLIER) cc_final: 0.8139 (pp20) REVERT: E 528 ASN cc_start: 0.8209 (m-40) cc_final: 0.8008 (m-40) REVERT: E 529 GLN cc_start: 0.7205 (tp40) cc_final: 0.6302 (mm-40) REVERT: E 530 ARG cc_start: 0.8556 (ptp-170) cc_final: 0.8333 (ptp-170) REVERT: E 532 ILE cc_start: 0.8942 (mm) cc_final: 0.8546 (tp) REVERT: E 533 GLU cc_start: 0.8436 (mt-10) cc_final: 0.7856 (mt-10) REVERT: G 9 GLU cc_start: 0.7977 (mt-10) cc_final: 0.7515 (mt-10) REVERT: G 21 LYS cc_start: 0.8180 (mmtm) cc_final: 0.7596 (mmmt) REVERT: G 25 LYS cc_start: 0.8485 (mttt) cc_final: 0.8135 (mttt) REVERT: G 51 TYR cc_start: 0.7346 (m-80) cc_final: 0.6952 (m-80) REVERT: G 52 MET cc_start: 0.7124 (ttp) cc_final: 0.6413 (tmm) REVERT: G 634 LYS cc_start: 0.5907 (ttpp) cc_final: 0.5466 (tptp) REVERT: G 643 MET cc_start: 0.7722 (ptp) cc_final: 0.7431 (ptp) REVERT: G 1068 LYS cc_start: 0.8665 (ptmm) cc_final: 0.8293 (ptmm) REVERT: G 1074 ARG cc_start: 0.8337 (ttp80) cc_final: 0.7790 (ttp-170) REVERT: G 1079 PHE cc_start: 0.8977 (m-10) cc_final: 0.8648 (m-80) REVERT: G 1082 LYS cc_start: 0.8831 (mttt) cc_final: 0.8392 (mttt) REVERT: G 1083 HIS cc_start: 0.8596 (m90) cc_final: 0.8312 (m-70) REVERT: G 1084 GLU cc_start: 0.7885 (tp30) cc_final: 0.7190 (tp30) REVERT: G 1123 LYS cc_start: 0.7840 (tttt) cc_final: 0.7577 (tttt) REVERT: G 1156 GLU cc_start: 0.8487 (mt-10) cc_final: 0.8171 (mt-10) REVERT: G 1159 GLU cc_start: 0.8833 (tt0) cc_final: 0.8447 (tt0) REVERT: G 1163 ARG cc_start: 0.8881 (tpp80) cc_final: 0.8255 (ttt180) REVERT: G 1165 GLN cc_start: 0.8974 (mt0) cc_final: 0.8516 (mt0) REVERT: G 1166 ASN cc_start: 0.9041 (m-40) cc_final: 0.8838 (m110) REVERT: G 1173 MET cc_start: 0.8718 (mtm) cc_final: 0.8346 (mtm) REVERT: H 1282 LYS cc_start: 0.8323 (mtpt) cc_final: 0.8020 (mtpt) REVERT: H 1283 GLU cc_start: 0.8165 (tp30) cc_final: 0.7762 (mp0) outliers start: 89 outliers final: 68 residues processed: 1011 average time/residue: 0.2425 time to fit residues: 383.3694 Evaluate side-chains 1028 residues out of total 3824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 953 time to evaluate : 1.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 435 TYR Chi-restraints excluded: chain A residue 457 PHE Chi-restraints excluded: chain A residue 488 MET Chi-restraints excluded: chain A residue 491 CYS Chi-restraints excluded: chain A residue 503 ILE Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 546 ILE Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 590 LEU Chi-restraints excluded: chain A residue 661 ILE Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain A residue 701 ILE Chi-restraints excluded: chain A residue 721 LEU Chi-restraints excluded: chain A residue 854 LEU Chi-restraints excluded: chain A residue 905 LEU Chi-restraints excluded: chain A residue 935 LEU Chi-restraints excluded: chain A residue 958 VAL Chi-restraints excluded: chain A residue 1030 SER Chi-restraints excluded: chain A residue 1073 PHE Chi-restraints excluded: chain A residue 1185 LEU Chi-restraints excluded: chain A residue 1191 LEU Chi-restraints excluded: chain A residue 1382 THR Chi-restraints excluded: chain A residue 1544 VAL Chi-restraints excluded: chain A residue 1635 LEU Chi-restraints excluded: chain A residue 1696 SER Chi-restraints excluded: chain A residue 1810 VAL Chi-restraints excluded: chain A residue 1816 LEU Chi-restraints excluded: chain A residue 1912 LEU Chi-restraints excluded: chain A residue 1922 SER Chi-restraints excluded: chain A residue 1944 VAL Chi-restraints excluded: chain A residue 1951 LEU Chi-restraints excluded: chain A residue 1961 VAL Chi-restraints excluded: chain A residue 1973 ASP Chi-restraints excluded: chain A residue 2025 LEU Chi-restraints excluded: chain A residue 2155 GLU Chi-restraints excluded: chain A residue 2329 GLU Chi-restraints excluded: chain B residue 14 ILE Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 269 SER Chi-restraints excluded: chain B residue 283 GLU Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 292 HIS Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain C residue 309 ASP Chi-restraints excluded: chain C residue 364 LEU Chi-restraints excluded: chain C residue 384 ASP Chi-restraints excluded: chain C residue 482 SER Chi-restraints excluded: chain C residue 687 VAL Chi-restraints excluded: chain C residue 712 ILE Chi-restraints excluded: chain C residue 713 ASP Chi-restraints excluded: chain C residue 725 ILE Chi-restraints excluded: chain C residue 813 TYR Chi-restraints excluded: chain C residue 831 MET Chi-restraints excluded: chain C residue 852 MET Chi-restraints excluded: chain C residue 940 VAL Chi-restraints excluded: chain C residue 1022 ARG Chi-restraints excluded: chain C residue 1083 SER Chi-restraints excluded: chain C residue 1218 CYS Chi-restraints excluded: chain C residue 1401 LEU Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 119 ASN Chi-restraints excluded: chain E residue 322 ILE Chi-restraints excluded: chain E residue 354 GLU Chi-restraints excluded: chain E residue 541 MET Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain G residue 59 LEU Chi-restraints excluded: chain G residue 628 THR Chi-restraints excluded: chain G residue 1067 HIS Chi-restraints excluded: chain G residue 1096 ILE Chi-restraints excluded: chain G residue 1113 SER Chi-restraints excluded: chain G residue 1126 LYS Chi-restraints excluded: chain G residue 1174 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 419 random chunks: chunk 220 optimal weight: 0.7980 chunk 125 optimal weight: 1.9990 chunk 337 optimal weight: 0.3980 chunk 352 optimal weight: 0.9990 chunk 238 optimal weight: 0.9990 chunk 127 optimal weight: 0.9990 chunk 24 optimal weight: 0.0980 chunk 91 optimal weight: 0.9980 chunk 334 optimal weight: 1.9990 chunk 390 optimal weight: 0.9990 chunk 355 optimal weight: 0.0070 overall best weight: 0.4598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 481 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1691 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1977 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2419 ASN B 74 HIS ** B 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 843 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 952 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 498 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.147782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.117433 restraints weight = 73375.402| |-----------------------------------------------------------------------------| r_work (start): 0.3724 rms_B_bonded: 2.80 r_work: 0.3607 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.4485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 34823 Z= 0.133 Angle : 0.646 13.553 47098 Z= 0.325 Chirality : 0.042 0.325 5383 Planarity : 0.004 0.062 5944 Dihedral : 4.509 70.942 4602 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.62 % Favored : 97.33 % Rotamer: Outliers : 2.22 % Allowed : 21.42 % Favored : 76.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.55 (0.13), residues: 4165 helix: 1.67 (0.10), residues: 2771 sheet: 0.41 (0.36), residues: 215 loop : -0.29 (0.19), residues: 1179 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG A 444 TYR 0.057 0.001 TYR E 386 PHE 0.047 0.002 PHE E 380 TRP 0.029 0.001 TRP E 323 HIS 0.011 0.001 HIS C 952 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.13 (34823) covalent geometry : angle 0.64554 / 0.33 (47098) hydrogen bonds : bond 0.03647 / 2.44 ( 2004) hydrogen bonds : angle 4.06265 / 2.93 ( 5913) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8330 Ramachandran restraints generated. 4165 Oldfield, 0 Emsley, 4165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8330 Ramachandran restraints generated. 4165 Oldfield, 0 Emsley, 4165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1051 residues out of total 3824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 966 time to evaluate : 1.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 324 ASP cc_start: 0.7249 (m-30) cc_final: 0.6728 (m-30) REVERT: A 414 LYS cc_start: 0.7861 (tttt) cc_final: 0.7400 (ttpp) REVERT: A 442 ASN cc_start: 0.7210 (m-40) cc_final: 0.6946 (m-40) REVERT: A 512 GLU cc_start: 0.7952 (pm20) cc_final: 0.7579 (pm20) REVERT: A 548 LYS cc_start: 0.8579 (tttt) cc_final: 0.8168 (tptp) REVERT: A 555 GLN cc_start: 0.7096 (pp30) cc_final: 0.6334 (tp-100) REVERT: A 563 GLU cc_start: 0.6596 (mt-10) cc_final: 0.5885 (tm-30) REVERT: A 605 GLU cc_start: 0.7979 (pm20) cc_final: 0.7700 (pm20) REVERT: A 670 ASP cc_start: 0.7463 (m-30) cc_final: 0.7247 (t0) REVERT: A 804 PRO cc_start: 0.7909 (Cg_exo) cc_final: 0.7548 (Cg_endo) REVERT: A 808 ASN cc_start: 0.8148 (m-40) cc_final: 0.7856 (m-40) REVERT: A 927 MET cc_start: 0.8373 (mmm) cc_final: 0.8138 (tpp) REVERT: A 947 MET cc_start: 0.8011 (mmm) cc_final: 0.6736 (tmm) REVERT: A 948 HIS cc_start: 0.8236 (t-90) cc_final: 0.7784 (t70) REVERT: A 951 GLN cc_start: 0.8700 (mt0) cc_final: 0.8179 (mt0) REVERT: A 962 ASP cc_start: 0.8551 (p0) cc_final: 0.8155 (p0) REVERT: A 985 GLN cc_start: 0.8255 (mt0) cc_final: 0.7798 (mp10) REVERT: A 1030 SER cc_start: 0.9101 (OUTLIER) cc_final: 0.8778 (p) REVERT: A 1068 LYS cc_start: 0.8455 (tttp) cc_final: 0.8217 (ttmm) REVERT: A 1170 ARG cc_start: 0.8153 (ttp-110) cc_final: 0.7946 (ttp-110) REVERT: A 1172 ARG cc_start: 0.8670 (mpp80) cc_final: 0.8402 (mtt90) REVERT: A 1179 ASP cc_start: 0.8465 (m-30) cc_final: 0.8053 (m-30) REVERT: A 1221 ASN cc_start: 0.8069 (t0) cc_final: 0.7266 (p0) REVERT: A 1222 GLN cc_start: 0.8032 (pm20) cc_final: 0.7657 (pm20) REVERT: A 1243 TRP cc_start: 0.8193 (t60) cc_final: 0.7992 (t60) REVERT: A 1245 ARG cc_start: 0.7812 (mtt-85) cc_final: 0.7562 (mtt90) REVERT: A 1250 GLN cc_start: 0.8527 (tp-100) cc_final: 0.8013 (tp-100) REVERT: A 1328 ASP cc_start: 0.8672 (t0) cc_final: 0.8102 (t0) REVERT: A 1390 LYS cc_start: 0.8591 (tttm) cc_final: 0.8021 (tptm) REVERT: A 1393 GLN cc_start: 0.7542 (mp10) cc_final: 0.6955 (mp10) REVERT: A 1433 MET cc_start: 0.7633 (mmm) cc_final: 0.7047 (mmm) REVERT: A 1438 SER cc_start: 0.8587 (m) cc_final: 0.8291 (p) REVERT: A 1439 LEU cc_start: 0.8455 (mt) cc_final: 0.8090 (mt) REVERT: A 1465 LYS cc_start: 0.8795 (mttt) cc_final: 0.8517 (mtpp) REVERT: A 1480 GLN cc_start: 0.8409 (mp10) cc_final: 0.8208 (mp10) REVERT: A 1514 LYS cc_start: 0.8328 (tttt) cc_final: 0.7845 (ttpp) REVERT: A 1575 GLU cc_start: 0.8044 (mm-30) cc_final: 0.7731 (mp0) REVERT: A 1605 LYS cc_start: 0.9002 (mttm) cc_final: 0.8797 (mttm) REVERT: A 1676 ASN cc_start: 0.8902 (t0) cc_final: 0.8667 (t0) REVERT: A 1681 MET cc_start: 0.9119 (mmm) cc_final: 0.8808 (mmm) REVERT: A 1766 ASN cc_start: 0.8586 (m110) cc_final: 0.8172 (m-40) REVERT: A 1817 ILE cc_start: 0.8705 (mm) cc_final: 0.8441 (tp) REVERT: A 1818 HIS cc_start: 0.7695 (m90) cc_final: 0.7319 (m-70) REVERT: A 1864 HIS cc_start: 0.8351 (m90) cc_final: 0.7857 (m-70) REVERT: A 1917 MET cc_start: 0.8212 (mtm) cc_final: 0.7996 (mtt) REVERT: A 1928 GLN cc_start: 0.8642 (tt0) cc_final: 0.8279 (tt0) REVERT: A 1959 MET cc_start: 0.8616 (mtp) cc_final: 0.8250 (mtp) REVERT: A 1977 GLN cc_start: 0.8444 (tt0) cc_final: 0.7923 (tm-30) REVERT: A 1983 ASN cc_start: 0.8003 (t0) cc_final: 0.7324 (t0) REVERT: A 1996 GLU cc_start: 0.8038 (mt-10) cc_final: 0.7776 (mt-10) REVERT: A 2023 GLU cc_start: 0.8066 (tm-30) cc_final: 0.7548 (tm-30) REVERT: A 2121 LYS cc_start: 0.8688 (mttt) cc_final: 0.8338 (mttt) REVERT: A 2204 ILE cc_start: 0.8534 (tp) cc_final: 0.8307 (pt) REVERT: A 2218 ASN cc_start: 0.8280 (m-40) cc_final: 0.7902 (t0) REVERT: A 2268 MET cc_start: 0.8999 (tpt) cc_final: 0.8774 (tpt) REVERT: A 2329 GLU cc_start: 0.8777 (OUTLIER) cc_final: 0.8519 (mp0) REVERT: A 2418 ARG cc_start: 0.7636 (ttp-170) cc_final: 0.7418 (ttp-170) REVERT: A 2440 ARG cc_start: 0.8392 (ptp90) cc_final: 0.8161 (ptp90) REVERT: B 141 ARG cc_start: 0.7363 (mtp85) cc_final: 0.7088 (mtp85) REVERT: B 182 ASN cc_start: 0.7048 (t0) cc_final: 0.6529 (t0) REVERT: B 188 MET cc_start: 0.1841 (mmm) cc_final: 0.1016 (mmm) REVERT: B 212 ARG cc_start: 0.6139 (tpm170) cc_final: 0.5659 (tpm170) REVERT: B 232 ARG cc_start: 0.7007 (ttm170) cc_final: 0.6460 (ttm-80) REVERT: B 275 ARG cc_start: 0.6799 (mpp80) cc_final: 0.6509 (mtt180) REVERT: B 286 ARG cc_start: 0.8303 (mmm160) cc_final: 0.7897 (tpp-160) REVERT: C 351 MET cc_start: 0.8010 (mmm) cc_final: 0.7772 (mmm) REVERT: C 360 ASN cc_start: 0.8261 (p0) cc_final: 0.8020 (p0) REVERT: C 373 CYS cc_start: 0.8574 (t) cc_final: 0.8213 (t) REVERT: C 388 GLU cc_start: 0.8249 (tp30) cc_final: 0.7770 (tp30) REVERT: C 422 TYR cc_start: 0.8443 (m-80) cc_final: 0.7924 (m-80) REVERT: C 465 LYS cc_start: 0.8798 (tttt) cc_final: 0.8436 (tttm) REVERT: C 497 MET cc_start: 0.8816 (mmt) cc_final: 0.7228 (mmt) REVERT: C 642 GLU cc_start: 0.8221 (mm-30) cc_final: 0.7844 (mm-30) REVERT: C 713 ASP cc_start: 0.7805 (OUTLIER) cc_final: 0.7380 (t70) REVERT: C 740 ARG cc_start: 0.7146 (tpt170) cc_final: 0.6931 (tpt170) REVERT: C 742 MET cc_start: 0.8164 (mtm) cc_final: 0.7877 (mtt) REVERT: C 759 TRP cc_start: 0.6684 (m-10) cc_final: 0.6073 (m-10) REVERT: C 813 TYR cc_start: 0.7633 (OUTLIER) cc_final: 0.7268 (m-10) REVERT: C 824 LEU cc_start: 0.8525 (mt) cc_final: 0.8040 (tp) REVERT: C 848 MET cc_start: 0.8162 (mtp) cc_final: 0.7452 (mmp) REVERT: C 864 ASN cc_start: 0.8931 (m-40) cc_final: 0.8664 (t0) REVERT: C 893 ARG cc_start: 0.8526 (ptm-80) cc_final: 0.8053 (ptm-80) REVERT: C 923 ASP cc_start: 0.7992 (t0) cc_final: 0.7339 (t70) REVERT: C 982 MET cc_start: 0.7295 (tpp) cc_final: 0.6790 (tpp) REVERT: C 1072 HIS cc_start: 0.7308 (t70) cc_final: 0.7085 (t70) REVERT: C 1076 GLU cc_start: 0.8526 (tt0) cc_final: 0.8214 (tt0) REVERT: C 1081 ASN cc_start: 0.8942 (m-40) cc_final: 0.8728 (m-40) REVERT: C 1082 GLU cc_start: 0.7891 (mt-10) cc_final: 0.7611 (tt0) REVERT: C 1096 ARG cc_start: 0.7935 (ptm160) cc_final: 0.7579 (ptm160) REVERT: C 1103 GLU cc_start: 0.7884 (tt0) cc_final: 0.7481 (tt0) REVERT: C 1342 LYS cc_start: 0.8583 (mmtt) cc_final: 0.8179 (mtmt) REVERT: C 1364 THR cc_start: 0.8501 (t) cc_final: 0.8239 (t) REVERT: C 1380 MET cc_start: 0.8266 (tpp) cc_final: 0.7928 (tpp) REVERT: C 1383 LYS cc_start: 0.7038 (mttt) cc_final: 0.6733 (mtmm) REVERT: D 53 TYR cc_start: 0.7849 (t80) cc_final: 0.7632 (t80) REVERT: D 110 ARG cc_start: 0.7959 (mtt180) cc_final: 0.7408 (ttm110) REVERT: D 119 ASN cc_start: 0.8725 (OUTLIER) cc_final: 0.7882 (t0) REVERT: D 123 GLN cc_start: 0.8623 (mp10) cc_final: 0.8306 (mp10) REVERT: D 178 ASN cc_start: 0.7217 (t0) cc_final: 0.6813 (t0) REVERT: E 354 GLU cc_start: 0.8617 (OUTLIER) cc_final: 0.8139 (pp20) REVERT: E 390 ASN cc_start: 0.8529 (m-40) cc_final: 0.8301 (m110) REVERT: E 407 LYS cc_start: 0.8010 (ptpp) cc_final: 0.7743 (ptpp) REVERT: E 529 GLN cc_start: 0.7100 (tp40) cc_final: 0.6645 (mm-40) REVERT: E 530 ARG cc_start: 0.8552 (ptp-170) cc_final: 0.8335 (ptp-170) REVERT: E 532 ILE cc_start: 0.8924 (mm) cc_final: 0.8545 (tp) REVERT: E 533 GLU cc_start: 0.8436 (mt-10) cc_final: 0.7866 (mt-10) REVERT: G 21 LYS cc_start: 0.8187 (mmtm) cc_final: 0.7605 (mmmt) REVERT: G 25 LYS cc_start: 0.8504 (mttt) cc_final: 0.8176 (mttt) REVERT: G 51 TYR cc_start: 0.7473 (m-80) cc_final: 0.7094 (m-80) REVERT: G 52 MET cc_start: 0.7216 (ttp) cc_final: 0.6502 (tmm) REVERT: G 634 LYS cc_start: 0.5953 (ttpp) cc_final: 0.5484 (tptp) REVERT: G 643 MET cc_start: 0.7573 (ptp) cc_final: 0.7292 (ptp) REVERT: G 1068 LYS cc_start: 0.8606 (ptmm) cc_final: 0.8216 (ptmm) REVERT: G 1074 ARG cc_start: 0.8310 (ttp80) cc_final: 0.7826 (ttp-170) REVERT: G 1079 PHE cc_start: 0.8969 (m-10) cc_final: 0.8680 (m-80) REVERT: G 1082 LYS cc_start: 0.8903 (mttt) cc_final: 0.8496 (mttt) REVERT: G 1083 HIS cc_start: 0.8526 (m90) cc_final: 0.8243 (m-70) REVERT: G 1113 SER cc_start: 0.9200 (OUTLIER) cc_final: 0.8815 (m) REVERT: G 1123 LYS cc_start: 0.7908 (tttt) cc_final: 0.7594 (tttt) REVERT: G 1156 GLU cc_start: 0.8640 (mt-10) cc_final: 0.8312 (mt-10) REVERT: G 1159 GLU cc_start: 0.8924 (tt0) cc_final: 0.8554 (tt0) REVERT: G 1163 ARG cc_start: 0.8939 (tpp80) cc_final: 0.8342 (ttt180) REVERT: G 1165 GLN cc_start: 0.8853 (mt0) cc_final: 0.8391 (mt0) REVERT: G 1173 MET cc_start: 0.8675 (mtm) cc_final: 0.8317 (mtm) REVERT: H 1282 LYS cc_start: 0.8309 (mtpt) cc_final: 0.8016 (mtpt) REVERT: H 1283 GLU cc_start: 0.8186 (tp30) cc_final: 0.7793 (mp0) outliers start: 85 outliers final: 59 residues processed: 1007 average time/residue: 0.2455 time to fit residues: 386.5642 Evaluate side-chains 1012 residues out of total 3824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 946 time to evaluate : 1.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 389 TYR Chi-restraints excluded: chain A residue 435 TYR Chi-restraints excluded: chain A residue 457 PHE Chi-restraints excluded: chain A residue 491 CYS Chi-restraints excluded: chain A residue 503 ILE Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 546 ILE Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 590 LEU Chi-restraints excluded: chain A residue 661 ILE Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain A residue 698 ILE Chi-restraints excluded: chain A residue 721 LEU Chi-restraints excluded: chain A residue 958 VAL Chi-restraints excluded: chain A residue 1030 SER Chi-restraints excluded: chain A residue 1073 PHE Chi-restraints excluded: chain A residue 1185 LEU Chi-restraints excluded: chain A residue 1191 LEU Chi-restraints excluded: chain A residue 1502 ASP Chi-restraints excluded: chain A residue 1544 VAL Chi-restraints excluded: chain A residue 1696 SER Chi-restraints excluded: chain A residue 1810 VAL Chi-restraints excluded: chain A residue 1816 LEU Chi-restraints excluded: chain A residue 1912 LEU Chi-restraints excluded: chain A residue 1922 SER Chi-restraints excluded: chain A residue 1944 VAL Chi-restraints excluded: chain A residue 1951 LEU Chi-restraints excluded: chain A residue 1961 VAL Chi-restraints excluded: chain A residue 1973 ASP Chi-restraints excluded: chain A residue 2329 GLU Chi-restraints excluded: chain B residue 14 ILE Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 269 SER Chi-restraints excluded: chain B residue 283 GLU Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 292 HIS Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain C residue 309 ASP Chi-restraints excluded: chain C residue 364 LEU Chi-restraints excluded: chain C residue 384 ASP Chi-restraints excluded: chain C residue 482 SER Chi-restraints excluded: chain C residue 687 VAL Chi-restraints excluded: chain C residue 712 ILE Chi-restraints excluded: chain C residue 713 ASP Chi-restraints excluded: chain C residue 725 ILE Chi-restraints excluded: chain C residue 813 TYR Chi-restraints excluded: chain C residue 940 VAL Chi-restraints excluded: chain C residue 1022 ARG Chi-restraints excluded: chain C residue 1083 SER Chi-restraints excluded: chain C residue 1218 CYS Chi-restraints excluded: chain C residue 1401 LEU Chi-restraints excluded: chain D residue 11 GLU Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 119 ASN Chi-restraints excluded: chain E residue 354 GLU Chi-restraints excluded: chain E residue 541 MET Chi-restraints excluded: chain G residue 59 LEU Chi-restraints excluded: chain G residue 628 THR Chi-restraints excluded: chain G residue 1067 HIS Chi-restraints excluded: chain G residue 1096 ILE Chi-restraints excluded: chain G residue 1113 SER Chi-restraints excluded: chain G residue 1126 LYS Chi-restraints excluded: chain G residue 1174 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 419 random chunks: chunk 267 optimal weight: 2.9990 chunk 101 optimal weight: 0.6980 chunk 242 optimal weight: 6.9990 chunk 184 optimal weight: 0.9980 chunk 310 optimal weight: 0.9980 chunk 328 optimal weight: 0.9980 chunk 411 optimal weight: 8.9990 chunk 384 optimal weight: 0.7980 chunk 41 optimal weight: 0.6980 chunk 362 optimal weight: 0.7980 chunk 354 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 481 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1691 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1977 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2223 GLN A2419 ASN ** B 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 329 ASN ** C 843 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 952 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 979 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1345 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.146893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.116415 restraints weight = 72898.658| |-----------------------------------------------------------------------------| r_work (start): 0.3672 rms_B_bonded: 2.79 r_work: 0.3530 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.4560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 34823 Z= 0.160 Angle : 0.653 12.142 47098 Z= 0.332 Chirality : 0.043 0.279 5383 Planarity : 0.004 0.057 5944 Dihedral : 4.528 71.195 4602 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.95 % Favored : 97.00 % Rotamer: Outliers : 1.99 % Allowed : 21.84 % Favored : 76.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.49 (0.13), residues: 4165 helix: 1.62 (0.10), residues: 2769 sheet: 0.30 (0.35), residues: 225 loop : -0.28 (0.19), residues: 1171 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG A 444 TYR 0.051 0.001 TYR E 386 PHE 0.036 0.001 PHE E 380 TRP 0.023 0.001 TRP C 757 HIS 0.010 0.001 HIS C 952 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.16 (34823) covalent geometry : angle 0.65287 / 0.33 (47098) hydrogen bonds : bond 0.03753 / 2.52 ( 2004) hydrogen bonds : angle 4.12948 / 2.97 ( 5913) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12915.10 seconds wall clock time: 220 minutes 44.87 seconds (13244.87 seconds total)