Starting phenix.real_space_refine on Wed Oct 28 05:03:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9xe6_66783/10_2026/9xe6_66783.cif Found real_map, /net/cci-nas-00/data/ceres_data/9xe6_66783/10_2026/9xe6_66783.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.09 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9xe6_66783/10_2026/9xe6_66783.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9xe6_66783/10_2026/9xe6_66783.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9xe6_66783/10_2026/9xe6_66783.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9xe6_66783/10_2026/9xe6_66783.map" } resolution = 3.09 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= 0.046 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: 8 Type Number sf(0) Gaussians Mn 4 7.51 5 Zn 1 6.06 5 P 49 5.49 5 S 164 5.16 5 C 16603 2.51 5 N 4532 2.21 5 O 5101 1.98 5 F 1 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 26455 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 25428 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3179, 25428 Classifications: {'peptide': 3179} Link IDs: {'PCIS': 1, 'PTRANS': 95, 'TRANS': 3082} Chain breaks: 21 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': 4, 'rna3p_pur': 3, 'rna3p_pyr': 4} Link IDs: {'rna2p': 3, 'rna3p': 7} Chain: "C" Number of atoms: 300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 300 Classifications: {'RNA': 14} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 1, 'rna3p_pur': 7, 'rna3p_pyr': 5} Link IDs: {'rna2p': 2, 'rna3p': 11} Chain: "D" Number of atoms: 211 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 211 Unusual residues: {'CFZ': 1} Classifications: {'DNA_mixed': 1, 'RNA': 9} Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 5, 'rna3p_pyr': 3} Link IDs: {'rna2p': 1, 'rna3p': 7, None: 1} Not linked: pdbres=" A D 9 " pdbres="CFZ D 10 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 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: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 81 Classifications: {'RNA': 4} Modifications used: {'p5*END': 1, 'rna2p_pyr': 1, 'rna3p_pyr': 3} Link IDs: {'rna2p': 1, '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 4865 SG CYS A1028 43.459 98.359 96.422 1.00 81.70 S ATOM 4884 SG CYS A1031 45.945 101.096 97.050 1.00 79.61 S ATOM 5127 SG CYS A1062 44.089 99.795 100.031 1.00102.36 S ATOM 5147 SG CYS A1065 46.619 97.590 98.412 1.00 82.97 S Time building chain proxies: 5.85, per 1000 atoms: 0.22 Number of scatterers: 26455 At special positions: 0 Unit cell: (145.416, 136.656, 138.408, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 1 29.99 Mn 4 24.99 S 164 16.00 P 49 15.00 F 1 9.00 O 5101 8.00 N 4532 7.00 C 16603 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.93 Conformation dependent library (CDL) restraints added in 1.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A4006 " pdb="ZN ZN A4006 " - pdb=" SG CYS A1031 " pdb="ZN ZN A4006 " - pdb=" SG CYS A1065 " pdb="ZN ZN A4006 " - pdb=" SG CYS A1062 " pdb="ZN ZN A4006 " - pdb=" SG CYS A1028 " Number of angles added : 6 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6096 Finding SS restraints... Secondary structure from input PDB file: 160 helices and 20 sheets defined 61.8% alpha, 7.4% beta 8 base pairs and 20 stacking pairs defined. Time for finding SS restraints: 4.37 Creating SS restraints... Processing helix chain 'A' and resid 316 through 325 Processing helix chain 'A' and resid 329 through 333 Processing helix chain 'A' and resid 338 through 352 removed outlier: 3.546A pdb=" N ILE A 342 " --> pdb=" O HIS A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 412 removed outlier: 4.207A pdb=" N THR A 406 " --> pdb=" O LYS A 402 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ALA A 410 " --> pdb=" O THR A 406 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N PHE A 412 " --> pdb=" O CYS A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 425 Processing helix chain 'A' and resid 427 through 436 Processing helix chain 'A' and resid 445 through 459 Processing helix chain 'A' and resid 466 through 485 Processing helix chain 'A' and resid 487 through 494 removed outlier: 3.614A pdb=" N LEU A 490 " --> pdb=" O ASP A 487 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 523 removed outlier: 3.957A pdb=" N PHE A 514 " --> pdb=" O ASN A 510 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LYS A 523 " --> pdb=" O PHE A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 554 removed outlier: 3.676A pdb=" N VAL A 544 " --> pdb=" O LYS A 540 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SER A 554 " --> pdb=" O ASN A 550 " (cutoff:3.500A) Processing helix chain 'A' and resid 564 through 580 Processing helix chain 'A' and resid 586 through 604 removed outlier: 3.500A pdb=" N ILE A 590 " --> pdb=" O PRO A 586 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N SER A 596 " --> pdb=" O ASP A 592 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N ASN A 597 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N GLN A 600 " --> pdb=" O SER A 596 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU A 601 " --> pdb=" O ASN A 597 " (cutoff:3.500A) Processing helix chain 'A' and resid 606 through 622 removed outlier: 3.679A pdb=" N ARG A 611 " --> pdb=" O PRO A 607 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N GLU A 612 " --> pdb=" O ASP A 608 " (cutoff:3.500A) Processing helix chain 'A' and resid 626 through 649 removed outlier: 3.895A 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 681 Processing helix chain 'A' and resid 684 through 690 removed outlier: 4.064A pdb=" N LEU A 690 " --> pdb=" O PHE A 687 " (cutoff:3.500A) Processing helix chain 'A' and resid 748 through 761 removed outlier: 3.670A pdb=" N ILE A 752 " --> pdb=" O SER A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 811 through 817 removed outlier: 3.525A pdb=" N GLN A 815 " --> pdb=" O GLY A 812 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N LEU A 816 " --> pdb=" O GLU A 813 " (cutoff:3.500A) Processing helix chain 'A' and resid 832 through 843 Processing helix chain 'A' and resid 844 through 854 removed outlier: 3.661A pdb=" N LYS A 848 " --> pdb=" O LYS A 844 " (cutoff:3.500A) Processing helix chain 'A' and resid 869 through 873 removed outlier: 3.967A pdb=" N TRP A 873 " --> pdb=" O PRO A 870 " (cutoff:3.500A) Processing helix chain 'A' and resid 876 through 897 removed outlier: 3.800A pdb=" N VAL A 882 " --> pdb=" O ASP A 878 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ARG A 896 " --> pdb=" O ASN A 892 " (cutoff:3.500A) Processing helix chain 'A' and resid 899 through 911 Processing helix chain 'A' and resid 912 through 917 Processing helix chain 'A' and resid 930 through 946 removed outlier: 5.198A pdb=" N GLU A 943 " --> pdb=" O GLU A 939 " (cutoff:3.500A) removed outlier: 5.932A 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 removed outlier: 3.697A pdb=" N LYS A1024 " --> pdb=" O SER A1020 " (cutoff:3.500A) Processing helix chain 'A' and resid 1028 through 1042 Processing helix chain 'A' and resid 1044 through 1055 Processing helix chain 'A' and resid 1057 through 1061 removed outlier: 3.561A pdb=" N ASN A1060 " --> pdb=" O GLN A1057 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N HIS A1061 " --> pdb=" O LEU A1058 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1057 through 1061' Processing helix chain 'A' and resid 1076 through 1082 Processing helix chain 'A' and resid 1084 through 1088 Processing helix chain 'A' and resid 1104 through 1111 removed outlier: 3.714A pdb=" N ARG A1111 " --> pdb=" O ASP A1107 " (cutoff:3.500A) Processing helix chain 'A' and resid 1118 through 1138 Processing helix chain 'A' and resid 1178 through 1184 removed outlier: 3.638A pdb=" N THR A1182 " --> pdb=" O GLU A1178 " (cutoff:3.500A) Processing helix chain 'A' and resid 1196 through 1208 Processing helix chain 'A' and resid 1209 through 1213 removed outlier: 3.977A pdb=" N GLN A1213 " --> pdb=" O LEU A1210 " (cutoff:3.500A) Processing helix chain 'A' and resid 1221 through 1229 removed outlier: 3.967A pdb=" N LEU A1225 " --> pdb=" O PRO A1221 " (cutoff:3.500A) Processing helix chain 'A' and resid 1237 through 1254 Processing helix chain 'A' and resid 1266 through 1281 removed outlier: 3.507A pdb=" N LEU A1270 " --> pdb=" O SER A1266 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLN A1277 " --> pdb=" O CYS A1273 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N PHE A1279 " --> pdb=" O ASP A1275 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N LYS A1280 " --> pdb=" O VAL A1276 " (cutoff:3.500A) Processing helix chain 'A' and resid 1291 through 1295 Processing helix chain 'A' and resid 1297 through 1309 Processing helix chain 'A' and resid 1315 through 1328 removed outlier: 3.638A 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: 3.800A pdb=" N LEU A1407 " --> pdb=" O ARG A1403 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N LEU A1412 " --> pdb=" O GLY A1408 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N TYR A1413 " --> pdb=" O SER A1409 " (cutoff:3.500A) removed outlier: 3.900A 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: 3.512A pdb=" N GLU A1463 " --> pdb=" O THR A1459 " (cutoff:3.500A) Processing helix chain 'A' and resid 1465 through 1481 removed outlier: 3.666A pdb=" N SER A1469 " --> pdb=" O ARG A1465 " (cutoff:3.500A) Processing helix chain 'A' and resid 1487 through 1505 Processing helix chain 'A' and resid 1508 through 1514 removed outlier: 3.961A pdb=" N ASN A1514 " --> pdb=" O ASN A1510 " (cutoff:3.500A) Processing helix chain 'A' and resid 1515 through 1524 Processing helix chain 'A' and resid 1524 through 1531 Processing helix chain 'A' and resid 1542 through 1547 removed outlier: 3.511A pdb=" N SER A1547 " --> pdb=" O LYS A1544 " (cutoff:3.500A) Processing helix chain 'A' and resid 1552 through 1571 Processing helix chain 'A' and resid 1572 through 1581 removed outlier: 3.740A 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: 3.989A pdb=" N HIS A1615 " --> pdb=" O TYR A1612 " (cutoff:3.500A) Processing helix chain 'A' and resid 1623 through 1651 removed outlier: 3.614A pdb=" N ARG A1638 " --> pdb=" O GLU A1634 " (cutoff:3.500A) Processing helix chain 'A' and resid 1659 through 1666 Processing helix chain 'A' and resid 1760 through 1773 Processing helix chain 'A' and resid 1780 through 1792 Processing helix chain 'A' and resid 1793 through 1795 No H-bonds generated for 'chain 'A' and resid 1793 through 1795' Processing helix chain 'A' and resid 1796 through 1805 Processing helix chain 'A' and resid 1806 through 1810 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: 3.942A 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: 3.931A pdb=" N LEU A1908 " --> pdb=" O HIS A1904 " (cutoff:3.500A) Processing helix chain 'A' and resid 1912 through 1917 removed outlier: 3.766A pdb=" N VAL A1916 " --> pdb=" O ASN A1912 " (cutoff:3.500A) Processing helix chain 'A' and resid 1922 through 1937 Processing helix chain 'A' and resid 1937 through 1944 Processing helix chain 'A' and resid 1945 through 1948 Processing helix chain 'A' and resid 1962 through 1977 removed outlier: 3.609A pdb=" N LEU A1977 " --> pdb=" O LYS A1973 " (cutoff:3.500A) Processing helix chain 'A' and resid 1988 through 2002 Processing helix chain 'A' and resid 2003 through 2006 Processing helix chain 'A' and resid 2007 through 2014 removed outlier: 3.539A pdb=" N LYS A2011 " --> pdb=" O ILE A2008 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N ILE A2012 " --> pdb=" O ASN A2009 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N GLN A2013 " --> pdb=" O ASP A2010 " (cutoff:3.500A) Processing helix chain 'A' and resid 2015 through 2040 Processing helix chain 'A' and resid 2045 through 2063 Processing helix chain 'A' and resid 2063 through 2079 Processing helix chain 'A' and resid 2080 through 2085 removed outlier: 6.046A pdb=" N TRP A2083 " --> pdb=" O SER A2080 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LEU A2085 " --> pdb=" O PRO A2082 " (cutoff:3.500A) Processing helix chain 'A' and resid 2117 through 2124 removed outlier: 4.247A pdb=" N CYS A2124 " --> pdb=" O LYS A2120 " (cutoff:3.500A) Processing helix chain 'A' and resid 2138 through 2155 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 2219 removed outlier: 3.899A pdb=" N CYS A2215 " --> pdb=" O ASN A2211 " (cutoff:3.500A) Processing helix chain 'A' and resid 2235 through 2247 Processing helix chain 'A' and resid 2250 through 2260 removed outlier: 3.753A pdb=" N LEU A2260 " --> pdb=" O PHE A2256 " (cutoff:3.500A) Processing helix chain 'A' and resid 2286 through 2305 Processing helix chain 'A' and resid 2316 through 2335 Processing helix chain 'A' and resid 2361 through 2366 removed outlier: 3.956A pdb=" N HIS A2366 " --> pdb=" O TRP A2362 " (cutoff:3.500A) Processing helix chain 'A' and resid 2367 through 2379 Processing helix chain 'A' and resid 2382 through 2398 removed outlier: 3.663A pdb=" N PHE A2388 " --> pdb=" O ASP A2384 " (cutoff:3.500A) Processing helix chain 'A' and resid 2404 through 2422 removed outlier: 3.508A pdb=" N LEU A2415 " --> pdb=" O ILE A2411 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N SER A2421 " --> pdb=" O TYR A2417 " (cutoff:3.500A) removed outlier: 4.159A 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: 3.681A pdb=" N ASP A2445 " --> pdb=" O ASP A2442 " (cutoff:3.500A) Processing helix chain 'A' and resid 2447 through 2457 removed outlier: 3.871A pdb=" N LEU A2453 " --> pdb=" O THR A2449 " (cutoff:3.500A) Processing helix chain 'A' and resid 2458 through 2461 removed outlier: 3.591A pdb=" N GLY A2461 " --> pdb=" O ILE A2458 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2458 through 2461' Processing helix chain 'A' and resid 2477 through 2503 removed outlier: 3.874A pdb=" N VAL A2489 " --> pdb=" O SER A2485 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LEU A2490 " --> pdb=" O LEU A2486 " (cutoff:3.500A) Processing helix chain 'A' and resid 2530 through 2558 removed outlier: 4.936A pdb=" N TRP A2542 " --> pdb=" O ASP A2538 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N LYS A2543 " --> pdb=" O GLU A2539 " (cutoff:3.500A) Processing helix chain 'A' and resid 2590 through 2594 removed outlier: 3.592A pdb=" N MET A2594 " --> pdb=" O ILE A2591 " (cutoff:3.500A) Processing helix chain 'A' and resid 2595 through 2600 removed outlier: 4.021A pdb=" N ILE A2599 " --> pdb=" O PHE A2595 " (cutoff:3.500A) removed outlier: 3.852A 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 2643 removed outlier: 3.538A pdb=" N PHE A2641 " --> pdb=" O ARG A2637 " (cutoff:3.500A) Processing helix chain 'A' and resid 2645 through 2657 removed outlier: 6.493A pdb=" N ILE A2654 " --> pdb=" O ARG A2650 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N LEU A2655 " --> pdb=" O ARG A2651 " (cutoff:3.500A) Processing helix chain 'A' and resid 2660 through 2664 removed outlier: 3.628A pdb=" N GLY A2664 " --> pdb=" O SER A2661 " (cutoff:3.500A) Processing helix chain 'A' and resid 2670 through 2676 removed outlier: 4.265A pdb=" N SER A2676 " --> pdb=" O SER A2672 " (cutoff:3.500A) Processing helix chain 'A' and resid 2678 through 2697 Processing helix chain 'A' and resid 2753 through 2764 Processing helix chain 'A' and resid 2770 through 2783 Processing helix chain 'A' and resid 2806 through 2816 Processing helix chain 'A' and resid 2816 through 2834 removed outlier: 3.542A pdb=" N SER A2826 " --> pdb=" O ASN A2822 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N VAL A2827 " --> pdb=" O ARG A2823 " (cutoff:3.500A) Processing helix chain 'A' and resid 2869 through 2889 removed outlier: 3.805A pdb=" N GLU A2875 " --> pdb=" O LYS A2871 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ARG A2878 " --> pdb=" O ARG A2874 " (cutoff:3.500A) Processing helix chain 'A' and resid 2898 through 2908 removed outlier: 3.503A pdb=" N LYS A2906 " --> pdb=" O LEU A2902 " (cutoff:3.500A) Processing helix chain 'A' and resid 2916 through 2929 Processing helix chain 'A' and resid 2932 through 2938 removed outlier: 4.176A pdb=" N GLY A2936 " --> pdb=" O ASN A2932 " (cutoff:3.500A) Processing helix chain 'A' and resid 2944 through 2953 removed outlier: 3.533A pdb=" N MET A2953 " --> pdb=" O TYR A2949 " (cutoff:3.500A) Processing helix chain 'A' and resid 2994 through 3003 Processing helix chain 'A' and resid 3043 through 3060 Processing helix chain 'A' and resid 3062 through 3073 Processing helix chain 'A' and resid 3104 through 3114 removed outlier: 3.510A pdb=" N VAL A3108 " --> pdb=" O ASN A3104 " (cutoff:3.500A) Processing helix chain 'A' and resid 3116 through 3121 Processing helix chain 'A' and resid 3127 through 3131 removed outlier: 3.824A pdb=" N LEU A3131 " --> pdb=" O PHE A3128 " (cutoff:3.500A) Processing helix chain 'A' and resid 3133 through 3140 Processing helix chain 'A' and resid 3142 through 3163 Processing helix chain 'A' and resid 3167 through 3187 removed outlier: 3.657A pdb=" N VAL A3171 " --> pdb=" O ASP A3167 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ALA A3172 " --> pdb=" O LEU A3168 " (cutoff:3.500A) Processing helix chain 'A' and resid 3209 through 3217 removed outlier: 3.699A pdb=" N VAL A3213 " --> pdb=" O VAL A3209 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ILE A3217 " --> pdb=" O VAL A3213 " (cutoff:3.500A) Processing helix chain 'A' and resid 3237 through 3251 Processing helix chain 'A' and resid 3255 through 3268 Processing helix chain 'A' and resid 3272 through 3276 removed outlier: 3.579A pdb=" N ILE A3275 " --> pdb=" O ASN A3272 " (cutoff:3.500A) Processing helix chain 'A' and resid 3285 through 3293 removed outlier: 3.548A pdb=" N LEU A3290 " --> pdb=" O GLU A3286 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N GLU A3292 " --> pdb=" O SER A3288 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N PHE A3293 " --> pdb=" O ILE A3289 " (cutoff:3.500A) Processing helix chain 'A' and resid 3298 through 3305 Processing helix chain 'A' and resid 3306 through 3309 removed outlier: 3.597A 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 3312 through 3326 removed outlier: 3.608A pdb=" N GLU A3316 " --> pdb=" O ASP A3312 " (cutoff:3.500A) Processing helix chain 'A' and resid 3327 through 3334 Processing helix chain 'A' and resid 3382 through 3398 Processing helix chain 'A' and resid 3406 through 3417 removed outlier: 3.504A pdb=" N LEU A3416 " --> pdb=" O LEU A3412 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU A3417 " --> pdb=" O PHE A3413 " (cutoff:3.500A) Processing helix chain 'A' and resid 3503 through 3515 Processing helix chain 'A' and resid 3543 through 3555 removed outlier: 3.658A pdb=" N LEU A3547 " --> pdb=" O LEU A3543 " (cutoff:3.500A) Processing helix chain 'A' and resid 3555 through 3567 removed outlier: 4.581A pdb=" N SER A3559 " --> pdb=" O LYS A3555 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ASP A3560 " --> pdb=" O HIS A3556 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ILE A3562 " --> pdb=" O PRO A3558 " (cutoff:3.500A) Processing helix chain 'A' and resid 3569 through 3579 removed outlier: 3.771A pdb=" N HIS A3573 " --> pdb=" O SER A3569 " (cutoff:3.500A) Processing helix chain 'A' and resid 3586 through 3592 removed outlier: 3.560A pdb=" N PHE A3590 " --> pdb=" O THR A3586 " (cutoff:3.500A) Processing helix chain 'A' and resid 3607 through 3624 Processing helix chain 'A' and resid 3627 through 3629 No H-bonds generated for 'chain 'A' and resid 3627 through 3629' Processing helix chain 'A' and resid 3630 through 3640 removed outlier: 3.698A pdb=" N GLN A3635 " --> pdb=" O TRP A3631 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ASN A3636 " --> pdb=" O SER A3632 " (cutoff:3.500A) Processing helix chain 'A' and resid 3677 through 3687 removed outlier: 3.547A pdb=" N THR A3687 " --> pdb=" O SER A3683 " (cutoff:3.500A) Processing helix chain 'A' and resid 3694 through 3698 Processing helix chain 'A' and resid 3700 through 3722 Processing helix chain 'A' and resid 3724 through 3739 removed outlier: 3.536A pdb=" N PHE A3737 " --> pdb=" O THR A3733 " (cutoff:3.500A) Processing helix chain 'A' and resid 3754 through 3760 removed outlier: 3.530A pdb=" N LEU A3757 " --> pdb=" O ALA A3754 " (cutoff:3.500A) Processing helix chain 'A' and resid 3792 through 3796 Processing helix chain 'A' and resid 3799 through 3819 Processing helix chain 'A' and resid 3824 through 3831 Processing helix chain 'A' and resid 3859 through 3866 removed outlier: 3.548A pdb=" N HIS A3866 " --> pdb=" O LYS A3862 " (cutoff:3.500A) Processing helix chain 'A' and resid 3873 through 3888 removed outlier: 3.755A pdb=" N VAL A3877 " --> pdb=" O LYS A3873 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 744 through 745 removed outlier: 4.190A pdb=" N SER A 744 " --> pdb=" O SER A 695 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR A 697 " --> pdb=" O SER A 744 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N LEU A 821 " --> pdb=" O SER A 858 " (cutoff:3.500A) removed outlier: 8.132A pdb=" N ILE A 860 " --> pdb=" O LEU A 821 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N LEU A 823 " --> pdb=" O ILE A 860 " (cutoff:3.500A) removed outlier: 7.758A pdb=" N CYS A 862 " --> pdb=" O LEU A 823 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N GLU A 825 " --> pdb=" O CYS A 862 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 728 through 729 removed outlier: 3.658A pdb=" N TYR A1755 " --> pdb=" O VAL A 971 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1003 through 1004 Processing sheet with id=AA4, first strand: chain 'A' and resid 1143 through 1145 Processing sheet with id=AA5, first strand: chain 'A' and resid 1357 through 1362 removed outlier: 4.154A pdb=" N LEU A1383 " --> pdb=" O LYS A1373 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N LEU A1386 " --> pdb=" O GLY A1396 " (cutoff:3.500A) removed outlier: 5.394A pdb=" N GLY A1396 " --> pdb=" O LEU A1386 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1821 through 1825 removed outlier: 6.942A 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: 7.637A 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: 3.627A pdb=" N TYR A2519 " --> pdb=" O GLY A2357 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 2574 through 2576 removed outlier: 3.540A pdb=" N PHE A2580 " --> pdb=" O THR A2587 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 2956 through 2959 Processing sheet with id=AB2, first strand: chain 'A' and resid 3006 through 3009 removed outlier: 6.585A pdb=" N SER A3007 " --> pdb=" O VAL A3041 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 3079 through 3081 Processing sheet with id=AB4, first strand: chain 'A' and resid 3086 through 3094 Processing sheet with id=AB5, first strand: chain 'A' and resid 3270 through 3271 removed outlier: 3.988A pdb=" N GLN A3296 " --> pdb=" O VAL A3271 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 3343 through 3346 removed outlier: 7.677A pdb=" N LEU A3374 " --> pdb=" O VAL A3456 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N LYS A3458 " --> pdb=" O LEU A3374 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N ILE A3376 " --> pdb=" O LYS A3458 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N ALA A3455 " --> pdb=" O VAL A3435 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 3466 through 3468 Processing sheet with id=AB8, first strand: chain 'A' and resid 3478 through 3481 removed outlier: 3.648A pdb=" N ILE A3489 " --> pdb=" O SER A3534 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N SER A3534 " --> pdb=" O ILE A3489 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N TYR A3491 " --> pdb=" O VAL A3532 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N VAL A3532 " --> pdb=" O TYR A3491 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 3647 through 3650 Processing sheet with id=AC1, first strand: chain 'A' and resid 3765 through 3767 Processing sheet with id=AC2, first strand: chain 'A' and resid 3765 through 3767 removed outlier: 5.038A pdb=" N GLN A3843 " --> pdb=" O ASN A3839 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N ASN A3839 " --> pdb=" O GLN A3843 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N CYS A3845 " --> pdb=" O MET A3837 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N MET A3837 " --> pdb=" O CYS A3845 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N GLU A3847 " --> pdb=" O CYS A3835 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N CYS A3835 " --> pdb=" O GLU A3847 " (cutoff:3.500A) 1388 hydrogen bonds defined for protein. 3927 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 19 hydrogen bonds 38 hydrogen bond angles 0 basepair planarities 8 basepair parallelities 20 stacking parallelities Total time for adding SS restraints: 11.30 Time building geometry restraints manager: 2.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 4271 1.31 - 1.43: 6891 1.43 - 1.56: 15496 1.56 - 1.69: 94 1.69 - 1.81: 241 Bond restraints: 26993 Sorted by residual: bond pdb=" C2' 2KH A4001 " pdb=" C3' 2KH A4001 " ideal model delta sigma weight residual 1.548 1.290 0.258 2.00e-02 2.50e+03 1.66e+02 bond pdb=" N3A 2KH A4001 " pdb=" PA 2KH A4001 " ideal model delta sigma weight residual 1.933 1.696 0.237 2.00e-02 2.50e+03 1.40e+02 bond pdb=" O3G 2KH A4001 " pdb=" PG 2KH A4001 " ideal model delta sigma weight residual 1.669 1.469 0.200 2.00e-02 2.50e+03 1.00e+02 bond pdb=" C1' 2KH A4001 " pdb=" N1 2KH A4001 " ideal model delta sigma weight residual 1.502 1.336 0.166 2.00e-02 2.50e+03 6.91e+01 bond pdb=" N3A 2KH A4001 " pdb=" PB 2KH A4001 " ideal model delta sigma weight residual 1.890 1.726 0.164 2.00e-02 2.50e+03 6.75e+01 ... (remaining 26988 not shown) Histogram of bond angle deviations from ideal: 0.00 - 12.22: 36615 12.22 - 24.43: 7 24.43 - 36.65: 0 36.65 - 48.86: 0 48.86 - 61.08: 2 Bond angle restraints: 36624 Sorted by residual: angle pdb=" N3A 2KH A4001 " pdb=" PA 2KH A4001 " pdb=" O2A 2KH A4001 " ideal model delta sigma weight residual 48.17 109.25 -61.08 3.00e+00 1.11e-01 4.15e+02 angle pdb=" O2G 2KH A4001 " pdb=" PG 2KH A4001 " pdb=" O3G 2KH A4001 " ideal model delta sigma weight residual 53.94 109.30 -55.36 3.00e+00 1.11e-01 3.41e+02 angle pdb=" O1A 2KH A4001 " pdb=" PA 2KH A4001 " pdb=" O2A 2KH A4001 " ideal model delta sigma weight residual 130.82 109.10 21.72 3.00e+00 1.11e-01 5.24e+01 angle pdb=" O1B 2KH A4001 " pdb=" PB 2KH A4001 " pdb=" O2B 2KH A4001 " ideal model delta sigma weight residual 130.56 109.22 21.34 3.00e+00 1.11e-01 5.06e+01 angle pdb=" O1G 2KH A4001 " pdb=" PG 2KH A4001 " pdb=" O3G 2KH A4001 " ideal model delta sigma weight residual 130.17 109.50 20.67 3.00e+00 1.11e-01 4.75e+01 ... (remaining 36619 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.35: 16386 35.35 - 70.69: 202 70.69 - 106.04: 15 106.04 - 141.39: 0 141.39 - 176.73: 1 Dihedral angle restraints: 16604 sinusoidal: 7271 harmonic: 9333 Sorted by residual: dihedral pdb=" O4' C E 12 " pdb=" C1' C E 12 " pdb=" N1 C E 12 " pdb=" C2 C E 12 " ideal model delta sinusoidal sigma weight residual -128.00 48.73 -176.73 1 1.70e+01 3.46e-03 6.64e+01 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 68.00 133.70 -65.70 1 1.70e+01 3.46e-03 1.95e+01 dihedral pdb=" CA ASP A1806 " pdb=" CB ASP A1806 " pdb=" CG ASP A1806 " pdb=" OD1 ASP A1806 " ideal model delta sinusoidal sigma weight residual -30.00 -87.34 57.34 1 2.00e+01 2.50e-03 1.10e+01 ... (remaining 16601 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.088: 4056 0.088 - 0.176: 216 0.176 - 0.265: 3 0.265 - 0.353: 0 0.353 - 0.441: 1 Chirality restraints: 4276 Sorted by residual: chirality pdb=" C2' 2KH A4001 " pdb=" C1' 2KH A4001 " pdb=" C3' 2KH A4001 " pdb=" O2' 2KH A4001 " both_signs ideal model delta sigma weight residual False -2.85 -2.41 -0.44 2.00e-01 2.50e+01 4.86e+00 chirality pdb=" CB ILE A 594 " pdb=" CA ILE A 594 " pdb=" CG1 ILE A 594 " pdb=" CG2 ILE A 594 " both_signs ideal model delta sigma weight residual False 2.64 2.83 -0.19 2.00e-01 2.50e+01 8.58e-01 chirality pdb=" C1' U F 1 " pdb=" O4' U F 1 " pdb=" C2' U F 1 " pdb=" N1 U F 1 " both_signs ideal model delta sigma weight residual False 2.47 2.29 0.18 2.00e-01 2.50e+01 8.41e-01 ... (remaining 4273 not shown) Planarity restraints: 4445 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A1311 " 0.035 5.00e-02 4.00e+02 5.30e-02 4.49e+00 pdb=" N PRO A1312 " -0.092 5.00e-02 4.00e+02 pdb=" CA PRO A1312 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A1312 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A2503 " -0.033 5.00e-02 4.00e+02 5.02e-02 4.04e+00 pdb=" N PRO A2504 " 0.087 5.00e-02 4.00e+02 pdb=" CA PRO A2504 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A2504 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 885 " 0.010 2.00e-02 2.50e+03 1.97e-02 3.87e+00 pdb=" C ASN A 885 " -0.034 2.00e-02 2.50e+03 pdb=" O ASN A 885 " 0.013 2.00e-02 2.50e+03 pdb=" N SER A 886 " 0.011 2.00e-02 2.50e+03 ... (remaining 4442 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 380 2.71 - 3.26: 25994 3.26 - 3.81: 42924 3.81 - 4.35: 56024 4.35 - 4.90: 91972 Nonbonded interactions: 217294 Sorted by model distance: nonbonded pdb=" O2A 2KH A4001 " pdb="MN MN A4004 " model vdw 2.165 2.320 nonbonded pdb=" OP3 U F 1 " pdb="MN MN A4003 " model vdw 2.167 2.320 nonbonded pdb=" O1B 2KH A4001 " pdb="MN MN A4005 " model vdw 2.175 2.320 nonbonded pdb=" OD1 ASP A2358 " pdb="MN MN A4005 " model vdw 2.181 2.320 nonbonded pdb=" OP2 U F 1 " pdb="MN MN A4002 " model vdw 2.189 2.320 ... (remaining 217289 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: 2.600 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: 0.510 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 38.980 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 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 : 0.004 0.258 26998 Z= 0.224 Angle : 0.753 61.080 36630 Z= 0.367 Chirality : 0.042 0.441 4276 Planarity : 0.004 0.053 4445 Dihedral : 12.223 176.735 10508 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 0.00 % Allowed : 0.17 % Favored : 99.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.04 % 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: -0.09 (0.15), residues: 3135 helix: 0.54 (0.12), residues: 1803 sheet: 0.02 (0.36), residues: 213 loop : -0.93 (0.18), residues: 1119 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1552 TYR 0.021 0.001 TYR A3239 PHE 0.028 0.001 PHE A1966 TRP 0.021 0.001 TRP A1928 HIS 0.006 0.001 HIS A2512 Details of bonding type rmsd/Z covalent geometry : bond 0.00438 / 0.22 (26993) covalent geometry : angle 0.75201 / 0.37 (36624) hydrogen bonds : bond 0.13347 / 8.85 ( 1401) hydrogen bonds : angle 5.48153 / 3.85 ( 3965) metal coordination : bond 0.00426 / 0.21 ( 4) metal coordination : angle 2.99334 / 1.11 ( 6) Misc. bond : bond 0.00038 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 786 residues out of total 2917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 786 time to evaluate : 1.152 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 472 LEU cc_start: 0.8200 (tt) cc_final: 0.7206 (tp) REVERT: A 494 TRP cc_start: 0.8183 (m-10) cc_final: 0.7815 (m-10) REVERT: A 510 ASN cc_start: 0.7091 (m-40) cc_final: 0.6724 (t0) REVERT: A 521 LYS cc_start: 0.8198 (tptt) cc_final: 0.7975 (tptt) REVERT: A 573 LYS cc_start: 0.8699 (mttt) cc_final: 0.8466 (mtpp) REVERT: A 584 VAL cc_start: 0.7953 (t) cc_final: 0.7462 (p) REVERT: A 594 ILE cc_start: 0.7438 (mt) cc_final: 0.7172 (tt) REVERT: A 599 LYS cc_start: 0.8265 (tptm) cc_final: 0.8062 (tptm) REVERT: A 645 PHE cc_start: 0.8193 (t80) cc_final: 0.7871 (t80) REVERT: A 672 ASP cc_start: 0.7719 (p0) cc_final: 0.7462 (p0) REVERT: A 682 GLN cc_start: 0.8222 (mt0) cc_final: 0.8015 (mt0) REVERT: A 844 LYS cc_start: 0.8606 (tttt) cc_final: 0.8198 (ttpp) REVERT: A 897 ASN cc_start: 0.8166 (m-40) cc_final: 0.7426 (m-40) REVERT: A 968 GLU cc_start: 0.7127 (mt-10) cc_final: 0.6825 (mt-10) REVERT: A 1084 LYS cc_start: 0.7921 (mtpt) cc_final: 0.7685 (mppt) REVERT: A 1086 GLU cc_start: 0.8003 (mp0) cc_final: 0.7688 (mp0) REVERT: A 1107 ASP cc_start: 0.7171 (m-30) cc_final: 0.6933 (m-30) REVERT: A 1123 ARG cc_start: 0.6698 (tmm160) cc_final: 0.6108 (mtp-110) REVERT: A 1203 ILE cc_start: 0.8450 (mt) cc_final: 0.8241 (mt) REVERT: A 1230 PHE cc_start: 0.8266 (t80) cc_final: 0.7918 (t80) REVERT: A 1292 VAL cc_start: 0.8101 (t) cc_final: 0.7124 (m) REVERT: A 1361 VAL cc_start: 0.7814 (t) cc_final: 0.7596 (p) REVERT: A 1455 PHE cc_start: 0.7597 (t80) cc_final: 0.7356 (t80) REVERT: A 1564 THR cc_start: 0.7889 (p) cc_final: 0.7457 (p) REVERT: A 1645 ASP cc_start: 0.7666 (t70) cc_final: 0.7450 (t0) REVERT: A 1845 LYS cc_start: 0.8176 (mtpt) cc_final: 0.7945 (mtpt) REVERT: A 1846 LYS cc_start: 0.8043 (mttt) cc_final: 0.7764 (mtmt) REVERT: A 1848 VAL cc_start: 0.8601 (t) cc_final: 0.8387 (p) REVERT: A 1879 VAL cc_start: 0.8219 (t) cc_final: 0.7869 (m) REVERT: A 1947 MET cc_start: 0.6091 (mmm) cc_final: 0.5884 (mmm) REVERT: A 2206 MET cc_start: 0.6328 (mmm) cc_final: 0.5905 (mmm) REVERT: A 2581 MET cc_start: 0.7622 (tmm) cc_final: 0.7180 (tmm) REVERT: A 2755 THR cc_start: 0.7746 (m) cc_final: 0.6908 (p) REVERT: A 2769 THR cc_start: 0.8578 (m) cc_final: 0.8334 (p) REVERT: A 2802 MET cc_start: 0.7899 (ttt) cc_final: 0.7649 (ttp) REVERT: A 2864 MET cc_start: 0.8211 (mmt) cc_final: 0.7538 (mmt) REVERT: A 2994 TYR cc_start: 0.7689 (t80) cc_final: 0.7423 (t80) REVERT: A 3146 PHE cc_start: 0.8347 (t80) cc_final: 0.8146 (t80) REVERT: A 3204 ASN cc_start: 0.8251 (m-40) cc_final: 0.8005 (t0) REVERT: A 3264 MET cc_start: 0.7621 (mmm) cc_final: 0.6918 (mmm) REVERT: A 3273 MET cc_start: 0.8498 (ttp) cc_final: 0.8093 (ttp) REVERT: A 3274 ASP cc_start: 0.8266 (m-30) cc_final: 0.8037 (m-30) REVERT: A 3286 GLU cc_start: 0.6385 (pt0) cc_final: 0.5321 (tt0) REVERT: A 3325 LEU cc_start: 0.8205 (tt) cc_final: 0.7934 (tp) REVERT: A 3356 PHE cc_start: 0.7463 (p90) cc_final: 0.7229 (p90) REVERT: A 3436 ILE cc_start: 0.8476 (pt) cc_final: 0.8249 (pt) REVERT: A 3481 GLN cc_start: 0.7666 (tm-30) cc_final: 0.7165 (tm-30) REVERT: A 3502 GLU cc_start: 0.8084 (tt0) cc_final: 0.7773 (tt0) REVERT: A 3662 LYS cc_start: 0.7921 (mttt) cc_final: 0.7662 (mmmm) REVERT: A 3715 LYS cc_start: 0.8186 (tttt) cc_final: 0.7915 (ttpt) REVERT: A 3727 GLU cc_start: 0.8044 (mt-10) cc_final: 0.7844 (mt-10) REVERT: A 3867 CYS cc_start: 0.8081 (m) cc_final: 0.7766 (t) REVERT: A 3875 GLU cc_start: 0.7918 (mt-10) cc_final: 0.7654 (mt-10) outliers start: 0 outliers final: 0 residues processed: 786 average time/residue: 0.2048 time to fit residues: 244.6343 Evaluate side-chains 603 residues out of total 2917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 603 time to evaluate : 0.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: [197, 215, 20, 132, 261, 248, 207, 155, 244, 183, 298] chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 0.7980 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 5.9990 chunk 298 optimal weight: 2.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 415 GLN A 474 GLN A 597 ASN A 632 HIS A 698 GLN ** A 806 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 947 ASN A 960 GLN A1034 ASN A1247 ASN A1284 ASN A1424 GLN A1518 GLN A1519 ASN A1576 ASN A1829 HIS ** A2275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2413 ASN ** A2477 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2560 GLN A2607 GLN A2614 GLN A2623 ASN A2695 GLN A2901 GLN ** A3045 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3285 HIS A3326 ASN A3375 HIS A3615 ASN A3624 ASN A3653 ASN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.158019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.131036 restraints weight = 36624.041| |-----------------------------------------------------------------------------| r_work (start): 0.3612 rms_B_bonded: 2.02 r_work: 0.3491 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3336 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.1939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 26998 Z= 0.259 Angle : 0.603 9.271 36630 Z= 0.314 Chirality : 0.044 0.240 4276 Planarity : 0.005 0.050 4445 Dihedral : 10.331 173.225 4127 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.25 % Favored : 96.71 % Rotamer: Outliers : 2.26 % Allowed : 9.29 % Favored : 88.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.04 % 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: 0.25 (0.15), residues: 3135 helix: 0.87 (0.12), residues: 1820 sheet: -0.12 (0.34), residues: 228 loop : -0.87 (0.19), residues: 1087 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG A1123 TYR 0.018 0.002 TYR A2350 PHE 0.029 0.002 PHE A2633 TRP 0.020 0.002 TRP A2808 HIS 0.008 0.001 HIS A2996 Details of bonding type rmsd/Z covalent geometry : bond 0.00594 / 0.26 (26993) covalent geometry : angle 0.60147 / 0.31 (36624) hydrogen bonds : bond 0.04501 / 3.04 ( 1401) hydrogen bonds : angle 4.49973 / 3.18 ( 3965) metal coordination : bond 0.01044 / 0.51 ( 4) metal coordination : angle 3.38617 / 1.31 ( 6) Misc. bond : bond 0.00147 / 0.08 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 691 residues out of total 2917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 625 time to evaluate : 1.016 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 490 LEU cc_start: 0.7501 (mt) cc_final: 0.7250 (mt) REVERT: A 494 TRP cc_start: 0.8159 (m-10) cc_final: 0.7805 (m-10) REVERT: A 510 ASN cc_start: 0.7260 (m-40) cc_final: 0.6721 (t0) REVERT: A 521 LYS cc_start: 0.8317 (tptt) cc_final: 0.8030 (tptt) REVERT: A 556 SER cc_start: 0.8142 (m) cc_final: 0.7914 (p) REVERT: A 573 LYS cc_start: 0.8699 (mttt) cc_final: 0.8490 (mtpp) REVERT: A 584 VAL cc_start: 0.7987 (t) cc_final: 0.7398 (p) REVERT: A 594 ILE cc_start: 0.7460 (mt) cc_final: 0.7148 (tt) REVERT: A 599 LYS cc_start: 0.8291 (tptm) cc_final: 0.8002 (tptm) REVERT: A 614 GLU cc_start: 0.7513 (tp30) cc_final: 0.7263 (tp30) REVERT: A 679 ASP cc_start: 0.8258 (t0) cc_final: 0.8002 (t0) REVERT: A 753 MET cc_start: 0.7747 (mmm) cc_final: 0.7106 (mmm) REVERT: A 805 GLU cc_start: 0.7600 (tt0) cc_final: 0.7313 (tt0) REVERT: A 806 ASN cc_start: 0.7418 (OUTLIER) cc_final: 0.7216 (p0) REVERT: A 844 LYS cc_start: 0.8655 (tttt) cc_final: 0.8188 (ttpp) REVERT: A 881 ARG cc_start: 0.8131 (ttm170) cc_final: 0.7782 (ttm170) REVERT: A 963 ARG cc_start: 0.8149 (ttt-90) cc_final: 0.7945 (ttt-90) REVERT: A 968 GLU cc_start: 0.7825 (mt-10) cc_final: 0.7504 (mt-10) REVERT: A 1084 LYS cc_start: 0.7700 (mtpt) cc_final: 0.7370 (mppt) REVERT: A 1086 GLU cc_start: 0.8203 (mp0) cc_final: 0.7903 (mp0) REVERT: A 1107 ASP cc_start: 0.7398 (m-30) cc_final: 0.7109 (m-30) REVERT: A 1122 ARG cc_start: 0.7417 (mpt-90) cc_final: 0.7068 (mmt90) REVERT: A 1130 TYR cc_start: 0.7862 (m-10) cc_final: 0.7621 (m-10) REVERT: A 1207 LEU cc_start: 0.8189 (OUTLIER) cc_final: 0.7956 (mm) REVERT: A 1210 LEU cc_start: 0.8176 (OUTLIER) cc_final: 0.7966 (tp) REVERT: A 1277 GLN cc_start: 0.7548 (mm-40) cc_final: 0.7216 (mt0) REVERT: A 1292 VAL cc_start: 0.8015 (t) cc_final: 0.7105 (m) REVERT: A 1589 VAL cc_start: 0.8559 (m) cc_final: 0.8317 (p) REVERT: A 1621 MET cc_start: 0.7652 (mtm) cc_final: 0.7440 (mtp) REVERT: A 1760 GLU cc_start: 0.7905 (tt0) cc_final: 0.7664 (tm-30) REVERT: A 1831 MET cc_start: 0.8160 (mtp) cc_final: 0.7864 (mmm) REVERT: A 1845 LYS cc_start: 0.8115 (mtpt) cc_final: 0.7850 (mtpt) REVERT: A 1846 LYS cc_start: 0.7859 (mttt) cc_final: 0.7505 (mtmt) REVERT: A 1887 LYS cc_start: 0.8181 (mtmt) cc_final: 0.7596 (mtmm) REVERT: A 2037 LYS cc_start: 0.8409 (mttt) cc_final: 0.8193 (mttp) REVERT: A 2206 MET cc_start: 0.6235 (mmm) cc_final: 0.5876 (mmm) REVERT: A 2239 MET cc_start: 0.8187 (mmt) cc_final: 0.7977 (mmp) REVERT: A 2581 MET cc_start: 0.7727 (tmm) cc_final: 0.6423 (tmm) REVERT: A 2692 GLN cc_start: 0.7986 (mm-40) cc_final: 0.7655 (mm-40) REVERT: A 2755 THR cc_start: 0.7875 (m) cc_final: 0.6873 (p) REVERT: A 2802 MET cc_start: 0.8276 (ttt) cc_final: 0.8010 (ttm) REVERT: A 2856 ASP cc_start: 0.6411 (t0) cc_final: 0.6127 (t0) REVERT: A 2906 LYS cc_start: 0.8088 (tptp) cc_final: 0.7884 (tptp) REVERT: A 2959 LYS cc_start: 0.8236 (ptmt) cc_final: 0.7969 (ptpp) REVERT: A 2994 TYR cc_start: 0.7768 (t80) cc_final: 0.7466 (t80) REVERT: A 3050 GLU cc_start: 0.7781 (tt0) cc_final: 0.7418 (tt0) REVERT: A 3146 PHE cc_start: 0.8361 (t80) cc_final: 0.8116 (t80) REVERT: A 3204 ASN cc_start: 0.8321 (m-40) cc_final: 0.8084 (m110) REVERT: A 3247 SER cc_start: 0.7946 (m) cc_final: 0.7564 (p) REVERT: A 3264 MET cc_start: 0.7642 (mmm) cc_final: 0.7147 (mmm) REVERT: A 3282 LEU cc_start: 0.8553 (mp) cc_final: 0.8349 (mt) REVERT: A 3356 PHE cc_start: 0.7810 (p90) cc_final: 0.7419 (p90) REVERT: A 3391 ARG cc_start: 0.7943 (ttm-80) cc_final: 0.7627 (ttt90) REVERT: A 3408 GLU cc_start: 0.7718 (mp0) cc_final: 0.7479 (mp0) REVERT: A 3435 VAL cc_start: 0.8443 (t) cc_final: 0.8198 (m) REVERT: A 3481 GLN cc_start: 0.7759 (tm-30) cc_final: 0.7188 (tm-30) REVERT: A 3491 TYR cc_start: 0.7516 (m-80) cc_final: 0.7246 (m-80) REVERT: A 3502 GLU cc_start: 0.8224 (tt0) cc_final: 0.7895 (tt0) REVERT: A 3537 LYS cc_start: 0.8016 (mttt) cc_final: 0.7741 (mmmm) REVERT: A 3555 LYS cc_start: 0.8437 (mmtt) cc_final: 0.8230 (mmtt) REVERT: A 3620 THR cc_start: 0.8273 (OUTLIER) cc_final: 0.8040 (p) REVERT: A 3662 LYS cc_start: 0.7917 (mttt) cc_final: 0.7516 (mmmm) REVERT: A 3727 GLU cc_start: 0.7952 (mt-10) cc_final: 0.7451 (mt-10) REVERT: A 3750 ARG cc_start: 0.6406 (mtt90) cc_final: 0.6005 (mtt180) REVERT: A 3867 CYS cc_start: 0.8165 (m) cc_final: 0.7772 (t) REVERT: A 3875 GLU cc_start: 0.7921 (mt-10) cc_final: 0.7651 (mt-10) REVERT: A 3884 ILE cc_start: 0.8183 (mt) cc_final: 0.7937 (mp) outliers start: 66 outliers final: 40 residues processed: 656 average time/residue: 0.1857 time to fit residues: 186.9023 Evaluate side-chains 623 residues out of total 2917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 579 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain A residue 597 ASN Chi-restraints excluded: chain A residue 648 CYS Chi-restraints excluded: chain A residue 799 GLU Chi-restraints excluded: chain A residue 806 ASN Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 865 CYS Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain A residue 944 HIS Chi-restraints excluded: chain A residue 1025 SER Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1137 SER Chi-restraints excluded: chain A residue 1183 VAL Chi-restraints excluded: chain A residue 1207 LEU Chi-restraints excluded: chain A residue 1210 LEU Chi-restraints excluded: chain A residue 1412 LEU Chi-restraints excluded: chain A residue 1553 ILE Chi-restraints excluded: chain A residue 1620 GLU Chi-restraints excluded: chain A residue 1753 SER Chi-restraints excluded: chain A residue 1812 SER Chi-restraints excluded: chain A residue 1851 LEU Chi-restraints excluded: chain A residue 2467 SER Chi-restraints excluded: chain A residue 2507 THR Chi-restraints excluded: chain A residue 2526 THR Chi-restraints excluded: chain A residue 2533 LEU Chi-restraints excluded: chain A residue 2645 VAL Chi-restraints excluded: chain A residue 2675 VAL Chi-restraints excluded: chain A residue 2757 LEU Chi-restraints excluded: chain A residue 2805 SER Chi-restraints excluded: chain A residue 2965 SER Chi-restraints excluded: chain A residue 3080 LEU Chi-restraints excluded: chain A residue 3184 MET Chi-restraints excluded: chain A residue 3243 LEU Chi-restraints excluded: chain A residue 3265 SER Chi-restraints excluded: chain A residue 3277 THR Chi-restraints excluded: chain A residue 3451 LYS Chi-restraints excluded: chain A residue 3466 VAL Chi-restraints excluded: chain A residue 3499 THR Chi-restraints excluded: chain A residue 3504 LEU Chi-restraints excluded: chain A residue 3510 LEU Chi-restraints excluded: chain A residue 3548 THR Chi-restraints excluded: chain A residue 3620 THR Chi-restraints excluded: chain A residue 3686 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: [141, 72, 212, 79, 3, 217, 124, 159, 166, 30, 262] chunk 141 optimal weight: 30.0000 chunk 72 optimal weight: 0.9990 chunk 212 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 chunk 3 optimal weight: 30.0000 chunk 217 optimal weight: 3.9990 chunk 124 optimal weight: 0.8980 chunk 159 optimal weight: 0.9990 chunk 166 optimal weight: 0.9990 chunk 30 optimal weight: 0.3980 chunk 262 optimal weight: 0.9990 overall best weight: 0.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 474 GLN A 597 ASN A 806 ASN A1034 ASN A1068 ASN A1424 GLN A1576 ASN A1768 GLN A1829 HIS ** A2275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2413 ASN A3023 ASN ** A3045 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3375 HIS A3615 ASN A3765 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.159384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.132606 restraints weight = 36634.587| |-----------------------------------------------------------------------------| r_work (start): 0.3633 rms_B_bonded: 2.02 r_work: 0.3513 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3357 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.2117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 26998 Z= 0.132 Angle : 0.505 8.002 36630 Z= 0.264 Chirality : 0.039 0.303 4276 Planarity : 0.004 0.049 4445 Dihedral : 10.216 176.247 4127 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.97 % Favored : 97.00 % Rotamer: Outliers : 2.09 % Allowed : 12.07 % Favored : 85.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.04 % 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: 0.52 (0.15), residues: 3135 helix: 1.14 (0.12), residues: 1826 sheet: -0.16 (0.34), residues: 231 loop : -0.83 (0.19), residues: 1078 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A3135 TYR 0.020 0.001 TYR A3239 PHE 0.023 0.001 PHE A1966 TRP 0.013 0.001 TRP A3482 HIS 0.010 0.001 HIS A2996 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 (26993) covalent geometry : angle 0.50455 / 0.26 (36624) hydrogen bonds : bond 0.03777 / 2.57 ( 1401) hydrogen bonds : angle 4.23552 / 3.01 ( 3965) metal coordination : bond 0.00479 / 0.23 ( 4) metal coordination : angle 2.16883 / 0.79 ( 6) Misc. bond : bond 0.00011 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 656 residues out of total 2917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 595 time to evaluate : 0.891 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 490 LEU cc_start: 0.7468 (mt) cc_final: 0.7255 (mt) REVERT: A 494 TRP cc_start: 0.8133 (m-10) cc_final: 0.7810 (m-10) REVERT: A 510 ASN cc_start: 0.7235 (m-40) cc_final: 0.6716 (t0) REVERT: A 521 LYS cc_start: 0.8313 (tptt) cc_final: 0.8038 (tptt) REVERT: A 556 SER cc_start: 0.8175 (m) cc_final: 0.7939 (p) REVERT: A 573 LYS cc_start: 0.8677 (mttt) cc_final: 0.8470 (mtpp) REVERT: A 584 VAL cc_start: 0.8018 (t) cc_final: 0.7589 (p) REVERT: A 599 LYS cc_start: 0.8274 (tptm) cc_final: 0.7938 (tptm) REVERT: A 614 GLU cc_start: 0.7511 (tp30) cc_final: 0.7219 (tp30) REVERT: A 679 ASP cc_start: 0.8272 (t0) cc_final: 0.7930 (t0) REVERT: A 753 MET cc_start: 0.7729 (mmm) cc_final: 0.7095 (mmm) REVERT: A 805 GLU cc_start: 0.7610 (tt0) cc_final: 0.7387 (tt0) REVERT: A 806 ASN cc_start: 0.7264 (OUTLIER) cc_final: 0.7045 (p0) REVERT: A 844 LYS cc_start: 0.8621 (tttt) cc_final: 0.8147 (ttpp) REVERT: A 881 ARG cc_start: 0.8093 (ttm170) cc_final: 0.7756 (ttm170) REVERT: A 963 ARG cc_start: 0.8167 (ttt-90) cc_final: 0.7890 (ttt-90) REVERT: A 968 GLU cc_start: 0.7778 (mt-10) cc_final: 0.7321 (mt-10) REVERT: A 1071 ASN cc_start: 0.7931 (t0) cc_final: 0.7629 (t0) REVERT: A 1084 LYS cc_start: 0.7694 (mtpt) cc_final: 0.7343 (mppt) REVERT: A 1086 GLU cc_start: 0.8226 (mp0) cc_final: 0.7896 (mp0) REVERT: A 1107 ASP cc_start: 0.7410 (m-30) cc_final: 0.7111 (m-30) REVERT: A 1122 ARG cc_start: 0.7356 (mpt-90) cc_final: 0.6995 (mmt90) REVERT: A 1123 ARG cc_start: 0.7426 (ttm110) cc_final: 0.7000 (mtp85) REVERT: A 1130 TYR cc_start: 0.7905 (m-10) cc_final: 0.7625 (m-10) REVERT: A 1292 VAL cc_start: 0.7994 (t) cc_final: 0.7085 (m) REVERT: A 1589 VAL cc_start: 0.8542 (m) cc_final: 0.8320 (p) REVERT: A 1760 GLU cc_start: 0.7859 (tt0) cc_final: 0.7616 (tm-30) REVERT: A 1846 LYS cc_start: 0.7884 (mttt) cc_final: 0.7517 (mtmt) REVERT: A 1887 LYS cc_start: 0.8148 (mtmt) cc_final: 0.7577 (mtmm) REVERT: A 2037 LYS cc_start: 0.8403 (mttt) cc_final: 0.8141 (mttp) REVERT: A 2239 MET cc_start: 0.8139 (mmt) cc_final: 0.7907 (mmp) REVERT: A 2297 GLU cc_start: 0.6805 (mm-30) cc_final: 0.6486 (mm-30) REVERT: A 2581 MET cc_start: 0.7682 (tmm) cc_final: 0.6449 (tmm) REVERT: A 2692 GLN cc_start: 0.8007 (mm-40) cc_final: 0.7620 (mm-40) REVERT: A 2755 THR cc_start: 0.7837 (m) cc_final: 0.6936 (p) REVERT: A 2856 ASP cc_start: 0.6399 (t0) cc_final: 0.6092 (t0) REVERT: A 2906 LYS cc_start: 0.8082 (tptp) cc_final: 0.7860 (tptp) REVERT: A 2959 LYS cc_start: 0.8235 (ptmt) cc_final: 0.7943 (ptpp) REVERT: A 2994 TYR cc_start: 0.7683 (t80) cc_final: 0.7373 (t80) REVERT: A 3050 GLU cc_start: 0.7793 (tt0) cc_final: 0.7405 (tt0) REVERT: A 3146 PHE cc_start: 0.8344 (t80) cc_final: 0.8093 (t80) REVERT: A 3160 GLU cc_start: 0.6839 (OUTLIER) cc_final: 0.6612 (mp0) REVERT: A 3204 ASN cc_start: 0.8357 (m-40) cc_final: 0.8084 (m110) REVERT: A 3236 SER cc_start: 0.8275 (m) cc_final: 0.8045 (t) REVERT: A 3391 ARG cc_start: 0.7876 (ttm-80) cc_final: 0.7476 (ttt90) REVERT: A 3419 GLN cc_start: 0.7906 (mt0) cc_final: 0.7671 (mm-40) REVERT: A 3435 VAL cc_start: 0.8443 (t) cc_final: 0.8207 (m) REVERT: A 3481 GLN cc_start: 0.7767 (tm-30) cc_final: 0.7416 (tm-30) REVERT: A 3491 TYR cc_start: 0.7521 (m-80) cc_final: 0.7233 (m-80) REVERT: A 3502 GLU cc_start: 0.8221 (tt0) cc_final: 0.7882 (tt0) REVERT: A 3555 LYS cc_start: 0.8325 (mmtt) cc_final: 0.8035 (mmtt) REVERT: A 3612 GLU cc_start: 0.7658 (OUTLIER) cc_final: 0.7433 (mt-10) REVERT: A 3662 LYS cc_start: 0.7887 (mttt) cc_final: 0.7470 (mmmm) REVERT: A 3727 GLU cc_start: 0.7915 (mt-10) cc_final: 0.7373 (mt-10) REVERT: A 3746 ARG cc_start: 0.7817 (ptt90) cc_final: 0.7594 (ptt90) REVERT: A 3750 ARG cc_start: 0.6346 (mtt90) cc_final: 0.6046 (mtt90) REVERT: A 3867 CYS cc_start: 0.8148 (m) cc_final: 0.7790 (t) outliers start: 61 outliers final: 37 residues processed: 624 average time/residue: 0.1819 time to fit residues: 173.7841 Evaluate side-chains 609 residues out of total 2917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 569 time to evaluate : 0.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain A residue 597 ASN Chi-restraints excluded: chain A residue 648 CYS Chi-restraints excluded: chain A residue 799 GLU Chi-restraints excluded: chain A residue 806 ASN Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain A residue 936 GLU Chi-restraints excluded: chain A residue 1025 SER Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1134 LEU Chi-restraints excluded: chain A residue 1137 SER Chi-restraints excluded: chain A residue 1210 LEU Chi-restraints excluded: chain A residue 1250 LYS Chi-restraints excluded: chain A residue 1553 ILE Chi-restraints excluded: chain A residue 1603 SER Chi-restraints excluded: chain A residue 1667 CYS Chi-restraints excluded: chain A residue 1753 SER Chi-restraints excluded: chain A residue 1812 SER Chi-restraints excluded: chain A residue 1851 LEU Chi-restraints excluded: chain A residue 2470 HIS Chi-restraints excluded: chain A residue 2526 THR Chi-restraints excluded: chain A residue 2645 VAL Chi-restraints excluded: chain A residue 2675 VAL Chi-restraints excluded: chain A residue 2757 LEU Chi-restraints excluded: chain A residue 2787 ASN Chi-restraints excluded: chain A residue 2965 SER Chi-restraints excluded: chain A residue 3029 LEU Chi-restraints excluded: chain A residue 3080 LEU Chi-restraints excluded: chain A residue 3160 GLU Chi-restraints excluded: chain A residue 3184 MET Chi-restraints excluded: chain A residue 3243 LEU Chi-restraints excluded: chain A residue 3441 ASN Chi-restraints excluded: chain A residue 3451 LYS Chi-restraints excluded: chain A residue 3499 THR Chi-restraints excluded: chain A residue 3504 LEU Chi-restraints excluded: chain A residue 3510 LEU Chi-restraints excluded: chain A residue 3548 THR Chi-restraints excluded: chain A residue 3612 GLU Chi-restraints excluded: chain A residue 3828 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: [208, 91, 263, 224, 37, 142, 212, 237, 102, 10, 46] chunk 208 optimal weight: 0.0170 chunk 91 optimal weight: 3.9990 chunk 263 optimal weight: 0.9990 chunk 224 optimal weight: 0.9980 chunk 37 optimal weight: 0.2980 chunk 142 optimal weight: 8.9990 chunk 212 optimal weight: 5.9990 chunk 237 optimal weight: 0.9980 chunk 102 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 overall best weight: 0.6620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 474 GLN A 597 ASN A1034 ASN A1576 ASN A2275 GLN ** A2366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2413 ASN A2470 HIS A2901 GLN A3023 ASN ** A3045 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3375 HIS A3615 ASN A3710 GLN A3765 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.159763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.132994 restraints weight = 36479.325| |-----------------------------------------------------------------------------| r_work (start): 0.3639 rms_B_bonded: 2.02 r_work: 0.3519 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3364 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.2225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 26998 Z= 0.116 Angle : 0.485 8.043 36630 Z= 0.254 Chirality : 0.038 0.231 4276 Planarity : 0.004 0.050 4445 Dihedral : 10.140 176.418 4127 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.16 % Favored : 96.81 % Rotamer: Outliers : 1.95 % Allowed : 12.92 % Favored : 85.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.04 % 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: 0.70 (0.15), residues: 3135 helix: 1.32 (0.12), residues: 1828 sheet: -0.17 (0.34), residues: 232 loop : -0.81 (0.19), residues: 1075 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1307 TYR 0.019 0.001 TYR A3239 PHE 0.023 0.001 PHE A1966 TRP 0.012 0.001 TRP A3482 HIS 0.008 0.001 HIS A 840 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.12 (26993) covalent geometry : angle 0.48406 / 0.25 (36624) hydrogen bonds : bond 0.03485 / 2.37 ( 1401) hydrogen bonds : angle 4.09040 / 2.91 ( 3965) metal coordination : bond 0.00423 / 0.21 ( 4) metal coordination : angle 1.93077 / 0.70 ( 6) Misc. bond : bond 0.00050 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 635 residues out of total 2917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 578 time to evaluate : 0.912 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 490 LEU cc_start: 0.7482 (mt) cc_final: 0.7273 (mt) REVERT: A 494 TRP cc_start: 0.8134 (m-10) cc_final: 0.7806 (m-10) REVERT: A 510 ASN cc_start: 0.7215 (m-40) cc_final: 0.6722 (t0) REVERT: A 521 LYS cc_start: 0.8294 (tptt) cc_final: 0.8018 (tptt) REVERT: A 552 TYR cc_start: 0.8738 (t80) cc_final: 0.8454 (t80) REVERT: A 556 SER cc_start: 0.8160 (m) cc_final: 0.7937 (p) REVERT: A 573 LYS cc_start: 0.8688 (mttt) cc_final: 0.8438 (mtpp) REVERT: A 584 VAL cc_start: 0.8078 (t) cc_final: 0.7573 (p) REVERT: A 614 GLU cc_start: 0.7533 (tp30) cc_final: 0.7215 (tp30) REVERT: A 753 MET cc_start: 0.7761 (mmm) cc_final: 0.7153 (mmm) REVERT: A 805 GLU cc_start: 0.7585 (OUTLIER) cc_final: 0.7380 (tt0) REVERT: A 806 ASN cc_start: 0.7065 (OUTLIER) cc_final: 0.6775 (p0) REVERT: A 844 LYS cc_start: 0.8578 (tttt) cc_final: 0.8123 (ttpp) REVERT: A 881 ARG cc_start: 0.8105 (ttm170) cc_final: 0.7764 (ttm170) REVERT: A 963 ARG cc_start: 0.8162 (ttt-90) cc_final: 0.7853 (ttt-90) REVERT: A 968 GLU cc_start: 0.7829 (mt-10) cc_final: 0.7318 (mt-10) REVERT: A 1071 ASN cc_start: 0.7938 (t0) cc_final: 0.7645 (t0) REVERT: A 1084 LYS cc_start: 0.7680 (mtpt) cc_final: 0.7308 (mppt) REVERT: A 1086 GLU cc_start: 0.8216 (mp0) cc_final: 0.7865 (mp0) REVERT: A 1107 ASP cc_start: 0.7456 (m-30) cc_final: 0.7162 (m-30) REVERT: A 1122 ARG cc_start: 0.7348 (mpt-90) cc_final: 0.6964 (mmt90) REVERT: A 1123 ARG cc_start: 0.7413 (ttm110) cc_final: 0.6936 (mtp85) REVERT: A 1130 TYR cc_start: 0.7920 (m-10) cc_final: 0.7624 (m-10) REVERT: A 1230 PHE cc_start: 0.8454 (t80) cc_final: 0.8225 (t80) REVERT: A 1292 VAL cc_start: 0.8003 (t) cc_final: 0.7088 (m) REVERT: A 1589 VAL cc_start: 0.8517 (m) cc_final: 0.8297 (p) REVERT: A 1647 MET cc_start: 0.8243 (ttm) cc_final: 0.8040 (ttm) REVERT: A 1760 GLU cc_start: 0.7808 (tt0) cc_final: 0.7554 (tm-30) REVERT: A 1846 LYS cc_start: 0.7889 (mttt) cc_final: 0.7547 (mtmt) REVERT: A 1887 LYS cc_start: 0.8187 (mtmt) cc_final: 0.7638 (mtmm) REVERT: A 2037 LYS cc_start: 0.8445 (mttt) cc_final: 0.8195 (mttp) REVERT: A 2206 MET cc_start: 0.6117 (mmm) cc_final: 0.5870 (mmm) REVERT: A 2239 MET cc_start: 0.8131 (mmt) cc_final: 0.7877 (mmp) REVERT: A 2297 GLU cc_start: 0.6789 (mm-30) cc_final: 0.6480 (mm-30) REVERT: A 2581 MET cc_start: 0.7674 (tmm) cc_final: 0.6494 (tmm) REVERT: A 2692 GLN cc_start: 0.7991 (mm-40) cc_final: 0.7612 (mm-40) REVERT: A 2755 THR cc_start: 0.7871 (m) cc_final: 0.7009 (p) REVERT: A 2856 ASP cc_start: 0.6487 (t0) cc_final: 0.6145 (t0) REVERT: A 2906 LYS cc_start: 0.8081 (tptp) cc_final: 0.7874 (tptp) REVERT: A 2916 GLU cc_start: 0.7213 (tp30) cc_final: 0.6932 (tp30) REVERT: A 2959 LYS cc_start: 0.8237 (ptmt) cc_final: 0.7949 (ptpp) REVERT: A 2994 TYR cc_start: 0.7688 (t80) cc_final: 0.7341 (t80) REVERT: A 3050 GLU cc_start: 0.7782 (tt0) cc_final: 0.7363 (tt0) REVERT: A 3146 PHE cc_start: 0.8336 (t80) cc_final: 0.8090 (t80) REVERT: A 3160 GLU cc_start: 0.6820 (OUTLIER) cc_final: 0.6581 (mp0) REVERT: A 3204 ASN cc_start: 0.8359 (m-40) cc_final: 0.7939 (t0) REVERT: A 3236 SER cc_start: 0.8245 (m) cc_final: 0.8030 (t) REVERT: A 3356 PHE cc_start: 0.7719 (p90) cc_final: 0.7111 (p90) REVERT: A 3435 VAL cc_start: 0.8435 (t) cc_final: 0.8204 (m) REVERT: A 3481 GLN cc_start: 0.7746 (tm-30) cc_final: 0.7377 (tm-30) REVERT: A 3491 TYR cc_start: 0.7498 (m-80) cc_final: 0.7227 (m-80) REVERT: A 3502 GLU cc_start: 0.8212 (tt0) cc_final: 0.7879 (tt0) REVERT: A 3537 LYS cc_start: 0.7921 (mttt) cc_final: 0.7649 (mmmm) REVERT: A 3612 GLU cc_start: 0.7658 (OUTLIER) cc_final: 0.7437 (mt-10) REVERT: A 3637 TYR cc_start: 0.7906 (t80) cc_final: 0.7673 (t80) REVERT: A 3662 LYS cc_start: 0.7859 (mttt) cc_final: 0.7482 (mmmm) REVERT: A 3727 GLU cc_start: 0.7947 (mt-10) cc_final: 0.7417 (mt-10) REVERT: A 3750 ARG cc_start: 0.6380 (mtt90) cc_final: 0.6084 (mtt90) REVERT: A 3867 CYS cc_start: 0.8161 (m) cc_final: 0.7804 (t) outliers start: 57 outliers final: 38 residues processed: 606 average time/residue: 0.1845 time to fit residues: 171.3605 Evaluate side-chains 607 residues out of total 2917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 565 time to evaluate : 0.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain A residue 597 ASN Chi-restraints excluded: chain A residue 604 ILE Chi-restraints excluded: chain A residue 648 CYS Chi-restraints excluded: chain A residue 805 GLU Chi-restraints excluded: chain A residue 806 ASN Chi-restraints excluded: chain A residue 865 CYS Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain A residue 936 GLU Chi-restraints excluded: chain A residue 952 LEU Chi-restraints excluded: chain A residue 1025 SER Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1137 SER Chi-restraints excluded: chain A residue 1250 LYS Chi-restraints excluded: chain A residue 1553 ILE Chi-restraints excluded: chain A residue 1620 GLU Chi-restraints excluded: chain A residue 1667 CYS Chi-restraints excluded: chain A residue 1753 SER Chi-restraints excluded: chain A residue 1812 SER Chi-restraints excluded: chain A residue 1851 LEU Chi-restraints excluded: chain A residue 2275 GLN Chi-restraints excluded: chain A residue 2470 HIS Chi-restraints excluded: chain A residue 2526 THR Chi-restraints excluded: chain A residue 2529 LEU Chi-restraints excluded: chain A residue 2675 VAL Chi-restraints excluded: chain A residue 2787 ASN Chi-restraints excluded: chain A residue 2965 SER Chi-restraints excluded: chain A residue 3029 LEU Chi-restraints excluded: chain A residue 3080 LEU Chi-restraints excluded: chain A residue 3160 GLU Chi-restraints excluded: chain A residue 3184 MET Chi-restraints excluded: chain A residue 3243 LEU Chi-restraints excluded: chain A residue 3441 ASN Chi-restraints excluded: chain A residue 3451 LYS Chi-restraints excluded: chain A residue 3499 THR Chi-restraints excluded: chain A residue 3504 LEU Chi-restraints excluded: chain A residue 3510 LEU Chi-restraints excluded: chain A residue 3548 THR Chi-restraints excluded: chain A residue 3612 GLU Chi-restraints excluded: chain A residue 3710 GLN Chi-restraints excluded: chain A residue 3828 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: [242, 79, 262, 89, 168, 229, 142, 21, 26, 115, 260] chunk 242 optimal weight: 0.8980 chunk 79 optimal weight: 0.4980 chunk 262 optimal weight: 0.8980 chunk 89 optimal weight: 2.9990 chunk 168 optimal weight: 2.9990 chunk 229 optimal weight: 6.9990 chunk 142 optimal weight: 5.9990 chunk 21 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 115 optimal weight: 2.9990 chunk 260 optimal weight: 3.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 474 GLN A 597 ASN A 806 ASN A1034 ASN A1068 ASN A1576 ASN ** A2366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2413 ASN A2614 GLN A2817 ASN ** A3045 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3285 HIS A3375 HIS A3615 ASN A3710 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.158916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.131910 restraints weight = 36395.218| |-----------------------------------------------------------------------------| r_work (start): 0.3628 rms_B_bonded: 2.02 r_work: 0.3505 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3348 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.2345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 26998 Z= 0.145 Angle : 0.494 8.381 36630 Z= 0.258 Chirality : 0.039 0.189 4276 Planarity : 0.004 0.051 4445 Dihedral : 10.096 175.651 4127 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.25 % Favored : 96.68 % Rotamer: Outliers : 2.16 % Allowed : 13.95 % Favored : 83.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.04 % 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: 0.75 (0.15), residues: 3135 helix: 1.38 (0.12), residues: 1827 sheet: -0.14 (0.34), residues: 228 loop : -0.83 (0.19), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A3746 TYR 0.017 0.001 TYR A3239 PHE 0.023 0.001 PHE A1966 TRP 0.014 0.001 TRP A3482 HIS 0.006 0.001 HIS A2996 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.14 (26993) covalent geometry : angle 0.49304 / 0.26 (36624) hydrogen bonds : bond 0.03556 / 2.41 ( 1401) hydrogen bonds : angle 4.03812 / 2.88 ( 3965) metal coordination : bond 0.00547 / 0.27 ( 4) metal coordination : angle 1.98208 / 0.73 ( 6) Misc. bond : bond 0.00063 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 633 residues out of total 2917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 570 time to evaluate : 0.807 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 482 LEU cc_start: 0.8555 (OUTLIER) cc_final: 0.8298 (tt) REVERT: A 490 LEU cc_start: 0.7506 (mt) cc_final: 0.7282 (mt) REVERT: A 494 TRP cc_start: 0.8146 (m-10) cc_final: 0.7835 (m-10) REVERT: A 510 ASN cc_start: 0.7222 (m-40) cc_final: 0.6673 (t0) REVERT: A 521 LYS cc_start: 0.8335 (tptt) cc_final: 0.8057 (tptt) REVERT: A 552 TYR cc_start: 0.8733 (t80) cc_final: 0.8447 (t80) REVERT: A 556 SER cc_start: 0.8173 (m) cc_final: 0.7956 (p) REVERT: A 614 GLU cc_start: 0.7576 (tp30) cc_final: 0.7268 (tp30) REVERT: A 753 MET cc_start: 0.7768 (mmm) cc_final: 0.7146 (mmm) REVERT: A 844 LYS cc_start: 0.8592 (tttt) cc_final: 0.8123 (ttpp) REVERT: A 881 ARG cc_start: 0.8069 (ttm170) cc_final: 0.7734 (ttm170) REVERT: A 963 ARG cc_start: 0.8167 (ttt-90) cc_final: 0.7823 (ttt-90) REVERT: A 968 GLU cc_start: 0.7858 (mt-10) cc_final: 0.7300 (mt-10) REVERT: A 1071 ASN cc_start: 0.7960 (t0) cc_final: 0.7673 (t0) REVERT: A 1086 GLU cc_start: 0.8236 (mp0) cc_final: 0.7886 (mp0) REVERT: A 1107 ASP cc_start: 0.7443 (m-30) cc_final: 0.7139 (m-30) REVERT: A 1122 ARG cc_start: 0.7369 (mpt-90) cc_final: 0.7069 (mpt-90) REVERT: A 1123 ARG cc_start: 0.7378 (ttm110) cc_final: 0.6877 (mtp85) REVERT: A 1130 TYR cc_start: 0.7898 (m-10) cc_final: 0.7605 (m-10) REVERT: A 1207 LEU cc_start: 0.8103 (mm) cc_final: 0.7810 (mp) REVERT: A 1230 PHE cc_start: 0.8494 (t80) cc_final: 0.8237 (t80) REVERT: A 1260 ASP cc_start: 0.7781 (p0) cc_final: 0.7443 (p0) REVERT: A 1292 VAL cc_start: 0.7998 (t) cc_final: 0.7093 (m) REVERT: A 1589 VAL cc_start: 0.8529 (m) cc_final: 0.8307 (p) REVERT: A 1760 GLU cc_start: 0.7898 (tt0) cc_final: 0.7633 (tm-30) REVERT: A 1792 MET cc_start: 0.8213 (mmm) cc_final: 0.7817 (mmm) REVERT: A 1830 MET cc_start: 0.8439 (ppp) cc_final: 0.8206 (ptm) REVERT: A 1831 MET cc_start: 0.8079 (mmm) cc_final: 0.7630 (mmm) REVERT: A 1846 LYS cc_start: 0.7886 (mttt) cc_final: 0.7517 (mtmt) REVERT: A 1849 LYS cc_start: 0.7564 (OUTLIER) cc_final: 0.6216 (mttt) REVERT: A 1887 LYS cc_start: 0.8168 (mtmt) cc_final: 0.7615 (mtmm) REVERT: A 2037 LYS cc_start: 0.8445 (mttt) cc_final: 0.8200 (mttp) REVERT: A 2239 MET cc_start: 0.8126 (mmt) cc_final: 0.7877 (mmp) REVERT: A 2275 GLN cc_start: 0.8183 (tt0) cc_final: 0.7957 (tt0) REVERT: A 2280 ARG cc_start: 0.7662 (ttm-80) cc_final: 0.7305 (ttm170) REVERT: A 2297 GLU cc_start: 0.6808 (mm-30) cc_final: 0.6496 (mm-30) REVERT: A 2581 MET cc_start: 0.7686 (tmm) cc_final: 0.6489 (tmm) REVERT: A 2692 GLN cc_start: 0.8000 (mm-40) cc_final: 0.7591 (mm-40) REVERT: A 2755 THR cc_start: 0.7931 (m) cc_final: 0.7063 (p) REVERT: A 2856 ASP cc_start: 0.6501 (t0) cc_final: 0.6164 (t0) REVERT: A 2906 LYS cc_start: 0.8071 (tptp) cc_final: 0.7851 (tptp) REVERT: A 2959 LYS cc_start: 0.8252 (ptmt) cc_final: 0.7960 (ptpp) REVERT: A 2994 TYR cc_start: 0.7697 (t80) cc_final: 0.7359 (t80) REVERT: A 3050 GLU cc_start: 0.7818 (tt0) cc_final: 0.6938 (tt0) REVERT: A 3146 PHE cc_start: 0.8352 (t80) cc_final: 0.8119 (t80) REVERT: A 3151 MET cc_start: 0.7715 (tmm) cc_final: 0.7329 (tmm) REVERT: A 3160 GLU cc_start: 0.6840 (OUTLIER) cc_final: 0.6609 (mp0) REVERT: A 3204 ASN cc_start: 0.8354 (m-40) cc_final: 0.8102 (m110) REVERT: A 3236 SER cc_start: 0.8243 (m) cc_final: 0.8027 (t) REVERT: A 3337 TYR cc_start: 0.8151 (t80) cc_final: 0.7572 (t80) REVERT: A 3356 PHE cc_start: 0.7757 (p90) cc_final: 0.7169 (p90) REVERT: A 3397 MET cc_start: 0.8301 (mmm) cc_final: 0.8029 (mmm) REVERT: A 3435 VAL cc_start: 0.8440 (t) cc_final: 0.8204 (m) REVERT: A 3481 GLN cc_start: 0.7774 (tm-30) cc_final: 0.7403 (tm-30) REVERT: A 3491 TYR cc_start: 0.7511 (m-80) cc_final: 0.7246 (m-80) REVERT: A 3502 GLU cc_start: 0.8202 (tt0) cc_final: 0.7837 (tt0) REVERT: A 3537 LYS cc_start: 0.7955 (mttt) cc_final: 0.7693 (mmmm) REVERT: A 3612 GLU cc_start: 0.7685 (OUTLIER) cc_final: 0.7463 (mt-10) REVERT: A 3637 TYR cc_start: 0.7892 (t80) cc_final: 0.7668 (t80) REVERT: A 3662 LYS cc_start: 0.7855 (mttt) cc_final: 0.7458 (mmmm) REVERT: A 3727 GLU cc_start: 0.7984 (mt-10) cc_final: 0.7453 (mt-10) REVERT: A 3750 ARG cc_start: 0.6417 (mtt90) cc_final: 0.6107 (mtt90) REVERT: A 3867 CYS cc_start: 0.8165 (m) cc_final: 0.7807 (t) outliers start: 63 outliers final: 45 residues processed: 603 average time/residue: 0.1872 time to fit residues: 171.6687 Evaluate side-chains 609 residues out of total 2917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 560 time to evaluate : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 597 ASN Chi-restraints excluded: chain A residue 604 ILE Chi-restraints excluded: chain A residue 648 CYS Chi-restraints excluded: chain A residue 806 ASN Chi-restraints excluded: chain A residue 865 CYS Chi-restraints excluded: chain A residue 866 SER Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain A residue 936 GLU Chi-restraints excluded: chain A residue 1025 SER Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1250 LYS Chi-restraints excluded: chain A residue 1317 VAL Chi-restraints excluded: chain A residue 1553 ILE Chi-restraints excluded: chain A residue 1620 GLU Chi-restraints excluded: chain A residue 1667 CYS Chi-restraints excluded: chain A residue 1753 SER Chi-restraints excluded: chain A residue 1812 SER Chi-restraints excluded: chain A residue 1849 LYS Chi-restraints excluded: chain A residue 2467 SER Chi-restraints excluded: chain A residue 2507 THR Chi-restraints excluded: chain A residue 2526 THR Chi-restraints excluded: chain A residue 2529 LEU Chi-restraints excluded: chain A residue 2563 ASP Chi-restraints excluded: chain A residue 2621 MET Chi-restraints excluded: chain A residue 2645 VAL Chi-restraints excluded: chain A residue 2675 VAL Chi-restraints excluded: chain A residue 2757 LEU Chi-restraints excluded: chain A residue 2787 ASN Chi-restraints excluded: chain A residue 2805 SER Chi-restraints excluded: chain A residue 2965 SER Chi-restraints excluded: chain A residue 3029 LEU Chi-restraints excluded: chain A residue 3080 LEU Chi-restraints excluded: chain A residue 3160 GLU Chi-restraints excluded: chain A residue 3184 MET Chi-restraints excluded: chain A residue 3243 LEU Chi-restraints excluded: chain A residue 3277 THR Chi-restraints excluded: chain A residue 3441 ASN Chi-restraints excluded: chain A residue 3451 LYS Chi-restraints excluded: chain A residue 3499 THR Chi-restraints excluded: chain A residue 3504 LEU Chi-restraints excluded: chain A residue 3510 LEU Chi-restraints excluded: chain A residue 3548 THR Chi-restraints excluded: chain A residue 3612 GLU Chi-restraints excluded: chain A residue 3676 LYS Chi-restraints excluded: chain A residue 3828 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: [86, 300, 194, 307, 196, 3, 316, 161, 166, 228, 113] chunk 86 optimal weight: 0.9980 chunk 300 optimal weight: 6.9990 chunk 194 optimal weight: 3.9990 chunk 307 optimal weight: 20.0000 chunk 196 optimal weight: 0.0980 chunk 3 optimal weight: 30.0000 chunk 316 optimal weight: 0.5980 chunk 161 optimal weight: 2.9990 chunk 166 optimal weight: 1.9990 chunk 228 optimal weight: 0.3980 chunk 113 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 474 GLN A 597 ASN ** A 806 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1576 ASN A2275 GLN ** A2366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2413 ASN ** A3045 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3098 GLN A3375 HIS A3615 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.159453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.132574 restraints weight = 36340.282| |-----------------------------------------------------------------------------| r_work (start): 0.3640 rms_B_bonded: 2.01 r_work: 0.3519 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3364 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.2399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 26998 Z= 0.112 Angle : 0.477 8.356 36630 Z= 0.250 Chirality : 0.038 0.282 4276 Planarity : 0.003 0.050 4445 Dihedral : 10.075 176.558 4127 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.16 % Favored : 96.78 % Rotamer: Outliers : 1.99 % Allowed : 14.91 % Favored : 83.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.04 % 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: 0.85 (0.15), residues: 3135 helix: 1.47 (0.12), residues: 1828 sheet: -0.17 (0.34), residues: 232 loop : -0.80 (0.19), residues: 1075 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A3746 TYR 0.016 0.001 TYR A3358 PHE 0.023 0.001 PHE A1966 TRP 0.012 0.001 TRP A3482 HIS 0.006 0.001 HIS A 840 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.11 (26993) covalent geometry : angle 0.47608 / 0.25 (36624) hydrogen bonds : bond 0.03348 / 2.28 ( 1401) hydrogen bonds : angle 3.96492 / 2.83 ( 3965) metal coordination : bond 0.00374 / 0.18 ( 4) metal coordination : angle 1.73233 / 0.63 ( 6) Misc. bond : bond 0.00057 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 635 residues out of total 2917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 577 time to evaluate : 0.905 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 482 LEU cc_start: 0.8539 (OUTLIER) cc_final: 0.8278 (tt) REVERT: A 494 TRP cc_start: 0.8158 (m-10) cc_final: 0.7879 (m-10) REVERT: A 510 ASN cc_start: 0.7213 (m-40) cc_final: 0.6700 (t0) REVERT: A 521 LYS cc_start: 0.8281 (tptt) cc_final: 0.8007 (tptt) REVERT: A 556 SER cc_start: 0.8149 (m) cc_final: 0.7943 (p) REVERT: A 614 GLU cc_start: 0.7558 (tp30) cc_final: 0.7218 (tp30) REVERT: A 753 MET cc_start: 0.7679 (mmm) cc_final: 0.7039 (mmm) REVERT: A 844 LYS cc_start: 0.8555 (tttt) cc_final: 0.8062 (ttpp) REVERT: A 881 ARG cc_start: 0.8080 (ttm170) cc_final: 0.7748 (ttm170) REVERT: A 920 LYS cc_start: 0.7631 (tttt) cc_final: 0.7338 (tttt) REVERT: A 963 ARG cc_start: 0.8178 (ttt-90) cc_final: 0.7833 (ttt-90) REVERT: A 968 GLU cc_start: 0.7900 (mt-10) cc_final: 0.7361 (mt-10) REVERT: A 1071 ASN cc_start: 0.7952 (t0) cc_final: 0.7666 (t0) REVERT: A 1086 GLU cc_start: 0.8238 (mp0) cc_final: 0.7870 (mp0) REVERT: A 1107 ASP cc_start: 0.7429 (m-30) cc_final: 0.7127 (m-30) REVERT: A 1122 ARG cc_start: 0.7346 (mpt-90) cc_final: 0.7040 (mpt-90) REVERT: A 1123 ARG cc_start: 0.7354 (ttm110) cc_final: 0.6898 (mtp85) REVERT: A 1130 TYR cc_start: 0.7911 (m-10) cc_final: 0.7590 (m-10) REVERT: A 1230 PHE cc_start: 0.8476 (t80) cc_final: 0.8212 (t80) REVERT: A 1285 LYS cc_start: 0.8049 (mtmm) cc_final: 0.7841 (mtmm) REVERT: A 1292 VAL cc_start: 0.8007 (t) cc_final: 0.7095 (m) REVERT: A 1589 VAL cc_start: 0.8515 (m) cc_final: 0.8299 (p) REVERT: A 1760 GLU cc_start: 0.7840 (tt0) cc_final: 0.7574 (tm-30) REVERT: A 1830 MET cc_start: 0.8426 (ppp) cc_final: 0.8223 (ptm) REVERT: A 1846 LYS cc_start: 0.7886 (mttt) cc_final: 0.7560 (mtmt) REVERT: A 1849 LYS cc_start: 0.7563 (OUTLIER) cc_final: 0.6219 (mttt) REVERT: A 1887 LYS cc_start: 0.8188 (mtmt) cc_final: 0.7687 (mtmm) REVERT: A 2037 LYS cc_start: 0.8446 (mttt) cc_final: 0.8198 (mttp) REVERT: A 2239 MET cc_start: 0.8130 (mmt) cc_final: 0.7860 (mmp) REVERT: A 2280 ARG cc_start: 0.7622 (ttm-80) cc_final: 0.7398 (ttm170) REVERT: A 2297 GLU cc_start: 0.6796 (mm-30) cc_final: 0.6478 (mm-30) REVERT: A 2581 MET cc_start: 0.7684 (tmm) cc_final: 0.6481 (tmm) REVERT: A 2655 LEU cc_start: 0.6951 (OUTLIER) cc_final: 0.6476 (pt) REVERT: A 2692 GLN cc_start: 0.8045 (mm-40) cc_final: 0.7590 (mm-40) REVERT: A 2755 THR cc_start: 0.7940 (m) cc_final: 0.7118 (p) REVERT: A 2856 ASP cc_start: 0.6420 (t0) cc_final: 0.6102 (t0) REVERT: A 2868 ILE cc_start: 0.8068 (mm) cc_final: 0.7806 (mm) REVERT: A 2906 LYS cc_start: 0.8050 (tptp) cc_final: 0.7834 (tptp) REVERT: A 2959 LYS cc_start: 0.8262 (ptmt) cc_final: 0.7954 (ptpp) REVERT: A 2994 TYR cc_start: 0.7668 (t80) cc_final: 0.7301 (t80) REVERT: A 3050 GLU cc_start: 0.7792 (tt0) cc_final: 0.6864 (tt0) REVERT: A 3146 PHE cc_start: 0.8328 (t80) cc_final: 0.8077 (t80) REVERT: A 3151 MET cc_start: 0.7681 (tmm) cc_final: 0.7301 (tmm) REVERT: A 3160 GLU cc_start: 0.6841 (OUTLIER) cc_final: 0.6607 (mp0) REVERT: A 3204 ASN cc_start: 0.8354 (m-40) cc_final: 0.7943 (t0) REVERT: A 3236 SER cc_start: 0.8276 (m) cc_final: 0.8062 (t) REVERT: A 3333 LYS cc_start: 0.8351 (mttt) cc_final: 0.8078 (mttm) REVERT: A 3356 PHE cc_start: 0.7731 (p90) cc_final: 0.7158 (p90) REVERT: A 3397 MET cc_start: 0.8276 (mmm) cc_final: 0.8015 (mmm) REVERT: A 3435 VAL cc_start: 0.8423 (t) cc_final: 0.8188 (m) REVERT: A 3481 GLN cc_start: 0.7753 (tm-30) cc_final: 0.7364 (tm-30) REVERT: A 3491 TYR cc_start: 0.7491 (m-80) cc_final: 0.7211 (m-80) REVERT: A 3502 GLU cc_start: 0.8172 (tt0) cc_final: 0.7811 (tt0) REVERT: A 3537 LYS cc_start: 0.7947 (mttt) cc_final: 0.7690 (mmmm) REVERT: A 3612 GLU cc_start: 0.7693 (OUTLIER) cc_final: 0.7470 (mt-10) REVERT: A 3637 TYR cc_start: 0.7879 (t80) cc_final: 0.7628 (t80) REVERT: A 3662 LYS cc_start: 0.7839 (mttt) cc_final: 0.7455 (mmmm) REVERT: A 3727 GLU cc_start: 0.7959 (mt-10) cc_final: 0.7419 (mt-10) REVERT: A 3750 ARG cc_start: 0.6417 (mtt90) cc_final: 0.6100 (mtt90) REVERT: A 3823 MET cc_start: 0.4495 (pmm) cc_final: 0.3418 (pmm) REVERT: A 3867 CYS cc_start: 0.8163 (m) cc_final: 0.7828 (t) outliers start: 58 outliers final: 41 residues processed: 608 average time/residue: 0.1909 time to fit residues: 179.1446 Evaluate side-chains 602 residues out of total 2917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 556 time to evaluate : 0.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 594 ILE Chi-restraints excluded: chain A residue 597 ASN Chi-restraints excluded: chain A residue 648 CYS Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain A residue 952 LEU Chi-restraints excluded: chain A residue 1025 SER Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1250 LYS Chi-restraints excluded: chain A residue 1317 VAL Chi-restraints excluded: chain A residue 1432 ILE Chi-restraints excluded: chain A residue 1553 ILE Chi-restraints excluded: chain A residue 1620 GLU Chi-restraints excluded: chain A residue 1667 CYS Chi-restraints excluded: chain A residue 1753 SER Chi-restraints excluded: chain A residue 1812 SER Chi-restraints excluded: chain A residue 1849 LYS Chi-restraints excluded: chain A residue 2470 HIS Chi-restraints excluded: chain A residue 2526 THR Chi-restraints excluded: chain A residue 2529 LEU Chi-restraints excluded: chain A residue 2563 ASP Chi-restraints excluded: chain A residue 2621 MET Chi-restraints excluded: chain A residue 2645 VAL Chi-restraints excluded: chain A residue 2655 LEU Chi-restraints excluded: chain A residue 2675 VAL Chi-restraints excluded: chain A residue 2787 ASN Chi-restraints excluded: chain A residue 2805 SER Chi-restraints excluded: chain A residue 2965 SER Chi-restraints excluded: chain A residue 3029 LEU Chi-restraints excluded: chain A residue 3080 LEU Chi-restraints excluded: chain A residue 3160 GLU Chi-restraints excluded: chain A residue 3184 MET Chi-restraints excluded: chain A residue 3243 LEU Chi-restraints excluded: chain A residue 3277 THR Chi-restraints excluded: chain A residue 3306 LEU Chi-restraints excluded: chain A residue 3441 ASN Chi-restraints excluded: chain A residue 3451 LYS Chi-restraints excluded: chain A residue 3499 THR Chi-restraints excluded: chain A residue 3504 LEU Chi-restraints excluded: chain A residue 3510 LEU Chi-restraints excluded: chain A residue 3548 THR Chi-restraints excluded: chain A residue 3612 GLU Chi-restraints excluded: chain A residue 3828 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: [235, 268, 234, 126, 82, 22, 279, 253, 291, 179, 241] chunk 235 optimal weight: 2.9990 chunk 268 optimal weight: 6.9990 chunk 234 optimal weight: 2.9990 chunk 126 optimal weight: 2.9990 chunk 82 optimal weight: 4.9990 chunk 22 optimal weight: 0.5980 chunk 279 optimal weight: 1.9990 chunk 253 optimal weight: 0.5980 chunk 291 optimal weight: 6.9990 chunk 179 optimal weight: 5.9990 chunk 241 optimal weight: 0.0370 overall best weight: 1.2462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 474 GLN A 597 ASN A 667 GLN A 806 ASN A1576 ASN A2275 GLN ** A2366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3023 ASN ** A3045 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3375 HIS A3556 HIS A3615 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.158526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.131569 restraints weight = 36361.256| |-----------------------------------------------------------------------------| r_work (start): 0.3621 rms_B_bonded: 2.01 r_work: 0.3500 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3345 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.2506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 26998 Z= 0.161 Angle : 0.500 8.686 36630 Z= 0.262 Chirality : 0.039 0.258 4276 Planarity : 0.004 0.049 4445 Dihedral : 10.039 175.172 4127 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.41 % Favored : 96.52 % Rotamer: Outliers : 2.13 % Allowed : 15.53 % Favored : 82.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.04 % 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: 0.80 (0.15), residues: 3135 helix: 1.43 (0.12), residues: 1828 sheet: -0.18 (0.34), residues: 222 loop : -0.84 (0.19), residues: 1085 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A3746 TYR 0.015 0.001 TYR A3358 PHE 0.023 0.002 PHE A1966 TRP 0.015 0.001 TRP A3482 HIS 0.005 0.001 HIS A3045 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.16 (26993) covalent geometry : angle 0.49970 / 0.26 (36624) hydrogen bonds : bond 0.03573 / 2.43 ( 1401) hydrogen bonds : angle 4.00672 / 2.86 ( 3965) metal coordination : bond 0.00628 / 0.31 ( 4) metal coordination : angle 1.94994 / 0.73 ( 6) Misc. bond : bond 0.00061 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 626 residues out of total 2917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 564 time to evaluate : 0.711 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 482 LEU cc_start: 0.8579 (OUTLIER) cc_final: 0.8313 (tt) REVERT: A 494 TRP cc_start: 0.8154 (m-10) cc_final: 0.7881 (m-10) REVERT: A 510 ASN cc_start: 0.7206 (m-40) cc_final: 0.6651 (t0) REVERT: A 521 LYS cc_start: 0.8262 (tptt) cc_final: 0.7989 (tptt) REVERT: A 575 LEU cc_start: 0.8424 (OUTLIER) cc_final: 0.8210 (mp) REVERT: A 599 LYS cc_start: 0.8256 (tptm) cc_final: 0.7851 (tppp) REVERT: A 614 GLU cc_start: 0.7563 (tp30) cc_final: 0.7231 (tp30) REVERT: A 657 ASP cc_start: 0.7789 (p0) cc_final: 0.7531 (p0) REVERT: A 753 MET cc_start: 0.7675 (mmm) cc_final: 0.7075 (mmm) REVERT: A 844 LYS cc_start: 0.8579 (tttt) cc_final: 0.8104 (ttpp) REVERT: A 881 ARG cc_start: 0.8112 (ttm170) cc_final: 0.7778 (ttm170) REVERT: A 936 GLU cc_start: 0.7822 (mm-30) cc_final: 0.7565 (mm-30) REVERT: A 963 ARG cc_start: 0.8169 (ttt-90) cc_final: 0.7901 (ttt-90) REVERT: A 968 GLU cc_start: 0.7918 (mt-10) cc_final: 0.7538 (mt-10) REVERT: A 1071 ASN cc_start: 0.7938 (t0) cc_final: 0.7646 (t0) REVERT: A 1086 GLU cc_start: 0.8243 (mp0) cc_final: 0.7868 (mp0) REVERT: A 1107 ASP cc_start: 0.7384 (m-30) cc_final: 0.7086 (m-30) REVERT: A 1122 ARG cc_start: 0.7400 (mpt-90) cc_final: 0.7117 (mpt-90) REVERT: A 1123 ARG cc_start: 0.7391 (ttm110) cc_final: 0.6947 (mtp85) REVERT: A 1130 TYR cc_start: 0.7914 (m-10) cc_final: 0.7581 (m-10) REVERT: A 1183 VAL cc_start: 0.8531 (m) cc_final: 0.8073 (p) REVERT: A 1230 PHE cc_start: 0.8505 (t80) cc_final: 0.8250 (t80) REVERT: A 1260 ASP cc_start: 0.7787 (p0) cc_final: 0.7453 (p0) REVERT: A 1277 GLN cc_start: 0.7475 (mt0) cc_final: 0.7136 (mt0) REVERT: A 1285 LYS cc_start: 0.8064 (mtmm) cc_final: 0.7804 (mtmm) REVERT: A 1292 VAL cc_start: 0.8014 (t) cc_final: 0.7101 (m) REVERT: A 1550 CYS cc_start: 0.7996 (m) cc_final: 0.7176 (p) REVERT: A 1589 VAL cc_start: 0.8512 (m) cc_final: 0.8302 (p) REVERT: A 1628 CYS cc_start: 0.7578 (OUTLIER) cc_final: 0.7341 (m) REVERT: A 1760 GLU cc_start: 0.7899 (tt0) cc_final: 0.7629 (tm-30) REVERT: A 1792 MET cc_start: 0.8211 (mmm) cc_final: 0.7840 (mmm) REVERT: A 1846 LYS cc_start: 0.7926 (mttt) cc_final: 0.7601 (mtmt) REVERT: A 1849 LYS cc_start: 0.7575 (OUTLIER) cc_final: 0.6209 (mttt) REVERT: A 1887 LYS cc_start: 0.8209 (mtmt) cc_final: 0.7700 (mtmm) REVERT: A 2037 LYS cc_start: 0.8471 (mttt) cc_final: 0.8231 (mttp) REVERT: A 2239 MET cc_start: 0.8116 (mmt) cc_final: 0.7857 (mmp) REVERT: A 2297 GLU cc_start: 0.6825 (mm-30) cc_final: 0.6515 (mm-30) REVERT: A 2581 MET cc_start: 0.7707 (tmm) cc_final: 0.6502 (tmm) REVERT: A 2655 LEU cc_start: 0.6934 (OUTLIER) cc_final: 0.6525 (pt) REVERT: A 2692 GLN cc_start: 0.8015 (mm-40) cc_final: 0.7651 (mt0) REVERT: A 2755 THR cc_start: 0.7981 (m) cc_final: 0.7146 (p) REVERT: A 2856 ASP cc_start: 0.6512 (t0) cc_final: 0.6181 (t0) REVERT: A 2906 LYS cc_start: 0.8051 (tptp) cc_final: 0.7850 (tptp) REVERT: A 2959 LYS cc_start: 0.8265 (ptmt) cc_final: 0.7967 (ptpp) REVERT: A 2994 TYR cc_start: 0.7697 (t80) cc_final: 0.7353 (t80) REVERT: A 3090 THR cc_start: 0.8348 (p) cc_final: 0.8122 (p) REVERT: A 3146 PHE cc_start: 0.8342 (t80) cc_final: 0.8100 (t80) REVERT: A 3151 MET cc_start: 0.7706 (tmm) cc_final: 0.7309 (tmm) REVERT: A 3160 GLU cc_start: 0.6812 (OUTLIER) cc_final: 0.6584 (mp0) REVERT: A 3204 ASN cc_start: 0.8316 (m-40) cc_final: 0.7887 (t0) REVERT: A 3236 SER cc_start: 0.8288 (m) cc_final: 0.8065 (t) REVERT: A 3356 PHE cc_start: 0.7805 (p90) cc_final: 0.7165 (p90) REVERT: A 3435 VAL cc_start: 0.8442 (t) cc_final: 0.8204 (m) REVERT: A 3481 GLN cc_start: 0.7772 (tm-30) cc_final: 0.7380 (tm-30) REVERT: A 3491 TYR cc_start: 0.7545 (m-80) cc_final: 0.7291 (m-80) REVERT: A 3502 GLU cc_start: 0.8173 (tt0) cc_final: 0.7812 (tt0) REVERT: A 3612 GLU cc_start: 0.7689 (OUTLIER) cc_final: 0.7482 (mt-10) REVERT: A 3637 TYR cc_start: 0.7888 (t80) cc_final: 0.7679 (t80) REVERT: A 3662 LYS cc_start: 0.7848 (mttt) cc_final: 0.7454 (mmmm) REVERT: A 3727 GLU cc_start: 0.7923 (mt-10) cc_final: 0.7390 (mt-10) REVERT: A 3750 ARG cc_start: 0.6469 (mtt90) cc_final: 0.6136 (mtt90) REVERT: A 3765 GLN cc_start: 0.7038 (mm-40) cc_final: 0.6825 (mm-40) REVERT: A 3823 MET cc_start: 0.4622 (pmm) cc_final: 0.3602 (pmm) REVERT: A 3867 CYS cc_start: 0.8155 (m) cc_final: 0.7843 (t) outliers start: 62 outliers final: 46 residues processed: 597 average time/residue: 0.1860 time to fit residues: 169.1122 Evaluate side-chains 607 residues out of total 2917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 554 time to evaluate : 0.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 575 LEU Chi-restraints excluded: chain A residue 594 ILE Chi-restraints excluded: chain A residue 597 ASN Chi-restraints excluded: chain A residue 648 CYS Chi-restraints excluded: chain A residue 698 GLN Chi-restraints excluded: chain A residue 866 SER Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain A residue 1025 SER Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1250 LYS Chi-restraints excluded: chain A residue 1317 VAL Chi-restraints excluded: chain A residue 1432 ILE Chi-restraints excluded: chain A residue 1553 ILE Chi-restraints excluded: chain A residue 1620 GLU Chi-restraints excluded: chain A residue 1628 CYS Chi-restraints excluded: chain A residue 1634 GLU Chi-restraints excluded: chain A residue 1667 CYS Chi-restraints excluded: chain A residue 1753 SER Chi-restraints excluded: chain A residue 1812 SER Chi-restraints excluded: chain A residue 1849 LYS Chi-restraints excluded: chain A residue 2275 GLN Chi-restraints excluded: chain A residue 2470 HIS Chi-restraints excluded: chain A residue 2507 THR Chi-restraints excluded: chain A residue 2526 THR Chi-restraints excluded: chain A residue 2529 LEU Chi-restraints excluded: chain A residue 2563 ASP Chi-restraints excluded: chain A residue 2621 MET Chi-restraints excluded: chain A residue 2645 VAL Chi-restraints excluded: chain A residue 2655 LEU Chi-restraints excluded: chain A residue 2675 VAL Chi-restraints excluded: chain A residue 2757 LEU Chi-restraints excluded: chain A residue 2805 SER Chi-restraints excluded: chain A residue 2965 SER Chi-restraints excluded: chain A residue 3030 ILE Chi-restraints excluded: chain A residue 3080 LEU Chi-restraints excluded: chain A residue 3160 GLU Chi-restraints excluded: chain A residue 3184 MET Chi-restraints excluded: chain A residue 3243 LEU Chi-restraints excluded: chain A residue 3277 THR Chi-restraints excluded: chain A residue 3306 LEU Chi-restraints excluded: chain A residue 3441 ASN Chi-restraints excluded: chain A residue 3451 LYS Chi-restraints excluded: chain A residue 3499 THR Chi-restraints excluded: chain A residue 3504 LEU Chi-restraints excluded: chain A residue 3510 LEU Chi-restraints excluded: chain A residue 3548 THR Chi-restraints excluded: chain A residue 3612 GLU Chi-restraints excluded: chain A residue 3676 LYS Chi-restraints excluded: chain A residue 3885 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: [55, 132, 206, 14, 66, 74, 56, 127, 138, 183, 190] chunk 55 optimal weight: 4.9990 chunk 132 optimal weight: 0.8980 chunk 206 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 chunk 66 optimal weight: 0.0980 chunk 74 optimal weight: 3.9990 chunk 56 optimal weight: 0.6980 chunk 127 optimal weight: 1.9990 chunk 138 optimal weight: 8.9990 chunk 183 optimal weight: 0.4980 chunk 190 optimal weight: 0.0870 overall best weight: 0.4558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 474 GLN A 667 GLN A 806 ASN A1576 ASN A2275 GLN ** A2366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3023 ASN ** A3045 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3375 HIS A3615 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.159829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.132931 restraints weight = 36512.055| |-----------------------------------------------------------------------------| r_work (start): 0.3641 rms_B_bonded: 2.02 r_work: 0.3519 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3364 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.2525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 26998 Z= 0.105 Angle : 0.481 8.437 36630 Z= 0.252 Chirality : 0.037 0.208 4276 Planarity : 0.003 0.050 4445 Dihedral : 10.030 176.801 4127 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.19 % Favored : 96.75 % Rotamer: Outliers : 1.89 % Allowed : 16.22 % Favored : 81.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.04 % 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: 0.93 (0.15), residues: 3135 helix: 1.54 (0.12), residues: 1827 sheet: -0.11 (0.34), residues: 222 loop : -0.78 (0.19), residues: 1086 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A3746 TYR 0.017 0.001 TYR A3239 PHE 0.023 0.001 PHE A1966 TRP 0.014 0.001 TRP A2542 HIS 0.009 0.001 HIS A2996 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.10 (26993) covalent geometry : angle 0.48046 / 0.25 (36624) hydrogen bonds : bond 0.03290 / 2.24 ( 1401) hydrogen bonds : angle 3.93572 / 2.80 ( 3965) metal coordination : bond 0.00324 / 0.16 ( 4) metal coordination : angle 1.52413 / 0.55 ( 6) Misc. bond : bond 0.00048 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 608 residues out of total 2917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 553 time to evaluate : 0.804 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 482 LEU cc_start: 0.8563 (OUTLIER) cc_final: 0.8303 (tt) REVERT: A 494 TRP cc_start: 0.8139 (m-10) cc_final: 0.7862 (m-10) REVERT: A 510 ASN cc_start: 0.7149 (m-40) cc_final: 0.6618 (t0) REVERT: A 521 LYS cc_start: 0.8220 (tptt) cc_final: 0.7927 (tptt) REVERT: A 599 LYS cc_start: 0.8220 (tptm) cc_final: 0.7828 (tppp) REVERT: A 614 GLU cc_start: 0.7553 (tp30) cc_final: 0.7152 (tp30) REVERT: A 657 ASP cc_start: 0.7783 (p0) cc_final: 0.7512 (p0) REVERT: A 753 MET cc_start: 0.7712 (mmm) cc_final: 0.7127 (mmm) REVERT: A 844 LYS cc_start: 0.8565 (tttt) cc_final: 0.8085 (ttpp) REVERT: A 881 ARG cc_start: 0.8101 (ttm170) cc_final: 0.7759 (ttm170) REVERT: A 936 GLU cc_start: 0.7827 (mm-30) cc_final: 0.7575 (mm-30) REVERT: A 963 ARG cc_start: 0.8184 (ttt-90) cc_final: 0.7907 (ttt-90) REVERT: A 968 GLU cc_start: 0.7910 (mt-10) cc_final: 0.7546 (mt-10) REVERT: A 1071 ASN cc_start: 0.7956 (t0) cc_final: 0.7665 (t0) REVERT: A 1086 GLU cc_start: 0.8241 (mp0) cc_final: 0.7867 (mp0) REVERT: A 1107 ASP cc_start: 0.7401 (m-30) cc_final: 0.7054 (m-30) REVERT: A 1122 ARG cc_start: 0.7357 (mpt-90) cc_final: 0.7080 (mpt-90) REVERT: A 1123 ARG cc_start: 0.7363 (ttm110) cc_final: 0.6930 (mtp85) REVERT: A 1130 TYR cc_start: 0.7893 (m-10) cc_final: 0.7568 (m-10) REVERT: A 1183 VAL cc_start: 0.8544 (m) cc_final: 0.8105 (p) REVERT: A 1230 PHE cc_start: 0.8495 (t80) cc_final: 0.8235 (t80) REVERT: A 1285 LYS cc_start: 0.8061 (mtmm) cc_final: 0.7802 (mtmm) REVERT: A 1292 VAL cc_start: 0.7993 (t) cc_final: 0.7091 (m) REVERT: A 1550 CYS cc_start: 0.7964 (m) cc_final: 0.7166 (p) REVERT: A 1628 CYS cc_start: 0.7600 (OUTLIER) cc_final: 0.7368 (m) REVERT: A 1760 GLU cc_start: 0.7878 (tt0) cc_final: 0.7605 (tm-30) REVERT: A 1846 LYS cc_start: 0.7925 (mttt) cc_final: 0.7601 (mtmt) REVERT: A 1849 LYS cc_start: 0.7559 (OUTLIER) cc_final: 0.6179 (mttt) REVERT: A 1879 VAL cc_start: 0.8268 (p) cc_final: 0.7968 (m) REVERT: A 1887 LYS cc_start: 0.8175 (mtmt) cc_final: 0.7672 (mtmm) REVERT: A 2239 MET cc_start: 0.8112 (mmt) cc_final: 0.7848 (mmp) REVERT: A 2275 GLN cc_start: 0.8274 (OUTLIER) cc_final: 0.7647 (mt0) REVERT: A 2280 ARG cc_start: 0.7753 (ttm-80) cc_final: 0.7287 (ttm170) REVERT: A 2292 MET cc_start: 0.7740 (OUTLIER) cc_final: 0.7459 (mtp) REVERT: A 2297 GLU cc_start: 0.6797 (mm-30) cc_final: 0.6574 (mm-30) REVERT: A 2563 ASP cc_start: 0.7749 (OUTLIER) cc_final: 0.7519 (t70) REVERT: A 2581 MET cc_start: 0.7687 (tmm) cc_final: 0.6520 (tmm) REVERT: A 2655 LEU cc_start: 0.6965 (OUTLIER) cc_final: 0.6488 (pt) REVERT: A 2755 THR cc_start: 0.7996 (m) cc_final: 0.7196 (p) REVERT: A 2856 ASP cc_start: 0.6434 (t0) cc_final: 0.6173 (t0) REVERT: A 2868 ILE cc_start: 0.8086 (mm) cc_final: 0.7825 (mm) REVERT: A 2906 LYS cc_start: 0.8032 (tptp) cc_final: 0.7801 (tptp) REVERT: A 2912 VAL cc_start: 0.8400 (m) cc_final: 0.8189 (p) REVERT: A 2959 LYS cc_start: 0.8260 (ptmt) cc_final: 0.7958 (ptpp) REVERT: A 2994 TYR cc_start: 0.7648 (t80) cc_final: 0.7279 (t80) REVERT: A 3146 PHE cc_start: 0.8320 (t80) cc_final: 0.8063 (t80) REVERT: A 3151 MET cc_start: 0.7676 (tmm) cc_final: 0.7330 (tmt) REVERT: A 3160 GLU cc_start: 0.6815 (OUTLIER) cc_final: 0.6577 (mp0) REVERT: A 3204 ASN cc_start: 0.8319 (m-40) cc_final: 0.7894 (t0) REVERT: A 3236 SER cc_start: 0.8246 (m) cc_final: 0.8031 (t) REVERT: A 3356 PHE cc_start: 0.7739 (p90) cc_final: 0.7272 (p90) REVERT: A 3435 VAL cc_start: 0.8417 (t) cc_final: 0.8185 (m) REVERT: A 3481 GLN cc_start: 0.7773 (tm-30) cc_final: 0.7381 (tm-30) REVERT: A 3491 TYR cc_start: 0.7514 (m-80) cc_final: 0.7258 (m-80) REVERT: A 3502 GLU cc_start: 0.8126 (tt0) cc_final: 0.7782 (tt0) REVERT: A 3612 GLU cc_start: 0.7661 (OUTLIER) cc_final: 0.7443 (mt-10) REVERT: A 3637 TYR cc_start: 0.7864 (t80) cc_final: 0.7629 (t80) REVERT: A 3662 LYS cc_start: 0.7853 (mttt) cc_final: 0.7464 (mmmm) REVERT: A 3727 GLU cc_start: 0.7963 (mt-10) cc_final: 0.7428 (mt-10) REVERT: A 3750 ARG cc_start: 0.6484 (mtt90) cc_final: 0.6152 (mtt90) REVERT: A 3765 GLN cc_start: 0.7003 (mm-40) cc_final: 0.6733 (mm-40) REVERT: A 3774 ARG cc_start: 0.7933 (ttm-80) cc_final: 0.7537 (tpp-160) REVERT: A 3823 MET cc_start: 0.4646 (pmm) cc_final: 0.3647 (pmm) REVERT: A 3867 CYS cc_start: 0.8139 (m) cc_final: 0.7839 (t) outliers start: 55 outliers final: 37 residues processed: 584 average time/residue: 0.1900 time to fit residues: 168.1806 Evaluate side-chains 595 residues out of total 2917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 549 time to evaluate : 0.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 594 ILE Chi-restraints excluded: chain A residue 648 CYS Chi-restraints excluded: chain A residue 698 GLN Chi-restraints excluded: chain A residue 866 SER Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain A residue 952 LEU Chi-restraints excluded: chain A residue 1025 SER Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1317 VAL Chi-restraints excluded: chain A residue 1432 ILE Chi-restraints excluded: chain A residue 1553 ILE Chi-restraints excluded: chain A residue 1620 GLU Chi-restraints excluded: chain A residue 1628 CYS Chi-restraints excluded: chain A residue 1667 CYS Chi-restraints excluded: chain A residue 1753 SER Chi-restraints excluded: chain A residue 1812 SER Chi-restraints excluded: chain A residue 1849 LYS Chi-restraints excluded: chain A residue 2275 GLN Chi-restraints excluded: chain A residue 2292 MET Chi-restraints excluded: chain A residue 2470 HIS Chi-restraints excluded: chain A residue 2526 THR Chi-restraints excluded: chain A residue 2529 LEU Chi-restraints excluded: chain A residue 2563 ASP Chi-restraints excluded: chain A residue 2621 MET Chi-restraints excluded: chain A residue 2645 VAL Chi-restraints excluded: chain A residue 2655 LEU Chi-restraints excluded: chain A residue 2675 VAL Chi-restraints excluded: chain A residue 2965 SER Chi-restraints excluded: chain A residue 3080 LEU Chi-restraints excluded: chain A residue 3160 GLU Chi-restraints excluded: chain A residue 3184 MET Chi-restraints excluded: chain A residue 3277 THR Chi-restraints excluded: chain A residue 3306 LEU Chi-restraints excluded: chain A residue 3441 ASN Chi-restraints excluded: chain A residue 3451 LYS Chi-restraints excluded: chain A residue 3499 THR Chi-restraints excluded: chain A residue 3504 LEU Chi-restraints excluded: chain A residue 3510 LEU Chi-restraints excluded: chain A residue 3548 THR Chi-restraints excluded: chain A residue 3612 GLU Chi-restraints excluded: chain A residue 3676 LYS Chi-restraints excluded: chain A residue 3885 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: [254, 262, 144, 179, 283, 253, 218, 289, 222, 79, 158] chunk 254 optimal weight: 3.9990 chunk 262 optimal weight: 3.9990 chunk 144 optimal weight: 0.9990 chunk 179 optimal weight: 0.0020 chunk 283 optimal weight: 0.9980 chunk 253 optimal weight: 0.7980 chunk 218 optimal weight: 2.9990 chunk 289 optimal weight: 3.9990 chunk 222 optimal weight: 4.9990 chunk 79 optimal weight: 0.5980 chunk 158 optimal weight: 9.9990 overall best weight: 0.6790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 474 GLN A 597 ASN A 667 GLN A1077 ASN A1576 ASN A2275 GLN ** A2366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3023 ASN ** A3045 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3375 HIS A3615 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.159975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.133113 restraints weight = 36462.071| |-----------------------------------------------------------------------------| r_work (start): 0.3639 rms_B_bonded: 2.01 r_work: 0.3517 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3363 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.2575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 26998 Z= 0.116 Angle : 0.484 8.357 36630 Z= 0.254 Chirality : 0.038 0.178 4276 Planarity : 0.003 0.050 4445 Dihedral : 9.992 176.313 4127 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.32 % Favored : 96.62 % Rotamer: Outliers : 1.82 % Allowed : 16.39 % Favored : 81.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.04 % 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: 0.94 (0.15), residues: 3135 helix: 1.55 (0.12), residues: 1828 sheet: -0.05 (0.34), residues: 222 loop : -0.80 (0.19), residues: 1085 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A3746 TYR 0.016 0.001 TYR A3239 PHE 0.023 0.001 PHE A1966 TRP 0.013 0.001 TRP A3482 HIS 0.004 0.001 HIS A 840 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 (26993) covalent geometry : angle 0.48393 / 0.25 (36624) hydrogen bonds : bond 0.03302 / 2.25 ( 1401) hydrogen bonds : angle 3.92505 / 2.80 ( 3965) metal coordination : bond 0.00414 / 0.20 ( 4) metal coordination : angle 1.57819 / 0.58 ( 6) Misc. bond : bond 0.00060 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 611 residues out of total 2917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 558 time to evaluate : 0.877 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 482 LEU cc_start: 0.8583 (OUTLIER) cc_final: 0.8319 (tt) REVERT: A 494 TRP cc_start: 0.8155 (m-10) cc_final: 0.7918 (m-10) REVERT: A 510 ASN cc_start: 0.7154 (m-40) cc_final: 0.6594 (t0) REVERT: A 521 LYS cc_start: 0.8202 (tptt) cc_final: 0.7918 (tptt) REVERT: A 575 LEU cc_start: 0.8330 (mp) cc_final: 0.8119 (mt) REVERT: A 614 GLU cc_start: 0.7590 (tp30) cc_final: 0.7180 (tp30) REVERT: A 657 ASP cc_start: 0.7787 (p0) cc_final: 0.7514 (p0) REVERT: A 753 MET cc_start: 0.7634 (mmm) cc_final: 0.7056 (mmm) REVERT: A 844 LYS cc_start: 0.8559 (tttt) cc_final: 0.8080 (ttpp) REVERT: A 881 ARG cc_start: 0.8082 (ttm170) cc_final: 0.7744 (ttm170) REVERT: A 936 GLU cc_start: 0.7809 (mm-30) cc_final: 0.7566 (mm-30) REVERT: A 963 ARG cc_start: 0.8179 (ttt-90) cc_final: 0.7899 (ttt-90) REVERT: A 968 GLU cc_start: 0.7937 (mt-10) cc_final: 0.7615 (mt-10) REVERT: A 1071 ASN cc_start: 0.7962 (t0) cc_final: 0.7673 (t0) REVERT: A 1086 GLU cc_start: 0.8247 (mp0) cc_final: 0.7864 (mp0) REVERT: A 1107 ASP cc_start: 0.7390 (m-30) cc_final: 0.7037 (m-30) REVERT: A 1122 ARG cc_start: 0.7387 (mpt-90) cc_final: 0.7101 (mpt-90) REVERT: A 1123 ARG cc_start: 0.7382 (ttm110) cc_final: 0.6954 (mtp85) REVERT: A 1130 TYR cc_start: 0.7909 (m-10) cc_final: 0.7588 (m-10) REVERT: A 1183 VAL cc_start: 0.8548 (m) cc_final: 0.8116 (p) REVERT: A 1230 PHE cc_start: 0.8503 (t80) cc_final: 0.8250 (t80) REVERT: A 1285 LYS cc_start: 0.8044 (mtmm) cc_final: 0.7790 (mtmm) REVERT: A 1292 VAL cc_start: 0.8009 (t) cc_final: 0.7100 (m) REVERT: A 1550 CYS cc_start: 0.7988 (m) cc_final: 0.7200 (p) REVERT: A 1589 VAL cc_start: 0.8508 (m) cc_final: 0.8294 (p) REVERT: A 1628 CYS cc_start: 0.7602 (OUTLIER) cc_final: 0.7364 (m) REVERT: A 1760 GLU cc_start: 0.7886 (tt0) cc_final: 0.7606 (tm-30) REVERT: A 1846 LYS cc_start: 0.7936 (mttt) cc_final: 0.7582 (mtmt) REVERT: A 1849 LYS cc_start: 0.7589 (OUTLIER) cc_final: 0.6187 (mttt) REVERT: A 1879 VAL cc_start: 0.8253 (p) cc_final: 0.7957 (m) REVERT: A 1887 LYS cc_start: 0.8175 (mtmt) cc_final: 0.7893 (mtmm) REVERT: A 2239 MET cc_start: 0.8119 (mmt) cc_final: 0.7842 (mmp) REVERT: A 2275 GLN cc_start: 0.8192 (OUTLIER) cc_final: 0.7771 (mt0) REVERT: A 2280 ARG cc_start: 0.7769 (ttm-80) cc_final: 0.7384 (ttm170) REVERT: A 2297 GLU cc_start: 0.6771 (mm-30) cc_final: 0.6532 (mm-30) REVERT: A 2563 ASP cc_start: 0.7752 (OUTLIER) cc_final: 0.7538 (t70) REVERT: A 2581 MET cc_start: 0.7689 (tmm) cc_final: 0.6532 (tmm) REVERT: A 2655 LEU cc_start: 0.6934 (OUTLIER) cc_final: 0.6541 (pt) REVERT: A 2755 THR cc_start: 0.8017 (m) cc_final: 0.7213 (p) REVERT: A 2856 ASP cc_start: 0.6412 (t0) cc_final: 0.6154 (t0) REVERT: A 2868 ILE cc_start: 0.8076 (mm) cc_final: 0.7837 (mm) REVERT: A 2906 LYS cc_start: 0.8024 (tptp) cc_final: 0.7823 (tptp) REVERT: A 2912 VAL cc_start: 0.8407 (m) cc_final: 0.8197 (p) REVERT: A 2959 LYS cc_start: 0.8270 (ptmt) cc_final: 0.7958 (ptpp) REVERT: A 2994 TYR cc_start: 0.7658 (t80) cc_final: 0.7260 (t80) REVERT: A 3139 MET cc_start: 0.8426 (tpp) cc_final: 0.7551 (mmm) REVERT: A 3146 PHE cc_start: 0.8311 (t80) cc_final: 0.7608 (t80) REVERT: A 3151 MET cc_start: 0.7665 (tmm) cc_final: 0.7327 (tmm) REVERT: A 3160 GLU cc_start: 0.6788 (OUTLIER) cc_final: 0.6554 (mp0) REVERT: A 3204 ASN cc_start: 0.8300 (m-40) cc_final: 0.7889 (t0) REVERT: A 3211 GLU cc_start: 0.7705 (mm-30) cc_final: 0.7499 (mm-30) REVERT: A 3236 SER cc_start: 0.8240 (m) cc_final: 0.8021 (t) REVERT: A 3356 PHE cc_start: 0.7753 (p90) cc_final: 0.7160 (p90) REVERT: A 3435 VAL cc_start: 0.8418 (t) cc_final: 0.8188 (m) REVERT: A 3481 GLN cc_start: 0.7777 (tm-30) cc_final: 0.7375 (tm-30) REVERT: A 3491 TYR cc_start: 0.7503 (m-80) cc_final: 0.7252 (m-80) REVERT: A 3502 GLU cc_start: 0.8134 (tt0) cc_final: 0.7785 (tt0) REVERT: A 3612 GLU cc_start: 0.7641 (mt-10) cc_final: 0.7435 (mt-10) REVERT: A 3637 TYR cc_start: 0.7871 (t80) cc_final: 0.7646 (t80) REVERT: A 3662 LYS cc_start: 0.7851 (mttt) cc_final: 0.7472 (mmmm) REVERT: A 3727 GLU cc_start: 0.7950 (mt-10) cc_final: 0.7412 (mt-10) REVERT: A 3750 ARG cc_start: 0.6502 (mtt90) cc_final: 0.6171 (mtt90) REVERT: A 3765 GLN cc_start: 0.7002 (mm-40) cc_final: 0.6710 (mm-40) REVERT: A 3774 ARG cc_start: 0.7938 (ttm-80) cc_final: 0.7459 (tpp-160) REVERT: A 3823 MET cc_start: 0.4725 (pmm) cc_final: 0.3799 (pmm) REVERT: A 3867 CYS cc_start: 0.8134 (m) cc_final: 0.7868 (t) outliers start: 53 outliers final: 40 residues processed: 588 average time/residue: 0.1870 time to fit residues: 167.1675 Evaluate side-chains 597 residues out of total 2917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 550 time to evaluate : 0.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 594 ILE Chi-restraints excluded: chain A residue 597 ASN Chi-restraints excluded: chain A residue 648 CYS Chi-restraints excluded: chain A residue 698 GLN Chi-restraints excluded: chain A residue 866 SER Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain A residue 952 LEU Chi-restraints excluded: chain A residue 1025 SER Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1143 CYS Chi-restraints excluded: chain A residue 1250 LYS Chi-restraints excluded: chain A residue 1317 VAL Chi-restraints excluded: chain A residue 1432 ILE Chi-restraints excluded: chain A residue 1553 ILE Chi-restraints excluded: chain A residue 1620 GLU Chi-restraints excluded: chain A residue 1628 CYS Chi-restraints excluded: chain A residue 1667 CYS Chi-restraints excluded: chain A residue 1753 SER Chi-restraints excluded: chain A residue 1812 SER Chi-restraints excluded: chain A residue 1849 LYS Chi-restraints excluded: chain A residue 2275 GLN Chi-restraints excluded: chain A residue 2276 LEU Chi-restraints excluded: chain A residue 2470 HIS Chi-restraints excluded: chain A residue 2526 THR Chi-restraints excluded: chain A residue 2529 LEU Chi-restraints excluded: chain A residue 2563 ASP Chi-restraints excluded: chain A residue 2621 MET Chi-restraints excluded: chain A residue 2645 VAL Chi-restraints excluded: chain A residue 2655 LEU Chi-restraints excluded: chain A residue 2675 VAL Chi-restraints excluded: chain A residue 2965 SER Chi-restraints excluded: chain A residue 3080 LEU Chi-restraints excluded: chain A residue 3160 GLU Chi-restraints excluded: chain A residue 3184 MET Chi-restraints excluded: chain A residue 3277 THR Chi-restraints excluded: chain A residue 3306 LEU Chi-restraints excluded: chain A residue 3441 ASN Chi-restraints excluded: chain A residue 3451 LYS Chi-restraints excluded: chain A residue 3499 THR Chi-restraints excluded: chain A residue 3504 LEU Chi-restraints excluded: chain A residue 3510 LEU Chi-restraints excluded: chain A residue 3548 THR Chi-restraints excluded: chain A residue 3885 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: [286, 43, 156, 236, 98, 259, 31, 141, 194, 272, 142] chunk 286 optimal weight: 7.9990 chunk 43 optimal weight: 1.9990 chunk 156 optimal weight: 3.9990 chunk 236 optimal weight: 0.7980 chunk 98 optimal weight: 0.8980 chunk 259 optimal weight: 5.9990 chunk 31 optimal weight: 0.8980 chunk 141 optimal weight: 20.0000 chunk 194 optimal weight: 1.9990 chunk 272 optimal weight: 0.7980 chunk 142 optimal weight: 8.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 474 GLN A 597 ASN A 667 GLN A1077 ASN A1576 ASN ** A2366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3023 ASN A3170 GLN A3375 HIS A3615 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.158700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.131729 restraints weight = 36218.366| |-----------------------------------------------------------------------------| r_work (start): 0.3629 rms_B_bonded: 1.99 r_work: 0.3509 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3354 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.2633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 26998 Z= 0.147 Angle : 0.506 8.350 36630 Z= 0.264 Chirality : 0.039 0.170 4276 Planarity : 0.004 0.049 4445 Dihedral : 9.990 175.644 4127 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.35 % Favored : 96.59 % Rotamer: Outliers : 1.61 % Allowed : 16.70 % Favored : 81.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.04 % 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: 0.91 (0.15), residues: 3135 helix: 1.55 (0.12), residues: 1821 sheet: -0.04 (0.34), residues: 222 loop : -0.83 (0.19), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 574 TYR 0.015 0.001 TYR A3358 PHE 0.023 0.001 PHE A 674 TRP 0.014 0.001 TRP A3482 HIS 0.006 0.001 HIS A2996 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.15 (26993) covalent geometry : angle 0.50563 / 0.26 (36624) hydrogen bonds : bond 0.03428 / 2.34 ( 1401) hydrogen bonds : angle 3.96084 / 2.83 ( 3965) metal coordination : bond 0.00560 / 0.27 ( 4) metal coordination : angle 1.70863 / 0.64 ( 6) Misc. bond : bond 0.00075 / 0.04 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 608 residues out of total 2917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 561 time to evaluate : 0.967 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 482 LEU cc_start: 0.8584 (OUTLIER) cc_final: 0.8315 (tt) REVERT: A 494 TRP cc_start: 0.8158 (m-10) cc_final: 0.7922 (m-10) REVERT: A 510 ASN cc_start: 0.7201 (m-40) cc_final: 0.6611 (t0) REVERT: A 521 LYS cc_start: 0.8223 (tptt) cc_final: 0.7939 (tptt) REVERT: A 574 ARG cc_start: 0.8378 (ttm110) cc_final: 0.7961 (mtp180) REVERT: A 575 LEU cc_start: 0.8376 (mp) cc_final: 0.8136 (mt) REVERT: A 597 ASN cc_start: 0.8109 (OUTLIER) cc_final: 0.7804 (t0) REVERT: A 614 GLU cc_start: 0.7580 (tp30) cc_final: 0.7242 (tp30) REVERT: A 657 ASP cc_start: 0.7791 (p0) cc_final: 0.7510 (p0) REVERT: A 667 GLN cc_start: 0.8152 (OUTLIER) cc_final: 0.7768 (mm110) REVERT: A 753 MET cc_start: 0.7732 (mmm) cc_final: 0.7178 (mmm) REVERT: A 804 GLU cc_start: 0.8121 (mt-10) cc_final: 0.7889 (mt-10) REVERT: A 844 LYS cc_start: 0.8567 (tttt) cc_final: 0.8101 (ttpp) REVERT: A 881 ARG cc_start: 0.8080 (ttm170) cc_final: 0.7757 (ttm170) REVERT: A 936 GLU cc_start: 0.7823 (mm-30) cc_final: 0.7583 (mm-30) REVERT: A 963 ARG cc_start: 0.8183 (ttt-90) cc_final: 0.7904 (ttt-90) REVERT: A 968 GLU cc_start: 0.7942 (mt-10) cc_final: 0.7608 (mt-10) REVERT: A 1071 ASN cc_start: 0.7969 (t0) cc_final: 0.7681 (t0) REVERT: A 1086 GLU cc_start: 0.8229 (mp0) cc_final: 0.7848 (mp0) REVERT: A 1107 ASP cc_start: 0.7365 (m-30) cc_final: 0.7025 (m-30) REVERT: A 1122 ARG cc_start: 0.7419 (mpt-90) cc_final: 0.7128 (mpt-90) REVERT: A 1123 ARG cc_start: 0.7408 (ttm110) cc_final: 0.6887 (mtp85) REVERT: A 1130 TYR cc_start: 0.7909 (m-10) cc_final: 0.7580 (m-10) REVERT: A 1183 VAL cc_start: 0.8579 (m) cc_final: 0.8165 (p) REVERT: A 1230 PHE cc_start: 0.8508 (t80) cc_final: 0.8282 (t80) REVERT: A 1260 ASP cc_start: 0.7777 (p0) cc_final: 0.7452 (p0) REVERT: A 1285 LYS cc_start: 0.8029 (mtmm) cc_final: 0.7785 (mtmm) REVERT: A 1292 VAL cc_start: 0.8024 (t) cc_final: 0.7120 (m) REVERT: A 1550 CYS cc_start: 0.8006 (m) cc_final: 0.7193 (p) REVERT: A 1589 VAL cc_start: 0.8511 (m) cc_final: 0.8302 (p) REVERT: A 1628 CYS cc_start: 0.7610 (OUTLIER) cc_final: 0.7365 (m) REVERT: A 1760 GLU cc_start: 0.7945 (tt0) cc_final: 0.7710 (tm-30) REVERT: A 1846 LYS cc_start: 0.7880 (mttt) cc_final: 0.7532 (mtmt) REVERT: A 1879 VAL cc_start: 0.8226 (p) cc_final: 0.7928 (m) REVERT: A 1887 LYS cc_start: 0.8183 (mtmt) cc_final: 0.7899 (mtmm) REVERT: A 2239 MET cc_start: 0.8124 (mmt) cc_final: 0.7858 (mmp) REVERT: A 2297 GLU cc_start: 0.6774 (mm-30) cc_final: 0.6547 (mm-30) REVERT: A 2563 ASP cc_start: 0.7752 (OUTLIER) cc_final: 0.7526 (t70) REVERT: A 2581 MET cc_start: 0.7693 (tmm) cc_final: 0.6519 (tmm) REVERT: A 2655 LEU cc_start: 0.6992 (OUTLIER) cc_final: 0.6536 (pt) REVERT: A 2755 THR cc_start: 0.8079 (m) cc_final: 0.7281 (p) REVERT: A 2856 ASP cc_start: 0.6441 (t0) cc_final: 0.6179 (t0) REVERT: A 2868 ILE cc_start: 0.8085 (mm) cc_final: 0.7838 (mm) REVERT: A 2906 LYS cc_start: 0.8018 (tptp) cc_final: 0.7813 (tptp) REVERT: A 2912 VAL cc_start: 0.8434 (m) cc_final: 0.8225 (p) REVERT: A 2959 LYS cc_start: 0.8269 (ptmt) cc_final: 0.7966 (ptpp) REVERT: A 2994 TYR cc_start: 0.7665 (t80) cc_final: 0.7261 (t80) REVERT: A 3146 PHE cc_start: 0.8313 (t80) cc_final: 0.8063 (t80) REVERT: A 3151 MET cc_start: 0.7665 (tmm) cc_final: 0.7345 (tmm) REVERT: A 3160 GLU cc_start: 0.6791 (OUTLIER) cc_final: 0.6578 (mp0) REVERT: A 3204 ASN cc_start: 0.8293 (m-40) cc_final: 0.7886 (t0) REVERT: A 3236 SER cc_start: 0.8258 (m) cc_final: 0.8038 (t) REVERT: A 3356 PHE cc_start: 0.7762 (p90) cc_final: 0.7141 (p90) REVERT: A 3435 VAL cc_start: 0.8423 (t) cc_final: 0.8195 (m) REVERT: A 3481 GLN cc_start: 0.7808 (tm-30) cc_final: 0.7349 (tm-30) REVERT: A 3491 TYR cc_start: 0.7557 (m-80) cc_final: 0.7305 (m-80) REVERT: A 3502 GLU cc_start: 0.8179 (tt0) cc_final: 0.7838 (tt0) REVERT: A 3536 ILE cc_start: 0.8235 (mt) cc_final: 0.7971 (tt) REVERT: A 3612 GLU cc_start: 0.7667 (mt-10) cc_final: 0.7463 (mt-10) REVERT: A 3637 TYR cc_start: 0.7878 (t80) cc_final: 0.7656 (t80) REVERT: A 3662 LYS cc_start: 0.7847 (mttt) cc_final: 0.7441 (mmmm) REVERT: A 3727 GLU cc_start: 0.7924 (mt-10) cc_final: 0.7393 (mt-10) REVERT: A 3750 ARG cc_start: 0.6509 (mtt90) cc_final: 0.6140 (mtt90) REVERT: A 3823 MET cc_start: 0.4694 (pmm) cc_final: 0.3763 (pmm) REVERT: A 3867 CYS cc_start: 0.8139 (m) cc_final: 0.7885 (t) outliers start: 47 outliers final: 37 residues processed: 589 average time/residue: 0.1864 time to fit residues: 166.9278 Evaluate side-chains 595 residues out of total 2917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 551 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 594 ILE Chi-restraints excluded: chain A residue 597 ASN Chi-restraints excluded: chain A residue 648 CYS Chi-restraints excluded: chain A residue 667 GLN Chi-restraints excluded: chain A residue 698 GLN Chi-restraints excluded: chain A residue 866 SER Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain A residue 1025 SER Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1250 LYS Chi-restraints excluded: chain A residue 1317 VAL Chi-restraints excluded: chain A residue 1432 ILE Chi-restraints excluded: chain A residue 1553 ILE Chi-restraints excluded: chain A residue 1620 GLU Chi-restraints excluded: chain A residue 1628 CYS Chi-restraints excluded: chain A residue 1667 CYS Chi-restraints excluded: chain A residue 1753 SER Chi-restraints excluded: chain A residue 1812 SER Chi-restraints excluded: chain A residue 2470 HIS Chi-restraints excluded: chain A residue 2526 THR Chi-restraints excluded: chain A residue 2529 LEU Chi-restraints excluded: chain A residue 2563 ASP Chi-restraints excluded: chain A residue 2621 MET Chi-restraints excluded: chain A residue 2645 VAL Chi-restraints excluded: chain A residue 2655 LEU Chi-restraints excluded: chain A residue 2675 VAL Chi-restraints excluded: chain A residue 2757 LEU Chi-restraints excluded: chain A residue 2965 SER Chi-restraints excluded: chain A residue 3080 LEU Chi-restraints excluded: chain A residue 3160 GLU Chi-restraints excluded: chain A residue 3184 MET Chi-restraints excluded: chain A residue 3277 THR Chi-restraints excluded: chain A residue 3306 LEU Chi-restraints excluded: chain A residue 3441 ASN Chi-restraints excluded: chain A residue 3451 LYS Chi-restraints excluded: chain A residue 3499 THR Chi-restraints excluded: chain A residue 3504 LEU Chi-restraints excluded: chain A residue 3510 LEU Chi-restraints excluded: chain A residue 3548 THR Chi-restraints excluded: chain A residue 3885 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: [304, 0, 130, 256, 64, 89, 62, 207, 22, 56, 154] chunk 304 optimal weight: 4.9990 chunk 0 optimal weight: 20.0000 chunk 130 optimal weight: 0.8980 chunk 256 optimal weight: 0.6980 chunk 64 optimal weight: 0.1980 chunk 89 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 chunk 207 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 154 optimal weight: 0.0770 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 474 GLN A 667 GLN A1077 ASN A1576 ASN A2275 GLN ** A2366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3023 ASN A3375 HIS ** A3409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3615 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.158991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.132033 restraints weight = 36223.931| |-----------------------------------------------------------------------------| r_work (start): 0.3632 rms_B_bonded: 2.00 r_work: 0.3511 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3356 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.2652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.220 26998 Z= 0.197 Angle : 0.709 59.174 36630 Z= 0.416 Chirality : 0.039 0.341 4276 Planarity : 0.005 0.175 4445 Dihedral : 9.991 175.748 4127 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.29 % Favored : 96.65 % Rotamer: Outliers : 1.68 % Allowed : 16.59 % Favored : 81.73 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 1.04 % 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: 0.93 (0.15), residues: 3135 helix: 1.56 (0.12), residues: 1821 sheet: -0.04 (0.34), residues: 222 loop : -0.82 (0.19), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 574 TYR 0.015 0.001 TYR A3239 PHE 0.061 0.002 PHE A1505 TRP 0.060 0.001 TRP A3482 HIS 0.025 0.001 HIS A 840 Details of bonding type rmsd/Z covalent geometry : bond 0.00426 / 0.20 (26993) covalent geometry : angle 0.70894 / 0.42 (36624) hydrogen bonds : bond 0.03440 / 2.35 ( 1401) hydrogen bonds : angle 3.97161 / 2.83 ( 3965) metal coordination : bond 0.00459 / 0.22 ( 4) metal coordination : angle 1.69237 / 0.63 ( 6) Misc. bond : bond 0.00050 / 0.03 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7970.38 seconds wall clock time: 136 minutes 54.45 seconds (8214.45 seconds total)