Starting phenix.real_space_refine on Tue Nov 18 15:07:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6l42_0828/11_2025/6l42_0828.cif Found real_map, /net/cci-nas-00/data/ceres_data/6l42_0828/11_2025/6l42_0828.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6l42_0828/11_2025/6l42_0828.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6l42_0828/11_2025/6l42_0828.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6l42_0828/11_2025/6l42_0828.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6l42_0828/11_2025/6l42_0828.map" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 Mg 1 5.21 5 S 91 5.16 5 C 9388 2.51 5 N 2574 2.21 5 O 2773 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 47 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14827 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 14826 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1864, 14826 Classifications: {'peptide': 1864} Link IDs: {'CIS': 2, 'PTRANS': 66, 'TRANS': 1795} Chain breaks: 15 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.04, per 1000 atoms: 0.27 Number of scatterers: 14827 At special positions: 0 Unit cell: (90.72, 112.32, 138.24, 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 91 16.00 Mg 1 11.99 O 2773 8.00 N 2574 7.00 C 9388 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=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.25 Conformation dependent library (CDL) restraints added in 796.5 milliseconds 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3488 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 14 sheets defined 42.2% alpha, 6.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.67 Creating SS restraints... Processing helix chain 'A' and resid 3 through 10 removed outlier: 4.038A pdb=" N ILE A 10 " --> pdb=" O LEU A 6 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 83 removed outlier: 4.484A pdb=" N THR A 83 " --> pdb=" O ASN A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 158 removed outlier: 3.780A pdb=" N ILE A 146 " --> pdb=" O TYR A 142 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LYS A 148 " --> pdb=" O THR A 144 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N TYR A 149 " --> pdb=" O LYS A 145 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N ASP A 151 " --> pdb=" O GLU A 147 " (cutoff:3.500A) Proline residue: A 152 - end of helix removed outlier: 3.515A pdb=" N ASP A 158 " --> pdb=" O SER A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 206 removed outlier: 3.798A pdb=" N ALA A 188 " --> pdb=" O THR A 184 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLU A 189 " --> pdb=" O GLN A 185 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N MET A 192 " --> pdb=" O ALA A 188 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N PHE A 195 " --> pdb=" O LEU A 191 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N LYS A 204 " --> pdb=" O GLU A 200 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ALA A 205 " --> pdb=" O ILE A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 232 removed outlier: 4.224A pdb=" N ARG A 226 " --> pdb=" O GLU A 222 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA A 227 " --> pdb=" O ALA A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 245 Processing helix chain 'A' and resid 251 through 258 removed outlier: 3.630A pdb=" N GLN A 255 " --> pdb=" O GLU A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 285 removed outlier: 3.852A pdb=" N LYS A 271 " --> pdb=" O THR A 267 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N VAL A 275 " --> pdb=" O LYS A 271 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLU A 276 " --> pdb=" O ALA A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 318 removed outlier: 3.739A pdb=" N GLU A 298 " --> pdb=" O GLN A 294 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ILE A 299 " --> pdb=" O GLU A 295 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ASN A 300 " --> pdb=" O ARG A 296 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ARG A 301 " --> pdb=" O LEU A 297 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ARG A 318 " --> pdb=" O GLY A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 375 removed outlier: 3.637A pdb=" N TRP A 365 " --> pdb=" O TYR A 361 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N LEU A 374 " --> pdb=" O LEU A 370 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N GLY A 375 " --> pdb=" O ASP A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 406 removed outlier: 3.571A pdb=" N ILE A 406 " --> pdb=" O GLU A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 427 removed outlier: 4.037A pdb=" N LEU A 425 " --> pdb=" O GLN A 421 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLN A 426 " --> pdb=" O GLU A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 465 removed outlier: 4.044A pdb=" N GLY A 460 " --> pdb=" O VAL A 456 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 482 removed outlier: 3.992A pdb=" N ALA A 482 " --> pdb=" O SER A 478 " (cutoff:3.500A) Processing helix chain 'A' and resid 482 through 492 removed outlier: 3.725A pdb=" N LEU A 486 " --> pdb=" O ALA A 482 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLU A 488 " --> pdb=" O SER A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 503 Processing helix chain 'A' and resid 506 through 511 Processing helix chain 'A' and resid 514 through 531 removed outlier: 4.138A pdb=" N TRP A 520 " --> pdb=" O GLN A 516 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N VAL A 521 " --> pdb=" O TRP A 517 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N SER A 530 " --> pdb=" O GLN A 526 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ALA A 531 " --> pdb=" O GLU A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 605 through 611 removed outlier: 4.379A pdb=" N LEU A 609 " --> pdb=" O LYS A 605 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N ASN A 611 " --> pdb=" O THR A 607 " (cutoff:3.500A) Processing helix chain 'A' and resid 612 through 615 Processing helix chain 'A' and resid 616 through 621 Processing helix chain 'A' and resid 621 through 627 Processing helix chain 'A' and resid 638 through 652 removed outlier: 3.846A pdb=" N GLU A 643 " --> pdb=" O SER A 639 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N GLN A 644 " --> pdb=" O GLU A 640 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N THR A 648 " --> pdb=" O GLN A 644 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU A 650 " --> pdb=" O GLY A 646 " (cutoff:3.500A) Processing helix chain 'A' and resid 656 through 661 removed outlier: 3.951A pdb=" N GLU A 660 " --> pdb=" O LYS A 656 " (cutoff:3.500A) Processing helix chain 'A' and resid 663 through 667 Processing helix chain 'A' and resid 670 through 675 removed outlier: 3.623A pdb=" N VAL A 675 " --> pdb=" O GLU A 672 " (cutoff:3.500A) Processing helix chain 'A' and resid 683 through 690 removed outlier: 3.567A pdb=" N LEU A 687 " --> pdb=" O GLN A 684 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N GLY A 688 " --> pdb=" O LYS A 685 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LYS A 689 " --> pdb=" O MET A 686 " (cutoff:3.500A) Processing helix chain 'A' and resid 697 through 713 removed outlier: 3.581A pdb=" N TYR A 701 " --> pdb=" O LYS A 697 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N ASP A 708 " --> pdb=" O ARG A 704 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N CYS A 709 " --> pdb=" O LYS A 705 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N MET A 710 " --> pdb=" O HIS A 706 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N VAL A 711 " --> pdb=" O LEU A 707 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ILE A 713 " --> pdb=" O CYS A 709 " (cutoff:3.500A) Processing helix chain 'A' and resid 742 through 750 removed outlier: 4.419A pdb=" N ASN A 748 " --> pdb=" O GLU A 744 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N SER A 749 " --> pdb=" O ASN A 745 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N TRP A 750 " --> pdb=" O MET A 746 " (cutoff:3.500A) Processing helix chain 'A' and resid 763 through 776 removed outlier: 3.521A pdb=" N LEU A 767 " --> pdb=" O GLU A 763 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLU A 769 " --> pdb=" O ASN A 765 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ILE A 774 " --> pdb=" O MET A 770 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N VAL A 775 " --> pdb=" O TYR A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 802 through 819 removed outlier: 3.546A pdb=" N LEU A 806 " --> pdb=" O SER A 802 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N SER A 812 " --> pdb=" O ALA A 808 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N LEU A 813 " --> pdb=" O ALA A 809 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N GLU A 814 " --> pdb=" O CYS A 810 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N ARG A 815 " --> pdb=" O SER A 811 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ALA A 818 " --> pdb=" O GLU A 814 " (cutoff:3.500A) Processing helix chain 'A' and resid 825 through 838 removed outlier: 4.610A pdb=" N GLU A 831 " --> pdb=" O GLN A 827 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ARG A 835 " --> pdb=" O GLU A 831 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N GLY A 838 " --> pdb=" O LEU A 834 " (cutoff:3.500A) Processing helix chain 'A' and resid 855 through 859 removed outlier: 3.536A pdb=" N GLU A 859 " --> pdb=" O LYS A 856 " (cutoff:3.500A) Processing helix chain 'A' and resid 875 through 883 removed outlier: 3.579A pdb=" N LEU A 881 " --> pdb=" O LYS A 877 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 902 Processing helix chain 'A' and resid 929 through 945 removed outlier: 3.959A pdb=" N VAL A 936 " --> pdb=" O VAL A 932 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N THR A 938 " --> pdb=" O PHE A 934 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N MET A 939 " --> pdb=" O GLY A 935 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N VAL A 943 " --> pdb=" O MET A 939 " (cutoff:3.500A) Processing helix chain 'A' and resid 956 through 960 Processing helix chain 'A' and resid 961 through 969 removed outlier: 4.294A pdb=" N GLY A 966 " --> pdb=" O ILE A 962 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N LEU A 967 " --> pdb=" O GLU A 963 " (cutoff:3.500A) Processing helix chain 'A' and resid 994 through 1006 removed outlier: 4.357A pdb=" N LEU A 998 " --> pdb=" O TYR A 994 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA A 999 " --> pdb=" O THR A 995 " (cutoff:3.500A) Processing helix chain 'A' and resid 1010 through 1019 removed outlier: 4.181A pdb=" N ALA A1016 " --> pdb=" O ARG A1012 " (cutoff:3.500A) Processing helix chain 'A' and resid 1029 through 1037 removed outlier: 3.667A pdb=" N LEU A1033 " --> pdb=" O ASP A1029 " (cutoff:3.500A) Processing helix chain 'A' and resid 1047 through 1058 Processing helix chain 'A' and resid 1086 through 1107 removed outlier: 3.562A pdb=" N LEU A1090 " --> pdb=" O THR A1086 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N SER A1104 " --> pdb=" O SER A1100 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1155 removed outlier: 3.583A pdb=" N PHE A1147 " --> pdb=" O VAL A1143 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N PHE A1148 " --> pdb=" O ARG A1144 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LEU A1152 " --> pdb=" O PHE A1148 " (cutoff:3.500A) Processing helix chain 'A' and resid 1156 through 1158 No H-bonds generated for 'chain 'A' and resid 1156 through 1158' Processing helix chain 'A' and resid 1195 through 1200 removed outlier: 3.742A pdb=" N ALA A1200 " --> pdb=" O LEU A1196 " (cutoff:3.500A) Processing helix chain 'A' and resid 1212 through 1228 removed outlier: 3.767A pdb=" N GLU A1216 " --> pdb=" O ALA A1212 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLN A1224 " --> pdb=" O ASN A1220 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N CYS A1225 " --> pdb=" O LEU A1221 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N LEU A1226 " --> pdb=" O LEU A1222 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N GLU A1227 " --> pdb=" O THR A1223 " (cutoff:3.500A) Processing helix chain 'A' and resid 1236 through 1252 removed outlier: 3.610A pdb=" N LEU A1244 " --> pdb=" O CYS A1240 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N LEU A1249 " --> pdb=" O HIS A1245 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU A1250 " --> pdb=" O HIS A1246 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLY A1251 " --> pdb=" O TYR A1247 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N LEU A1252 " --> pdb=" O MET A1248 " (cutoff:3.500A) Processing helix chain 'A' and resid 1257 through 1266 removed outlier: 3.802A pdb=" N LEU A1265 " --> pdb=" O PHE A1261 " (cutoff:3.500A) Processing helix chain 'A' and resid 1288 through 1299 removed outlier: 3.721A pdb=" N ASN A1292 " --> pdb=" O GLY A1288 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N THR A1299 " --> pdb=" O ARG A1295 " (cutoff:3.500A) Processing helix chain 'A' and resid 1306 through 1311 Processing helix chain 'A' and resid 1345 through 1350 Processing helix chain 'A' and resid 1360 through 1367 Processing helix chain 'A' and resid 1369 through 1373 removed outlier: 3.570A pdb=" N TYR A1373 " --> pdb=" O GLY A1370 " (cutoff:3.500A) Processing helix chain 'A' and resid 1378 through 1392 removed outlier: 3.683A pdb=" N HIS A1391 " --> pdb=" O ALA A1387 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N SER A1392 " --> pdb=" O GLU A1388 " (cutoff:3.500A) Processing helix chain 'A' and resid 1403 through 1418 removed outlier: 3.766A pdb=" N ARG A1407 " --> pdb=" O HIS A1403 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL A1409 " --> pdb=" O VAL A1405 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ALA A1411 " --> pdb=" O ARG A1407 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N LEU A1415 " --> pdb=" O ALA A1411 " (cutoff:3.500A) Processing helix chain 'A' and resid 1435 through 1443 removed outlier: 3.513A pdb=" N ILE A1439 " --> pdb=" O LYS A1435 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LYS A1440 " --> pdb=" O ALA A1436 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEU A1441 " --> pdb=" O SER A1437 " (cutoff:3.500A) Processing helix chain 'A' and resid 1451 through 1457 Processing helix chain 'A' and resid 1514 through 1522 removed outlier: 4.108A pdb=" N SER A1518 " --> pdb=" O GLU A1514 " (cutoff:3.500A) Processing helix chain 'A' and resid 1536 through 1544 removed outlier: 3.695A pdb=" N LYS A1540 " --> pdb=" O GLU A1536 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER A1544 " --> pdb=" O LYS A1540 " (cutoff:3.500A) Processing helix chain 'A' and resid 1553 through 1558 removed outlier: 3.614A pdb=" N ARG A1557 " --> pdb=" O SER A1553 " (cutoff:3.500A) Processing helix chain 'A' and resid 1563 through 1572 removed outlier: 3.616A pdb=" N PHE A1567 " --> pdb=" O SER A1563 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N ASN A1569 " --> pdb=" O VAL A1565 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N PHE A1570 " --> pdb=" O GLN A1566 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ILE A1571 " --> pdb=" O PHE A1567 " (cutoff:3.500A) Processing helix chain 'A' and resid 1617 through 1628 Processing helix chain 'A' and resid 1635 through 1638 Processing helix chain 'A' and resid 1639 through 1647 removed outlier: 3.744A pdb=" N GLU A1643 " --> pdb=" O GLY A1639 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLU A1644 " --> pdb=" O PRO A1640 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N TYR A1645 " --> pdb=" O TYR A1641 " (cutoff:3.500A) Processing helix chain 'A' and resid 1671 through 1676 Processing helix chain 'A' and resid 1688 through 1694 removed outlier: 3.883A pdb=" N ILE A1692 " --> pdb=" O ILE A1688 " (cutoff:3.500A) Processing helix chain 'A' and resid 1758 through 1773 removed outlier: 3.956A pdb=" N GLU A1763 " --> pdb=" O TYR A1759 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LEU A1768 " --> pdb=" O SER A1764 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ASP A1770 " --> pdb=" O ARG A1766 " (cutoff:3.500A) Processing helix chain 'A' and resid 1797 through 1801 Processing helix chain 'A' and resid 1859 through 1866 removed outlier: 3.631A pdb=" N ALA A1863 " --> pdb=" O GLU A1859 " (cutoff:3.500A) Processing helix chain 'A' and resid 1871 through 1875 Processing helix chain 'A' and resid 1900 through 1909 removed outlier: 3.614A pdb=" N ASP A1904 " --> pdb=" O LEU A1900 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ARG A1905 " --> pdb=" O LEU A1901 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N LYS A1906 " --> pdb=" O ALA A1902 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLN A1908 " --> pdb=" O ASP A1904 " (cutoff:3.500A) Processing helix chain 'A' and resid 1922 through 1924 No H-bonds generated for 'chain 'A' and resid 1922 through 1924' Processing helix chain 'A' and resid 1925 through 1933 removed outlier: 4.243A pdb=" N LYS A1929 " --> pdb=" O GLY A1925 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LEU A1932 " --> pdb=" O ARG A1928 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N MET A1933 " --> pdb=" O LYS A1929 " (cutoff:3.500A) Processing helix chain 'A' and resid 1936 through 1941 removed outlier: 3.666A pdb=" N MET A1940 " --> pdb=" O LYS A1936 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL A1941 " --> pdb=" O LEU A1937 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1936 through 1941' Processing helix chain 'A' and resid 2012 through 2019 removed outlier: 3.663A pdb=" N ASP A2016 " --> pdb=" O LEU A2012 " (cutoff:3.500A) Processing helix chain 'A' and resid 2029 through 2034 Processing helix chain 'A' and resid 2041 through 2049 removed outlier: 3.880A pdb=" N GLN A2047 " --> pdb=" O ALA A2043 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 15 through 17 removed outlier: 6.076A pdb=" N GLY A 15 " --> pdb=" O VAL A 165 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N PHE A 167 " --> pdb=" O GLY A 15 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N SER A 17 " --> pdb=" O PHE A 167 " (cutoff:3.500A) removed outlier: 8.378A pdb=" N VAL A 169 " --> pdb=" O SER A 17 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 15 through 17 removed outlier: 6.076A pdb=" N GLY A 15 " --> pdb=" O VAL A 165 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N PHE A 167 " --> pdb=" O GLY A 15 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N SER A 17 " --> pdb=" O PHE A 167 " (cutoff:3.500A) removed outlier: 8.378A pdb=" N VAL A 169 " --> pdb=" O SER A 17 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ILE A 122 " --> pdb=" O PHE A 166 " (cutoff:3.500A) removed outlier: 7.890A pdb=" N GLY A 168 " --> pdb=" O ILE A 122 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N VAL A 124 " --> pdb=" O GLY A 168 " (cutoff:3.500A) removed outlier: 8.080A pdb=" N ILE A 170 " --> pdb=" O VAL A 124 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N GLU A 126 " --> pdb=" O ILE A 170 " (cutoff:3.500A) removed outlier: 8.373A pdb=" N VAL A 172 " --> pdb=" O GLU A 126 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N THR A 128 " --> pdb=" O VAL A 172 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL A 113 " --> pdb=" O VAL A 125 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 336 through 337 Processing sheet with id=AA4, first strand: chain 'A' and resid 544 through 545 removed outlier: 3.502A pdb=" N ILE A 570 " --> pdb=" O GLU A 594 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLU A 594 " --> pdb=" O ILE A 570 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU A 595 " --> pdb=" O ILE A 588 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 563 through 566 Processing sheet with id=AA6, first strand: chain 'A' and resid 720 through 721 removed outlier: 3.510A pdb=" N ILE A 721 " --> pdb=" O GLU A 728 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLU A 728 " --> pdb=" O ILE A 721 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 921 through 923 removed outlier: 4.393A pdb=" N LEU A 910 " --> pdb=" O MET A1027 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LYS A1024 " --> pdb=" O THR A1074 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 980 through 981 Processing sheet with id=AA9, first strand: chain 'A' and resid 1179 through 1180 Processing sheet with id=AB1, first strand: chain 'A' and resid 1328 through 1330 removed outlier: 3.816A pdb=" N ALA A1328 " --> pdb=" O SER A1335 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 1699 through 1700 removed outlier: 3.709A pdb=" N LEU A1700 " --> pdb=" O VAL A1728 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1709 through 1712 removed outlier: 3.912A pdb=" N GLY A1716 " --> pdb=" O ARG A1712 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 1723 through 1726 removed outlier: 6.589A pdb=" N GLN A1735 " --> pdb=" O ILE A1750 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N ILE A1750 " --> pdb=" O GLN A1735 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N LEU A1737 " --> pdb=" O GLU A1748 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1825 through 1829 removed outlier: 3.860A pdb=" N ARG A1829 " --> pdb=" O ILE A1832 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ILE A1832 " --> pdb=" O ARG A1829 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N LEU A1833 " --> pdb=" O SER A1849 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N SER A1849 " --> pdb=" O LEU A1833 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N LEU A1835 " --> pdb=" O ILE A1847 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE A1847 " --> pdb=" O LEU A1835 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N ARG A1843 " --> pdb=" O ILE A1839 " (cutoff:3.500A) 405 hydrogen bonds defined for protein. 1122 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: 3.42 Time building geometry restraints manager: 1.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.00 - 1.16: 4 1.16 - 1.33: 2757 1.33 - 1.49: 5739 1.49 - 1.65: 6461 1.65 - 1.81: 156 Bond restraints: 15117 Sorted by residual: bond pdb=" CA VAL A1520 " pdb=" C VAL A1520 " ideal model delta sigma weight residual 1.522 1.174 0.348 1.50e-02 4.44e+03 5.39e+02 bond pdb=" C ALA A 892 " pdb=" N VAL A 893 " ideal model delta sigma weight residual 1.336 1.591 -0.255 1.17e-02 7.31e+03 4.75e+02 bond pdb=" C THR A 348 " pdb=" N ASP A 349 " ideal model delta sigma weight residual 1.333 1.596 -0.262 1.34e-02 5.57e+03 3.83e+02 bond pdb=" CA THR A 348 " pdb=" C THR A 348 " ideal model delta sigma weight residual 1.533 1.638 -0.104 5.60e-03 3.19e+04 3.48e+02 bond pdb=" C MET A 1 " pdb=" N ASN A 2 " ideal model delta sigma weight residual 1.332 1.576 -0.243 1.40e-02 5.10e+03 3.02e+02 ... (remaining 15112 not shown) Histogram of bond angle deviations from ideal: 0.00 - 10.12: 19984 10.12 - 20.23: 260 20.23 - 30.35: 76 30.35 - 40.47: 47 40.47 - 50.59: 12 Bond angle restraints: 20379 Sorted by residual: angle pdb=" O THR A 348 " pdb=" C THR A 348 " pdb=" N ASP A 349 " ideal model delta sigma weight residual 121.47 79.92 41.55 7.50e-01 1.78e+00 3.07e+03 angle pdb=" CA THR A 348 " pdb=" C THR A 348 " pdb=" N ASP A 349 " ideal model delta sigma weight residual 120.47 157.47 -37.00 1.03e+00 9.43e-01 1.29e+03 angle pdb=" O SER A1580 " pdb=" C SER A1580 " pdb=" N VAL A1581 " ideal model delta sigma weight residual 122.97 78.20 44.77 1.39e+00 5.18e-01 1.04e+03 angle pdb=" O LEU A1584 " pdb=" C LEU A1584 " pdb=" N GLY A1585 " ideal model delta sigma weight residual 123.13 89.16 33.97 1.07e+00 8.73e-01 1.01e+03 angle pdb=" O VAL A1581 " pdb=" C VAL A1581 " pdb=" N ARG A1582 " ideal model delta sigma weight residual 122.57 161.28 -38.71 1.25e+00 6.40e-01 9.59e+02 ... (remaining 20374 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.74: 8465 25.74 - 51.48: 611 51.48 - 77.23: 65 77.23 - 102.97: 10 102.97 - 128.71: 2 Dihedral angle restraints: 9153 sinusoidal: 3763 harmonic: 5390 Sorted by residual: dihedral pdb=" CA THR A 348 " pdb=" C THR A 348 " pdb=" N ASP A 349 " pdb=" CA ASP A 349 " ideal model delta harmonic sigma weight residual -180.00 -51.29 -128.71 0 5.00e+00 4.00e-02 6.63e+02 dihedral pdb=" CA VAL A1574 " pdb=" C VAL A1574 " pdb=" N ASP A1575 " pdb=" CA ASP A1575 " ideal model delta harmonic sigma weight residual 180.00 65.64 114.36 0 5.00e+00 4.00e-02 5.23e+02 dihedral pdb=" CA LEU A 95 " pdb=" C LEU A 95 " pdb=" N SER A 96 " pdb=" CA SER A 96 " ideal model delta harmonic sigma weight residual 180.00 87.25 92.75 0 5.00e+00 4.00e-02 3.44e+02 ... (remaining 9150 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.310: 2134 0.310 - 0.620: 92 0.620 - 0.930: 16 0.930 - 1.240: 4 1.240 - 1.550: 10 Chirality restraints: 2256 Sorted by residual: chirality pdb=" CA PHE A1793 " pdb=" N PHE A1793 " pdb=" C PHE A1793 " pdb=" CB PHE A1793 " both_signs ideal model delta sigma weight residual False 2.51 0.96 1.55 2.00e-01 2.50e+01 6.01e+01 chirality pdb=" CA TRP A 790 " pdb=" N TRP A 790 " pdb=" C TRP A 790 " pdb=" CB TRP A 790 " both_signs ideal model delta sigma weight residual False 2.51 0.98 1.53 2.00e-01 2.50e+01 5.83e+01 chirality pdb=" CA GLN A 824 " pdb=" N GLN A 824 " pdb=" C GLN A 824 " pdb=" CB GLN A 824 " both_signs ideal model delta sigma weight residual False 2.51 0.99 1.52 2.00e-01 2.50e+01 5.80e+01 ... (remaining 2253 not shown) Planarity restraints: 2599 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO A1393 " -0.153 2.00e-02 2.50e+03 3.09e-01 9.54e+02 pdb=" C PRO A1393 " 0.522 2.00e-02 2.50e+03 pdb=" O PRO A1393 " -0.280 2.00e-02 2.50e+03 pdb=" N GLY A1394 " -0.088 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A1687 " -0.158 2.00e-02 2.50e+03 2.47e-01 6.11e+02 pdb=" C SER A1687 " 0.422 2.00e-02 2.50e+03 pdb=" O SER A1687 " -0.187 2.00e-02 2.50e+03 pdb=" N ILE A1688 " -0.077 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A1584 " -0.141 2.00e-02 2.50e+03 2.43e-01 5.92e+02 pdb=" C LEU A1584 " 0.418 2.00e-02 2.50e+03 pdb=" O LEU A1584 " -0.180 2.00e-02 2.50e+03 pdb=" N GLY A1585 " -0.097 2.00e-02 2.50e+03 ... (remaining 2596 not shown) Histogram of nonbonded interaction distances: 1.22 - 1.96: 51 1.96 - 2.69: 1035 2.69 - 3.43: 21032 3.43 - 4.16: 32655 4.16 - 4.90: 56204 Nonbonded interactions: 110977 Sorted by model distance: nonbonded pdb=" CZ PHE A1567 " pdb=" CD1 ILE A1571 " model vdw 1.223 3.760 nonbonded pdb=" O ASP A1515 " pdb=" OE1 GLU A1519 " model vdw 1.260 3.040 nonbonded pdb=" O PHE A 84 " pdb=" OG SER A 88 " model vdw 1.354 3.040 nonbonded pdb=" CB ALA A1296 " pdb=" OD2 ASP A1301 " model vdw 1.363 3.460 nonbonded pdb=" CE2 TYR A1348 " pdb=" CB SER A1397 " model vdw 1.393 3.740 ... (remaining 110972 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.250 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 16.500 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 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:1.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7471 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 : 0.013 0.352 15121 Z= 1.020 Angle : 3.318 50.587 20379 Z= 2.152 Chirality : 0.171 1.550 2256 Planarity : 0.021 0.309 2599 Dihedral : 16.555 128.708 5665 Min Nonbonded Distance : 1.223 Molprobity Statistics. All-atom Clashscore : 41.49 Ramachandran Plot: Outliers : 2.02 % Allowed : 11.41 % Favored : 86.57 % Rotamer: Outliers : 6.61 % Allowed : 7.40 % Favored : 85.99 % Cbeta Deviations : 6.25 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.55 % Twisted General : 1.80 % 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: -5.16 (0.15), residues: 1832 helix: -3.17 (0.14), residues: 663 sheet: -2.42 (0.41), residues: 136 loop : -3.92 (0.16), residues: 1033 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A1568 TYR 0.010 0.001 TYR A1101 PHE 0.127 0.002 PHE A 352 TRP 0.019 0.001 TRP A 520 HIS 0.004 0.001 HIS A 916 Details of bonding type rmsd covalent geometry : bond 0.01280 (15117) covalent geometry : angle 3.31769 (20379) hydrogen bonds : bond 0.23007 ( 405) hydrogen bonds : angle 8.24036 ( 1122) Misc. bond : bond 0.25417 ( 4) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 442 residues out of total 1635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 334 time to evaluate : 0.599 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: A 126 GLU cc_start: 0.7288 (tt0) cc_final: 0.7047 (mt-10) REVERT: A 420 ARG cc_start: 0.7990 (mtp-110) cc_final: 0.7575 (mtp-110) REVERT: A 672 GLU cc_start: 0.7523 (mt-10) cc_final: 0.7301 (mt-10) REVERT: A 773 LYS cc_start: 0.9095 (tttt) cc_final: 0.8802 (ttmm) REVERT: A 777 MET cc_start: 0.8179 (ttm) cc_final: 0.7872 (ttm) REVERT: A 778 GLU cc_start: 0.8119 (tp30) cc_final: 0.7882 (tp30) REVERT: A 913 LYS cc_start: 0.7383 (OUTLIER) cc_final: 0.7176 (ptmt) REVERT: A 933 GLN cc_start: 0.8743 (tm-30) cc_final: 0.8491 (tm-30) REVERT: A 1020 MET cc_start: 0.8014 (mtp) cc_final: 0.7746 (mtm) REVERT: A 1067 LYS cc_start: 0.8517 (OUTLIER) cc_final: 0.8154 (tppt) REVERT: A 1131 MET cc_start: 0.7983 (mtm) cc_final: 0.7644 (mtt) REVERT: A 1527 THR cc_start: 0.6439 (OUTLIER) cc_final: 0.5840 (m) REVERT: A 1544 SER cc_start: 0.5449 (OUTLIER) cc_final: 0.5127 (p) REVERT: A 1637 LEU cc_start: 0.9154 (pp) cc_final: 0.8943 (pp) REVERT: A 1791 SER cc_start: 0.8188 (OUTLIER) cc_final: 0.7722 (p) REVERT: A 1800 ARG cc_start: 0.8133 (ttm-80) cc_final: 0.7671 (ttm-80) REVERT: A 2015 MET cc_start: 0.8374 (tpp) cc_final: 0.8097 (tpt) outliers start: 108 outliers final: 53 residues processed: 415 average time/residue: 0.1534 time to fit residues: 87.4574 Evaluate side-chains 281 residues out of total 1635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 223 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 CYS Chi-restraints excluded: chain A residue 13 GLU Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 30 ARG Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 109 MET Chi-restraints excluded: chain A residue 155 ARG Chi-restraints excluded: chain A residue 161 GLU Chi-restraints excluded: chain A residue 181 MET Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 239 GLU Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 348 THR Chi-restraints excluded: chain A residue 349 ASP Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 387 GLU Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 408 TYR Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain A residue 699 GLN Chi-restraints excluded: chain A residue 888 TRP Chi-restraints excluded: chain A residue 913 LYS Chi-restraints excluded: chain A residue 921 GLU Chi-restraints excluded: chain A residue 949 HIS Chi-restraints excluded: chain A residue 971 ARG Chi-restraints excluded: chain A residue 1024 LYS Chi-restraints excluded: chain A residue 1064 TRP Chi-restraints excluded: chain A residue 1067 LYS Chi-restraints excluded: chain A residue 1071 TYR Chi-restraints excluded: chain A residue 1107 LYS Chi-restraints excluded: chain A residue 1399 LEU Chi-restraints excluded: chain A residue 1428 HIS Chi-restraints excluded: chain A residue 1460 GLN Chi-restraints excluded: chain A residue 1477 LEU Chi-restraints excluded: chain A residue 1514 GLU Chi-restraints excluded: chain A residue 1521 TRP Chi-restraints excluded: chain A residue 1527 THR Chi-restraints excluded: chain A residue 1534 LEU Chi-restraints excluded: chain A residue 1537 GLU Chi-restraints excluded: chain A residue 1538 TRP Chi-restraints excluded: chain A residue 1541 LEU Chi-restraints excluded: chain A residue 1542 ARG Chi-restraints excluded: chain A residue 1544 SER Chi-restraints excluded: chain A residue 1545 PHE Chi-restraints excluded: chain A residue 1589 LYS Chi-restraints excluded: chain A residue 1649 MET Chi-restraints excluded: chain A residue 1652 GLU Chi-restraints excluded: chain A residue 1657 LEU Chi-restraints excluded: chain A residue 1790 LEU Chi-restraints excluded: chain A residue 1791 SER Chi-restraints excluded: chain A residue 1796 LYS Chi-restraints excluded: chain A residue 1810 GLU Chi-restraints excluded: chain A residue 1911 ASP Chi-restraints excluded: chain A residue 1976 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 0.3980 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 0.9990 overall best weight: 2.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 237 ASN A 376 ASN A 466 ASN A 513 ASN A 618 ASN A 841 ASN A 915 GLN A 964 ASN A1035 HIS A1190 HIS A1204 GLN A1930 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.111074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.085062 restraints weight = 35285.010| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 4.23 r_work: 0.3173 rms_B_bonded: 4.73 restraints_weight: 0.5000 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.2867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 15121 Z= 0.213 Angle : 0.919 17.203 20379 Z= 0.477 Chirality : 0.051 0.266 2256 Planarity : 0.007 0.097 2599 Dihedral : 10.809 77.446 2165 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 12.79 Ramachandran Plot: Outliers : 0.66 % Allowed : 11.19 % Favored : 88.16 % Rotamer: Outliers : 4.10 % Allowed : 18.17 % Favored : 77.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.11 % Twisted Proline : 3.03 % Twisted General : 0.67 % 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: -4.32 (0.17), residues: 1832 helix: -2.25 (0.17), residues: 708 sheet: -1.76 (0.42), residues: 140 loop : -3.66 (0.17), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A1060 TYR 0.027 0.002 TYR A 193 PHE 0.019 0.002 PHE A1570 TRP 0.018 0.002 TRP A 520 HIS 0.014 0.001 HIS A 916 Details of bonding type rmsd covalent geometry : bond 0.00460 (15117) covalent geometry : angle 0.91935 (20379) hydrogen bonds : bond 0.05054 ( 405) hydrogen bonds : angle 5.50740 ( 1122) Misc. bond : bond 0.00416 ( 4) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 1635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 246 time to evaluate : 0.616 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 ASN cc_start: 0.8330 (m-40) cc_final: 0.7892 (t0) REVERT: A 126 GLU cc_start: 0.7734 (tt0) cc_final: 0.7307 (mt-10) REVERT: A 160 MET cc_start: 0.8139 (OUTLIER) cc_final: 0.7897 (mmm) REVERT: A 189 GLU cc_start: 0.8906 (mt-10) cc_final: 0.8567 (mm-30) REVERT: A 356 MET cc_start: 0.8715 (mmp) cc_final: 0.8196 (mtp) REVERT: A 420 ARG cc_start: 0.8309 (mtp-110) cc_final: 0.8064 (mtp-110) REVERT: A 689 LYS cc_start: 0.9235 (mttp) cc_final: 0.8999 (mttm) REVERT: A 773 LYS cc_start: 0.9232 (tttt) cc_final: 0.8933 (ttmm) REVERT: A 777 MET cc_start: 0.8543 (ttm) cc_final: 0.8224 (ttm) REVERT: A 888 TRP cc_start: 0.8519 (OUTLIER) cc_final: 0.8257 (m-10) REVERT: A 913 LYS cc_start: 0.8142 (OUTLIER) cc_final: 0.7726 (ptmt) REVERT: A 971 ARG cc_start: 0.9260 (OUTLIER) cc_final: 0.8943 (ttm110) REVERT: A 1020 MET cc_start: 0.8740 (mtp) cc_final: 0.8460 (mtm) REVERT: A 1111 MET cc_start: 0.9023 (mpp) cc_final: 0.8260 (ppp) REVERT: A 1131 MET cc_start: 0.8808 (mtm) cc_final: 0.8480 (mtt) REVERT: A 1463 MET cc_start: 0.3406 (ttm) cc_final: 0.2351 (tmm) REVERT: A 1532 ARG cc_start: 0.8777 (OUTLIER) cc_final: 0.8539 (mmm-85) REVERT: A 1556 LEU cc_start: 0.8979 (tp) cc_final: 0.8481 (mp) REVERT: A 1564 HIS cc_start: 0.6597 (m-70) cc_final: 0.5959 (m-70) REVERT: A 1575 ASP cc_start: 0.7824 (OUTLIER) cc_final: 0.7364 (t70) REVERT: A 1620 GLN cc_start: 0.9502 (tp40) cc_final: 0.9235 (tp-100) REVERT: A 1746 TRP cc_start: 0.8760 (p90) cc_final: 0.8051 (p90) REVERT: A 1800 ARG cc_start: 0.8455 (ttm-80) cc_final: 0.8076 (ttm-80) REVERT: A 1865 LEU cc_start: 0.9262 (tp) cc_final: 0.9055 (tp) REVERT: A 1950 THR cc_start: 0.3967 (OUTLIER) cc_final: 0.3653 (p) REVERT: A 2015 MET cc_start: 0.8360 (tpp) cc_final: 0.7996 (tpt) outliers start: 67 outliers final: 41 residues processed: 285 average time/residue: 0.1413 time to fit residues: 57.4275 Evaluate side-chains 255 residues out of total 1635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 207 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 160 MET Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 237 ASN Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 348 THR Chi-restraints excluded: chain A residue 352 PHE Chi-restraints excluded: chain A residue 387 GLU Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 408 TYR Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain A residue 607 THR Chi-restraints excluded: chain A residue 663 ILE Chi-restraints excluded: chain A residue 699 GLN Chi-restraints excluded: chain A residue 724 GLU Chi-restraints excluded: chain A residue 762 THR Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 888 TRP Chi-restraints excluded: chain A residue 913 LYS Chi-restraints excluded: chain A residue 971 ARG Chi-restraints excluded: chain A residue 1064 TRP Chi-restraints excluded: chain A residue 1071 TYR Chi-restraints excluded: chain A residue 1160 ASN Chi-restraints excluded: chain A residue 1178 CYS Chi-restraints excluded: chain A residue 1361 TRP Chi-restraints excluded: chain A residue 1399 LEU Chi-restraints excluded: chain A residue 1514 GLU Chi-restraints excluded: chain A residue 1532 ARG Chi-restraints excluded: chain A residue 1534 LEU Chi-restraints excluded: chain A residue 1537 GLU Chi-restraints excluded: chain A residue 1541 LEU Chi-restraints excluded: chain A residue 1557 ARG Chi-restraints excluded: chain A residue 1573 HIS Chi-restraints excluded: chain A residue 1575 ASP Chi-restraints excluded: chain A residue 1595 THR Chi-restraints excluded: chain A residue 1672 MET Chi-restraints excluded: chain A residue 1738 ILE Chi-restraints excluded: chain A residue 1769 CYS Chi-restraints excluded: chain A residue 1796 LYS Chi-restraints excluded: chain A residue 1868 ASN Chi-restraints excluded: chain A residue 1883 TRP Chi-restraints excluded: chain A residue 1910 ILE Chi-restraints excluded: chain A residue 1950 THR Chi-restraints excluded: chain A residue 1957 LEU Chi-restraints excluded: chain A residue 2007 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 104 optimal weight: 8.9990 chunk 162 optimal weight: 7.9990 chunk 44 optimal weight: 4.9990 chunk 21 optimal weight: 3.9990 chunk 51 optimal weight: 0.0170 chunk 132 optimal weight: 6.9990 chunk 55 optimal weight: 2.9990 chunk 126 optimal weight: 1.9990 chunk 138 optimal weight: 10.0000 chunk 28 optimal weight: 0.4980 chunk 25 optimal weight: 2.9990 overall best weight: 1.7024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 ASN A 513 ASN A 959 ASN A1255 HIS A1292 ASN A1391 HIS A1566 GLN ** A1846 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.110726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.084491 restraints weight = 35668.992| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 4.26 r_work: 0.3159 rms_B_bonded: 4.78 restraints_weight: 0.5000 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.3371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 15121 Z= 0.158 Angle : 0.790 10.851 20379 Z= 0.406 Chirality : 0.046 0.235 2256 Planarity : 0.006 0.096 2599 Dihedral : 8.385 60.751 2067 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.49 % Allowed : 10.86 % Favored : 88.65 % Rotamer: Outliers : 4.34 % Allowed : 20.61 % Favored : 75.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.11 % Twisted Proline : 4.55 % Twisted General : 0.51 % 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: -3.76 (0.18), residues: 1832 helix: -1.74 (0.18), residues: 715 sheet: -1.32 (0.42), residues: 143 loop : -3.41 (0.18), residues: 974 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1023 TYR 0.020 0.001 TYR A1348 PHE 0.022 0.001 PHE A1561 TRP 0.017 0.001 TRP A 520 HIS 0.004 0.001 HIS A 103 Details of bonding type rmsd covalent geometry : bond 0.00350 (15117) covalent geometry : angle 0.78973 (20379) hydrogen bonds : bond 0.03954 ( 405) hydrogen bonds : angle 4.85578 ( 1122) Misc. bond : bond 0.00317 ( 4) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 221 time to evaluate : 0.597 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6950 (mmm) cc_final: 0.6708 (mmm) REVERT: A 2 ASN cc_start: 0.8520 (m-40) cc_final: 0.8184 (t0) REVERT: A 126 GLU cc_start: 0.7790 (tt0) cc_final: 0.7302 (mt-10) REVERT: A 160 MET cc_start: 0.8042 (OUTLIER) cc_final: 0.7807 (mmm) REVERT: A 189 GLU cc_start: 0.8925 (mt-10) cc_final: 0.8604 (mt-10) REVERT: A 252 MET cc_start: 0.8348 (mtp) cc_final: 0.8064 (mmt) REVERT: A 406 ILE cc_start: 0.7681 (OUTLIER) cc_final: 0.7077 (pt) REVERT: A 420 ARG cc_start: 0.8337 (mtp-110) cc_final: 0.8036 (mtp-110) REVERT: A 689 LYS cc_start: 0.9213 (mttp) cc_final: 0.8937 (mttm) REVERT: A 773 LYS cc_start: 0.9243 (tttt) cc_final: 0.8951 (ttmm) REVERT: A 848 MET cc_start: 0.7780 (tpp) cc_final: 0.6939 (tpt) REVERT: A 874 LEU cc_start: 0.8907 (tp) cc_final: 0.8637 (tp) REVERT: A 878 MET cc_start: 0.8950 (mtt) cc_final: 0.8603 (mtt) REVERT: A 1079 MET cc_start: 0.8470 (mmp) cc_final: 0.7284 (mmp) REVERT: A 1131 MET cc_start: 0.8792 (mtm) cc_final: 0.8500 (mtt) REVERT: A 1381 GLU cc_start: 0.9099 (pm20) cc_final: 0.8587 (pm20) REVERT: A 1463 MET cc_start: 0.3273 (ttm) cc_final: 0.2406 (tmm) REVERT: A 1514 GLU cc_start: 0.8715 (OUTLIER) cc_final: 0.8379 (pp20) REVERT: A 1544 SER cc_start: 0.8826 (m) cc_final: 0.8584 (p) REVERT: A 1557 ARG cc_start: 0.8836 (OUTLIER) cc_final: 0.8595 (mtm110) REVERT: A 1568 ARG cc_start: 0.8419 (OUTLIER) cc_final: 0.8129 (tpt-90) REVERT: A 1569 ASN cc_start: 0.8963 (m-40) cc_final: 0.7734 (t0) REVERT: A 1620 GLN cc_start: 0.9548 (tp40) cc_final: 0.9316 (tp-100) REVERT: A 1637 LEU cc_start: 0.9329 (pp) cc_final: 0.8947 (pp) REVERT: A 1746 TRP cc_start: 0.8533 (p90) cc_final: 0.8197 (p90) REVERT: A 1800 ARG cc_start: 0.8333 (ttm-80) cc_final: 0.8085 (ttm-80) REVERT: A 1865 LEU cc_start: 0.9261 (tp) cc_final: 0.9026 (tp) REVERT: A 2015 MET cc_start: 0.8397 (tpp) cc_final: 0.8029 (tpt) outliers start: 71 outliers final: 39 residues processed: 270 average time/residue: 0.1308 time to fit residues: 51.4123 Evaluate side-chains 235 residues out of total 1635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 191 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ILE Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 151 ASP Chi-restraints excluded: chain A residue 160 MET Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 237 ASN Chi-restraints excluded: chain A residue 352 PHE Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 408 TYR Chi-restraints excluded: chain A residue 633 LEU Chi-restraints excluded: chain A residue 663 ILE Chi-restraints excluded: chain A residue 664 THR Chi-restraints excluded: chain A residue 699 GLN Chi-restraints excluded: chain A residue 721 ILE Chi-restraints excluded: chain A residue 724 GLU Chi-restraints excluded: chain A residue 762 THR Chi-restraints excluded: chain A residue 837 ILE Chi-restraints excluded: chain A residue 1064 TRP Chi-restraints excluded: chain A residue 1160 ASN Chi-restraints excluded: chain A residue 1178 CYS Chi-restraints excluded: chain A residue 1300 THR Chi-restraints excluded: chain A residue 1395 VAL Chi-restraints excluded: chain A residue 1396 THR Chi-restraints excluded: chain A residue 1399 LEU Chi-restraints excluded: chain A residue 1514 GLU Chi-restraints excluded: chain A residue 1534 LEU Chi-restraints excluded: chain A residue 1541 LEU Chi-restraints excluded: chain A residue 1556 LEU Chi-restraints excluded: chain A residue 1557 ARG Chi-restraints excluded: chain A residue 1568 ARG Chi-restraints excluded: chain A residue 1573 HIS Chi-restraints excluded: chain A residue 1574 VAL Chi-restraints excluded: chain A residue 1595 THR Chi-restraints excluded: chain A residue 1769 CYS Chi-restraints excluded: chain A residue 1806 VAL Chi-restraints excluded: chain A residue 1868 ASN Chi-restraints excluded: chain A residue 1910 ILE Chi-restraints excluded: chain A residue 1954 VAL Chi-restraints excluded: chain A residue 1957 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 15 optimal weight: 8.9990 chunk 103 optimal weight: 8.9990 chunk 180 optimal weight: 20.0000 chunk 51 optimal weight: 10.0000 chunk 94 optimal weight: 4.9990 chunk 66 optimal weight: 8.9990 chunk 179 optimal weight: 6.9990 chunk 118 optimal weight: 0.9980 chunk 167 optimal weight: 0.8980 chunk 41 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 GLN A1292 ASN A1403 HIS A1566 GLN ** A1846 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.109461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.082918 restraints weight = 35596.470| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 4.17 r_work: 0.3134 rms_B_bonded: 4.65 restraints_weight: 0.5000 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.3729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 15121 Z= 0.191 Angle : 0.779 10.284 20379 Z= 0.401 Chirality : 0.047 0.242 2256 Planarity : 0.006 0.097 2599 Dihedral : 7.514 60.283 2042 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.38 % Allowed : 11.68 % Favored : 87.94 % Rotamer: Outliers : 4.40 % Allowed : 21.04 % Favored : 74.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.11 % Twisted Proline : 4.55 % Twisted General : 0.56 % 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: -3.42 (0.18), residues: 1832 helix: -1.49 (0.18), residues: 724 sheet: -1.28 (0.42), residues: 150 loop : -3.18 (0.18), residues: 958 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1189 TYR 0.020 0.001 TYR A1348 PHE 0.020 0.002 PHE A 352 TRP 0.018 0.001 TRP A1064 HIS 0.005 0.001 HIS A1564 Details of bonding type rmsd covalent geometry : bond 0.00420 (15117) covalent geometry : angle 0.77929 (20379) hydrogen bonds : bond 0.03979 ( 405) hydrogen bonds : angle 4.74373 ( 1122) Misc. bond : bond 0.00135 ( 4) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 207 time to evaluate : 0.591 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7084 (mmm) cc_final: 0.6827 (mmm) REVERT: A 2 ASN cc_start: 0.8543 (m-40) cc_final: 0.8315 (t0) REVERT: A 126 GLU cc_start: 0.7833 (tt0) cc_final: 0.7394 (mt-10) REVERT: A 160 MET cc_start: 0.8025 (OUTLIER) cc_final: 0.7775 (mmm) REVERT: A 193 TYR cc_start: 0.8673 (t80) cc_final: 0.8435 (t80) REVERT: A 252 MET cc_start: 0.8322 (mtp) cc_final: 0.8046 (mmt) REVERT: A 664 THR cc_start: 0.9295 (OUTLIER) cc_final: 0.9027 (p) REVERT: A 689 LYS cc_start: 0.9229 (mttp) cc_final: 0.8947 (mttm) REVERT: A 773 LYS cc_start: 0.9220 (tttt) cc_final: 0.8957 (ttmm) REVERT: A 878 MET cc_start: 0.8946 (mtt) cc_final: 0.8638 (mtt) REVERT: A 1111 MET cc_start: 0.9043 (mpp) cc_final: 0.8271 (ppp) REVERT: A 1131 MET cc_start: 0.8812 (mtm) cc_final: 0.8421 (mtp) REVERT: A 1180 GLU cc_start: 0.7783 (tm-30) cc_final: 0.7377 (tm-30) REVERT: A 1381 GLU cc_start: 0.9071 (pm20) cc_final: 0.8595 (pm20) REVERT: A 1463 MET cc_start: 0.2537 (ttm) cc_final: 0.1743 (tmm) REVERT: A 1477 LEU cc_start: 0.4230 (OUTLIER) cc_final: 0.3914 (tp) REVERT: A 1557 ARG cc_start: 0.8838 (OUTLIER) cc_final: 0.8566 (mtm110) REVERT: A 1568 ARG cc_start: 0.8374 (OUTLIER) cc_final: 0.6664 (ttm-80) REVERT: A 1569 ASN cc_start: 0.9046 (m-40) cc_final: 0.7840 (t0) REVERT: A 1746 TRP cc_start: 0.8503 (p90) cc_final: 0.7862 (p90) REVERT: A 1865 LEU cc_start: 0.9257 (tp) cc_final: 0.8961 (tp) REVERT: A 2015 MET cc_start: 0.8329 (tpp) cc_final: 0.7995 (tpt) outliers start: 72 outliers final: 52 residues processed: 259 average time/residue: 0.1281 time to fit residues: 48.5782 Evaluate side-chains 247 residues out of total 1635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 190 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 10 ILE Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 109 MET Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 160 MET Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 352 PHE Chi-restraints excluded: chain A residue 408 TYR Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain A residue 607 THR Chi-restraints excluded: chain A residue 633 LEU Chi-restraints excluded: chain A residue 663 ILE Chi-restraints excluded: chain A residue 664 THR Chi-restraints excluded: chain A residue 699 GLN Chi-restraints excluded: chain A residue 721 ILE Chi-restraints excluded: chain A residue 724 GLU Chi-restraints excluded: chain A residue 762 THR Chi-restraints excluded: chain A residue 837 ILE Chi-restraints excluded: chain A residue 844 ASP Chi-restraints excluded: chain A residue 847 SER Chi-restraints excluded: chain A residue 1064 TRP Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain A residue 1160 ASN Chi-restraints excluded: chain A residue 1178 CYS Chi-restraints excluded: chain A residue 1254 LEU Chi-restraints excluded: chain A residue 1300 THR Chi-restraints excluded: chain A residue 1395 VAL Chi-restraints excluded: chain A residue 1396 THR Chi-restraints excluded: chain A residue 1399 LEU Chi-restraints excluded: chain A residue 1433 THR Chi-restraints excluded: chain A residue 1474 VAL Chi-restraints excluded: chain A residue 1477 LEU Chi-restraints excluded: chain A residue 1534 LEU Chi-restraints excluded: chain A residue 1541 LEU Chi-restraints excluded: chain A residue 1557 ARG Chi-restraints excluded: chain A residue 1568 ARG Chi-restraints excluded: chain A residue 1573 HIS Chi-restraints excluded: chain A residue 1574 VAL Chi-restraints excluded: chain A residue 1595 THR Chi-restraints excluded: chain A residue 1672 MET Chi-restraints excluded: chain A residue 1709 THR Chi-restraints excluded: chain A residue 1739 ASP Chi-restraints excluded: chain A residue 1769 CYS Chi-restraints excluded: chain A residue 1806 VAL Chi-restraints excluded: chain A residue 1868 ASN Chi-restraints excluded: chain A residue 1886 LEU Chi-restraints excluded: chain A residue 1910 ILE Chi-restraints excluded: chain A residue 1955 ASP Chi-restraints excluded: chain A residue 1957 LEU Chi-restraints excluded: chain A residue 1969 VAL Chi-restraints excluded: chain A residue 2007 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 174 optimal weight: 8.9990 chunk 170 optimal weight: 6.9990 chunk 133 optimal weight: 9.9990 chunk 148 optimal weight: 5.9990 chunk 176 optimal weight: 6.9990 chunk 155 optimal weight: 7.9990 chunk 181 optimal weight: 6.9990 chunk 122 optimal weight: 0.0370 chunk 143 optimal weight: 0.0370 chunk 30 optimal weight: 9.9990 chunk 66 optimal weight: 7.9990 overall best weight: 4.0142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 618 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 799 HIS A 915 GLN ** A1203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1204 GLN ** A1846 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.106405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.080688 restraints weight = 36057.015| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 4.07 r_work: 0.3091 rms_B_bonded: 4.54 restraints_weight: 0.5000 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.3985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 15121 Z= 0.265 Angle : 0.816 10.182 20379 Z= 0.417 Chirality : 0.048 0.254 2256 Planarity : 0.006 0.104 2599 Dihedral : 7.441 62.482 2035 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 11.95 Ramachandran Plot: Outliers : 0.33 % Allowed : 12.34 % Favored : 87.34 % Rotamer: Outliers : 5.32 % Allowed : 21.41 % Favored : 73.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.11 % Twisted Proline : 4.55 % Twisted General : 0.51 % 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: -3.29 (0.18), residues: 1832 helix: -1.34 (0.19), residues: 730 sheet: -1.40 (0.41), residues: 164 loop : -3.12 (0.19), residues: 938 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A1928 TYR 0.022 0.002 TYR A1348 PHE 0.019 0.002 PHE A 352 TRP 0.022 0.002 TRP A1064 HIS 0.005 0.001 HIS A 706 Details of bonding type rmsd covalent geometry : bond 0.00582 (15117) covalent geometry : angle 0.81569 (20379) hydrogen bonds : bond 0.04415 ( 405) hydrogen bonds : angle 4.85720 ( 1122) Misc. bond : bond 0.00255 ( 4) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 1635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 203 time to evaluate : 0.562 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: A 2 ASN cc_start: 0.8761 (m-40) cc_final: 0.8484 (t0) REVERT: A 189 GLU cc_start: 0.9085 (mt-10) cc_final: 0.8810 (mm-30) REVERT: A 193 TYR cc_start: 0.8758 (t80) cc_final: 0.8491 (t80) REVERT: A 252 MET cc_start: 0.8501 (mtp) cc_final: 0.8250 (mmt) REVERT: A 347 LYS cc_start: 0.8950 (tmmt) cc_final: 0.8639 (ttpp) REVERT: A 411 PHE cc_start: 0.6971 (m-10) cc_final: 0.6544 (m-10) REVERT: A 726 ARG cc_start: 0.7248 (mtm-85) cc_final: 0.6926 (ptt180) REVERT: A 773 LYS cc_start: 0.9259 (tttt) cc_final: 0.8996 (ttmm) REVERT: A 848 MET cc_start: 0.7973 (tpp) cc_final: 0.7069 (tpt) REVERT: A 878 MET cc_start: 0.9010 (mtt) cc_final: 0.8694 (mtt) REVERT: A 925 MET cc_start: 0.8724 (mmm) cc_final: 0.8444 (mmm) REVERT: A 947 SER cc_start: 0.9392 (p) cc_final: 0.8878 (p) REVERT: A 950 GLU cc_start: 0.8171 (mm-30) cc_final: 0.7773 (mt-10) REVERT: A 1079 MET cc_start: 0.8518 (mmp) cc_final: 0.8295 (mmp) REVERT: A 1131 MET cc_start: 0.8837 (mtm) cc_final: 0.8531 (mtt) REVERT: A 1140 MET cc_start: 0.9162 (ttp) cc_final: 0.8586 (tmm) REVERT: A 1381 GLU cc_start: 0.9040 (pm20) cc_final: 0.8586 (pm20) REVERT: A 1416 LEU cc_start: 0.9071 (tp) cc_final: 0.8722 (tp) REVERT: A 1463 MET cc_start: 0.2730 (ttm) cc_final: 0.1870 (tmm) REVERT: A 1477 LEU cc_start: 0.4212 (OUTLIER) cc_final: 0.3850 (tp) REVERT: A 1554 GLU cc_start: 0.8289 (tp30) cc_final: 0.8054 (tp30) REVERT: A 1568 ARG cc_start: 0.8519 (OUTLIER) cc_final: 0.6679 (tpm-80) REVERT: A 1569 ASN cc_start: 0.9052 (m-40) cc_final: 0.7809 (t0) REVERT: A 1635 MET cc_start: 0.8696 (ppp) cc_final: 0.8226 (ppp) REVERT: A 1677 LEU cc_start: 0.8645 (OUTLIER) cc_final: 0.8431 (mm) REVERT: A 1700 LEU cc_start: 0.6784 (OUTLIER) cc_final: 0.6554 (pt) REVERT: A 1746 TRP cc_start: 0.8501 (p90) cc_final: 0.7883 (p90) REVERT: A 1865 LEU cc_start: 0.9301 (tp) cc_final: 0.9001 (tp) REVERT: A 2015 MET cc_start: 0.8398 (tpp) cc_final: 0.8093 (tpt) outliers start: 87 outliers final: 59 residues processed: 265 average time/residue: 0.1285 time to fit residues: 49.7874 Evaluate side-chains 249 residues out of total 1635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 186 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ILE Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 151 ASP Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 352 PHE Chi-restraints excluded: chain A residue 408 TYR Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain A residue 607 THR Chi-restraints excluded: chain A residue 633 LEU Chi-restraints excluded: chain A residue 664 THR Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain A residue 699 GLN Chi-restraints excluded: chain A residue 724 GLU Chi-restraints excluded: chain A residue 762 THR Chi-restraints excluded: chain A residue 799 HIS Chi-restraints excluded: chain A residue 810 CYS Chi-restraints excluded: chain A residue 837 ILE Chi-restraints excluded: chain A residue 844 ASP Chi-restraints excluded: chain A residue 847 SER Chi-restraints excluded: chain A residue 954 ASN Chi-restraints excluded: chain A residue 967 LEU Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain A residue 1103 VAL Chi-restraints excluded: chain A residue 1160 ASN Chi-restraints excluded: chain A residue 1178 CYS Chi-restraints excluded: chain A residue 1191 LEU Chi-restraints excluded: chain A residue 1254 LEU Chi-restraints excluded: chain A residue 1300 THR Chi-restraints excluded: chain A residue 1395 VAL Chi-restraints excluded: chain A residue 1396 THR Chi-restraints excluded: chain A residue 1399 LEU Chi-restraints excluded: chain A residue 1444 MET Chi-restraints excluded: chain A residue 1474 VAL Chi-restraints excluded: chain A residue 1477 LEU Chi-restraints excluded: chain A residue 1527 THR Chi-restraints excluded: chain A residue 1534 LEU Chi-restraints excluded: chain A residue 1557 ARG Chi-restraints excluded: chain A residue 1568 ARG Chi-restraints excluded: chain A residue 1573 HIS Chi-restraints excluded: chain A residue 1595 THR Chi-restraints excluded: chain A residue 1677 LEU Chi-restraints excluded: chain A residue 1700 LEU Chi-restraints excluded: chain A residue 1709 THR Chi-restraints excluded: chain A residue 1738 ILE Chi-restraints excluded: chain A residue 1739 ASP Chi-restraints excluded: chain A residue 1743 THR Chi-restraints excluded: chain A residue 1769 CYS Chi-restraints excluded: chain A residue 1806 VAL Chi-restraints excluded: chain A residue 1811 ARG Chi-restraints excluded: chain A residue 1868 ASN Chi-restraints excluded: chain A residue 1886 LEU Chi-restraints excluded: chain A residue 1910 ILE Chi-restraints excluded: chain A residue 1954 VAL Chi-restraints excluded: chain A residue 1957 LEU Chi-restraints excluded: chain A residue 1977 ASP Chi-restraints excluded: chain A residue 2007 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 100 optimal weight: 9.9990 chunk 11 optimal weight: 2.9990 chunk 162 optimal weight: 6.9990 chunk 61 optimal weight: 0.7980 chunk 27 optimal weight: 7.9990 chunk 77 optimal weight: 2.9990 chunk 155 optimal weight: 5.9990 chunk 124 optimal weight: 1.9990 chunk 133 optimal weight: 5.9990 chunk 60 optimal weight: 0.9990 chunk 52 optimal weight: 0.4980 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 HIS A 959 ASN ** A1255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1292 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.108732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.082924 restraints weight = 35295.318| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 4.17 r_work: 0.3137 rms_B_bonded: 4.65 restraints_weight: 0.5000 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.4158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15121 Z= 0.143 Angle : 0.756 10.744 20379 Z= 0.382 Chirality : 0.045 0.276 2256 Planarity : 0.005 0.099 2599 Dihedral : 6.916 61.266 2031 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.33 % Allowed : 11.30 % Favored : 88.37 % Rotamer: Outliers : 4.10 % Allowed : 23.24 % Favored : 72.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.11 % Twisted Proline : 3.03 % Twisted General : 0.45 % 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: -3.05 (0.19), residues: 1832 helix: -1.12 (0.19), residues: 732 sheet: -1.08 (0.42), residues: 152 loop : -3.03 (0.19), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 30 TYR 0.020 0.001 TYR A 869 PHE 0.018 0.001 PHE A 352 TRP 0.019 0.001 TRP A 520 HIS 0.007 0.001 HIS A 799 Details of bonding type rmsd covalent geometry : bond 0.00321 (15117) covalent geometry : angle 0.75605 (20379) hydrogen bonds : bond 0.03565 ( 405) hydrogen bonds : angle 4.52112 ( 1122) Misc. bond : bond 0.00159 ( 4) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 209 time to evaluate : 0.486 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 ASN cc_start: 0.8725 (m-40) cc_final: 0.8485 (t0) REVERT: A 160 MET cc_start: 0.8121 (mmm) cc_final: 0.7766 (mmm) REVERT: A 181 MET cc_start: 0.8997 (mmp) cc_final: 0.8731 (mmp) REVERT: A 189 GLU cc_start: 0.9068 (mt-10) cc_final: 0.8770 (mm-30) REVERT: A 193 TYR cc_start: 0.8686 (t80) cc_final: 0.8452 (t80) REVERT: A 352 PHE cc_start: 0.7181 (OUTLIER) cc_final: 0.6817 (p90) REVERT: A 411 PHE cc_start: 0.6634 (m-10) cc_final: 0.6106 (m-10) REVERT: A 666 THR cc_start: 0.9511 (p) cc_final: 0.9206 (t) REVERT: A 726 ARG cc_start: 0.7342 (mtm-85) cc_final: 0.6930 (ptt180) REVERT: A 773 LYS cc_start: 0.9209 (tttt) cc_final: 0.8932 (ttmm) REVERT: A 848 MET cc_start: 0.7914 (tpp) cc_final: 0.6919 (tpt) REVERT: A 878 MET cc_start: 0.8968 (mtt) cc_final: 0.8639 (mtt) REVERT: A 887 MET cc_start: 0.7840 (tpp) cc_final: 0.7070 (tpp) REVERT: A 1079 MET cc_start: 0.8539 (mmp) cc_final: 0.8269 (mmp) REVERT: A 1111 MET cc_start: 0.9049 (mpp) cc_final: 0.8205 (ppp) REVERT: A 1131 MET cc_start: 0.8774 (mtm) cc_final: 0.8371 (mtp) REVERT: A 1140 MET cc_start: 0.9176 (ttp) cc_final: 0.8596 (tmm) REVERT: A 1253 CYS cc_start: 0.8119 (m) cc_final: 0.7878 (m) REVERT: A 1381 GLU cc_start: 0.9037 (pm20) cc_final: 0.8572 (pm20) REVERT: A 1416 LEU cc_start: 0.9055 (tp) cc_final: 0.8700 (tp) REVERT: A 1463 MET cc_start: 0.2715 (ttm) cc_final: 0.1585 (tmm) REVERT: A 1551 ASP cc_start: 0.9318 (m-30) cc_final: 0.9049 (t0) REVERT: A 1557 ARG cc_start: 0.8830 (OUTLIER) cc_final: 0.8537 (mtp85) REVERT: A 1568 ARG cc_start: 0.8441 (OUTLIER) cc_final: 0.6726 (tpm-80) REVERT: A 1635 MET cc_start: 0.8623 (ppp) cc_final: 0.7911 (ppp) REVERT: A 1672 MET cc_start: 0.7472 (pmm) cc_final: 0.7263 (pmm) REVERT: A 1677 LEU cc_start: 0.8659 (OUTLIER) cc_final: 0.8449 (mm) REVERT: A 1746 TRP cc_start: 0.8507 (p90) cc_final: 0.7918 (p90) REVERT: A 1810 GLU cc_start: 0.8171 (OUTLIER) cc_final: 0.7795 (tm-30) REVERT: A 1865 LEU cc_start: 0.9274 (tp) cc_final: 0.8924 (tp) REVERT: A 2015 MET cc_start: 0.8337 (tpp) cc_final: 0.8059 (tpt) outliers start: 67 outliers final: 42 residues processed: 257 average time/residue: 0.1199 time to fit residues: 45.5262 Evaluate side-chains 235 residues out of total 1635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 188 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 109 MET Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 347 LYS Chi-restraints excluded: chain A residue 352 PHE Chi-restraints excluded: chain A residue 408 TYR Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain A residue 633 LEU Chi-restraints excluded: chain A residue 699 GLN Chi-restraints excluded: chain A residue 724 GLU Chi-restraints excluded: chain A residue 762 THR Chi-restraints excluded: chain A residue 810 CYS Chi-restraints excluded: chain A residue 837 ILE Chi-restraints excluded: chain A residue 844 ASP Chi-restraints excluded: chain A residue 1160 ASN Chi-restraints excluded: chain A residue 1254 LEU Chi-restraints excluded: chain A residue 1300 THR Chi-restraints excluded: chain A residue 1395 VAL Chi-restraints excluded: chain A residue 1399 LEU Chi-restraints excluded: chain A residue 1444 MET Chi-restraints excluded: chain A residue 1534 LEU Chi-restraints excluded: chain A residue 1556 LEU Chi-restraints excluded: chain A residue 1557 ARG Chi-restraints excluded: chain A residue 1568 ARG Chi-restraints excluded: chain A residue 1595 THR Chi-restraints excluded: chain A residue 1676 LEU Chi-restraints excluded: chain A residue 1677 LEU Chi-restraints excluded: chain A residue 1738 ILE Chi-restraints excluded: chain A residue 1739 ASP Chi-restraints excluded: chain A residue 1743 THR Chi-restraints excluded: chain A residue 1769 CYS Chi-restraints excluded: chain A residue 1806 VAL Chi-restraints excluded: chain A residue 1810 GLU Chi-restraints excluded: chain A residue 1811 ARG Chi-restraints excluded: chain A residue 1868 ASN Chi-restraints excluded: chain A residue 1886 LEU Chi-restraints excluded: chain A residue 1910 ILE Chi-restraints excluded: chain A residue 1954 VAL Chi-restraints excluded: chain A residue 1957 LEU Chi-restraints excluded: chain A residue 1977 ASP Chi-restraints excluded: chain A residue 2007 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 78 optimal weight: 1.9990 chunk 38 optimal weight: 0.0870 chunk 89 optimal weight: 0.9990 chunk 45 optimal weight: 0.9990 chunk 11 optimal weight: 0.7980 chunk 0 optimal weight: 9.9990 chunk 175 optimal weight: 6.9990 chunk 123 optimal weight: 9.9990 chunk 95 optimal weight: 7.9990 chunk 133 optimal weight: 10.0000 chunk 1 optimal weight: 0.0870 overall best weight: 0.5940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 799 HIS A 959 ASN A1428 HIS ** A1638 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1834 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.110866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.085485 restraints weight = 34906.880| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 4.07 r_work: 0.3180 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.4373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 15121 Z= 0.128 Angle : 0.742 10.120 20379 Z= 0.374 Chirality : 0.045 0.240 2256 Planarity : 0.005 0.096 2599 Dihedral : 6.658 60.446 2031 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.22 % Allowed : 10.53 % Favored : 89.25 % Rotamer: Outliers : 3.67 % Allowed : 24.04 % Favored : 72.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.11 % Twisted Proline : 3.03 % Twisted General : 0.39 % 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: -2.87 (0.19), residues: 1832 helix: -0.94 (0.19), residues: 738 sheet: -0.96 (0.44), residues: 143 loop : -2.96 (0.19), residues: 951 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1829 TYR 0.016 0.001 TYR A1348 PHE 0.019 0.001 PHE A 352 TRP 0.023 0.001 TRP A1064 HIS 0.004 0.001 HIS A 799 Details of bonding type rmsd covalent geometry : bond 0.00290 (15117) covalent geometry : angle 0.74170 (20379) hydrogen bonds : bond 0.03267 ( 405) hydrogen bonds : angle 4.43180 ( 1122) Misc. bond : bond 0.00339 ( 4) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 212 time to evaluate : 0.595 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: A 160 MET cc_start: 0.8082 (mmm) cc_final: 0.7705 (mmm) REVERT: A 189 GLU cc_start: 0.8999 (mt-10) cc_final: 0.8774 (mt-10) REVERT: A 193 TYR cc_start: 0.8628 (t80) cc_final: 0.8421 (t80) REVERT: A 376 ASN cc_start: 0.7793 (OUTLIER) cc_final: 0.7291 (t0) REVERT: A 411 PHE cc_start: 0.6459 (m-10) cc_final: 0.6252 (m-10) REVERT: A 540 GLU cc_start: 0.7692 (pm20) cc_final: 0.7385 (pm20) REVERT: A 666 THR cc_start: 0.9485 (p) cc_final: 0.9251 (t) REVERT: A 726 ARG cc_start: 0.7476 (mtm-85) cc_final: 0.7053 (ptt180) REVERT: A 773 LYS cc_start: 0.9175 (tttt) cc_final: 0.8827 (ttmm) REVERT: A 777 MET cc_start: 0.8971 (mtp) cc_final: 0.8742 (mtp) REVERT: A 848 MET cc_start: 0.7882 (tpp) cc_final: 0.7382 (tpt) REVERT: A 887 MET cc_start: 0.7797 (tpp) cc_final: 0.7066 (tpp) REVERT: A 1079 MET cc_start: 0.8574 (mmp) cc_final: 0.8339 (mmp) REVERT: A 1111 MET cc_start: 0.9090 (mpp) cc_final: 0.8214 (ppp) REVERT: A 1131 MET cc_start: 0.8737 (mtm) cc_final: 0.8468 (mtt) REVERT: A 1140 MET cc_start: 0.9132 (ttp) cc_final: 0.8518 (tmm) REVERT: A 1253 CYS cc_start: 0.8047 (m) cc_final: 0.7809 (m) REVERT: A 1381 GLU cc_start: 0.9050 (pm20) cc_final: 0.8568 (pm20) REVERT: A 1416 LEU cc_start: 0.9048 (tp) cc_final: 0.8691 (tp) REVERT: A 1463 MET cc_start: 0.2616 (ttm) cc_final: 0.1888 (tmm) REVERT: A 1551 ASP cc_start: 0.9286 (m-30) cc_final: 0.9041 (t0) REVERT: A 1568 ARG cc_start: 0.8346 (OUTLIER) cc_final: 0.6603 (tpm-80) REVERT: A 1635 MET cc_start: 0.8660 (ppp) cc_final: 0.8203 (ppp) REVERT: A 1746 TRP cc_start: 0.8497 (p90) cc_final: 0.7921 (p90) REVERT: A 1810 GLU cc_start: 0.8170 (OUTLIER) cc_final: 0.7563 (tm-30) REVERT: A 1865 LEU cc_start: 0.9286 (tp) cc_final: 0.8961 (tp) REVERT: A 2015 MET cc_start: 0.8321 (tpp) cc_final: 0.8051 (tpt) outliers start: 60 outliers final: 40 residues processed: 258 average time/residue: 0.1244 time to fit residues: 47.0887 Evaluate side-chains 237 residues out of total 1635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 194 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 109 MET Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 347 LYS Chi-restraints excluded: chain A residue 376 ASN Chi-restraints excluded: chain A residue 408 TYR Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain A residue 699 GLN Chi-restraints excluded: chain A residue 724 GLU Chi-restraints excluded: chain A residue 762 THR Chi-restraints excluded: chain A residue 837 ILE Chi-restraints excluded: chain A residue 844 ASP Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 954 ASN Chi-restraints excluded: chain A residue 1064 TRP Chi-restraints excluded: chain A residue 1160 ASN Chi-restraints excluded: chain A residue 1254 LEU Chi-restraints excluded: chain A residue 1300 THR Chi-restraints excluded: chain A residue 1395 VAL Chi-restraints excluded: chain A residue 1399 LEU Chi-restraints excluded: chain A residue 1556 LEU Chi-restraints excluded: chain A residue 1557 ARG Chi-restraints excluded: chain A residue 1568 ARG Chi-restraints excluded: chain A residue 1573 HIS Chi-restraints excluded: chain A residue 1595 THR Chi-restraints excluded: chain A residue 1676 LEU Chi-restraints excluded: chain A residue 1738 ILE Chi-restraints excluded: chain A residue 1739 ASP Chi-restraints excluded: chain A residue 1743 THR Chi-restraints excluded: chain A residue 1769 CYS Chi-restraints excluded: chain A residue 1806 VAL Chi-restraints excluded: chain A residue 1810 GLU Chi-restraints excluded: chain A residue 1811 ARG Chi-restraints excluded: chain A residue 1868 ASN Chi-restraints excluded: chain A residue 1886 LEU Chi-restraints excluded: chain A residue 1910 ILE Chi-restraints excluded: chain A residue 1954 VAL Chi-restraints excluded: chain A residue 1957 LEU Chi-restraints excluded: chain A residue 1969 VAL Chi-restraints excluded: chain A residue 1977 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 92 optimal weight: 6.9990 chunk 24 optimal weight: 0.8980 chunk 43 optimal weight: 0.2980 chunk 23 optimal weight: 0.9980 chunk 123 optimal weight: 9.9990 chunk 178 optimal weight: 9.9990 chunk 122 optimal weight: 4.9990 chunk 70 optimal weight: 0.6980 chunk 64 optimal weight: 5.9990 chunk 114 optimal weight: 5.9990 chunk 37 optimal weight: 2.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 959 ASN A1245 HIS ** A1255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1638 ASN ** A1834 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.110418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.084703 restraints weight = 35252.607| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 4.22 r_work: 0.3159 rms_B_bonded: 4.72 restraints_weight: 0.5000 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.4507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15121 Z= 0.134 Angle : 0.751 10.756 20379 Z= 0.379 Chirality : 0.045 0.216 2256 Planarity : 0.005 0.096 2599 Dihedral : 6.489 60.359 2029 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.33 % Allowed : 10.75 % Favored : 88.92 % Rotamer: Outliers : 3.91 % Allowed : 24.40 % Favored : 71.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.11 % Twisted Proline : 4.55 % Twisted General : 0.34 % 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: -2.68 (0.19), residues: 1832 helix: -0.72 (0.19), residues: 725 sheet: -0.81 (0.42), residues: 150 loop : -2.90 (0.19), residues: 957 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 30 TYR 0.016 0.001 TYR A1850 PHE 0.029 0.001 PHE A 352 TRP 0.018 0.001 TRP A1064 HIS 0.003 0.001 HIS A 799 Details of bonding type rmsd covalent geometry : bond 0.00305 (15117) covalent geometry : angle 0.75088 (20379) hydrogen bonds : bond 0.03336 ( 405) hydrogen bonds : angle 4.40314 ( 1122) Misc. bond : bond 0.00244 ( 4) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 207 time to evaluate : 0.576 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: A 160 MET cc_start: 0.8121 (mmm) cc_final: 0.7750 (mmm) REVERT: A 189 GLU cc_start: 0.8953 (mt-10) cc_final: 0.8688 (mt-10) REVERT: A 376 ASN cc_start: 0.7779 (OUTLIER) cc_final: 0.7275 (t0) REVERT: A 540 GLU cc_start: 0.7608 (pm20) cc_final: 0.7305 (pm20) REVERT: A 726 ARG cc_start: 0.7601 (mtm-85) cc_final: 0.7149 (ptt180) REVERT: A 773 LYS cc_start: 0.9149 (tttt) cc_final: 0.8779 (ttmm) REVERT: A 777 MET cc_start: 0.9076 (mtp) cc_final: 0.8860 (mtp) REVERT: A 848 MET cc_start: 0.7874 (tpp) cc_final: 0.7588 (tpt) REVERT: A 887 MET cc_start: 0.7570 (tpp) cc_final: 0.6853 (tpp) REVERT: A 1111 MET cc_start: 0.9062 (mpp) cc_final: 0.8238 (ppp) REVERT: A 1131 MET cc_start: 0.8790 (mtm) cc_final: 0.8517 (mtt) REVERT: A 1140 MET cc_start: 0.9197 (ttp) cc_final: 0.8593 (tmm) REVERT: A 1203 HIS cc_start: 0.8321 (m-70) cc_final: 0.7882 (m170) REVERT: A 1253 CYS cc_start: 0.8047 (m) cc_final: 0.7845 (m) REVERT: A 1308 TYR cc_start: 0.9249 (t80) cc_final: 0.9015 (t80) REVERT: A 1381 GLU cc_start: 0.9038 (pm20) cc_final: 0.8555 (pm20) REVERT: A 1416 LEU cc_start: 0.9056 (tp) cc_final: 0.8697 (tp) REVERT: A 1463 MET cc_start: 0.2862 (ttm) cc_final: 0.2156 (tmm) REVERT: A 1551 ASP cc_start: 0.9299 (m-30) cc_final: 0.9046 (t0) REVERT: A 1568 ARG cc_start: 0.8300 (OUTLIER) cc_final: 0.6453 (tpm-80) REVERT: A 1635 MET cc_start: 0.8744 (ppp) cc_final: 0.8521 (ppp) REVERT: A 1746 TRP cc_start: 0.8475 (p90) cc_final: 0.7895 (p90) REVERT: A 1810 GLU cc_start: 0.8099 (OUTLIER) cc_final: 0.7491 (tm-30) REVERT: A 1845 MET cc_start: 0.9008 (ttm) cc_final: 0.8693 (ptp) REVERT: A 1865 LEU cc_start: 0.9302 (tp) cc_final: 0.8901 (tp) REVERT: A 2015 MET cc_start: 0.8357 (tpp) cc_final: 0.8083 (tpt) outliers start: 64 outliers final: 46 residues processed: 256 average time/residue: 0.1282 time to fit residues: 48.0304 Evaluate side-chains 241 residues out of total 1635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 192 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 347 LYS Chi-restraints excluded: chain A residue 376 ASN Chi-restraints excluded: chain A residue 408 TYR Chi-restraints excluded: chain A residue 633 LEU Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain A residue 689 LYS Chi-restraints excluded: chain A residue 699 GLN Chi-restraints excluded: chain A residue 724 GLU Chi-restraints excluded: chain A residue 762 THR Chi-restraints excluded: chain A residue 837 ILE Chi-restraints excluded: chain A residue 844 ASP Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain A residue 954 ASN Chi-restraints excluded: chain A residue 967 LEU Chi-restraints excluded: chain A residue 1064 TRP Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain A residue 1160 ASN Chi-restraints excluded: chain A residue 1173 VAL Chi-restraints excluded: chain A residue 1254 LEU Chi-restraints excluded: chain A residue 1300 THR Chi-restraints excluded: chain A residue 1395 VAL Chi-restraints excluded: chain A residue 1399 LEU Chi-restraints excluded: chain A residue 1557 ARG Chi-restraints excluded: chain A residue 1568 ARG Chi-restraints excluded: chain A residue 1573 HIS Chi-restraints excluded: chain A residue 1595 THR Chi-restraints excluded: chain A residue 1676 LEU Chi-restraints excluded: chain A residue 1709 THR Chi-restraints excluded: chain A residue 1738 ILE Chi-restraints excluded: chain A residue 1739 ASP Chi-restraints excluded: chain A residue 1743 THR Chi-restraints excluded: chain A residue 1769 CYS Chi-restraints excluded: chain A residue 1806 VAL Chi-restraints excluded: chain A residue 1810 GLU Chi-restraints excluded: chain A residue 1811 ARG Chi-restraints excluded: chain A residue 1868 ASN Chi-restraints excluded: chain A residue 1886 LEU Chi-restraints excluded: chain A residue 1954 VAL Chi-restraints excluded: chain A residue 1955 ASP Chi-restraints excluded: chain A residue 1957 LEU Chi-restraints excluded: chain A residue 1969 VAL Chi-restraints excluded: chain A residue 1977 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 103 optimal weight: 0.5980 chunk 36 optimal weight: 0.9990 chunk 97 optimal weight: 0.7980 chunk 95 optimal weight: 1.9990 chunk 154 optimal weight: 20.0000 chunk 59 optimal weight: 0.6980 chunk 129 optimal weight: 0.5980 chunk 99 optimal weight: 3.9990 chunk 135 optimal weight: 7.9990 chunk 182 optimal weight: 6.9990 chunk 101 optimal weight: 3.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 706 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 959 ASN ** A1255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1834 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.111694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.086194 restraints weight = 35437.992| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 4.18 r_work: 0.3182 rms_B_bonded: 4.72 restraints_weight: 0.5000 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.4670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15121 Z= 0.125 Angle : 0.743 10.806 20379 Z= 0.373 Chirality : 0.044 0.205 2256 Planarity : 0.005 0.095 2599 Dihedral : 6.403 59.702 2029 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.27 % Allowed : 10.21 % Favored : 89.52 % Rotamer: Outliers : 3.36 % Allowed : 25.38 % Favored : 71.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.11 % Twisted Proline : 3.03 % Twisted General : 0.39 % 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: -2.59 (0.19), residues: 1832 helix: -0.59 (0.19), residues: 729 sheet: -0.74 (0.42), residues: 150 loop : -2.92 (0.19), residues: 953 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 30 TYR 0.020 0.001 TYR A 193 PHE 0.024 0.001 PHE A 352 TRP 0.017 0.001 TRP A1064 HIS 0.002 0.000 HIS A 103 Details of bonding type rmsd covalent geometry : bond 0.00288 (15117) covalent geometry : angle 0.74279 (20379) hydrogen bonds : bond 0.03149 ( 405) hydrogen bonds : angle 4.35886 ( 1122) Misc. bond : bond 0.00314 ( 4) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 208 time to evaluate : 0.586 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 148 LYS cc_start: 0.9319 (ttpt) cc_final: 0.9083 (tttt) REVERT: A 160 MET cc_start: 0.8135 (mmm) cc_final: 0.7785 (mmm) REVERT: A 189 GLU cc_start: 0.8928 (mt-10) cc_final: 0.8698 (mt-10) REVERT: A 193 TYR cc_start: 0.8612 (t80) cc_final: 0.8224 (t80) REVERT: A 376 ASN cc_start: 0.7737 (OUTLIER) cc_final: 0.7220 (t0) REVERT: A 403 GLU cc_start: 0.8333 (pm20) cc_final: 0.7580 (pp20) REVERT: A 406 ILE cc_start: 0.6970 (OUTLIER) cc_final: 0.5961 (pt) REVERT: A 726 ARG cc_start: 0.7473 (mtm-85) cc_final: 0.7117 (ptt180) REVERT: A 773 LYS cc_start: 0.9142 (tttt) cc_final: 0.8758 (ttmm) REVERT: A 848 MET cc_start: 0.7433 (tpp) cc_final: 0.7218 (tpt) REVERT: A 960 SER cc_start: 0.9070 (m) cc_final: 0.8676 (p) REVERT: A 1111 MET cc_start: 0.9005 (mpp) cc_final: 0.8226 (ppp) REVERT: A 1131 MET cc_start: 0.8770 (mtm) cc_final: 0.8487 (mtt) REVERT: A 1140 MET cc_start: 0.9171 (ttp) cc_final: 0.8558 (tmm) REVERT: A 1203 HIS cc_start: 0.8299 (m-70) cc_final: 0.7828 (m170) REVERT: A 1253 CYS cc_start: 0.7992 (m) cc_final: 0.7772 (m) REVERT: A 1355 MET cc_start: 0.8815 (pmm) cc_final: 0.8459 (pmm) REVERT: A 1381 GLU cc_start: 0.9075 (pm20) cc_final: 0.8610 (pm20) REVERT: A 1416 LEU cc_start: 0.9042 (tp) cc_final: 0.8674 (tp) REVERT: A 1463 MET cc_start: 0.2653 (ttm) cc_final: 0.2004 (tmm) REVERT: A 1477 LEU cc_start: 0.4158 (OUTLIER) cc_final: 0.3834 (tp) REVERT: A 1551 ASP cc_start: 0.9248 (m-30) cc_final: 0.9012 (t0) REVERT: A 1568 ARG cc_start: 0.8240 (OUTLIER) cc_final: 0.6401 (tpm-80) REVERT: A 1635 MET cc_start: 0.8620 (ppp) cc_final: 0.8084 (ppp) REVERT: A 1672 MET cc_start: 0.7450 (pmm) cc_final: 0.7210 (pmm) REVERT: A 1746 TRP cc_start: 0.8462 (p90) cc_final: 0.7930 (p90) REVERT: A 1810 GLU cc_start: 0.8049 (OUTLIER) cc_final: 0.7478 (tm-30) REVERT: A 1845 MET cc_start: 0.8748 (ttm) cc_final: 0.8420 (ptm) REVERT: A 1865 LEU cc_start: 0.9296 (tp) cc_final: 0.9005 (tp) REVERT: A 2015 MET cc_start: 0.8383 (tpp) cc_final: 0.8122 (tpt) outliers start: 55 outliers final: 44 residues processed: 251 average time/residue: 0.1246 time to fit residues: 45.9502 Evaluate side-chains 242 residues out of total 1635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 193 time to evaluate : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 376 ASN Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 408 TYR Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain A residue 689 LYS Chi-restraints excluded: chain A residue 699 GLN Chi-restraints excluded: chain A residue 724 GLU Chi-restraints excluded: chain A residue 727 VAL Chi-restraints excluded: chain A residue 762 THR Chi-restraints excluded: chain A residue 799 HIS Chi-restraints excluded: chain A residue 810 CYS Chi-restraints excluded: chain A residue 837 ILE Chi-restraints excluded: chain A residue 844 ASP Chi-restraints excluded: chain A residue 954 ASN Chi-restraints excluded: chain A residue 967 LEU Chi-restraints excluded: chain A residue 1143 VAL Chi-restraints excluded: chain A residue 1160 ASN Chi-restraints excluded: chain A residue 1173 VAL Chi-restraints excluded: chain A residue 1178 CYS Chi-restraints excluded: chain A residue 1300 THR Chi-restraints excluded: chain A residue 1395 VAL Chi-restraints excluded: chain A residue 1399 LEU Chi-restraints excluded: chain A residue 1477 LEU Chi-restraints excluded: chain A residue 1557 ARG Chi-restraints excluded: chain A residue 1568 ARG Chi-restraints excluded: chain A residue 1595 THR Chi-restraints excluded: chain A residue 1676 LEU Chi-restraints excluded: chain A residue 1709 THR Chi-restraints excluded: chain A residue 1738 ILE Chi-restraints excluded: chain A residue 1739 ASP Chi-restraints excluded: chain A residue 1743 THR Chi-restraints excluded: chain A residue 1769 CYS Chi-restraints excluded: chain A residue 1806 VAL Chi-restraints excluded: chain A residue 1810 GLU Chi-restraints excluded: chain A residue 1811 ARG Chi-restraints excluded: chain A residue 1835 LEU Chi-restraints excluded: chain A residue 1868 ASN Chi-restraints excluded: chain A residue 1886 LEU Chi-restraints excluded: chain A residue 1954 VAL Chi-restraints excluded: chain A residue 1957 LEU Chi-restraints excluded: chain A residue 1969 VAL Chi-restraints excluded: chain A residue 1977 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 49 optimal weight: 9.9990 chunk 140 optimal weight: 0.8980 chunk 105 optimal weight: 0.6980 chunk 149 optimal weight: 9.9990 chunk 171 optimal weight: 0.0370 chunk 16 optimal weight: 10.0000 chunk 172 optimal weight: 0.9980 chunk 100 optimal weight: 7.9990 chunk 5 optimal weight: 9.9990 chunk 83 optimal weight: 10.0000 chunk 152 optimal weight: 0.3980 overall best weight: 0.6058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 706 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 959 ASN ** A1834 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.112498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.087061 restraints weight = 35189.802| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 4.16 r_work: 0.3201 rms_B_bonded: 4.68 restraints_weight: 0.5000 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.4850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15121 Z= 0.125 Angle : 0.762 12.205 20379 Z= 0.381 Chirality : 0.044 0.238 2256 Planarity : 0.005 0.094 2599 Dihedral : 6.308 59.106 2029 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.27 % Allowed : 10.21 % Favored : 89.52 % Rotamer: Outliers : 3.06 % Allowed : 25.87 % Favored : 71.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.11 % Twisted Proline : 3.03 % Twisted General : 0.39 % 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: -2.48 (0.19), residues: 1832 helix: -0.47 (0.19), residues: 728 sheet: -0.71 (0.42), residues: 150 loop : -2.87 (0.19), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 30 TYR 0.026 0.001 TYR A1308 PHE 0.025 0.001 PHE A 352 TRP 0.014 0.001 TRP A 520 HIS 0.003 0.000 HIS A1255 Details of bonding type rmsd covalent geometry : bond 0.00286 (15117) covalent geometry : angle 0.76196 (20379) hydrogen bonds : bond 0.03079 ( 405) hydrogen bonds : angle 4.27666 ( 1122) Misc. bond : bond 0.00289 ( 4) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 210 time to evaluate : 0.564 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 148 LYS cc_start: 0.9310 (ttpt) cc_final: 0.9062 (tttt) REVERT: A 160 MET cc_start: 0.8133 (mmm) cc_final: 0.7815 (mmm) REVERT: A 189 GLU cc_start: 0.8952 (mt-10) cc_final: 0.8680 (mt-10) REVERT: A 193 TYR cc_start: 0.8580 (t80) cc_final: 0.8220 (t80) REVERT: A 274 GLU cc_start: 0.8945 (mm-30) cc_final: 0.8588 (mm-30) REVERT: A 376 ASN cc_start: 0.7720 (OUTLIER) cc_final: 0.7209 (t0) REVERT: A 406 ILE cc_start: 0.6560 (OUTLIER) cc_final: 0.5662 (pt) REVERT: A 726 ARG cc_start: 0.7520 (mtm-85) cc_final: 0.7134 (ptt180) REVERT: A 763 GLU cc_start: 0.7280 (pp20) cc_final: 0.7068 (pp20) REVERT: A 773 LYS cc_start: 0.9093 (tttt) cc_final: 0.8677 (ttmm) REVERT: A 848 MET cc_start: 0.7292 (tpp) cc_final: 0.7050 (tpt) REVERT: A 878 MET cc_start: 0.9059 (ptp) cc_final: 0.8843 (mtm) REVERT: A 960 SER cc_start: 0.9054 (m) cc_final: 0.8657 (p) REVERT: A 1111 MET cc_start: 0.8983 (mpp) cc_final: 0.8232 (ppp) REVERT: A 1123 GLU cc_start: 0.8838 (pp20) cc_final: 0.8433 (pp20) REVERT: A 1131 MET cc_start: 0.8784 (mtm) cc_final: 0.8476 (mtt) REVERT: A 1140 MET cc_start: 0.9174 (ttp) cc_final: 0.8580 (tmm) REVERT: A 1203 HIS cc_start: 0.8279 (m-70) cc_final: 0.7821 (m170) REVERT: A 1355 MET cc_start: 0.8816 (pmm) cc_final: 0.8454 (pmm) REVERT: A 1381 GLU cc_start: 0.9060 (pm20) cc_final: 0.8599 (pm20) REVERT: A 1416 LEU cc_start: 0.9051 (tp) cc_final: 0.8692 (tp) REVERT: A 1463 MET cc_start: 0.2627 (ttm) cc_final: 0.2015 (tmm) REVERT: A 1473 ARG cc_start: 0.6518 (tpt170) cc_final: 0.5912 (tpt-90) REVERT: A 1551 ASP cc_start: 0.9206 (m-30) cc_final: 0.8989 (t0) REVERT: A 1557 ARG cc_start: 0.8896 (OUTLIER) cc_final: 0.8507 (mtp85) REVERT: A 1568 ARG cc_start: 0.8306 (OUTLIER) cc_final: 0.6448 (tpm-80) REVERT: A 1635 MET cc_start: 0.8648 (ppp) cc_final: 0.8389 (ppp) REVERT: A 1672 MET cc_start: 0.7265 (pmm) cc_final: 0.7008 (pmm) REVERT: A 1746 TRP cc_start: 0.8447 (p90) cc_final: 0.7969 (p90) REVERT: A 1810 GLU cc_start: 0.8105 (OUTLIER) cc_final: 0.7547 (tm-30) REVERT: A 1865 LEU cc_start: 0.9310 (tp) cc_final: 0.8902 (tp) REVERT: A 2012 LEU cc_start: 0.8515 (pp) cc_final: 0.8127 (tp) REVERT: A 2015 MET cc_start: 0.8428 (tpp) cc_final: 0.8194 (tpt) outliers start: 50 outliers final: 39 residues processed: 250 average time/residue: 0.1220 time to fit residues: 45.2765 Evaluate side-chains 242 residues out of total 1635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 198 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 376 ASN Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 408 TYR Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain A residue 689 LYS Chi-restraints excluded: chain A residue 699 GLN Chi-restraints excluded: chain A residue 724 GLU Chi-restraints excluded: chain A residue 727 VAL Chi-restraints excluded: chain A residue 762 THR Chi-restraints excluded: chain A residue 810 CYS Chi-restraints excluded: chain A residue 837 ILE Chi-restraints excluded: chain A residue 844 ASP Chi-restraints excluded: chain A residue 954 ASN Chi-restraints excluded: chain A residue 967 LEU Chi-restraints excluded: chain A residue 1143 VAL Chi-restraints excluded: chain A residue 1160 ASN Chi-restraints excluded: chain A residue 1173 VAL Chi-restraints excluded: chain A residue 1254 LEU Chi-restraints excluded: chain A residue 1300 THR Chi-restraints excluded: chain A residue 1395 VAL Chi-restraints excluded: chain A residue 1399 LEU Chi-restraints excluded: chain A residue 1557 ARG Chi-restraints excluded: chain A residue 1568 ARG Chi-restraints excluded: chain A residue 1595 THR Chi-restraints excluded: chain A residue 1676 LEU Chi-restraints excluded: chain A residue 1738 ILE Chi-restraints excluded: chain A residue 1739 ASP Chi-restraints excluded: chain A residue 1743 THR Chi-restraints excluded: chain A residue 1769 CYS Chi-restraints excluded: chain A residue 1806 VAL Chi-restraints excluded: chain A residue 1810 GLU Chi-restraints excluded: chain A residue 1811 ARG Chi-restraints excluded: chain A residue 1868 ASN Chi-restraints excluded: chain A residue 1886 LEU Chi-restraints excluded: chain A residue 1954 VAL Chi-restraints excluded: chain A residue 1969 VAL Chi-restraints excluded: chain A residue 1977 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 7 optimal weight: 2.9990 chunk 130 optimal weight: 0.9990 chunk 145 optimal weight: 0.9980 chunk 161 optimal weight: 10.0000 chunk 11 optimal weight: 0.6980 chunk 103 optimal weight: 10.0000 chunk 181 optimal weight: 6.9990 chunk 17 optimal weight: 0.0670 chunk 34 optimal weight: 0.9990 chunk 113 optimal weight: 5.9990 chunk 131 optimal weight: 9.9990 overall best weight: 0.7522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 706 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 959 ASN A 990 ASN A1912 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.112385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.086738 restraints weight = 35729.041| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 4.19 r_work: 0.3197 rms_B_bonded: 4.75 restraints_weight: 0.5000 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.4959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 15121 Z= 0.126 Angle : 0.753 11.155 20379 Z= 0.374 Chirality : 0.044 0.205 2256 Planarity : 0.005 0.094 2599 Dihedral : 6.150 58.614 2029 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.22 % Allowed : 9.93 % Favored : 89.85 % Rotamer: Outliers : 3.12 % Allowed : 25.69 % Favored : 71.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.11 % Twisted Proline : 3.03 % Twisted General : 0.22 % 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: -2.38 (0.19), residues: 1832 helix: -0.39 (0.19), residues: 737 sheet: -0.78 (0.43), residues: 151 loop : -2.82 (0.19), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 410 TYR 0.025 0.001 TYR A 923 PHE 0.022 0.001 PHE A 352 TRP 0.014 0.001 TRP A 520 HIS 0.003 0.000 HIS A1564 Details of bonding type rmsd covalent geometry : bond 0.00290 (15117) covalent geometry : angle 0.75345 (20379) hydrogen bonds : bond 0.02990 ( 405) hydrogen bonds : angle 4.21611 ( 1122) Misc. bond : bond 0.00336 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3232.41 seconds wall clock time: 56 minutes 31.45 seconds (3391.45 seconds total)