Starting phenix.real_space_refine on Sat Jun 6 07:26:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9xec_66787/06_2026/9xec_66787.cif Found real_map, /net/cci-nas-00/data/ceres_data/9xec_66787/06_2026/9xec_66787.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9xec_66787/06_2026/9xec_66787.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9xec_66787/06_2026/9xec_66787.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9xec_66787/06_2026/9xec_66787.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9xec_66787/06_2026/9xec_66787.map" } resolution = 2.98 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= 0.003 sd= 0.041 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: 7 Type Number sf(0) Gaussians Mn 4 7.51 5 Zn 1 6.06 5 P 46 5.49 5 S 164 5.16 5 C 16412 2.51 5 N 4476 2.21 5 O 5043 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 26146 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 25181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3148, 25181 Classifications: {'peptide': 3148} Link IDs: {'PCIS': 1, 'PTRANS': 96, 'TRANS': 3050} Chain breaks: 22 Chain: "B" Number of atoms: 231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 231 Classifications: {'RNA': 11} Modifications used: {'5*END': 1, 'rna2p_pur': 2, 'rna3p_pur': 5, 'rna3p_pyr': 4} Link IDs: {'rna2p': 2, 'rna3p': 8} Chain: "C" Number of atoms: 277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 277 Classifications: {'RNA': 13} Modifications used: {'rna3p_pur': 7, 'rna3p_pyr': 6} Link IDs: {'rna3p': 12} Chain: "D" Number of atoms: 192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 192 Classifications: {'RNA': 9} Modifications used: {'p5*END': 1, 'rna3p_pur': 5, 'rna3p_pyr': 4} Link IDs: {'rna3p': 8} Chain: "E" Number of atoms: 170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 170 Classifications: {'RNA': 8} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 4, 'rna3p_pur': 2} Link IDs: {'rna2p': 5, 'rna3p': 2} Chain: "F" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 61 Classifications: {'RNA': 3} Modifications used: {'p5*END': 1, 'rna3p_pyr': 3} Link IDs: {'rna3p': 2} Chain: "A" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 34 Unusual residues: {' MN': 4, ' ZN': 1, '2KH': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 4671 SG CYS A1028 18.028 86.589 41.095 1.00 60.69 S ATOM 4690 SG CYS A1031 16.611 83.242 40.656 1.00 61.18 S ATOM 4933 SG CYS A1062 17.027 84.688 37.693 1.00 57.73 S ATOM 4953 SG CYS A1065 20.358 83.906 39.822 1.00 60.89 S Time building chain proxies: 6.17, per 1000 atoms: 0.24 Number of scatterers: 26146 At special positions: 0 Unit cell: (120.888, 156.804, 141.036, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 Mn 4 24.99 S 164 16.00 P 46 15.00 O 5043 8.00 N 4476 7.00 C 16412 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.71 Conformation dependent library (CDL) restraints added in 822.8 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A4006 " pdb="ZN ZN A4006 " - pdb=" SG CYS A1031 " pdb="ZN ZN A4006 " - pdb=" SG CYS A1028 " pdb="ZN ZN A4006 " - pdb=" SG CYS A1062 " pdb="ZN ZN A4006 " - pdb=" SG CYS A1065 " Number of angles added : 6 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6038 Finding SS restraints... Secondary structure from input PDB file: 147 helices and 16 sheets defined 58.7% alpha, 6.2% beta 9 base pairs and 20 stacking pairs defined. Time for finding SS restraints: 4.02 Creating SS restraints... Processing helix chain 'A' and resid 339 through 356 Processing helix chain 'A' and resid 400 through 412 Processing helix chain 'A' and resid 412 through 424 removed outlier: 3.658A pdb=" N ASN A 417 " --> pdb=" O GLY A 413 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N LYS A 418 " --> pdb=" O LYS A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 436 Processing helix chain 'A' and resid 447 through 460 removed outlier: 3.728A pdb=" N ASN A 453 " --> pdb=" O GLY A 449 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N MET A 454 " --> pdb=" O MET A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 483 removed outlier: 3.596A pdb=" N LEU A 472 " --> pdb=" O GLU A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 494 Processing helix chain 'A' and resid 510 through 523 removed outlier: 3.959A pdb=" N LYS A 523 " --> pdb=" O PHE A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 553 removed outlier: 3.775A pdb=" N LEU A 553 " --> pdb=" O HIS A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 563 through 577 Processing helix chain 'A' and resid 586 through 602 removed outlier: 3.621A pdb=" N ILE A 590 " --> pdb=" O PRO A 586 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N GLY A 593 " --> pdb=" O ILE A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 608 through 622 removed outlier: 4.322A pdb=" N GLU A 612 " --> pdb=" O ASP A 608 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLU A 614 " --> pdb=" O ALA A 610 " (cutoff:3.500A) Processing helix chain 'A' and resid 626 through 648 removed outlier: 3.542A pdb=" N TRP A 630 " --> pdb=" O HIS A 626 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LYS A 631 " --> pdb=" O SER A 627 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N HIS A 632 " --> pdb=" O THR A 628 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ALA A 633 " --> pdb=" O ALA A 629 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ARG A 635 " --> pdb=" O LYS A 631 " (cutoff:3.500A) Processing helix chain 'A' and resid 655 through 659 Processing helix chain 'A' and resid 661 through 670 Processing helix chain 'A' and resid 673 through 680 Processing helix chain 'A' and resid 684 through 690 removed outlier: 3.758A pdb=" N LEU A 690 " --> pdb=" O PHE A 687 " (cutoff:3.500A) Processing helix chain 'A' and resid 748 through 761 removed outlier: 3.822A pdb=" N ILE A 752 " --> pdb=" O SER A 748 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N MET A 760 " --> pdb=" O PHE A 756 " (cutoff:3.500A) Processing helix chain 'A' and resid 831 through 843 Processing helix chain 'A' and resid 844 through 854 removed outlier: 3.838A pdb=" N LYS A 848 " --> pdb=" O LYS A 844 " (cutoff:3.500A) Processing helix chain 'A' and resid 876 through 878 No H-bonds generated for 'chain 'A' and resid 876 through 878' Processing helix chain 'A' and resid 879 through 894 removed outlier: 3.658A pdb=" N LEU A 883 " --> pdb=" O ARG A 879 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N SER A 886 " --> pdb=" O VAL A 882 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N PHE A 889 " --> pdb=" O ASN A 885 " (cutoff:3.500A) Processing helix chain 'A' and resid 899 through 911 Processing helix chain 'A' and resid 912 through 918 removed outlier: 3.553A pdb=" N SER A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N TYR A 918 " --> pdb=" O LYS A 914 " (cutoff:3.500A) Processing helix chain 'A' and resid 930 through 946 removed outlier: 5.048A pdb=" N GLU A 943 " --> pdb=" O GLU A 939 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N HIS A 944 " --> pdb=" O LYS A 940 " (cutoff:3.500A) Processing helix chain 'A' and resid 955 through 967 Processing helix chain 'A' and resid 973 through 987 Processing helix chain 'A' and resid 987 through 996 Processing helix chain 'A' and resid 1008 through 1024 Processing helix chain 'A' and resid 1028 through 1041 Processing helix chain 'A' and resid 1044 through 1057 Processing helix chain 'A' and resid 1058 through 1061 Processing helix chain 'A' and resid 1084 through 1088 removed outlier: 3.752A pdb=" N VAL A1088 " --> pdb=" O ILE A1085 " (cutoff:3.500A) Processing helix chain 'A' and resid 1104 through 1111 removed outlier: 3.583A pdb=" N ARG A1111 " --> pdb=" O ASP A1107 " (cutoff:3.500A) Processing helix chain 'A' and resid 1118 through 1136 Processing helix chain 'A' and resid 1181 through 1187 removed outlier: 3.944A pdb=" N LYS A1185 " --> pdb=" O ASP A1181 " (cutoff:3.500A) Processing helix chain 'A' and resid 1196 through 1208 removed outlier: 3.726A pdb=" N ASN A1205 " --> pdb=" O GLY A1201 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N SER A1206 " --> pdb=" O VAL A1202 " (cutoff:3.500A) Processing helix chain 'A' and resid 1209 through 1213 removed outlier: 4.247A pdb=" N GLN A1213 " --> pdb=" O LEU A1210 " (cutoff:3.500A) Processing helix chain 'A' and resid 1221 through 1232 removed outlier: 4.120A pdb=" N LEU A1225 " --> pdb=" O PRO A1221 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLU A1226 " --> pdb=" O ARG A1222 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ASP A1231 " --> pdb=" O LYS A1227 " (cutoff:3.500A) Processing helix chain 'A' and resid 1237 through 1252 Processing helix chain 'A' and resid 1266 through 1281 removed outlier: 3.664A pdb=" N CYS A1273 " --> pdb=" O GLU A1269 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N VAL A1276 " --> pdb=" O LYS A1272 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N GLN A1277 " --> pdb=" O CYS A1273 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N SER A1278 " --> pdb=" O PHE A1274 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N PHE A1279 " --> pdb=" O ASP A1275 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LYS A1280 " --> pdb=" O VAL A1276 " (cutoff:3.500A) Processing helix chain 'A' and resid 1297 through 1309 removed outlier: 3.522A pdb=" N ARG A1307 " --> pdb=" O GLU A1303 " (cutoff:3.500A) Processing helix chain 'A' and resid 1315 through 1328 removed outlier: 3.672A pdb=" N LEU A1323 " --> pdb=" O THR A1319 " (cutoff:3.500A) Processing helix chain 'A' and resid 1330 through 1350 Processing helix chain 'A' and resid 1401 through 1426 removed outlier: 3.925A pdb=" N LEU A1407 " --> pdb=" O ARG A1403 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N LEU A1412 " --> pdb=" O GLY A1408 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N TYR A1413 " --> pdb=" O SER A1409 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N GLN A1424 " --> pdb=" O ILE A1420 " (cutoff:3.500A) Processing helix chain 'A' and resid 1429 through 1434 Processing helix chain 'A' and resid 1436 through 1463 removed outlier: 3.630A pdb=" N ARG A1456 " --> pdb=" O GLU A1452 " (cutoff:3.500A) Processing helix chain 'A' and resid 1465 through 1481 removed outlier: 3.797A pdb=" N SER A1469 " --> pdb=" O ARG A1465 " (cutoff:3.500A) Processing helix chain 'A' and resid 1487 through 1506 Processing helix chain 'A' and resid 1507 through 1514 removed outlier: 3.906A pdb=" N ASN A1514 " --> pdb=" O ASN A1510 " (cutoff:3.500A) Processing helix chain 'A' and resid 1515 through 1530 removed outlier: 3.959A pdb=" N GLN A1521 " --> pdb=" O GLN A1517 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LEU A1522 " --> pdb=" O GLN A1518 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N ARG A1526 " --> pdb=" O LEU A1522 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N PHE A1527 " --> pdb=" O GLN A1523 " (cutoff:3.500A) Processing helix chain 'A' and resid 1543 through 1547 Processing helix chain 'A' and resid 1552 through 1572 removed outlier: 4.483A pdb=" N ASP A1572 " --> pdb=" O CYS A1568 " (cutoff:3.500A) Processing helix chain 'A' and resid 1572 through 1581 removed outlier: 4.073A pdb=" N LYS A1578 " --> pdb=" O GLU A1574 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LYS A1581 " --> pdb=" O VAL A1577 " (cutoff:3.500A) Processing helix chain 'A' and resid 1603 through 1611 Processing helix chain 'A' and resid 1612 through 1616 removed outlier: 3.758A pdb=" N HIS A1615 " --> pdb=" O TYR A1612 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE A1616 " --> pdb=" O ASN A1613 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1612 through 1616' Processing helix chain 'A' and resid 1623 through 1649 removed outlier: 3.552A pdb=" N ASP A1645 " --> pdb=" O LEU A1641 " (cutoff:3.500A) Processing helix chain 'A' and resid 1659 through 1666 Processing helix chain 'A' and resid 1758 through 1773 Processing helix chain 'A' and resid 1780 through 1791 Processing helix chain 'A' and resid 1796 through 1805 removed outlier: 3.569A pdb=" N LYS A1802 " --> pdb=" O GLU A1798 " (cutoff:3.500A) Processing helix chain 'A' and resid 1812 through 1816 Processing helix chain 'A' and resid 1831 through 1852 Processing helix chain 'A' and resid 1869 through 1878 removed outlier: 3.804A pdb=" N THR A1878 " --> pdb=" O ASP A1874 " (cutoff:3.500A) Processing helix chain 'A' and resid 1883 through 1896 Processing helix chain 'A' and resid 1904 through 1910 removed outlier: 3.574A pdb=" N LYS A1910 " --> pdb=" O LYS A1906 " (cutoff:3.500A) Processing helix chain 'A' and resid 1912 through 1917 Processing helix chain 'A' and resid 1922 through 1936 Processing helix chain 'A' and resid 1936 through 1944 removed outlier: 3.837A pdb=" N ARG A1943 " --> pdb=" O SER A1939 " (cutoff:3.500A) Processing helix chain 'A' and resid 1945 through 1948 Processing helix chain 'A' and resid 1962 through 1977 removed outlier: 3.534A pdb=" N LEU A1976 " --> pdb=" O LEU A1972 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU A1977 " --> pdb=" O LYS A1973 " (cutoff:3.500A) Processing helix chain 'A' and resid 1988 through 2001 Processing helix chain 'A' and resid 2004 through 2014 removed outlier: 3.683A pdb=" N ILE A2008 " --> pdb=" O ASP A2004 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LYS A2014 " --> pdb=" O ASP A2010 " (cutoff:3.500A) Processing helix chain 'A' and resid 2015 through 2040 removed outlier: 4.751A pdb=" N GLN A2029 " --> pdb=" O ASP A2025 " (cutoff:3.500A) Processing helix chain 'A' and resid 2045 through 2063 removed outlier: 3.712A pdb=" N HIS A2063 " --> pdb=" O PHE A2059 " (cutoff:3.500A) Processing helix chain 'A' and resid 2064 through 2080 Processing helix chain 'A' and resid 2138 through 2153 Processing helix chain 'A' and resid 2157 through 2162 Processing helix chain 'A' and resid 2199 through 2209 Processing helix chain 'A' and resid 2211 through 2220 Processing helix chain 'A' and resid 2235 through 2247 Processing helix chain 'A' and resid 2250 through 2260 removed outlier: 3.639A pdb=" N LEU A2260 " --> pdb=" O PHE A2256 " (cutoff:3.500A) Processing helix chain 'A' and resid 2286 through 2306 removed outlier: 3.873A pdb=" N THR A2306 " --> pdb=" O ASN A2302 " (cutoff:3.500A) Processing helix chain 'A' and resid 2316 through 2336 Processing helix chain 'A' and resid 2367 through 2379 Processing helix chain 'A' and resid 2382 through 2397 Processing helix chain 'A' and resid 2404 through 2422 removed outlier: 4.472A pdb=" N SER A2421 " --> pdb=" O TYR A2417 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N LYS A2422 " --> pdb=" O ARG A2418 " (cutoff:3.500A) Processing helix chain 'A' and resid 2429 through 2440 Processing helix chain 'A' and resid 2441 through 2445 removed outlier: 3.566A pdb=" N ASP A2445 " --> pdb=" O ASP A2442 " (cutoff:3.500A) Processing helix chain 'A' and resid 2447 through 2457 removed outlier: 3.832A pdb=" N LEU A2453 " --> pdb=" O THR A2449 " (cutoff:3.500A) Processing helix chain 'A' and resid 2477 through 2503 removed outlier: 3.946A pdb=" N VAL A2489 " --> pdb=" O SER A2485 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LEU A2490 " --> pdb=" O LEU A2486 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LYS A2500 " --> pdb=" O ILE A2496 " (cutoff:3.500A) Processing helix chain 'A' and resid 2530 through 2540 Processing helix chain 'A' and resid 2540 through 2558 removed outlier: 3.888A pdb=" N HIS A2544 " --> pdb=" O THR A2540 " (cutoff:3.500A) Processing helix chain 'A' and resid 2595 through 2600 removed outlier: 3.585A pdb=" N ILE A2599 " --> pdb=" O PHE A2595 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ASN A2600 " --> pdb=" O THR A2596 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2595 through 2600' Processing helix chain 'A' and resid 2605 through 2622 Processing helix chain 'A' and resid 2626 through 2644 removed outlier: 4.315A pdb=" N HIS A2644 " --> pdb=" O ILE A2640 " (cutoff:3.500A) Processing helix chain 'A' and resid 2645 through 2652 Processing helix chain 'A' and resid 2660 through 2664 removed outlier: 3.743A pdb=" N GLY A2664 " --> pdb=" O SER A2661 " (cutoff:3.500A) Processing helix chain 'A' and resid 2680 through 2697 Processing helix chain 'A' and resid 2753 through 2764 Processing helix chain 'A' and resid 2770 through 2780 Processing helix chain 'A' and resid 2802 through 2805 removed outlier: 3.759A pdb=" N SER A2805 " --> pdb=" O MET A2802 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2802 through 2805' Processing helix chain 'A' and resid 2806 through 2815 removed outlier: 3.630A pdb=" N ASP A2811 " --> pdb=" O ASP A2807 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N GLY A2812 " --> pdb=" O TRP A2808 " (cutoff:3.500A) Processing helix chain 'A' and resid 2818 through 2836 removed outlier: 4.223A pdb=" N VAL A2827 " --> pdb=" O ARG A2823 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ILE A2830 " --> pdb=" O SER A2826 " (cutoff:3.500A) Processing helix chain 'A' and resid 2869 through 2890 removed outlier: 3.797A pdb=" N GLU A2875 " --> pdb=" O LYS A2871 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ARG A2878 " --> pdb=" O ARG A2874 " (cutoff:3.500A) Processing helix chain 'A' and resid 2898 through 2908 Processing helix chain 'A' and resid 2916 through 2929 Processing helix chain 'A' and resid 2932 through 2938 removed outlier: 3.971A pdb=" N GLY A2936 " --> pdb=" O ASN A2932 " (cutoff:3.500A) Processing helix chain 'A' and resid 2944 through 2953 Processing helix chain 'A' and resid 2993 through 3003 Processing helix chain 'A' and resid 3043 through 3060 Processing helix chain 'A' and resid 3062 through 3074 removed outlier: 3.708A pdb=" N ILE A3070 " --> pdb=" O GLN A3066 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL A3071 " --> pdb=" O LYS A3067 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ARG A3074 " --> pdb=" O ILE A3070 " (cutoff:3.500A) Processing helix chain 'A' and resid 3104 through 3114 Processing helix chain 'A' and resid 3116 through 3121 Processing helix chain 'A' and resid 3133 through 3140 Processing helix chain 'A' and resid 3142 through 3161 removed outlier: 3.513A pdb=" N THR A3147 " --> pdb=" O PRO A3143 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N LEU A3148 " --> pdb=" O SER A3144 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N MET A3151 " --> pdb=" O THR A3147 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LYS A3161 " --> pdb=" O SER A3157 " (cutoff:3.500A) Processing helix chain 'A' and resid 3167 through 3189 removed outlier: 3.636A pdb=" N LYS A3189 " --> pdb=" O ILE A3185 " (cutoff:3.500A) Processing helix chain 'A' and resid 3208 through 3217 removed outlier: 4.280A pdb=" N LEU A3212 " --> pdb=" O THR A3208 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ILE A3217 " --> pdb=" O VAL A3213 " (cutoff:3.500A) Processing helix chain 'A' and resid 3237 through 3252 Processing helix chain 'A' and resid 3255 through 3268 Processing helix chain 'A' and resid 3281 through 3286 removed outlier: 4.064A pdb=" N HIS A3285 " --> pdb=" O LEU A3282 " (cutoff:3.500A) Processing helix chain 'A' and resid 3297 through 3305 Processing helix chain 'A' and resid 3306 through 3309 removed outlier: 3.611A pdb=" N VAL A3309 " --> pdb=" O LEU A3306 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 3306 through 3309' Processing helix chain 'A' and resid 3314 through 3327 removed outlier: 3.510A pdb=" N ASN A3326 " --> pdb=" O LEU A3322 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N SER A3327 " --> pdb=" O ASP A3323 " (cutoff:3.500A) Processing helix chain 'A' and resid 3329 through 3333 Processing helix chain 'A' and resid 3382 through 3397 Processing helix chain 'A' and resid 3406 through 3416 Processing helix chain 'A' and resid 3503 through 3510 Processing helix chain 'A' and resid 3543 through 3556 removed outlier: 4.477A pdb=" N LEU A3549 " --> pdb=" O ASN A3545 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N LEU A3550 " --> pdb=" O SER A3546 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N LEU A3554 " --> pdb=" O LEU A3550 " (cutoff:3.500A) Processing helix chain 'A' and resid 3556 through 3565 removed outlier: 4.173A pdb=" N ASP A3560 " --> pdb=" O HIS A3556 " (cutoff:3.500A) Processing helix chain 'A' and resid 3585 through 3591 removed outlier: 3.617A pdb=" N LEU A3589 " --> pdb=" O ASN A3585 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ARG A3591 " --> pdb=" O GLU A3587 " (cutoff:3.500A) Processing helix chain 'A' and resid 3591 through 3596 removed outlier: 4.403A pdb=" N LYS A3596 " --> pdb=" O GLU A3592 " (cutoff:3.500A) Processing helix chain 'A' and resid 3607 through 3624 Processing helix chain 'A' and resid 3627 through 3632 removed outlier: 4.292A pdb=" N SER A3632 " --> pdb=" O SER A3629 " (cutoff:3.500A) Processing helix chain 'A' and resid 3636 through 3642 removed outlier: 3.607A pdb=" N GLY A3642 " --> pdb=" O ILE A3638 " (cutoff:3.500A) Processing helix chain 'A' and resid 3677 through 3686 Processing helix chain 'A' and resid 3692 through 3698 removed outlier: 3.515A pdb=" N LEU A3695 " --> pdb=" O LYS A3692 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ALA A3696 " --> pdb=" O PHE A3693 " (cutoff:3.500A) Processing helix chain 'A' and resid 3700 through 3722 Processing helix chain 'A' and resid 3724 through 3739 Processing helix chain 'A' and resid 3754 through 3760 removed outlier: 3.640A pdb=" N LEU A3759 " --> pdb=" O LEU A3756 " (cutoff:3.500A) Processing helix chain 'A' and resid 3792 through 3796 Processing helix chain 'A' and resid 3799 through 3818 Processing helix chain 'A' and resid 3824 through 3830 Processing helix chain 'A' and resid 3839 through 3843 Processing helix chain 'A' and resid 3851 through 3855 Processing helix chain 'A' and resid 3859 through 3868 Processing helix chain 'A' and resid 3873 through 3888 Processing sheet with id=AA1, first strand: chain 'A' and resid 744 through 746 removed outlier: 6.752A pdb=" N SER A 695 " --> pdb=" O SER A 744 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N VAL A 746 " --> pdb=" O SER A 695 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N THR A 697 " --> pdb=" O VAL A 746 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 728 through 729 removed outlier: 6.670A pdb=" N GLY A 969 " --> pdb=" O SER A1753 " (cutoff:3.500A) removed outlier: 7.873A pdb=" N TYR A1755 " --> pdb=" O GLY A 969 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N VAL A 971 " --> pdb=" O TYR A1755 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1003 through 1004 removed outlier: 3.515A pdb=" N VAL A1537 " --> pdb=" O GLU A1003 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1357 through 1358 Processing sheet with id=AA5, first strand: chain 'A' and resid 1357 through 1358 removed outlier: 4.413A pdb=" N LEU A1383 " --> pdb=" O LYS A1373 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1821 through 1825 removed outlier: 7.003A pdb=" N VAL A2231 " --> pdb=" O ALA A1824 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 2281 through 2285 removed outlier: 3.576A pdb=" N ALA A2271 " --> pdb=" O LEU A2282 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N ALA A2268 " --> pdb=" O GLU A2402 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 2507 through 2515 removed outlier: 3.812A pdb=" N TYR A2519 " --> pdb=" O GLY A2357 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 2574 through 2575 Processing sheet with id=AB1, first strand: chain 'A' and resid 3006 through 3009 removed outlier: 6.356A pdb=" N SER A3007 " --> pdb=" O VAL A3041 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 3079 through 3081 Processing sheet with id=AB3, first strand: chain 'A' and resid 3086 through 3094 Processing sheet with id=AB4, first strand: chain 'A' and resid 3345 through 3346 removed outlier: 4.091A pdb=" N ILE A3368 " --> pdb=" O HIS A3375 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N LYS A3458 " --> pdb=" O LEU A3374 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N ILE A3376 " --> pdb=" O LYS A3458 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 3490 through 3491 Processing sheet with id=AB6, first strand: chain 'A' and resid 3649 through 3653 removed outlier: 3.785A pdb=" N LYS A3662 " --> pdb=" O ASN A3649 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 3765 through 3767 removed outlier: 3.516A pdb=" N LEU A3784 " --> pdb=" O ILE A3850 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N THR A3849 " --> pdb=" O ASN A3834 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N ASN A3834 " --> pdb=" O THR A3849 " (cutoff:3.500A) 1292 hydrogen bonds defined for protein. 3678 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 21 hydrogen bonds 42 hydrogen bond angles 0 basepair planarities 9 basepair parallelities 20 stacking parallelities Total time for adding SS restraints: 8.52 Time building geometry restraints manager: 2.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 4226 1.30 - 1.43: 6761 1.43 - 1.56: 15356 1.56 - 1.68: 89 1.68 - 1.81: 241 Bond restraints: 26673 Sorted by residual: bond pdb=" C2' 2KH A4005 " pdb=" C3' 2KH A4005 " ideal model delta sigma weight residual 1.548 1.291 0.257 2.00e-02 2.50e+03 1.66e+02 bond pdb=" N3A 2KH A4005 " pdb=" PA 2KH A4005 " ideal model delta sigma weight residual 1.933 1.691 0.242 2.00e-02 2.50e+03 1.46e+02 bond pdb=" O3G 2KH A4005 " pdb=" PG 2KH A4005 " ideal model delta sigma weight residual 1.669 1.466 0.203 2.00e-02 2.50e+03 1.03e+02 bond pdb=" C1' 2KH A4005 " pdb=" N1 2KH A4005 " ideal model delta sigma weight residual 1.502 1.330 0.172 2.00e-02 2.50e+03 7.41e+01 bond pdb=" N3A 2KH A4005 " pdb=" PB 2KH A4005 " ideal model delta sigma weight residual 1.890 1.720 0.170 2.00e-02 2.50e+03 7.19e+01 ... (remaining 26668 not shown) Histogram of bond angle deviations from ideal: 0.00 - 12.29: 36173 12.29 - 24.59: 8 24.59 - 36.88: 0 36.88 - 49.18: 0 49.18 - 61.47: 2 Bond angle restraints: 36183 Sorted by residual: angle pdb=" N3A 2KH A4005 " pdb=" PA 2KH A4005 " pdb=" O2A 2KH A4005 " ideal model delta sigma weight residual 48.17 109.64 -61.47 3.00e+00 1.11e-01 4.20e+02 angle pdb=" O2G 2KH A4005 " pdb=" PG 2KH A4005 " pdb=" O3G 2KH A4005 " ideal model delta sigma weight residual 53.94 109.74 -55.80 3.00e+00 1.11e-01 3.46e+02 angle pdb=" O1A 2KH A4005 " pdb=" PA 2KH A4005 " pdb=" O2A 2KH A4005 " ideal model delta sigma weight residual 130.82 109.35 21.47 3.00e+00 1.11e-01 5.12e+01 angle pdb=" O1B 2KH A4005 " pdb=" PB 2KH A4005 " pdb=" O2B 2KH A4005 " ideal model delta sigma weight residual 130.56 109.21 21.35 3.00e+00 1.11e-01 5.06e+01 angle pdb=" O1G 2KH A4005 " pdb=" PG 2KH A4005 " pdb=" O3G 2KH A4005 " ideal model delta sigma weight residual 130.17 109.53 20.64 3.00e+00 1.11e-01 4.73e+01 ... (remaining 36178 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.78: 15282 18.78 - 37.57: 941 37.57 - 56.35: 116 56.35 - 75.13: 51 75.13 - 93.91: 6 Dihedral angle restraints: 16396 sinusoidal: 7153 harmonic: 9243 Sorted by residual: dihedral pdb=" O4' A E 17 " pdb=" C1' A E 17 " pdb=" N9 A E 17 " pdb=" C4 A E 17 " ideal model delta sinusoidal sigma weight residual 68.00 148.56 -80.56 1 1.70e+01 3.46e-03 2.78e+01 dihedral pdb=" CA ALA A2833 " pdb=" C ALA A2833 " pdb=" N GLY A2834 " pdb=" CA GLY A2834 " ideal model delta harmonic sigma weight residual 180.00 156.44 23.56 0 5.00e+00 4.00e-02 2.22e+01 dihedral pdb=" CA LEU A2657 " pdb=" C LEU A2657 " pdb=" N GLY A2658 " pdb=" CA GLY A2658 " ideal model delta harmonic sigma weight residual 180.00 159.13 20.87 0 5.00e+00 4.00e-02 1.74e+01 ... (remaining 16393 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.091: 4005 0.091 - 0.181: 210 0.181 - 0.272: 4 0.272 - 0.362: 0 0.362 - 0.453: 1 Chirality restraints: 4220 Sorted by residual: chirality pdb=" C2' 2KH A4005 " pdb=" C1' 2KH A4005 " pdb=" C3' 2KH A4005 " pdb=" O2' 2KH A4005 " both_signs ideal model delta sigma weight residual False -2.85 -2.39 -0.45 2.00e-01 2.50e+01 5.13e+00 chirality pdb=" CB THR A3340 " pdb=" CA THR A3340 " pdb=" OG1 THR A3340 " pdb=" CG2 THR A3340 " both_signs ideal model delta sigma weight residual False 2.55 2.28 0.27 2.00e-01 2.50e+01 1.84e+00 chirality pdb=" CB ILE A2941 " pdb=" CA ILE A2941 " pdb=" CG1 ILE A2941 " pdb=" CG2 ILE A2941 " both_signs ideal model delta sigma weight residual False 2.64 2.90 -0.26 2.00e-01 2.50e+01 1.63e+00 ... (remaining 4217 not shown) Planarity restraints: 4402 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A3441 " -0.044 5.00e-02 4.00e+02 6.70e-02 7.17e+00 pdb=" N PRO A3442 " 0.116 5.00e-02 4.00e+02 pdb=" CA PRO A3442 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO A3442 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL A3471 " -0.012 2.00e-02 2.50e+03 2.36e-02 5.58e+00 pdb=" C VAL A3471 " 0.041 2.00e-02 2.50e+03 pdb=" O VAL A3471 " -0.016 2.00e-02 2.50e+03 pdb=" N PHE A3472 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A2024 " 0.023 2.00e-02 2.50e+03 1.47e-02 4.32e+00 pdb=" CG TYR A2024 " -0.034 2.00e-02 2.50e+03 pdb=" CD1 TYR A2024 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 TYR A2024 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR A2024 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR A2024 " 0.002 2.00e-02 2.50e+03 pdb=" CZ TYR A2024 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR A2024 " 0.007 2.00e-02 2.50e+03 ... (remaining 4399 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 61 2.64 - 3.21: 23600 3.21 - 3.77: 41296 3.77 - 4.34: 57623 4.34 - 4.90: 92167 Nonbonded interactions: 214747 Sorted by model distance: nonbonded pdb=" OP3 U F 1 " pdb="MN MN A4002 " model vdw 2.076 2.320 nonbonded pdb="MN MN A4004 " pdb=" O1B 2KH A4005 " model vdw 2.108 2.320 nonbonded pdb="MN MN A4003 " pdb=" O2A 2KH A4005 " model vdw 2.123 2.320 nonbonded pdb=" OD1 ASP A2358 " pdb="MN MN A4004 " model vdw 2.140 2.320 nonbonded pdb=" OD2 ASP A2517 " pdb="MN MN A4004 " model vdw 2.141 2.320 ... (remaining 214742 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.810 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: 0.410 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 33.020 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.040 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: 0.000 Load rotamer database and sin/cos tables:6.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6851 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 : 0.005 0.257 26677 Z= 0.241 Angle : 0.828 61.471 36189 Z= 0.373 Chirality : 0.043 0.453 4220 Planarity : 0.005 0.067 4402 Dihedral : 12.378 93.913 10358 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.37 (0.14), residues: 3102 helix: -0.24 (0.12), residues: 1700 sheet: -0.91 (0.35), residues: 239 loop : -1.81 (0.17), residues: 1163 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1027 TYR 0.034 0.002 TYR A2024 PHE 0.036 0.002 PHE A2633 TRP 0.024 0.002 TRP A3482 HIS 0.009 0.001 HIS A3501 Details of bonding type rmsd/Z covalent geometry : bond 0.00501 / 0.24 (26673) covalent geometry : angle 0.81810 / 0.37 (36183) hydrogen bonds : bond 0.16322 / 10.49 ( 1311) hydrogen bonds : angle 6.53363 / 4.62 ( 3720) metal coordination : bond 0.00900 / 0.44 ( 4) metal coordination : angle 9.74353 / 5.57 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 666 residues out of total 2891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 666 time to evaluate : 0.829 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 567 GLN cc_start: 0.7009 (tm-30) cc_final: 0.6432 (tm-30) REVERT: A 805 GLU cc_start: 0.7763 (pp20) cc_final: 0.7475 (pp20) REVERT: A 837 ARG cc_start: 0.7136 (mtt-85) cc_final: 0.6467 (mtt-85) REVERT: A 846 ILE cc_start: 0.8323 (mm) cc_final: 0.7949 (mt) REVERT: A 1021 GLU cc_start: 0.6964 (tp30) cc_final: 0.6259 (tp30) REVERT: A 1024 LYS cc_start: 0.8525 (mttt) cc_final: 0.7990 (mttt) REVERT: A 1119 GLU cc_start: 0.6851 (tp30) cc_final: 0.6650 (tp30) REVERT: A 1129 GLU cc_start: 0.7080 (mt-10) cc_final: 0.6867 (mp0) REVERT: A 1275 ASP cc_start: 0.7389 (m-30) cc_final: 0.7122 (m-30) REVERT: A 1303 GLU cc_start: 0.6990 (tp30) cc_final: 0.6667 (tp30) REVERT: A 1311 THR cc_start: 0.7872 (m) cc_final: 0.7445 (p) REVERT: A 1595 THR cc_start: 0.8321 (m) cc_final: 0.7905 (m) REVERT: A 1604 ASP cc_start: 0.7595 (p0) cc_final: 0.7253 (p0) REVERT: A 1778 MET cc_start: 0.7635 (tpt) cc_final: 0.7408 (tpp) REVERT: A 2029 GLN cc_start: 0.7883 (pm20) cc_final: 0.7539 (pm20) REVERT: A 2049 GLU cc_start: 0.7017 (mt-10) cc_final: 0.6684 (mt-10) REVERT: A 2239 MET cc_start: 0.7965 (mmt) cc_final: 0.6495 (mmt) REVERT: A 2308 SER cc_start: 0.8408 (p) cc_final: 0.8071 (t) REVERT: A 2467 SER cc_start: 0.8300 (t) cc_final: 0.8020 (m) REVERT: A 2543 LYS cc_start: 0.7751 (tttt) cc_final: 0.7513 (tttt) REVERT: A 2578 SER cc_start: 0.8217 (m) cc_final: 0.7927 (t) REVERT: A 2623 ASN cc_start: 0.7804 (m-40) cc_final: 0.7533 (m-40) REVERT: A 2659 THR cc_start: 0.7570 (m) cc_final: 0.7274 (p) REVERT: A 2666 LEU cc_start: 0.7845 (tp) cc_final: 0.7645 (tm) REVERT: A 2701 ILE cc_start: 0.8552 (mm) cc_final: 0.8315 (mm) REVERT: A 2804 ASP cc_start: 0.7156 (t0) cc_final: 0.6952 (t70) REVERT: A 2898 THR cc_start: 0.8282 (p) cc_final: 0.8072 (p) REVERT: A 2956 TYR cc_start: 0.7182 (m-80) cc_final: 0.6853 (m-80) REVERT: A 3153 THR cc_start: 0.7924 (m) cc_final: 0.7680 (p) REVERT: A 3175 SER cc_start: 0.8366 (t) cc_final: 0.8160 (t) REVERT: A 3176 ASN cc_start: 0.7884 (m-40) cc_final: 0.7460 (m110) REVERT: A 3268 ASN cc_start: 0.6385 (m-40) cc_final: 0.6161 (m-40) REVERT: A 3364 GLU cc_start: 0.6490 (mp0) cc_final: 0.6228 (mp0) REVERT: A 3457 VAL cc_start: 0.7679 (t) cc_final: 0.7438 (m) REVERT: A 3796 MET cc_start: 0.4781 (mmm) cc_final: 0.4487 (mmt) REVERT: A 3883 LEU cc_start: 0.7169 (tp) cc_final: 0.6949 (tm) REVERT: A 3890 ARG cc_start: 0.6633 (mmt180) cc_final: 0.6310 (mmt180) outliers start: 0 outliers final: 1 residues processed: 666 average time/residue: 0.6239 time to fit residues: 486.3858 Evaluate side-chains 536 residues out of total 2891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 535 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1640 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 0.0270 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 10.0000 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 0.8980 chunk 298 optimal weight: 4.9990 overall best weight: 1.3642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1057 GLN ** A1127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1284 ASN A1491 HIS A1510 ASN ** A2258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2509 HIS A2607 GLN A2614 GLN A2619 GLN A2623 ASN A2901 GLN A3616 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.178984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.152780 restraints weight = 37990.949| |-----------------------------------------------------------------------------| r_work (start): 0.3925 rms_B_bonded: 2.09 r_work: 0.3818 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3675 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7403 moved from start: 0.1726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 26677 Z= 0.186 Angle : 0.625 16.963 36189 Z= 0.318 Chirality : 0.042 0.258 4220 Planarity : 0.004 0.060 4402 Dihedral : 10.047 95.419 4038 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 2.18 % Allowed : 10.86 % Favored : 86.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.87 (0.15), residues: 3102 helix: 0.26 (0.12), residues: 1723 sheet: -0.90 (0.35), residues: 233 loop : -1.73 (0.18), residues: 1146 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 800 TYR 0.026 0.002 TYR A1597 PHE 0.027 0.002 PHE A3195 TRP 0.017 0.002 TRP A3482 HIS 0.005 0.001 HIS A2470 Details of bonding type rmsd/Z covalent geometry : bond 0.00408 / 0.19 (26673) covalent geometry : angle 0.61468 / 0.32 (36183) hydrogen bonds : bond 0.04538 / 2.91 ( 1311) hydrogen bonds : angle 5.02331 / 3.57 ( 3720) metal coordination : bond 0.00738 / 0.35 ( 4) metal coordination : angle 8.65929 / 4.92 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 620 residues out of total 2891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 557 time to evaluate : 0.983 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 555 LYS cc_start: 0.7118 (pttm) cc_final: 0.6761 (pttm) REVERT: A 567 GLN cc_start: 0.7765 (tm-30) cc_final: 0.7193 (tm-30) REVERT: A 663 THR cc_start: 0.8248 (m) cc_final: 0.8043 (t) REVERT: A 689 ASP cc_start: 0.8121 (t0) cc_final: 0.7837 (t0) REVERT: A 751 ARG cc_start: 0.7484 (mmp80) cc_final: 0.7161 (mmp80) REVERT: A 753 MET cc_start: 0.6589 (mmm) cc_final: 0.6160 (mmm) REVERT: A 805 GLU cc_start: 0.8209 (pp20) cc_final: 0.7802 (pp20) REVERT: A 833 ASP cc_start: 0.7889 (t0) cc_final: 0.6991 (t0) REVERT: A 837 ARG cc_start: 0.7657 (mtt-85) cc_final: 0.7273 (mtt-85) REVERT: A 940 LYS cc_start: 0.8049 (mttt) cc_final: 0.7609 (mttm) REVERT: A 959 GLU cc_start: 0.7067 (tm-30) cc_final: 0.6856 (tm-30) REVERT: A 1079 CYS cc_start: 0.8029 (t) cc_final: 0.7751 (t) REVERT: A 1119 GLU cc_start: 0.7575 (tp30) cc_final: 0.7150 (tp30) REVERT: A 1129 GLU cc_start: 0.7743 (mt-10) cc_final: 0.7155 (mp0) REVERT: A 1210 LEU cc_start: 0.7084 (mp) cc_final: 0.6844 (tp) REVERT: A 1240 GLU cc_start: 0.7605 (mp0) cc_final: 0.7388 (mp0) REVERT: A 1275 ASP cc_start: 0.7668 (m-30) cc_final: 0.7341 (m-30) REVERT: A 1311 THR cc_start: 0.8311 (m) cc_final: 0.7937 (p) REVERT: A 1418 LEU cc_start: 0.8508 (OUTLIER) cc_final: 0.8230 (tt) REVERT: A 1419 TYR cc_start: 0.7967 (m-80) cc_final: 0.7751 (m-80) REVERT: A 1833 LYS cc_start: 0.8108 (mttt) cc_final: 0.7710 (mttm) REVERT: A 1846 LYS cc_start: 0.7799 (tttt) cc_final: 0.7331 (mttp) REVERT: A 1947 MET cc_start: 0.3337 (mmm) cc_final: 0.2784 (mmm) REVERT: A 2029 GLN cc_start: 0.7941 (pm20) cc_final: 0.7524 (pm20) REVERT: A 2049 GLU cc_start: 0.7422 (mt-10) cc_final: 0.7001 (mt-10) REVERT: A 2308 SER cc_start: 0.8696 (p) cc_final: 0.8315 (t) REVERT: A 2336 ASP cc_start: 0.7724 (t0) cc_final: 0.7507 (t70) REVERT: A 2467 SER cc_start: 0.8653 (t) cc_final: 0.8326 (m) REVERT: A 2543 LYS cc_start: 0.8540 (tttt) cc_final: 0.8285 (tttt) REVERT: A 2579 GLU cc_start: 0.7301 (mt-10) cc_final: 0.7097 (mt-10) REVERT: A 2659 THR cc_start: 0.7939 (m) cc_final: 0.7581 (p) REVERT: A 2701 ILE cc_start: 0.8523 (mm) cc_final: 0.8226 (mm) REVERT: A 2908 ILE cc_start: 0.8754 (pt) cc_final: 0.8491 (mt) REVERT: A 2953 MET cc_start: 0.7723 (OUTLIER) cc_final: 0.7436 (mtm) REVERT: A 2956 TYR cc_start: 0.7864 (m-80) cc_final: 0.7305 (m-80) REVERT: A 3161 LYS cc_start: 0.7856 (mmtm) cc_final: 0.7648 (mmtm) REVERT: A 3180 LEU cc_start: 0.8263 (OUTLIER) cc_final: 0.8014 (mm) REVERT: A 3203 MET cc_start: 0.6295 (ttm) cc_final: 0.5818 (ttm) REVERT: A 3222 PHE cc_start: 0.7969 (t80) cc_final: 0.7697 (t80) REVERT: A 3223 PHE cc_start: 0.7374 (m-10) cc_final: 0.7080 (m-10) REVERT: A 3364 GLU cc_start: 0.7100 (mp0) cc_final: 0.6738 (mp0) REVERT: A 3539 LYS cc_start: 0.7643 (mmmm) cc_final: 0.7434 (mmmm) REVERT: A 3643 PHE cc_start: 0.7797 (m-10) cc_final: 0.7508 (m-10) REVERT: A 3715 LYS cc_start: 0.8229 (tppt) cc_final: 0.7903 (tppt) REVERT: A 3767 ILE cc_start: 0.8179 (OUTLIER) cc_final: 0.7373 (pp) REVERT: A 3796 MET cc_start: 0.5116 (mmm) cc_final: 0.4616 (mmt) REVERT: A 3818 MET cc_start: 0.7221 (mpm) cc_final: 0.6971 (mpm) REVERT: A 3883 LEU cc_start: 0.7271 (tp) cc_final: 0.6981 (tm) REVERT: A 3886 MET cc_start: 0.6058 (mtp) cc_final: 0.5809 (mtp) outliers start: 63 outliers final: 27 residues processed: 577 average time/residue: 0.6566 time to fit residues: 441.2131 Evaluate side-chains 550 residues out of total 2891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 519 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 341 MET Chi-restraints excluded: chain A residue 726 GLU Chi-restraints excluded: chain A residue 803 VAL Chi-restraints excluded: chain A residue 913 GLN Chi-restraints excluded: chain A residue 956 THR Chi-restraints excluded: chain A residue 972 ILE Chi-restraints excluded: chain A residue 1046 SER Chi-restraints excluded: chain A residue 1052 LEU Chi-restraints excluded: chain A residue 1366 CYS Chi-restraints excluded: chain A residue 1384 CYS Chi-restraints excluded: chain A residue 1418 LEU Chi-restraints excluded: chain A residue 1640 MET Chi-restraints excluded: chain A residue 1798 GLU Chi-restraints excluded: chain A residue 1849 LYS Chi-restraints excluded: chain A residue 2231 VAL Chi-restraints excluded: chain A residue 2305 LYS Chi-restraints excluded: chain A residue 2525 VAL Chi-restraints excluded: chain A residue 2661 SER Chi-restraints excluded: chain A residue 2810 LYS Chi-restraints excluded: chain A residue 2894 SER Chi-restraints excluded: chain A residue 2918 SER Chi-restraints excluded: chain A residue 2953 MET Chi-restraints excluded: chain A residue 3005 SER Chi-restraints excluded: chain A residue 3067 LYS Chi-restraints excluded: chain A residue 3119 SER Chi-restraints excluded: chain A residue 3180 LEU Chi-restraints excluded: chain A residue 3270 ARG Chi-restraints excluded: chain A residue 3307 SER Chi-restraints excluded: chain A residue 3375 HIS Chi-restraints excluded: chain A residue 3681 LEU Chi-restraints excluded: chain A residue 3767 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 190 optimal weight: 0.6980 chunk 71 optimal weight: 8.9990 chunk 313 optimal weight: 0.9980 chunk 117 optimal weight: 0.7980 chunk 155 optimal weight: 9.9990 chunk 110 optimal weight: 0.7980 chunk 48 optimal weight: 1.9990 chunk 118 optimal weight: 0.8980 chunk 173 optimal weight: 0.6980 chunk 55 optimal weight: 0.8980 chunk 297 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1284 ASN A2509 HIS A2614 GLN A2619 GLN ** A2638 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3043 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.179409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.153445 restraints weight = 38132.842| |-----------------------------------------------------------------------------| r_work (start): 0.3936 rms_B_bonded: 2.06 r_work: 0.3831 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3689 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7380 moved from start: 0.1982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 26677 Z= 0.136 Angle : 0.588 13.940 36189 Z= 0.295 Chirality : 0.040 0.226 4220 Planarity : 0.004 0.056 4402 Dihedral : 9.967 96.754 4038 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 2.28 % Allowed : 13.14 % Favored : 84.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.15), residues: 3102 helix: 0.49 (0.12), residues: 1725 sheet: -0.92 (0.34), residues: 231 loop : -1.68 (0.18), residues: 1146 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A3766 TYR 0.022 0.002 TYR A1597 PHE 0.027 0.002 PHE A3613 TRP 0.016 0.001 TRP A3631 HIS 0.006 0.001 HIS A 944 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.14 (26673) covalent geometry : angle 0.58061 / 0.29 (36183) hydrogen bonds : bond 0.03952 / 2.54 ( 1311) hydrogen bonds : angle 4.74047 / 3.37 ( 3720) metal coordination : bond 0.00595 / 0.29 ( 4) metal coordination : angle 7.41162 / 4.23 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 593 residues out of total 2891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 527 time to evaluate : 1.035 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: A 353 MET cc_start: 0.7529 (pmm) cc_final: 0.7202 (ppp) REVERT: A 526 MET cc_start: 0.6957 (tmm) cc_final: 0.6414 (mpp) REVERT: A 543 ASN cc_start: 0.6983 (t0) cc_final: 0.6619 (t0) REVERT: A 567 GLN cc_start: 0.7857 (tm-30) cc_final: 0.7275 (tm-30) REVERT: A 689 ASP cc_start: 0.8111 (t0) cc_final: 0.7692 (t0) REVERT: A 751 ARG cc_start: 0.7435 (mmp80) cc_final: 0.6889 (mmp-170) REVERT: A 755 ASN cc_start: 0.7189 (t0) cc_final: 0.6828 (m110) REVERT: A 805 GLU cc_start: 0.8208 (pp20) cc_final: 0.7956 (pp20) REVERT: A 889 PHE cc_start: 0.7230 (t80) cc_final: 0.7011 (t80) REVERT: A 897 ASN cc_start: 0.7709 (m-40) cc_final: 0.7444 (m110) REVERT: A 936 GLU cc_start: 0.7380 (tm-30) cc_final: 0.7114 (tm-30) REVERT: A 940 LYS cc_start: 0.8061 (mttt) cc_final: 0.7735 (mttp) REVERT: A 959 GLU cc_start: 0.7027 (tm-30) cc_final: 0.6785 (tm-30) REVERT: A 1079 CYS cc_start: 0.8061 (t) cc_final: 0.7469 (m) REVERT: A 1119 GLU cc_start: 0.7490 (tp30) cc_final: 0.7056 (tp30) REVERT: A 1129 GLU cc_start: 0.7671 (mt-10) cc_final: 0.7090 (mp0) REVERT: A 1210 LEU cc_start: 0.7038 (mp) cc_final: 0.6781 (tp) REVERT: A 1240 GLU cc_start: 0.7645 (mp0) cc_final: 0.7351 (mp0) REVERT: A 1273 CYS cc_start: 0.7983 (OUTLIER) cc_final: 0.7670 (m) REVERT: A 1275 ASP cc_start: 0.7712 (m-30) cc_final: 0.7378 (m-30) REVERT: A 1303 GLU cc_start: 0.7922 (tp30) cc_final: 0.7290 (tp30) REVERT: A 1311 THR cc_start: 0.8274 (m) cc_final: 0.7889 (p) REVERT: A 1418 LEU cc_start: 0.8521 (OUTLIER) cc_final: 0.8228 (tt) REVERT: A 1555 ASP cc_start: 0.7842 (m-30) cc_final: 0.7536 (m-30) REVERT: A 1577 VAL cc_start: 0.8470 (t) cc_final: 0.8206 (m) REVERT: A 1833 LYS cc_start: 0.8108 (mttt) cc_final: 0.7737 (mttm) REVERT: A 1846 LYS cc_start: 0.7758 (tttt) cc_final: 0.7298 (mttp) REVERT: A 1947 MET cc_start: 0.3373 (mmm) cc_final: 0.2725 (tmm) REVERT: A 2029 GLN cc_start: 0.7861 (pm20) cc_final: 0.7444 (pm20) REVERT: A 2049 GLU cc_start: 0.7431 (mt-10) cc_final: 0.7004 (mt-10) REVERT: A 2206 MET cc_start: 0.6604 (mmm) cc_final: 0.6010 (mmm) REVERT: A 2308 SER cc_start: 0.8673 (p) cc_final: 0.8274 (t) REVERT: A 2336 ASP cc_start: 0.7812 (t0) cc_final: 0.7576 (t70) REVERT: A 2467 SER cc_start: 0.8666 (t) cc_final: 0.8380 (m) REVERT: A 2543 LYS cc_start: 0.8507 (tttt) cc_final: 0.8257 (tttt) REVERT: A 2579 GLU cc_start: 0.7336 (mt-10) cc_final: 0.7129 (mt-10) REVERT: A 2659 THR cc_start: 0.7890 (m) cc_final: 0.7552 (p) REVERT: A 2701 ILE cc_start: 0.8464 (mm) cc_final: 0.8151 (mm) REVERT: A 2864 MET cc_start: 0.8241 (OUTLIER) cc_final: 0.7475 (mmt) REVERT: A 2881 VAL cc_start: 0.8712 (t) cc_final: 0.8475 (t) REVERT: A 2884 MET cc_start: 0.8110 (mpp) cc_final: 0.7605 (mpp) REVERT: A 2916 GLU cc_start: 0.7041 (tt0) cc_final: 0.6787 (tm-30) REVERT: A 2956 TYR cc_start: 0.7865 (m-80) cc_final: 0.7358 (m-80) REVERT: A 3161 LYS cc_start: 0.7879 (mmtm) cc_final: 0.7647 (mmtm) REVERT: A 3203 MET cc_start: 0.6401 (ttm) cc_final: 0.5898 (ttm) REVERT: A 3222 PHE cc_start: 0.7897 (t80) cc_final: 0.7686 (t80) REVERT: A 3364 GLU cc_start: 0.7041 (mp0) cc_final: 0.6667 (mp0) REVERT: A 3461 LYS cc_start: 0.8627 (mttt) cc_final: 0.8422 (mmtm) REVERT: A 3506 LYS cc_start: 0.7688 (tmtt) cc_final: 0.7325 (tptt) REVERT: A 3715 LYS cc_start: 0.8208 (tppt) cc_final: 0.7806 (tppt) REVERT: A 3766 ARG cc_start: 0.6194 (tpp-160) cc_final: 0.5896 (tpp-160) REVERT: A 3767 ILE cc_start: 0.7884 (OUTLIER) cc_final: 0.7462 (pp) REVERT: A 3796 MET cc_start: 0.5163 (mmm) cc_final: 0.4614 (mmt) REVERT: A 3870 MET cc_start: 0.6923 (pmm) cc_final: 0.6295 (ppp) REVERT: A 3883 LEU cc_start: 0.7212 (tp) cc_final: 0.6825 (tm) REVERT: A 3886 MET cc_start: 0.6008 (mtp) cc_final: 0.5797 (mtp) outliers start: 66 outliers final: 33 residues processed: 558 average time/residue: 0.6732 time to fit residues: 434.1032 Evaluate side-chains 540 residues out of total 2891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 503 time to evaluate : 0.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 341 MET Chi-restraints excluded: chain A residue 604 ILE Chi-restraints excluded: chain A residue 667 GLN Chi-restraints excluded: chain A residue 726 GLU Chi-restraints excluded: chain A residue 818 THR Chi-restraints excluded: chain A residue 913 GLN Chi-restraints excluded: chain A residue 929 VAL Chi-restraints excluded: chain A residue 935 LEU Chi-restraints excluded: chain A residue 972 ILE Chi-restraints excluded: chain A residue 1046 SER Chi-restraints excluded: chain A residue 1057 GLN Chi-restraints excluded: chain A residue 1273 CYS Chi-restraints excluded: chain A residue 1366 CYS Chi-restraints excluded: chain A residue 1418 LEU Chi-restraints excluded: chain A residue 1640 MET Chi-restraints excluded: chain A residue 1798 GLU Chi-restraints excluded: chain A residue 1849 LYS Chi-restraints excluded: chain A residue 2525 VAL Chi-restraints excluded: chain A residue 2530 SER Chi-restraints excluded: chain A residue 2661 SER Chi-restraints excluded: chain A residue 2768 SER Chi-restraints excluded: chain A residue 2810 LYS Chi-restraints excluded: chain A residue 2817 ASN Chi-restraints excluded: chain A residue 2864 MET Chi-restraints excluded: chain A residue 2894 SER Chi-restraints excluded: chain A residue 2943 GLU Chi-restraints excluded: chain A residue 2951 ILE Chi-restraints excluded: chain A residue 3067 LYS Chi-restraints excluded: chain A residue 3132 LEU Chi-restraints excluded: chain A residue 3270 ARG Chi-restraints excluded: chain A residue 3340 THR Chi-restraints excluded: chain A residue 3352 ARG Chi-restraints excluded: chain A residue 3375 HIS Chi-restraints excluded: chain A residue 3554 LEU Chi-restraints excluded: chain A residue 3681 LEU Chi-restraints excluded: chain A residue 3683 SER Chi-restraints excluded: chain A residue 3767 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 228 optimal weight: 0.9980 chunk 32 optimal weight: 5.9990 chunk 197 optimal weight: 4.9990 chunk 164 optimal weight: 0.9990 chunk 5 optimal weight: 6.9990 chunk 12 optimal weight: 8.9990 chunk 4 optimal weight: 8.9990 chunk 80 optimal weight: 0.8980 chunk 263 optimal weight: 4.9990 chunk 70 optimal weight: 3.9990 chunk 133 optimal weight: 20.0000 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1284 ASN A2509 HIS ** A2638 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3043 GLN A3501 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.180510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.152994 restraints weight = 37590.664| |-----------------------------------------------------------------------------| r_work (start): 0.3875 rms_B_bonded: 2.17 r_work: 0.3764 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3618 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7489 moved from start: 0.2390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 26677 Z= 0.286 Angle : 0.672 15.683 36189 Z= 0.341 Chirality : 0.045 0.227 4220 Planarity : 0.004 0.060 4402 Dihedral : 10.171 98.407 4038 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 3.22 % Allowed : 13.66 % Favored : 83.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.90 (0.15), residues: 3102 helix: 0.29 (0.12), residues: 1741 sheet: -1.14 (0.34), residues: 241 loop : -1.83 (0.18), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 837 TYR 0.030 0.002 TYR A1597 PHE 0.032 0.002 PHE A3613 TRP 0.027 0.002 TRP A3631 HIS 0.009 0.001 HIS A2470 Details of bonding type rmsd/Z covalent geometry : bond 0.00634 / 0.29 (26673) covalent geometry : angle 0.66367 / 0.34 (36183) hydrogen bonds : bond 0.04611 / 2.98 ( 1311) hydrogen bonds : angle 4.82244 / 3.43 ( 3720) metal coordination : bond 0.00916 / 0.44 ( 4) metal coordination : angle 8.22598 / 4.73 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 632 residues out of total 2891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 539 time to evaluate : 0.983 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 353 MET cc_start: 0.7561 (OUTLIER) cc_final: 0.7357 (ppp) REVERT: A 526 MET cc_start: 0.7034 (tmm) cc_final: 0.6795 (tmm) REVERT: A 543 ASN cc_start: 0.7166 (t0) cc_final: 0.6840 (t0) REVERT: A 567 GLN cc_start: 0.7925 (tm-30) cc_final: 0.7381 (tm-30) REVERT: A 689 ASP cc_start: 0.8201 (t0) cc_final: 0.7792 (t0) REVERT: A 699 LYS cc_start: 0.7670 (mttt) cc_final: 0.7037 (mmmt) REVERT: A 751 ARG cc_start: 0.7551 (mmp80) cc_final: 0.7049 (mmp-170) REVERT: A 753 MET cc_start: 0.6680 (mmm) cc_final: 0.6382 (mmm) REVERT: A 755 ASN cc_start: 0.7244 (t0) cc_final: 0.6817 (m110) REVERT: A 805 GLU cc_start: 0.8262 (pp20) cc_final: 0.7865 (pp20) REVERT: A 889 PHE cc_start: 0.7330 (t80) cc_final: 0.7079 (t80) REVERT: A 897 ASN cc_start: 0.7762 (m-40) cc_final: 0.7457 (m110) REVERT: A 929 VAL cc_start: 0.8434 (m) cc_final: 0.8190 (t) REVERT: A 940 LYS cc_start: 0.8082 (mttt) cc_final: 0.7840 (tppt) REVERT: A 959 GLU cc_start: 0.7102 (tm-30) cc_final: 0.6874 (tm-30) REVERT: A 1079 CYS cc_start: 0.8107 (t) cc_final: 0.7529 (m) REVERT: A 1119 GLU cc_start: 0.7478 (tp30) cc_final: 0.7049 (tp30) REVERT: A 1129 GLU cc_start: 0.7752 (mt-10) cc_final: 0.7197 (mp0) REVERT: A 1210 LEU cc_start: 0.7014 (mp) cc_final: 0.6746 (tp) REVERT: A 1240 GLU cc_start: 0.7710 (mp0) cc_final: 0.7366 (mp0) REVERT: A 1275 ASP cc_start: 0.7812 (m-30) cc_final: 0.7457 (m-30) REVERT: A 1311 THR cc_start: 0.8428 (m) cc_final: 0.8032 (p) REVERT: A 1418 LEU cc_start: 0.8560 (OUTLIER) cc_final: 0.8323 (tt) REVERT: A 1643 GLU cc_start: 0.7369 (mm-30) cc_final: 0.7098 (mm-30) REVERT: A 1846 LYS cc_start: 0.7854 (tttt) cc_final: 0.7362 (ttmt) REVERT: A 1947 MET cc_start: 0.3524 (mmm) cc_final: 0.3088 (tmm) REVERT: A 2029 GLN cc_start: 0.7887 (pm20) cc_final: 0.7410 (pm20) REVERT: A 2049 GLU cc_start: 0.7456 (mt-10) cc_final: 0.7048 (mt-10) REVERT: A 2206 MET cc_start: 0.6576 (mmm) cc_final: 0.6014 (mmm) REVERT: A 2308 SER cc_start: 0.8758 (p) cc_final: 0.8379 (t) REVERT: A 2336 ASP cc_start: 0.7894 (t0) cc_final: 0.7653 (t70) REVERT: A 2467 SER cc_start: 0.8667 (t) cc_final: 0.8373 (m) REVERT: A 2543 LYS cc_start: 0.8587 (tttt) cc_final: 0.8337 (tttt) REVERT: A 2579 GLU cc_start: 0.7238 (mt-10) cc_final: 0.6997 (mt-10) REVERT: A 2659 THR cc_start: 0.7999 (m) cc_final: 0.7650 (p) REVERT: A 2701 ILE cc_start: 0.8595 (mm) cc_final: 0.8277 (mm) REVERT: A 2881 VAL cc_start: 0.8751 (t) cc_final: 0.8506 (t) REVERT: A 2884 MET cc_start: 0.8150 (mpp) cc_final: 0.7629 (mpp) REVERT: A 2916 GLU cc_start: 0.7264 (tt0) cc_final: 0.7036 (tm-30) REVERT: A 2956 TYR cc_start: 0.7988 (m-80) cc_final: 0.7484 (m-80) REVERT: A 3120 GLU cc_start: 0.8520 (tt0) cc_final: 0.8008 (tp30) REVERT: A 3161 LYS cc_start: 0.7986 (mmtm) cc_final: 0.7726 (mmtm) REVERT: A 3211 GLU cc_start: 0.7168 (OUTLIER) cc_final: 0.6921 (pm20) REVERT: A 3222 PHE cc_start: 0.8127 (t80) cc_final: 0.7842 (t80) REVERT: A 3364 GLU cc_start: 0.7215 (mp0) cc_final: 0.6883 (mp0) REVERT: A 3506 LYS cc_start: 0.7744 (tmtt) cc_final: 0.7437 (tmtt) REVERT: A 3539 LYS cc_start: 0.7647 (mmmm) cc_final: 0.7443 (mmmm) REVERT: A 3715 LYS cc_start: 0.8215 (tppt) cc_final: 0.7981 (tppt) REVERT: A 3739 PHE cc_start: 0.7091 (m-80) cc_final: 0.6762 (m-80) REVERT: A 3767 ILE cc_start: 0.7944 (OUTLIER) cc_final: 0.7435 (pp) REVERT: A 3796 MET cc_start: 0.5162 (mmm) cc_final: 0.4603 (mmt) REVERT: A 3818 MET cc_start: 0.7235 (mpm) cc_final: 0.7007 (mpm) REVERT: A 3870 MET cc_start: 0.6959 (pmm) cc_final: 0.6424 (ppp) REVERT: A 3883 LEU cc_start: 0.7307 (tp) cc_final: 0.6843 (tm) REVERT: A 3886 MET cc_start: 0.6123 (mtp) cc_final: 0.5908 (mtp) outliers start: 93 outliers final: 42 residues processed: 581 average time/residue: 0.6608 time to fit residues: 445.1477 Evaluate side-chains 559 residues out of total 2891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 513 time to evaluate : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 341 MET Chi-restraints excluded: chain A residue 353 MET Chi-restraints excluded: chain A residue 604 ILE Chi-restraints excluded: chain A residue 625 THR Chi-restraints excluded: chain A residue 726 GLU Chi-restraints excluded: chain A residue 800 ARG Chi-restraints excluded: chain A residue 818 THR Chi-restraints excluded: chain A residue 913 GLN Chi-restraints excluded: chain A residue 956 THR Chi-restraints excluded: chain A residue 972 ILE Chi-restraints excluded: chain A residue 999 LYS Chi-restraints excluded: chain A residue 1025 SER Chi-restraints excluded: chain A residue 1075 THR Chi-restraints excluded: chain A residue 1104 THR Chi-restraints excluded: chain A residue 1144 ILE Chi-restraints excluded: chain A residue 1366 CYS Chi-restraints excluded: chain A residue 1384 CYS Chi-restraints excluded: chain A residue 1407 LEU Chi-restraints excluded: chain A residue 1418 LEU Chi-restraints excluded: chain A residue 1435 VAL Chi-restraints excluded: chain A residue 1516 GLN Chi-restraints excluded: chain A residue 1658 THR Chi-restraints excluded: chain A residue 1667 CYS Chi-restraints excluded: chain A residue 1753 SER Chi-restraints excluded: chain A residue 1798 GLU Chi-restraints excluded: chain A residue 1849 LYS Chi-restraints excluded: chain A residue 2231 VAL Chi-restraints excluded: chain A residue 2510 VAL Chi-restraints excluded: chain A residue 2661 SER Chi-restraints excluded: chain A residue 2768 SER Chi-restraints excluded: chain A residue 2810 LYS Chi-restraints excluded: chain A residue 2894 SER Chi-restraints excluded: chain A residue 2943 GLU Chi-restraints excluded: chain A residue 2951 ILE Chi-restraints excluded: chain A residue 3005 SER Chi-restraints excluded: chain A residue 3067 LYS Chi-restraints excluded: chain A residue 3208 THR Chi-restraints excluded: chain A residue 3209 VAL Chi-restraints excluded: chain A residue 3211 GLU Chi-restraints excluded: chain A residue 3279 ASP Chi-restraints excluded: chain A residue 3307 SER Chi-restraints excluded: chain A residue 3352 ARG Chi-restraints excluded: chain A residue 3375 HIS Chi-restraints excluded: chain A residue 3681 LEU Chi-restraints excluded: chain A residue 3683 SER Chi-restraints excluded: chain A residue 3767 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 277 optimal weight: 0.0870 chunk 231 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 290 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 chunk 47 optimal weight: 0.8980 chunk 293 optimal weight: 0.7980 chunk 90 optimal weight: 4.9990 chunk 128 optimal weight: 4.9990 chunk 204 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 overall best weight: 0.7358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1057 GLN ** A1127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1284 ASN A1510 ASN A2509 HIS A2619 GLN ** A2638 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3300 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.184025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.156533 restraints weight = 37631.438| |-----------------------------------------------------------------------------| r_work (start): 0.3920 rms_B_bonded: 2.19 r_work: 0.3812 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3668 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7419 moved from start: 0.2490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.126 26677 Z= 0.138 Angle : 0.597 14.969 36189 Z= 0.298 Chirality : 0.041 0.262 4220 Planarity : 0.004 0.057 4402 Dihedral : 9.975 98.336 4035 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 2.63 % Allowed : 15.84 % Favored : 81.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.55 (0.15), residues: 3102 helix: 0.57 (0.13), residues: 1730 sheet: -1.02 (0.34), residues: 241 loop : -1.65 (0.18), residues: 1131 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG A3766 TYR 0.022 0.002 TYR A3491 PHE 0.029 0.002 PHE A3613 TRP 0.025 0.001 TRP A3631 HIS 0.005 0.001 HIS A 944 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.14 (26673) covalent geometry : angle 0.59086 / 0.30 (36183) hydrogen bonds : bond 0.03800 / 2.47 ( 1311) hydrogen bonds : angle 4.56504 / 3.25 ( 3720) metal coordination : bond 0.00589 / 0.29 ( 4) metal coordination : angle 6.92109 / 3.97 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 594 residues out of total 2891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 518 time to evaluate : 0.928 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: A 526 MET cc_start: 0.6918 (tmm) cc_final: 0.6471 (mpp) REVERT: A 543 ASN cc_start: 0.7003 (t0) cc_final: 0.6778 (t0) REVERT: A 567 GLN cc_start: 0.7867 (tm-30) cc_final: 0.7297 (tm-30) REVERT: A 689 ASP cc_start: 0.8095 (t0) cc_final: 0.7629 (t0) REVERT: A 751 ARG cc_start: 0.7511 (mmp80) cc_final: 0.7014 (mmp-170) REVERT: A 753 MET cc_start: 0.6632 (mmm) cc_final: 0.6240 (mmm) REVERT: A 755 ASN cc_start: 0.7202 (t0) cc_final: 0.6879 (m110) REVERT: A 860 ILE cc_start: 0.8121 (mm) cc_final: 0.7816 (mm) REVERT: A 889 PHE cc_start: 0.7218 (t80) cc_final: 0.6995 (t80) REVERT: A 936 GLU cc_start: 0.7852 (mm-30) cc_final: 0.7380 (tm-30) REVERT: A 940 LYS cc_start: 0.8190 (mttt) cc_final: 0.7499 (ttmm) REVERT: A 1021 GLU cc_start: 0.7769 (tp30) cc_final: 0.7488 (tp30) REVERT: A 1026 SER cc_start: 0.8142 (p) cc_final: 0.7681 (t) REVERT: A 1079 CYS cc_start: 0.8101 (t) cc_final: 0.7534 (m) REVERT: A 1119 GLU cc_start: 0.7545 (tp30) cc_final: 0.7121 (tp30) REVERT: A 1129 GLU cc_start: 0.7682 (mt-10) cc_final: 0.7227 (mp0) REVERT: A 1240 GLU cc_start: 0.7763 (mp0) cc_final: 0.7383 (mp0) REVERT: A 1275 ASP cc_start: 0.7807 (m-30) cc_final: 0.7440 (m-30) REVERT: A 1299 GLU cc_start: 0.7911 (mp0) cc_final: 0.7700 (pm20) REVERT: A 1303 GLU cc_start: 0.7915 (tp30) cc_final: 0.7545 (tp30) REVERT: A 1311 THR cc_start: 0.8271 (m) cc_final: 0.7897 (p) REVERT: A 1418 LEU cc_start: 0.8498 (OUTLIER) cc_final: 0.8255 (tt) REVERT: A 1577 VAL cc_start: 0.8522 (t) cc_final: 0.8256 (m) REVERT: A 1590 THR cc_start: 0.8951 (OUTLIER) cc_final: 0.8696 (m) REVERT: A 1643 GLU cc_start: 0.7277 (mm-30) cc_final: 0.6993 (mm-30) REVERT: A 1648 ASN cc_start: 0.8264 (m-40) cc_final: 0.8014 (m-40) REVERT: A 1766 CYS cc_start: 0.8120 (OUTLIER) cc_final: 0.7788 (m) REVERT: A 1833 LYS cc_start: 0.8129 (mttt) cc_final: 0.7758 (mmtm) REVERT: A 1846 LYS cc_start: 0.7812 (tttt) cc_final: 0.7138 (ttmt) REVERT: A 1947 MET cc_start: 0.3632 (mmm) cc_final: 0.3230 (tmm) REVERT: A 2029 GLN cc_start: 0.7840 (pm20) cc_final: 0.7380 (pm20) REVERT: A 2049 GLU cc_start: 0.7463 (mt-10) cc_final: 0.7037 (mt-10) REVERT: A 2206 MET cc_start: 0.6554 (mmm) cc_final: 0.6008 (mmm) REVERT: A 2297 GLU cc_start: 0.7755 (mm-30) cc_final: 0.7514 (mt-10) REVERT: A 2308 SER cc_start: 0.8728 (p) cc_final: 0.8339 (t) REVERT: A 2336 ASP cc_start: 0.7861 (t0) cc_final: 0.7628 (t70) REVERT: A 2340 ILE cc_start: 0.7512 (pp) cc_final: 0.7280 (pt) REVERT: A 2345 ASN cc_start: 0.7540 (t0) cc_final: 0.7229 (t0) REVERT: A 2467 SER cc_start: 0.8634 (t) cc_final: 0.8360 (m) REVERT: A 2543 LYS cc_start: 0.8467 (tttt) cc_final: 0.8224 (tttt) REVERT: A 2676 SER cc_start: 0.8501 (t) cc_final: 0.8136 (m) REVERT: A 2701 ILE cc_start: 0.8629 (mm) cc_final: 0.8271 (mm) REVERT: A 2881 VAL cc_start: 0.8694 (t) cc_final: 0.8470 (t) REVERT: A 2916 GLU cc_start: 0.7089 (tt0) cc_final: 0.6830 (tm-30) REVERT: A 2956 TYR cc_start: 0.7868 (m-80) cc_final: 0.7411 (m-80) REVERT: A 3120 GLU cc_start: 0.8472 (tt0) cc_final: 0.8041 (tp30) REVERT: A 3161 LYS cc_start: 0.7886 (mmtm) cc_final: 0.7685 (mmtm) REVERT: A 3222 PHE cc_start: 0.7959 (t80) cc_final: 0.7715 (t80) REVERT: A 3364 GLU cc_start: 0.7120 (mp0) cc_final: 0.6776 (mp0) REVERT: A 3487 LEU cc_start: 0.6744 (OUTLIER) cc_final: 0.6420 (tp) REVERT: A 3506 LYS cc_start: 0.7729 (tmtt) cc_final: 0.7356 (tmtt) REVERT: A 3715 LYS cc_start: 0.8179 (tppt) cc_final: 0.7765 (tppt) REVERT: A 3796 MET cc_start: 0.5163 (mmm) cc_final: 0.4623 (mmt) REVERT: A 3818 MET cc_start: 0.7218 (mpm) cc_final: 0.6960 (mpm) REVERT: A 3870 MET cc_start: 0.6847 (pmm) cc_final: 0.6311 (ppp) REVERT: A 3883 LEU cc_start: 0.7314 (tp) cc_final: 0.6842 (tm) REVERT: A 3886 MET cc_start: 0.6124 (mtp) cc_final: 0.5856 (mtp) outliers start: 76 outliers final: 32 residues processed: 558 average time/residue: 0.6792 time to fit residues: 438.8632 Evaluate side-chains 537 residues out of total 2891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 501 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 341 MET Chi-restraints excluded: chain A residue 566 SER Chi-restraints excluded: chain A residue 667 GLN Chi-restraints excluded: chain A residue 726 GLU Chi-restraints excluded: chain A residue 818 THR Chi-restraints excluded: chain A residue 913 GLN Chi-restraints excluded: chain A residue 935 LEU Chi-restraints excluded: chain A residue 972 ILE Chi-restraints excluded: chain A residue 1060 ASN Chi-restraints excluded: chain A residue 1124 VAL Chi-restraints excluded: chain A residue 1136 MET Chi-restraints excluded: chain A residue 1366 CYS Chi-restraints excluded: chain A residue 1418 LEU Chi-restraints excluded: chain A residue 1590 THR Chi-restraints excluded: chain A residue 1658 THR Chi-restraints excluded: chain A residue 1667 CYS Chi-restraints excluded: chain A residue 1753 SER Chi-restraints excluded: chain A residue 1766 CYS Chi-restraints excluded: chain A residue 1798 GLU Chi-restraints excluded: chain A residue 2062 GLN Chi-restraints excluded: chain A residue 2577 TYR Chi-restraints excluded: chain A residue 2587 THR Chi-restraints excluded: chain A residue 2661 SER Chi-restraints excluded: chain A residue 2810 LYS Chi-restraints excluded: chain A residue 2817 ASN Chi-restraints excluded: chain A residue 2894 SER Chi-restraints excluded: chain A residue 2943 GLU Chi-restraints excluded: chain A residue 2951 ILE Chi-restraints excluded: chain A residue 3067 LYS Chi-restraints excluded: chain A residue 3307 SER Chi-restraints excluded: chain A residue 3352 ARG Chi-restraints excluded: chain A residue 3375 HIS Chi-restraints excluded: chain A residue 3487 LEU Chi-restraints excluded: chain A residue 3554 LEU Chi-restraints excluded: chain A residue 3681 LEU Chi-restraints excluded: chain A residue 3683 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 114 optimal weight: 1.9990 chunk 63 optimal weight: 0.8980 chunk 282 optimal weight: 0.9990 chunk 126 optimal weight: 3.9990 chunk 276 optimal weight: 0.9980 chunk 117 optimal weight: 2.9990 chunk 216 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 chunk 112 optimal weight: 1.9990 chunk 113 optimal weight: 0.7980 chunk 183 optimal weight: 0.9980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1057 GLN ** A1127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1284 ASN ** A2377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2509 HIS ** A2638 GLN ** 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 = 0.4256 r_free = 0.4256 target = 0.178813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.152701 restraints weight = 38055.296| |-----------------------------------------------------------------------------| r_work (start): 0.3922 rms_B_bonded: 2.07 r_work: 0.3819 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3674 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7413 moved from start: 0.2616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 26677 Z= 0.151 Angle : 0.617 15.207 36189 Z= 0.304 Chirality : 0.041 0.317 4220 Planarity : 0.004 0.069 4402 Dihedral : 9.949 98.866 4035 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 2.11 % Allowed : 17.61 % Favored : 80.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.42 (0.15), residues: 3102 helix: 0.66 (0.13), residues: 1728 sheet: -0.99 (0.35), residues: 232 loop : -1.53 (0.18), residues: 1142 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A1307 TYR 0.027 0.002 TYR A2126 PHE 0.029 0.002 PHE A3613 TRP 0.033 0.002 TRP A3631 HIS 0.005 0.001 HIS A1491 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.15 (26673) covalent geometry : angle 0.61079 / 0.30 (36183) hydrogen bonds : bond 0.03781 / 2.45 ( 1311) hydrogen bonds : angle 4.48217 / 3.20 ( 3720) metal coordination : bond 0.00567 / 0.27 ( 4) metal coordination : angle 6.73529 / 3.88 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 570 residues out of total 2891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 509 time to evaluate : 0.920 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 450 MET cc_start: 0.7458 (ttp) cc_final: 0.7240 (ttp) REVERT: A 468 GLU cc_start: 0.7307 (tp30) cc_final: 0.7106 (tp30) REVERT: A 526 MET cc_start: 0.7003 (tmm) cc_final: 0.6460 (mpp) REVERT: A 567 GLN cc_start: 0.7885 (tm-30) cc_final: 0.7322 (tm-30) REVERT: A 689 ASP cc_start: 0.8041 (t0) cc_final: 0.7581 (t0) REVERT: A 751 ARG cc_start: 0.7515 (mmp80) cc_final: 0.7006 (mmp-170) REVERT: A 753 MET cc_start: 0.6628 (mmm) cc_final: 0.6313 (mmm) REVERT: A 755 ASN cc_start: 0.7284 (t0) cc_final: 0.6942 (m110) REVERT: A 805 GLU cc_start: 0.8222 (pp20) cc_final: 0.7808 (pp20) REVERT: A 889 PHE cc_start: 0.7203 (t80) cc_final: 0.6991 (t80) REVERT: A 936 GLU cc_start: 0.7828 (mm-30) cc_final: 0.7215 (tm-30) REVERT: A 940 LYS cc_start: 0.8204 (mttt) cc_final: 0.7552 (tppt) REVERT: A 1021 GLU cc_start: 0.7794 (tp30) cc_final: 0.7506 (tp30) REVERT: A 1026 SER cc_start: 0.8126 (p) cc_final: 0.7624 (t) REVERT: A 1079 CYS cc_start: 0.8047 (t) cc_final: 0.7506 (m) REVERT: A 1119 GLU cc_start: 0.7434 (tp30) cc_final: 0.6999 (tp30) REVERT: A 1129 GLU cc_start: 0.7719 (mt-10) cc_final: 0.7304 (mp0) REVERT: A 1240 GLU cc_start: 0.7823 (mp0) cc_final: 0.7418 (mp0) REVERT: A 1275 ASP cc_start: 0.7850 (m-30) cc_final: 0.7495 (m-30) REVERT: A 1299 GLU cc_start: 0.7809 (mp0) cc_final: 0.7576 (pm20) REVERT: A 1303 GLU cc_start: 0.7916 (tp30) cc_final: 0.7674 (tp30) REVERT: A 1311 THR cc_start: 0.8222 (m) cc_final: 0.7846 (p) REVERT: A 1418 LEU cc_start: 0.8493 (OUTLIER) cc_final: 0.8283 (tt) REVERT: A 1465 ARG cc_start: 0.8171 (mtm-85) cc_final: 0.7955 (mtm-85) REVERT: A 1555 ASP cc_start: 0.7738 (m-30) cc_final: 0.7439 (m-30) REVERT: A 1577 VAL cc_start: 0.8505 (t) cc_final: 0.8247 (m) REVERT: A 1643 GLU cc_start: 0.7275 (mm-30) cc_final: 0.6986 (mm-30) REVERT: A 1648 ASN cc_start: 0.8269 (m-40) cc_final: 0.8010 (m-40) REVERT: A 1766 CYS cc_start: 0.8122 (OUTLIER) cc_final: 0.7782 (m) REVERT: A 1833 LYS cc_start: 0.8142 (mttt) cc_final: 0.7769 (mmtm) REVERT: A 1846 LYS cc_start: 0.7777 (tttt) cc_final: 0.7259 (ttmt) REVERT: A 1947 MET cc_start: 0.3581 (mmm) cc_final: 0.3186 (tmm) REVERT: A 2029 GLN cc_start: 0.7853 (pm20) cc_final: 0.7380 (pm20) REVERT: A 2049 GLU cc_start: 0.7489 (mt-10) cc_final: 0.7115 (mt-10) REVERT: A 2206 MET cc_start: 0.6564 (mmm) cc_final: 0.6014 (mmm) REVERT: A 2297 GLU cc_start: 0.7709 (mm-30) cc_final: 0.7477 (mt-10) REVERT: A 2308 SER cc_start: 0.8736 (p) cc_final: 0.8337 (t) REVERT: A 2336 ASP cc_start: 0.7882 (t0) cc_final: 0.7640 (t70) REVERT: A 2345 ASN cc_start: 0.7542 (t0) cc_final: 0.7201 (t0) REVERT: A 2397 LEU cc_start: 0.8788 (mt) cc_final: 0.8583 (mp) REVERT: A 2467 SER cc_start: 0.8632 (t) cc_final: 0.8369 (m) REVERT: A 2496 ILE cc_start: 0.8418 (mm) cc_final: 0.8152 (mp) REVERT: A 2543 LYS cc_start: 0.8483 (tttt) cc_final: 0.8239 (tttt) REVERT: A 2579 GLU cc_start: 0.6934 (mt-10) cc_final: 0.6726 (mt-10) REVERT: A 2676 SER cc_start: 0.8554 (t) cc_final: 0.8162 (m) REVERT: A 2701 ILE cc_start: 0.8651 (mm) cc_final: 0.8280 (mm) REVERT: A 2787 ASN cc_start: 0.8145 (t0) cc_final: 0.7853 (t0) REVERT: A 2881 VAL cc_start: 0.8684 (t) cc_final: 0.8455 (t) REVERT: A 2912 VAL cc_start: 0.8333 (m) cc_final: 0.8120 (p) REVERT: A 2956 TYR cc_start: 0.7876 (m-80) cc_final: 0.7341 (m-80) REVERT: A 3157 SER cc_start: 0.8675 (m) cc_final: 0.7930 (p) REVERT: A 3161 LYS cc_start: 0.7893 (mmtm) cc_final: 0.7431 (mptt) REVERT: A 3203 MET cc_start: 0.6498 (ttm) cc_final: 0.6065 (tpp) REVERT: A 3222 PHE cc_start: 0.7997 (t80) cc_final: 0.7745 (t80) REVERT: A 3241 LYS cc_start: 0.8142 (mttt) cc_final: 0.7779 (mttm) REVERT: A 3364 GLU cc_start: 0.7119 (mp0) cc_final: 0.6796 (mp0) REVERT: A 3506 LYS cc_start: 0.7695 (tmtt) cc_final: 0.7283 (tmtt) REVERT: A 3715 LYS cc_start: 0.8212 (tppt) cc_final: 0.7800 (tppt) REVERT: A 3766 ARG cc_start: 0.6452 (tpp-160) cc_final: 0.6224 (tpp-160) REVERT: A 3796 MET cc_start: 0.5131 (mmm) cc_final: 0.4596 (mmt) REVERT: A 3818 MET cc_start: 0.7328 (mpm) cc_final: 0.7076 (mpm) REVERT: A 3870 MET cc_start: 0.6932 (pmm) cc_final: 0.6431 (ppp) REVERT: A 3883 LEU cc_start: 0.7327 (tp) cc_final: 0.6854 (tm) REVERT: A 3886 MET cc_start: 0.6075 (mtp) cc_final: 0.5829 (mtp) outliers start: 61 outliers final: 38 residues processed: 540 average time/residue: 0.6638 time to fit residues: 415.9965 Evaluate side-chains 533 residues out of total 2891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 493 time to evaluate : 0.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 341 MET Chi-restraints excluded: chain A residue 726 GLU Chi-restraints excluded: chain A residue 866 SER Chi-restraints excluded: chain A residue 913 GLN Chi-restraints excluded: chain A residue 929 VAL Chi-restraints excluded: chain A residue 935 LEU Chi-restraints excluded: chain A residue 956 THR Chi-restraints excluded: chain A residue 972 ILE Chi-restraints excluded: chain A residue 999 LYS Chi-restraints excluded: chain A residue 1025 SER Chi-restraints excluded: chain A residue 1052 LEU Chi-restraints excluded: chain A residue 1060 ASN Chi-restraints excluded: chain A residue 1144 ILE Chi-restraints excluded: chain A residue 1366 CYS Chi-restraints excluded: chain A residue 1407 LEU Chi-restraints excluded: chain A residue 1418 LEU Chi-restraints excluded: chain A residue 1602 ASN Chi-restraints excluded: chain A residue 1658 THR Chi-restraints excluded: chain A residue 1667 CYS Chi-restraints excluded: chain A residue 1753 SER Chi-restraints excluded: chain A residue 1766 CYS Chi-restraints excluded: chain A residue 1798 GLU Chi-restraints excluded: chain A residue 2024 TYR Chi-restraints excluded: chain A residue 2062 GLN Chi-restraints excluded: chain A residue 2248 MET Chi-restraints excluded: chain A residue 2525 VAL Chi-restraints excluded: chain A residue 2587 THR Chi-restraints excluded: chain A residue 2661 SER Chi-restraints excluded: chain A residue 2817 ASN Chi-restraints excluded: chain A residue 2859 ILE Chi-restraints excluded: chain A residue 2894 SER Chi-restraints excluded: chain A residue 2943 GLU Chi-restraints excluded: chain A residue 2951 ILE Chi-restraints excluded: chain A residue 3067 LYS Chi-restraints excluded: chain A residue 3271 VAL Chi-restraints excluded: chain A residue 3352 ARG Chi-restraints excluded: chain A residue 3375 HIS Chi-restraints excluded: chain A residue 3554 LEU Chi-restraints excluded: chain A residue 3681 LEU Chi-restraints excluded: chain A residue 3683 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 313 optimal weight: 0.9990 chunk 242 optimal weight: 2.9990 chunk 49 optimal weight: 0.5980 chunk 272 optimal weight: 6.9990 chunk 291 optimal weight: 0.9990 chunk 276 optimal weight: 3.9990 chunk 12 optimal weight: 10.0000 chunk 93 optimal weight: 1.9990 chunk 201 optimal weight: 0.9980 chunk 129 optimal weight: 5.9990 chunk 66 optimal weight: 3.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1002 HIS A1057 GLN ** A1127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1284 ASN ** A2377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2509 HIS ** A2638 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2776 GLN A3098 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.178550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.152282 restraints weight = 37739.138| |-----------------------------------------------------------------------------| r_work (start): 0.3914 rms_B_bonded: 2.07 r_work: 0.3811 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3668 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7420 moved from start: 0.2719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 26677 Z= 0.162 Angle : 0.623 15.530 36189 Z= 0.308 Chirality : 0.041 0.353 4220 Planarity : 0.004 0.054 4402 Dihedral : 9.947 99.741 4035 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 2.53 % Allowed : 17.81 % Favored : 79.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.38 (0.15), residues: 3102 helix: 0.69 (0.13), residues: 1730 sheet: -1.04 (0.35), residues: 235 loop : -1.50 (0.18), residues: 1137 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 896 TYR 0.024 0.002 TYR A3337 PHE 0.027 0.002 PHE A3538 TRP 0.035 0.002 TRP A3631 HIS 0.005 0.001 HIS A2470 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.16 (26673) covalent geometry : angle 0.61741 / 0.31 (36183) hydrogen bonds : bond 0.03787 / 2.45 ( 1311) hydrogen bonds : angle 4.47528 / 3.18 ( 3720) metal coordination : bond 0.00567 / 0.27 ( 4) metal coordination : angle 6.70672 / 3.88 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 583 residues out of total 2891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 510 time to evaluate : 1.020 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: A 353 MET cc_start: 0.7647 (pmm) cc_final: 0.7355 (ppp) REVERT: A 468 GLU cc_start: 0.7318 (tp30) cc_final: 0.7111 (tp30) REVERT: A 526 MET cc_start: 0.6979 (tmm) cc_final: 0.6465 (mpt) REVERT: A 567 GLN cc_start: 0.7897 (tm-30) cc_final: 0.7321 (tm-30) REVERT: A 689 ASP cc_start: 0.8078 (t0) cc_final: 0.7609 (t0) REVERT: A 751 ARG cc_start: 0.7577 (mmp80) cc_final: 0.7257 (mmp-170) REVERT: A 753 MET cc_start: 0.6661 (mmm) cc_final: 0.6413 (mmm) REVERT: A 805 GLU cc_start: 0.8240 (pp20) cc_final: 0.7777 (pp20) REVERT: A 889 PHE cc_start: 0.7219 (t80) cc_final: 0.7000 (t80) REVERT: A 936 GLU cc_start: 0.7828 (mm-30) cc_final: 0.7196 (tm-30) REVERT: A 940 LYS cc_start: 0.8190 (mttt) cc_final: 0.7530 (tppt) REVERT: A 1026 SER cc_start: 0.8118 (p) cc_final: 0.7610 (t) REVERT: A 1079 CYS cc_start: 0.8017 (t) cc_final: 0.7480 (m) REVERT: A 1129 GLU cc_start: 0.7715 (mt-10) cc_final: 0.7315 (mp0) REVERT: A 1240 GLU cc_start: 0.7821 (mp0) cc_final: 0.7405 (mp0) REVERT: A 1275 ASP cc_start: 0.7883 (m-30) cc_final: 0.7565 (m-30) REVERT: A 1299 GLU cc_start: 0.7787 (mp0) cc_final: 0.7576 (pm20) REVERT: A 1303 GLU cc_start: 0.7919 (tp30) cc_final: 0.7232 (tp30) REVERT: A 1311 THR cc_start: 0.8237 (m) cc_final: 0.7864 (p) REVERT: A 1418 LEU cc_start: 0.8537 (pp) cc_final: 0.8299 (tt) REVERT: A 1577 VAL cc_start: 0.8511 (t) cc_final: 0.8239 (m) REVERT: A 1643 GLU cc_start: 0.7270 (mm-30) cc_final: 0.6988 (mm-30) REVERT: A 1648 ASN cc_start: 0.8261 (m-40) cc_final: 0.8001 (m-40) REVERT: A 1766 CYS cc_start: 0.8117 (OUTLIER) cc_final: 0.7758 (m) REVERT: A 1833 LYS cc_start: 0.8165 (mttt) cc_final: 0.7786 (mmtm) REVERT: A 1846 LYS cc_start: 0.7787 (tttt) cc_final: 0.7279 (ttmt) REVERT: A 1947 MET cc_start: 0.3557 (mmm) cc_final: 0.3195 (tmm) REVERT: A 2029 GLN cc_start: 0.7791 (pm20) cc_final: 0.7327 (pm20) REVERT: A 2049 GLU cc_start: 0.7507 (mt-10) cc_final: 0.7121 (mt-10) REVERT: A 2206 MET cc_start: 0.6563 (mmm) cc_final: 0.6013 (mmm) REVERT: A 2229 ARG cc_start: 0.8439 (ptp-110) cc_final: 0.8203 (ptp-110) REVERT: A 2297 GLU cc_start: 0.7701 (mm-30) cc_final: 0.7458 (mt-10) REVERT: A 2308 SER cc_start: 0.8735 (p) cc_final: 0.8333 (t) REVERT: A 2336 ASP cc_start: 0.7880 (t0) cc_final: 0.7641 (t70) REVERT: A 2345 ASN cc_start: 0.7577 (t0) cc_final: 0.7129 (t0) REVERT: A 2467 SER cc_start: 0.8636 (t) cc_final: 0.8378 (m) REVERT: A 2543 LYS cc_start: 0.8463 (tttt) cc_final: 0.8220 (tttt) REVERT: A 2676 SER cc_start: 0.8587 (t) cc_final: 0.8192 (m) REVERT: A 2701 ILE cc_start: 0.8662 (mm) cc_final: 0.8283 (mm) REVERT: A 2748 LEU cc_start: 0.8619 (OUTLIER) cc_final: 0.8316 (mt) REVERT: A 2787 ASN cc_start: 0.8168 (t0) cc_final: 0.7875 (t0) REVERT: A 2881 VAL cc_start: 0.8740 (t) cc_final: 0.8515 (t) REVERT: A 2912 VAL cc_start: 0.8326 (m) cc_final: 0.8112 (p) REVERT: A 2956 TYR cc_start: 0.7908 (m-80) cc_final: 0.7373 (m-80) REVERT: A 3157 SER cc_start: 0.8690 (m) cc_final: 0.7965 (p) REVERT: A 3161 LYS cc_start: 0.7909 (mmtm) cc_final: 0.7479 (mptt) REVERT: A 3203 MET cc_start: 0.6522 (ttm) cc_final: 0.6070 (tpp) REVERT: A 3222 PHE cc_start: 0.7974 (t80) cc_final: 0.7733 (t80) REVERT: A 3364 GLU cc_start: 0.7130 (mp0) cc_final: 0.6797 (mp0) REVERT: A 3446 LYS cc_start: 0.6781 (tttm) cc_final: 0.6528 (ttpp) REVERT: A 3506 LYS cc_start: 0.7699 (tmtt) cc_final: 0.7272 (tmtt) REVERT: A 3715 LYS cc_start: 0.8214 (tppt) cc_final: 0.7790 (tppt) REVERT: A 3796 MET cc_start: 0.5154 (mmm) cc_final: 0.4629 (mmt) REVERT: A 3818 MET cc_start: 0.7348 (mpm) cc_final: 0.7125 (mpm) REVERT: A 3837 MET cc_start: 0.7298 (tpp) cc_final: 0.6903 (tpp) REVERT: A 3870 MET cc_start: 0.6886 (pmm) cc_final: 0.6408 (ppp) REVERT: A 3883 LEU cc_start: 0.7311 (tp) cc_final: 0.6831 (tm) outliers start: 73 outliers final: 43 residues processed: 544 average time/residue: 0.6365 time to fit residues: 403.9270 Evaluate side-chains 544 residues out of total 2891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 499 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 341 MET Chi-restraints excluded: chain A residue 575 LEU Chi-restraints excluded: chain A residue 726 GLU Chi-restraints excluded: chain A residue 818 THR Chi-restraints excluded: chain A residue 866 SER Chi-restraints excluded: chain A residue 891 PHE Chi-restraints excluded: chain A residue 913 GLN Chi-restraints excluded: chain A residue 929 VAL Chi-restraints excluded: chain A residue 935 LEU Chi-restraints excluded: chain A residue 956 THR Chi-restraints excluded: chain A residue 972 ILE Chi-restraints excluded: chain A residue 999 LYS Chi-restraints excluded: chain A residue 1060 ASN Chi-restraints excluded: chain A residue 1124 VAL Chi-restraints excluded: chain A residue 1136 MET Chi-restraints excluded: chain A residue 1144 ILE Chi-restraints excluded: chain A residue 1366 CYS Chi-restraints excluded: chain A residue 1407 LEU Chi-restraints excluded: chain A residue 1529 MET Chi-restraints excluded: chain A residue 1602 ASN Chi-restraints excluded: chain A residue 1658 THR Chi-restraints excluded: chain A residue 1667 CYS Chi-restraints excluded: chain A residue 1753 SER Chi-restraints excluded: chain A residue 1763 LEU Chi-restraints excluded: chain A residue 1766 CYS Chi-restraints excluded: chain A residue 1798 GLU Chi-restraints excluded: chain A residue 1812 SER Chi-restraints excluded: chain A residue 1823 VAL Chi-restraints excluded: chain A residue 2024 TYR Chi-restraints excluded: chain A residue 2062 GLN Chi-restraints excluded: chain A residue 2525 VAL Chi-restraints excluded: chain A residue 2587 THR Chi-restraints excluded: chain A residue 2661 SER Chi-restraints excluded: chain A residue 2748 LEU Chi-restraints excluded: chain A residue 2768 SER Chi-restraints excluded: chain A residue 2894 SER Chi-restraints excluded: chain A residue 2943 GLU Chi-restraints excluded: chain A residue 2951 ILE Chi-restraints excluded: chain A residue 3067 LYS Chi-restraints excluded: chain A residue 3139 MET Chi-restraints excluded: chain A residue 3271 VAL Chi-restraints excluded: chain A residue 3352 ARG Chi-restraints excluded: chain A residue 3554 LEU Chi-restraints excluded: chain A residue 3681 LEU Chi-restraints excluded: chain A residue 3683 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 217 optimal weight: 2.9990 chunk 264 optimal weight: 0.8980 chunk 95 optimal weight: 0.9980 chunk 147 optimal weight: 6.9990 chunk 128 optimal weight: 5.9990 chunk 256 optimal weight: 0.0170 chunk 66 optimal weight: 2.9990 chunk 223 optimal weight: 4.9990 chunk 175 optimal weight: 0.0970 chunk 303 optimal weight: 3.9990 chunk 248 optimal weight: 0.0870 overall best weight: 0.4194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1002 HIS A1057 GLN ** A1127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1284 ASN A1514 ASN ** A2377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2509 HIS ** A2638 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3098 GLN A3410 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.180897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.154634 restraints weight = 38174.649| |-----------------------------------------------------------------------------| r_work (start): 0.3944 rms_B_bonded: 2.20 r_work: 0.3837 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3689 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7384 moved from start: 0.2819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 26677 Z= 0.118 Angle : 0.620 15.572 36189 Z= 0.301 Chirality : 0.040 0.357 4220 Planarity : 0.004 0.052 4402 Dihedral : 9.852 100.399 4035 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 2.08 % Allowed : 18.54 % Favored : 79.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.15), residues: 3102 helix: 0.86 (0.13), residues: 1730 sheet: -1.14 (0.34), residues: 241 loop : -1.40 (0.19), residues: 1131 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 896 TYR 0.025 0.002 TYR A 576 PHE 0.028 0.002 PHE A3753 TRP 0.036 0.001 TRP A3631 HIS 0.004 0.001 HIS A2509 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 (26673) covalent geometry : angle 0.61487 / 0.30 (36183) hydrogen bonds : bond 0.03427 / 2.23 ( 1311) hydrogen bonds : angle 4.32621 / 3.08 ( 3720) metal coordination : bond 0.00563 / 0.28 ( 4) metal coordination : angle 6.02923 / 3.47 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 562 residues out of total 2891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 502 time to evaluate : 0.920 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 353 MET cc_start: 0.7648 (pmm) cc_final: 0.7415 (ppp) REVERT: A 468 GLU cc_start: 0.7242 (tp30) cc_final: 0.7013 (tp30) REVERT: A 526 MET cc_start: 0.6922 (tmm) cc_final: 0.6265 (mpt) REVERT: A 567 GLN cc_start: 0.7937 (tm-30) cc_final: 0.7356 (tm-30) REVERT: A 689 ASP cc_start: 0.7973 (t0) cc_final: 0.7557 (t70) REVERT: A 694 PHE cc_start: 0.7545 (m-10) cc_final: 0.7214 (m-80) REVERT: A 751 ARG cc_start: 0.7551 (mmp80) cc_final: 0.7242 (mmp-170) REVERT: A 805 GLU cc_start: 0.8218 (pp20) cc_final: 0.7721 (pp20) REVERT: A 936 GLU cc_start: 0.7832 (mm-30) cc_final: 0.7118 (tm-30) REVERT: A 940 LYS cc_start: 0.8239 (mttt) cc_final: 0.7506 (tppt) REVERT: A 1021 GLU cc_start: 0.7787 (tp30) cc_final: 0.7407 (tp30) REVERT: A 1024 LYS cc_start: 0.8768 (mtmt) cc_final: 0.8370 (ttmt) REVERT: A 1026 SER cc_start: 0.8069 (p) cc_final: 0.7615 (t) REVERT: A 1079 CYS cc_start: 0.8041 (t) cc_final: 0.7763 (t) REVERT: A 1129 GLU cc_start: 0.7669 (mt-10) cc_final: 0.7271 (mp0) REVERT: A 1240 GLU cc_start: 0.7834 (mp0) cc_final: 0.7376 (mp0) REVERT: A 1275 ASP cc_start: 0.7873 (m-30) cc_final: 0.7479 (m-30) REVERT: A 1299 GLU cc_start: 0.7763 (mp0) cc_final: 0.7516 (pm20) REVERT: A 1303 GLU cc_start: 0.7938 (tp30) cc_final: 0.7698 (tp30) REVERT: A 1311 THR cc_start: 0.8160 (m) cc_final: 0.7776 (p) REVERT: A 1418 LEU cc_start: 0.8511 (pp) cc_final: 0.8244 (tt) REVERT: A 1489 ARG cc_start: 0.7915 (ttp-170) cc_final: 0.7709 (ttt-90) REVERT: A 1541 GLU cc_start: 0.7411 (mm-30) cc_final: 0.7164 (mm-30) REVERT: A 1555 ASP cc_start: 0.7798 (m-30) cc_final: 0.7577 (m-30) REVERT: A 1576 ASN cc_start: 0.8466 (m-40) cc_final: 0.8250 (m110) REVERT: A 1577 VAL cc_start: 0.8508 (t) cc_final: 0.8252 (m) REVERT: A 1643 GLU cc_start: 0.7275 (mm-30) cc_final: 0.6958 (mm-30) REVERT: A 1648 ASN cc_start: 0.8231 (m-40) cc_final: 0.7997 (m-40) REVERT: A 1766 CYS cc_start: 0.8129 (OUTLIER) cc_final: 0.7787 (m) REVERT: A 1831 MET cc_start: 0.7845 (mmm) cc_final: 0.7487 (mmm) REVERT: A 1833 LYS cc_start: 0.8119 (mttt) cc_final: 0.7729 (mmtm) REVERT: A 1846 LYS cc_start: 0.7780 (tttt) cc_final: 0.7260 (ttmt) REVERT: A 1947 MET cc_start: 0.3655 (mmm) cc_final: 0.3314 (tmm) REVERT: A 2029 GLN cc_start: 0.7750 (pm20) cc_final: 0.7274 (pm20) REVERT: A 2049 GLU cc_start: 0.7540 (mt-10) cc_final: 0.7136 (mt-10) REVERT: A 2206 MET cc_start: 0.6546 (mmm) cc_final: 0.5992 (mmm) REVERT: A 2231 VAL cc_start: 0.8818 (t) cc_final: 0.8543 (m) REVERT: A 2297 GLU cc_start: 0.7688 (mm-30) cc_final: 0.7444 (mt-10) REVERT: A 2308 SER cc_start: 0.8810 (p) cc_final: 0.8380 (t) REVERT: A 2336 ASP cc_start: 0.7905 (t0) cc_final: 0.7641 (t70) REVERT: A 2345 ASN cc_start: 0.7602 (t0) cc_final: 0.7226 (t0) REVERT: A 2397 LEU cc_start: 0.8792 (mt) cc_final: 0.8568 (mp) REVERT: A 2467 SER cc_start: 0.8616 (t) cc_final: 0.8404 (m) REVERT: A 2493 GLU cc_start: 0.7660 (tp30) cc_final: 0.7441 (tp30) REVERT: A 2543 LYS cc_start: 0.8451 (tttt) cc_final: 0.8186 (tmmm) REVERT: A 2676 SER cc_start: 0.8598 (t) cc_final: 0.8159 (m) REVERT: A 2787 ASN cc_start: 0.8115 (t0) cc_final: 0.7854 (t0) REVERT: A 2881 VAL cc_start: 0.8630 (t) cc_final: 0.8417 (t) REVERT: A 2912 VAL cc_start: 0.8233 (m) cc_final: 0.8009 (p) REVERT: A 2921 VAL cc_start: 0.8488 (t) cc_final: 0.8225 (m) REVERT: A 2956 TYR cc_start: 0.7877 (m-80) cc_final: 0.7356 (m-80) REVERT: A 3132 LEU cc_start: 0.7531 (mm) cc_final: 0.7288 (mm) REVERT: A 3157 SER cc_start: 0.8653 (m) cc_final: 0.7917 (p) REVERT: A 3161 LYS cc_start: 0.7842 (mmtm) cc_final: 0.7406 (mptt) REVERT: A 3203 MET cc_start: 0.6515 (ttm) cc_final: 0.5947 (ttt) REVERT: A 3222 PHE cc_start: 0.7960 (t80) cc_final: 0.7757 (t80) REVERT: A 3364 GLU cc_start: 0.7077 (mp0) cc_final: 0.6710 (mp0) REVERT: A 3487 LEU cc_start: 0.7349 (OUTLIER) cc_final: 0.7033 (tp) REVERT: A 3506 LYS cc_start: 0.7680 (tmtt) cc_final: 0.7250 (tmtt) REVERT: A 3715 LYS cc_start: 0.8218 (tppt) cc_final: 0.7855 (tppt) REVERT: A 3796 MET cc_start: 0.5116 (mmm) cc_final: 0.4604 (mmt) REVERT: A 3818 MET cc_start: 0.7354 (mpm) cc_final: 0.7100 (mpm) REVERT: A 3870 MET cc_start: 0.6964 (pmm) cc_final: 0.6463 (ppp) outliers start: 60 outliers final: 33 residues processed: 536 average time/residue: 0.6666 time to fit residues: 414.5795 Evaluate side-chains 521 residues out of total 2891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 486 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 341 MET Chi-restraints excluded: chain A residue 575 LEU Chi-restraints excluded: chain A residue 726 GLU Chi-restraints excluded: chain A residue 891 PHE Chi-restraints excluded: chain A residue 913 GLN Chi-restraints excluded: chain A residue 929 VAL Chi-restraints excluded: chain A residue 935 LEU Chi-restraints excluded: chain A residue 956 THR Chi-restraints excluded: chain A residue 999 LYS Chi-restraints excluded: chain A residue 1124 VAL Chi-restraints excluded: chain A residue 1326 VAL Chi-restraints excluded: chain A residue 1366 CYS Chi-restraints excluded: chain A residue 1529 MET Chi-restraints excluded: chain A residue 1602 ASN Chi-restraints excluded: chain A residue 1658 THR Chi-restraints excluded: chain A residue 1667 CYS Chi-restraints excluded: chain A residue 1753 SER Chi-restraints excluded: chain A residue 1766 CYS Chi-restraints excluded: chain A residue 1812 SER Chi-restraints excluded: chain A residue 1823 VAL Chi-restraints excluded: chain A residue 2024 TYR Chi-restraints excluded: chain A residue 2062 GLN Chi-restraints excluded: chain A residue 2577 TYR Chi-restraints excluded: chain A residue 2661 SER Chi-restraints excluded: chain A residue 2894 SER Chi-restraints excluded: chain A residue 2943 GLU Chi-restraints excluded: chain A residue 2951 ILE Chi-restraints excluded: chain A residue 3067 LYS Chi-restraints excluded: chain A residue 3139 MET Chi-restraints excluded: chain A residue 3175 SER Chi-restraints excluded: chain A residue 3271 VAL Chi-restraints excluded: chain A residue 3352 ARG Chi-restraints excluded: chain A residue 3470 VAL Chi-restraints excluded: chain A residue 3487 LEU Chi-restraints excluded: chain A residue 3683 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 157 optimal weight: 0.0970 chunk 244 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 6 optimal weight: 0.9980 chunk 18 optimal weight: 0.6980 chunk 266 optimal weight: 0.8980 chunk 214 optimal weight: 2.9990 chunk 277 optimal weight: 5.9990 chunk 112 optimal weight: 0.4980 chunk 23 optimal weight: 0.0670 chunk 40 optimal weight: 0.3980 overall best weight: 0.3516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 543 ASN A1002 HIS A1057 GLN ** A1127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1284 ASN ** A2377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2509 HIS A2607 GLN ** A2638 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3410 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.182381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.156311 restraints weight = 38234.011| |-----------------------------------------------------------------------------| r_work (start): 0.3951 rms_B_bonded: 2.19 r_work: 0.3841 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3696 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7363 moved from start: 0.2920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 26677 Z= 0.114 Angle : 0.624 15.716 36189 Z= 0.302 Chirality : 0.040 0.346 4220 Planarity : 0.004 0.053 4402 Dihedral : 9.801 101.227 4035 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 1.76 % Allowed : 19.65 % Favored : 78.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.13 (0.15), residues: 3102 helix: 0.93 (0.13), residues: 1729 sheet: -1.19 (0.34), residues: 234 loop : -1.38 (0.19), residues: 1139 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG A1805 TYR 0.025 0.001 TYR A 576 PHE 0.029 0.002 PHE A3613 TRP 0.035 0.001 TRP A3631 HIS 0.005 0.001 HIS A2509 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.11 (26673) covalent geometry : angle 0.61929 / 0.30 (36183) hydrogen bonds : bond 0.03355 / 2.18 ( 1311) hydrogen bonds : angle 4.26302 / 3.03 ( 3720) metal coordination : bond 0.00573 / 0.28 ( 4) metal coordination : angle 5.75155 / 3.32 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 548 residues out of total 2891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 497 time to evaluate : 1.056 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 353 MET cc_start: 0.7679 (pmm) cc_final: 0.7450 (ppp) REVERT: A 468 GLU cc_start: 0.7257 (tp30) cc_final: 0.7021 (tp30) REVERT: A 526 MET cc_start: 0.6902 (tmm) cc_final: 0.6156 (mpt) REVERT: A 567 GLN cc_start: 0.7970 (tm-30) cc_final: 0.7347 (tm-30) REVERT: A 689 ASP cc_start: 0.7929 (t0) cc_final: 0.7491 (t70) REVERT: A 694 PHE cc_start: 0.7518 (m-10) cc_final: 0.7282 (m-80) REVERT: A 699 LYS cc_start: 0.7585 (mttt) cc_final: 0.6928 (mmmt) REVERT: A 751 ARG cc_start: 0.7564 (mmp80) cc_final: 0.7200 (mmm160) REVERT: A 805 GLU cc_start: 0.8175 (pp20) cc_final: 0.7804 (pp20) REVERT: A 940 LYS cc_start: 0.8270 (mttt) cc_final: 0.7928 (tppt) REVERT: A 1026 SER cc_start: 0.8117 (p) cc_final: 0.7664 (t) REVERT: A 1079 CYS cc_start: 0.8069 (t) cc_final: 0.7782 (t) REVERT: A 1129 GLU cc_start: 0.7651 (mt-10) cc_final: 0.7255 (mp0) REVERT: A 1240 GLU cc_start: 0.7812 (mp0) cc_final: 0.7387 (mp0) REVERT: A 1275 ASP cc_start: 0.7814 (m-30) cc_final: 0.7412 (m-30) REVERT: A 1292 VAL cc_start: 0.7035 (p) cc_final: 0.6805 (t) REVERT: A 1299 GLU cc_start: 0.7709 (mp0) cc_final: 0.7466 (pm20) REVERT: A 1303 GLU cc_start: 0.7959 (tp30) cc_final: 0.7698 (tp30) REVERT: A 1311 THR cc_start: 0.8100 (m) cc_final: 0.7698 (p) REVERT: A 1418 LEU cc_start: 0.8544 (pp) cc_final: 0.8235 (tt) REVERT: A 1555 ASP cc_start: 0.7797 (m-30) cc_final: 0.7545 (m-30) REVERT: A 1576 ASN cc_start: 0.8457 (m-40) cc_final: 0.8232 (m110) REVERT: A 1643 GLU cc_start: 0.7332 (mm-30) cc_final: 0.6975 (mm-30) REVERT: A 1648 ASN cc_start: 0.8194 (m-40) cc_final: 0.7981 (m-40) REVERT: A 1766 CYS cc_start: 0.8139 (OUTLIER) cc_final: 0.7825 (m) REVERT: A 1831 MET cc_start: 0.7792 (mmm) cc_final: 0.7546 (mmm) REVERT: A 1833 LYS cc_start: 0.8095 (mttt) cc_final: 0.7691 (mmtm) REVERT: A 1846 LYS cc_start: 0.7723 (tttt) cc_final: 0.7090 (ttmt) REVERT: A 1947 MET cc_start: 0.3563 (mmm) cc_final: 0.3243 (tmm) REVERT: A 2029 GLN cc_start: 0.7755 (pm20) cc_final: 0.7314 (pm20) REVERT: A 2049 GLU cc_start: 0.7548 (mt-10) cc_final: 0.7193 (mt-10) REVERT: A 2206 MET cc_start: 0.6545 (mmm) cc_final: 0.6010 (mmm) REVERT: A 2231 VAL cc_start: 0.8779 (t) cc_final: 0.8469 (m) REVERT: A 2297 GLU cc_start: 0.7642 (mm-30) cc_final: 0.7398 (mt-10) REVERT: A 2308 SER cc_start: 0.8701 (p) cc_final: 0.8268 (t) REVERT: A 2336 ASP cc_start: 0.7946 (t0) cc_final: 0.7644 (t70) REVERT: A 2397 LEU cc_start: 0.8767 (mt) cc_final: 0.8507 (mp) REVERT: A 2525 VAL cc_start: 0.8361 (t) cc_final: 0.7969 (p) REVERT: A 2543 LYS cc_start: 0.8448 (tttt) cc_final: 0.8189 (tttt) REVERT: A 2676 SER cc_start: 0.8636 (t) cc_final: 0.8214 (m) REVERT: A 2787 ASN cc_start: 0.8074 (t0) cc_final: 0.7846 (t0) REVERT: A 2881 VAL cc_start: 0.8587 (t) cc_final: 0.8368 (t) REVERT: A 2921 VAL cc_start: 0.8479 (t) cc_final: 0.8199 (m) REVERT: A 2956 TYR cc_start: 0.7855 (m-80) cc_final: 0.7411 (m-80) REVERT: A 2999 ASP cc_start: 0.7320 (m-30) cc_final: 0.7078 (m-30) REVERT: A 3132 LEU cc_start: 0.7532 (mm) cc_final: 0.7297 (mm) REVERT: A 3157 SER cc_start: 0.8636 (m) cc_final: 0.7909 (p) REVERT: A 3161 LYS cc_start: 0.7804 (mmtm) cc_final: 0.7368 (mptt) REVERT: A 3203 MET cc_start: 0.6524 (ttm) cc_final: 0.5938 (ttt) REVERT: A 3364 GLU cc_start: 0.7095 (mp0) cc_final: 0.6720 (mp0) REVERT: A 3487 LEU cc_start: 0.7208 (OUTLIER) cc_final: 0.6824 (tp) REVERT: A 3506 LYS cc_start: 0.7635 (tmtt) cc_final: 0.7233 (tmtt) REVERT: A 3530 LYS cc_start: 0.7170 (tppt) cc_final: 0.6640 (mppt) REVERT: A 3715 LYS cc_start: 0.8215 (tppt) cc_final: 0.7788 (tppt) REVERT: A 3796 MET cc_start: 0.5125 (mmm) cc_final: 0.4613 (mmt) REVERT: A 3818 MET cc_start: 0.7271 (mpm) cc_final: 0.6805 (mpm) REVERT: A 3870 MET cc_start: 0.6896 (pmm) cc_final: 0.6434 (ppp) outliers start: 51 outliers final: 30 residues processed: 523 average time/residue: 0.6557 time to fit residues: 397.7768 Evaluate side-chains 508 residues out of total 2891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 476 time to evaluate : 0.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 341 MET Chi-restraints excluded: chain A residue 575 LEU Chi-restraints excluded: chain A residue 726 GLU Chi-restraints excluded: chain A residue 891 PHE Chi-restraints excluded: chain A residue 913 GLN Chi-restraints excluded: chain A residue 929 VAL Chi-restraints excluded: chain A residue 935 LEU Chi-restraints excluded: chain A residue 956 THR Chi-restraints excluded: chain A residue 999 LYS Chi-restraints excluded: chain A residue 1124 VAL Chi-restraints excluded: chain A residue 1326 VAL Chi-restraints excluded: chain A residue 1366 CYS Chi-restraints excluded: chain A residue 1529 MET Chi-restraints excluded: chain A residue 1602 ASN Chi-restraints excluded: chain A residue 1658 THR Chi-restraints excluded: chain A residue 1667 CYS Chi-restraints excluded: chain A residue 1753 SER Chi-restraints excluded: chain A residue 1766 CYS Chi-restraints excluded: chain A residue 2024 TYR Chi-restraints excluded: chain A residue 2062 GLN Chi-restraints excluded: chain A residue 2599 ILE Chi-restraints excluded: chain A residue 2661 SER Chi-restraints excluded: chain A residue 2894 SER Chi-restraints excluded: chain A residue 2943 GLU Chi-restraints excluded: chain A residue 2951 ILE Chi-restraints excluded: chain A residue 3139 MET Chi-restraints excluded: chain A residue 3175 SER Chi-restraints excluded: chain A residue 3271 VAL Chi-restraints excluded: chain A residue 3307 SER Chi-restraints excluded: chain A residue 3470 VAL Chi-restraints excluded: chain A residue 3487 LEU Chi-restraints excluded: chain A residue 3683 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 92 optimal weight: 0.9990 chunk 177 optimal weight: 3.9990 chunk 117 optimal weight: 0.6980 chunk 73 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 7 optimal weight: 10.0000 chunk 190 optimal weight: 0.5980 chunk 56 optimal weight: 0.8980 chunk 125 optimal weight: 0.0050 chunk 296 optimal weight: 0.9990 chunk 78 optimal weight: 5.9990 overall best weight: 0.6396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 543 ASN A1002 HIS A1057 GLN ** A1127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1284 ASN ** A2377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2509 HIS A2607 GLN ** A2638 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3410 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.181106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.154906 restraints weight = 38169.745| |-----------------------------------------------------------------------------| r_work (start): 0.3944 rms_B_bonded: 2.18 r_work: 0.3836 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3689 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7379 moved from start: 0.2979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 26677 Z= 0.129 Angle : 0.646 15.826 36189 Z= 0.313 Chirality : 0.041 0.335 4220 Planarity : 0.004 0.061 4402 Dihedral : 9.810 101.823 4035 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 1.42 % Allowed : 20.44 % Favored : 78.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.15), residues: 3102 helix: 0.88 (0.13), residues: 1749 sheet: -1.15 (0.35), residues: 233 loop : -1.37 (0.19), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A1805 TYR 0.023 0.002 TYR A 576 PHE 0.025 0.002 PHE A1966 TRP 0.034 0.001 TRP A2444 HIS 0.005 0.001 HIS A 944 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 (26673) covalent geometry : angle 0.64159 / 0.31 (36183) hydrogen bonds : bond 0.03427 / 2.24 ( 1311) hydrogen bonds : angle 4.27483 / 3.04 ( 3720) metal coordination : bond 0.00529 / 0.26 ( 4) metal coordination : angle 5.71713 / 3.32 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 528 residues out of total 2891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 487 time to evaluate : 1.028 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 353 MET cc_start: 0.7659 (pmm) cc_final: 0.7430 (ppp) REVERT: A 468 GLU cc_start: 0.7223 (tp30) cc_final: 0.6971 (tp30) REVERT: A 526 MET cc_start: 0.6978 (tmm) cc_final: 0.6246 (mpt) REVERT: A 567 GLN cc_start: 0.7940 (tm-30) cc_final: 0.7343 (tm-30) REVERT: A 617 PHE cc_start: 0.7291 (t80) cc_final: 0.7058 (t80) REVERT: A 689 ASP cc_start: 0.7941 (t0) cc_final: 0.7536 (t70) REVERT: A 699 LYS cc_start: 0.7605 (mttt) cc_final: 0.7255 (mttt) REVERT: A 751 ARG cc_start: 0.7579 (mmp80) cc_final: 0.6859 (mmp80) REVERT: A 805 GLU cc_start: 0.8185 (pp20) cc_final: 0.7835 (pp20) REVERT: A 940 LYS cc_start: 0.8265 (mttt) cc_final: 0.7931 (tppt) REVERT: A 1026 SER cc_start: 0.8107 (p) cc_final: 0.7673 (t) REVERT: A 1079 CYS cc_start: 0.7982 (t) cc_final: 0.7702 (t) REVERT: A 1129 GLU cc_start: 0.7664 (mt-10) cc_final: 0.7283 (mp0) REVERT: A 1240 GLU cc_start: 0.7811 (mp0) cc_final: 0.7353 (mp0) REVERT: A 1275 ASP cc_start: 0.7886 (m-30) cc_final: 0.7553 (m-30) REVERT: A 1299 GLU cc_start: 0.7690 (mp0) cc_final: 0.7460 (pm20) REVERT: A 1303 GLU cc_start: 0.7947 (tp30) cc_final: 0.7690 (tp30) REVERT: A 1311 THR cc_start: 0.8093 (m) cc_final: 0.7714 (p) REVERT: A 1418 LEU cc_start: 0.8543 (OUTLIER) cc_final: 0.8233 (tt) REVERT: A 1555 ASP cc_start: 0.7787 (m-30) cc_final: 0.7538 (m-30) REVERT: A 1562 LEU cc_start: 0.8669 (OUTLIER) cc_final: 0.8379 (mt) REVERT: A 1643 GLU cc_start: 0.7332 (mm-30) cc_final: 0.7006 (mm-30) REVERT: A 1648 ASN cc_start: 0.8202 (m-40) cc_final: 0.7971 (m-40) REVERT: A 1766 CYS cc_start: 0.8164 (OUTLIER) cc_final: 0.7829 (m) REVERT: A 1831 MET cc_start: 0.7822 (mmm) cc_final: 0.7577 (mmm) REVERT: A 1833 LYS cc_start: 0.8120 (mttt) cc_final: 0.7735 (mmtm) REVERT: A 1846 LYS cc_start: 0.7774 (tttt) cc_final: 0.7336 (ttmt) REVERT: A 1947 MET cc_start: 0.3570 (mmm) cc_final: 0.3243 (tmm) REVERT: A 2029 GLN cc_start: 0.7780 (pm20) cc_final: 0.7307 (pm20) REVERT: A 2049 GLU cc_start: 0.7490 (mt-10) cc_final: 0.7157 (mt-10) REVERT: A 2206 MET cc_start: 0.6585 (mmm) cc_final: 0.6040 (mmm) REVERT: A 2231 VAL cc_start: 0.8823 (t) cc_final: 0.8541 (m) REVERT: A 2297 GLU cc_start: 0.7644 (mm-30) cc_final: 0.7416 (mt-10) REVERT: A 2308 SER cc_start: 0.8668 (p) cc_final: 0.8238 (t) REVERT: A 2397 LEU cc_start: 0.8777 (mt) cc_final: 0.8517 (mp) REVERT: A 2525 VAL cc_start: 0.8382 (t) cc_final: 0.8018 (p) REVERT: A 2543 LYS cc_start: 0.8504 (tttt) cc_final: 0.8255 (tttt) REVERT: A 2676 SER cc_start: 0.8604 (t) cc_final: 0.8163 (m) REVERT: A 2787 ASN cc_start: 0.8074 (t0) cc_final: 0.7843 (t0) REVERT: A 2881 VAL cc_start: 0.8635 (t) cc_final: 0.8425 (t) REVERT: A 2956 TYR cc_start: 0.7872 (m-80) cc_final: 0.7479 (m-80) REVERT: A 3132 LEU cc_start: 0.7514 (mm) cc_final: 0.7300 (mm) REVERT: A 3150 LYS cc_start: 0.8530 (tptm) cc_final: 0.8320 (mptm) REVERT: A 3157 SER cc_start: 0.8688 (m) cc_final: 0.7962 (p) REVERT: A 3161 LYS cc_start: 0.7838 (mmtm) cc_final: 0.7418 (mptt) REVERT: A 3203 MET cc_start: 0.6564 (ttm) cc_final: 0.6002 (ttt) REVERT: A 3222 PHE cc_start: 0.7757 (t80) cc_final: 0.7555 (t80) REVERT: A 3264 MET cc_start: 0.7735 (mmm) cc_final: 0.7521 (mmp) REVERT: A 3364 GLU cc_start: 0.7079 (mp0) cc_final: 0.6694 (mp0) REVERT: A 3487 LEU cc_start: 0.7268 (OUTLIER) cc_final: 0.6889 (tp) REVERT: A 3506 LYS cc_start: 0.7699 (tmtt) cc_final: 0.7300 (tmtt) REVERT: A 3530 LYS cc_start: 0.7096 (tppt) cc_final: 0.6619 (mppt) REVERT: A 3715 LYS cc_start: 0.8256 (tppt) cc_final: 0.7929 (tppt) REVERT: A 3796 MET cc_start: 0.5190 (mmm) cc_final: 0.4688 (mmt) REVERT: A 3818 MET cc_start: 0.7351 (mpm) cc_final: 0.6881 (mpm) REVERT: A 3870 MET cc_start: 0.6846 (pmm) cc_final: 0.6446 (ppp) outliers start: 41 outliers final: 30 residues processed: 512 average time/residue: 0.6846 time to fit residues: 405.8132 Evaluate side-chains 514 residues out of total 2891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 480 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 341 MET Chi-restraints excluded: chain A residue 726 GLU Chi-restraints excluded: chain A residue 891 PHE Chi-restraints excluded: chain A residue 929 VAL Chi-restraints excluded: chain A residue 935 LEU Chi-restraints excluded: chain A residue 956 THR Chi-restraints excluded: chain A residue 999 LYS Chi-restraints excluded: chain A residue 1124 VAL Chi-restraints excluded: chain A residue 1326 VAL Chi-restraints excluded: chain A residue 1366 CYS Chi-restraints excluded: chain A residue 1418 LEU Chi-restraints excluded: chain A residue 1562 LEU Chi-restraints excluded: chain A residue 1602 ASN Chi-restraints excluded: chain A residue 1658 THR Chi-restraints excluded: chain A residue 1667 CYS Chi-restraints excluded: chain A residue 1753 SER Chi-restraints excluded: chain A residue 1766 CYS Chi-restraints excluded: chain A residue 1812 SER Chi-restraints excluded: chain A residue 2024 TYR Chi-restraints excluded: chain A residue 2062 GLN Chi-restraints excluded: chain A residue 2599 ILE Chi-restraints excluded: chain A residue 2661 SER Chi-restraints excluded: chain A residue 2768 SER Chi-restraints excluded: chain A residue 2894 SER Chi-restraints excluded: chain A residue 2943 GLU Chi-restraints excluded: chain A residue 2951 ILE Chi-restraints excluded: chain A residue 3139 MET Chi-restraints excluded: chain A residue 3271 VAL Chi-restraints excluded: chain A residue 3307 SER Chi-restraints excluded: chain A residue 3401 ARG Chi-restraints excluded: chain A residue 3470 VAL Chi-restraints excluded: chain A residue 3487 LEU Chi-restraints excluded: chain A residue 3554 LEU Chi-restraints excluded: chain A residue 3683 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 173 optimal weight: 0.8980 chunk 238 optimal weight: 0.7980 chunk 125 optimal weight: 0.6980 chunk 115 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 46 optimal weight: 2.9990 chunk 203 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 287 optimal weight: 0.9980 chunk 186 optimal weight: 6.9990 chunk 135 optimal weight: 4.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1002 HIS A1057 GLN ** A1127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1284 ASN A1576 ASN ** A2377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2509 HIS ** A2638 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3410 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.179416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.153292 restraints weight = 37879.375| |-----------------------------------------------------------------------------| r_work (start): 0.3926 rms_B_bonded: 2.08 r_work: 0.3821 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3680 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7401 moved from start: 0.3008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 26677 Z= 0.161 Angle : 0.657 15.973 36189 Z= 0.323 Chirality : 0.042 0.340 4220 Planarity : 0.004 0.059 4402 Dihedral : 9.881 101.719 4035 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 1.66 % Allowed : 20.41 % Favored : 77.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.15), residues: 3102 helix: 0.84 (0.13), residues: 1747 sheet: -1.25 (0.34), residues: 236 loop : -1.44 (0.18), residues: 1119 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A1805 TYR 0.024 0.002 TYR A3337 PHE 0.030 0.002 PHE A3613 TRP 0.036 0.002 TRP A2444 HIS 0.006 0.001 HIS A 944 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.16 (26673) covalent geometry : angle 0.65278 / 0.32 (36183) hydrogen bonds : bond 0.03647 / 2.38 ( 1311) hydrogen bonds : angle 4.33800 / 3.08 ( 3720) metal coordination : bond 0.00522 / 0.25 ( 4) metal coordination : angle 5.75312 / 3.35 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11967.29 seconds wall clock time: 204 minutes 5.01 seconds (12245.01 seconds total)