Starting phenix.real_space_refine on Sun Jul 5 08:02:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9xe9_66785/07_2026/9xe9_66785.cif Found real_map, /net/cci-nas-00/data/ceres_data/9xe9_66785/07_2026/9xe9_66785.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.81 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9xe9_66785/07_2026/9xe9_66785.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9xe9_66785/07_2026/9xe9_66785.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9xe9_66785/07_2026/9xe9_66785.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9xe9_66785/07_2026/9xe9_66785.map" } resolution = 2.81 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.041 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Mn 4 7.51 5 Zn 1 6.06 5 P 47 5.49 5 S 158 5.16 5 C 16075 2.51 5 N 4375 2.21 5 O 4945 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 25605 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 24614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3074, 24614 Classifications: {'peptide': 3074} Link IDs: {'PCIS': 1, 'PTRANS': 95, 'TRANS': 2977} Chain breaks: 22 Chain: "B" Number of atoms: 231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 231 Classifications: {'RNA': 11} Modifications used: {'5*END': 1, 'rna2p_pur': 4, 'rna3p_pur': 3, 'rna3p_pyr': 4} Link IDs: {'rna2p': 3, 'rna3p': 7} Chain: "C" Number of atoms: 280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 280 Classifications: {'RNA': 13} Modifications used: {'rna2p_pur': 2, 'rna3p_pur': 5, 'rna3p_pyr': 6} Link IDs: {'rna2p': 2, 'rna3p': 10} Chain: "D" Number of atoms: 215 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 215 Classifications: {'RNA': 10} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 6, 'rna3p_pyr': 3} Link IDs: {'rna2p': 1, 'rna3p': 8} Chain: "E" Number of atoms: 170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 170 Classifications: {'RNA': 8} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 4, 'rna3p_pur': 2} Link IDs: {'rna2p': 5, 'rna3p': 2} Chain: "F" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 61 Classifications: {'RNA': 3} Modifications used: {'p5*END': 1, 'rna2p_pyr': 1, 'rna3p_pyr': 2} Link IDs: {'rna2p': 1, 'rna3p': 1} Chain: "A" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 30 Ad-hoc single atom residues: {' MN': 4} Unusual residues: {' ZN': 1, '2KH': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain breaks: 4 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 4281 SG CYS A1028 43.139 97.164 96.552 1.00 74.48 S ATOM 4300 SG CYS A1031 45.710 99.879 97.089 1.00 63.59 S ATOM 4543 SG CYS A1062 43.958 98.746 100.111 1.00 81.09 S ATOM 4563 SG CYS A1065 46.322 96.457 98.647 1.00 77.73 S Time building chain proxies: 5.52, per 1000 atoms: 0.22 Number of scatterers: 25605 At special positions: 0 Unit cell: (138.218, 135.594, 138.218, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 Mn 4 24.99 S 158 16.00 P 47 15.00 O 4945 8.00 N 4375 7.00 C 16075 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.92 Conformation dependent library (CDL) restraints added in 1.0 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 A1062 " pdb="ZN ZN A4006 " - pdb=" SG CYS A1065 " pdb="ZN ZN A4006 " - pdb=" SG CYS A1028 " Number of angles added : 6 6056 Ramachandran restraints generated. 3028 Oldfield, 0 Emsley, 3028 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5904 Finding SS restraints... Secondary structure from input PDB file: 155 helices and 18 sheets defined 61.9% alpha, 7.4% beta 9 base pairs and 20 stacking pairs defined. Time for finding SS restraints: 3.88 Creating SS restraints... Processing helix chain 'A' and resid 427 through 436 Processing helix chain 'A' and resid 447 through 460 Processing helix chain 'A' and resid 466 through 485 Processing helix chain 'A' and resid 487 through 489 No H-bonds generated for 'chain 'A' and resid 487 through 489' Processing helix chain 'A' and resid 490 through 495 Processing helix chain 'A' and resid 510 through 523 removed outlier: 3.998A pdb=" N PHE A 514 " --> pdb=" O ASN A 510 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LYS A 523 " --> pdb=" O PHE A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 554 removed outlier: 3.758A pdb=" N VAL A 544 " --> pdb=" O LYS A 540 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N SER A 554 " --> pdb=" O ASN A 550 " (cutoff:3.500A) Processing helix chain 'A' and resid 561 through 580 removed outlier: 4.072A pdb=" N SER A 566 " --> pdb=" O SER A 562 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N GLN A 567 " --> pdb=" O GLU A 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 586 through 603 removed outlier: 5.160A pdb=" N SER A 596 " --> pdb=" O ASP A 592 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N ASN A 597 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N GLN A 600 " --> pdb=" O SER A 596 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LEU A 601 " --> pdb=" O ASN A 597 " (cutoff:3.500A) Processing helix chain 'A' and resid 606 through 622 removed outlier: 3.601A pdb=" N ARG A 611 " --> pdb=" O PRO A 607 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLU A 612 " --> pdb=" O ASP A 608 " (cutoff:3.500A) Processing helix chain 'A' and resid 625 through 649 removed outlier: 3.948A pdb=" N ALA A 629 " --> pdb=" O THR A 625 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ARG A 635 " --> pdb=" O LYS A 631 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N CYS A 648 " --> pdb=" O LEU A 644 " (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: 3.753A pdb=" N LEU A 690 " --> pdb=" O PHE A 687 " (cutoff:3.500A) Processing helix chain 'A' and resid 748 through 761 removed outlier: 3.693A pdb=" N ILE A 752 " --> pdb=" O SER A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 811 through 817 removed outlier: 4.130A pdb=" N LEU A 816 " --> pdb=" O GLU A 813 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLU A 817 " --> pdb=" O ASP A 814 " (cutoff:3.500A) Processing helix chain 'A' and resid 832 through 843 Processing helix chain 'A' and resid 844 through 854 removed outlier: 3.541A pdb=" N LYS A 848 " --> pdb=" O LYS A 844 " (cutoff:3.500A) Processing helix chain 'A' and resid 869 through 873 removed outlier: 3.685A pdb=" N TRP A 873 " --> pdb=" O PRO A 870 " (cutoff:3.500A) Processing helix chain 'A' and resid 876 through 897 removed outlier: 4.150A pdb=" N VAL A 882 " --> pdb=" O ASP A 878 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ARG A 896 " --> pdb=" O ASN A 892 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASN A 897 " --> pdb=" O LYS A 893 " (cutoff:3.500A) Processing helix chain 'A' and resid 899 through 912 Processing helix chain 'A' and resid 914 through 919 Processing helix chain 'A' and resid 930 through 946 removed outlier: 3.603A pdb=" N LYS A 940 " --> pdb=" O GLU A 936 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N GLU A 943 " --> pdb=" O GLU A 939 " (cutoff:3.500A) removed outlier: 5.470A 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 997 Processing helix chain 'A' and resid 1008 through 1024 removed outlier: 3.619A 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 1056 Processing helix chain 'A' and resid 1057 through 1061 removed outlier: 4.081A pdb=" N HIS A1061 " --> pdb=" O LEU A1058 " (cutoff:3.500A) Processing helix chain 'A' and resid 1076 through 1081 Processing helix chain 'A' and resid 1084 through 1088 Processing helix chain 'A' and resid 1104 through 1111 removed outlier: 3.536A 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 1187 removed outlier: 3.762A 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 1221 through 1232 removed outlier: 3.920A pdb=" N LEU A1225 " --> pdb=" O PRO A1221 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU A1232 " --> pdb=" O VAL A1228 " (cutoff:3.500A) Processing helix chain 'A' and resid 1237 through 1254 Processing helix chain 'A' and resid 1266 through 1277 removed outlier: 3.767A pdb=" N GLN A1277 " --> pdb=" O CYS A1273 " (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 1329 removed outlier: 3.516A pdb=" N SER A1322 " --> pdb=" O ASP A1318 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LEU A1323 " --> pdb=" O THR A1319 " (cutoff:3.500A) Processing helix chain 'A' and resid 1330 through 1350 removed outlier: 3.541A pdb=" N GLN A1334 " --> pdb=" O PHE A1330 " (cutoff:3.500A) Processing helix chain 'A' and resid 1401 through 1426 removed outlier: 3.969A pdb=" N LEU A1407 " --> pdb=" O ARG A1403 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLY A1408 " --> pdb=" O GLN A1404 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N LEU A1412 " --> pdb=" O GLY A1408 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N TYR A1413 " --> pdb=" O SER A1409 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N GLN A1424 " --> pdb=" O ILE A1420 " (cutoff:3.500A) Processing helix chain 'A' and resid 1428 through 1434 removed outlier: 3.635A pdb=" N VAL A1431 " --> pdb=" O CYS A1428 " (cutoff:3.500A) Processing helix chain 'A' and resid 1436 through 1463 Processing helix chain 'A' and resid 1465 through 1481 removed outlier: 3.636A 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: 3.972A 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 1532 through 1534 No H-bonds generated for 'chain 'A' and resid 1532 through 1534' Processing helix chain 'A' and resid 1542 through 1547 removed outlier: 3.574A 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: 3.960A 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: 3.908A pdb=" N HIS A1615 " --> pdb=" O TYR A1612 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE A1616 " --> pdb=" O ASN A1613 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1612 through 1616' Processing helix chain 'A' and resid 1623 through 1649 removed outlier: 3.579A 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 1853 removed outlier: 3.628A pdb=" N GLY A1853 " --> pdb=" O LYS A1849 " (cutoff:3.500A) Processing helix chain 'A' and resid 1869 through 1877 Processing helix chain 'A' and resid 1883 through 1896 Processing helix chain 'A' and resid 1904 through 1910 removed outlier: 3.766A pdb=" N LYS A1910 " --> pdb=" O LYS A1906 " (cutoff:3.500A) Processing helix chain 'A' and resid 1912 through 1917 removed outlier: 3.639A pdb=" N VAL A1916 " --> pdb=" O ASN A1912 " (cutoff:3.500A) Processing helix chain 'A' and resid 1922 through 1945 removed outlier: 3.802A pdb=" N LYS A1937 " --> pdb=" O SER A1933 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N GLY A1938 " --> pdb=" O SER A1934 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N SER A1939 " --> pdb=" O SER A1935 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ARG A1943 " --> pdb=" O SER A1939 " (cutoff:3.500A) Processing helix chain 'A' and resid 1946 through 1948 No H-bonds generated for 'chain 'A' and resid 1946 through 1948' Processing helix chain 'A' and resid 1962 through 1977 Processing helix chain 'A' and resid 1988 through 2002 Processing helix chain 'A' and resid 2005 through 2014 removed outlier: 4.212A pdb=" N LYS A2014 " --> 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 2117 through 2122 Processing helix chain 'A' and resid 2122 through 2127 removed outlier: 4.564A pdb=" N TYR A2126 " --> pdb=" O LEU A2122 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLN A2127 " --> pdb=" O VAL A2123 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2122 through 2127' Processing helix chain 'A' and resid 2138 through 2154 Processing helix chain 'A' and resid 2157 through 2163 Processing helix chain 'A' and resid 2199 through 2209 removed outlier: 3.503A pdb=" N ASN A2209 " --> pdb=" O GLN A2205 " (cutoff:3.500A) Processing helix chain 'A' and resid 2211 through 2219 removed outlier: 3.749A 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 2259 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: 3.816A pdb=" N HIS A2366 " --> pdb=" O TRP A2362 " (cutoff:3.500A) Processing helix chain 'A' and resid 2367 through 2379 removed outlier: 3.522A pdb=" N PHE A2371 " --> pdb=" O CYS A2367 " (cutoff:3.500A) Processing helix chain 'A' and resid 2382 through 2397 removed outlier: 3.746A pdb=" N PHE A2388 " --> pdb=" O ASP A2384 " (cutoff:3.500A) Processing helix chain 'A' and resid 2404 through 2420 removed outlier: 3.547A pdb=" N LEU A2415 " --> pdb=" O ILE A2411 " (cutoff:3.500A) Processing helix chain 'A' and resid 2429 through 2440 removed outlier: 3.549A pdb=" N THR A2438 " --> pdb=" O ARG A2434 " (cutoff:3.500A) Processing helix chain 'A' and resid 2441 through 2445 removed outlier: 3.635A pdb=" N ASP A2445 " --> pdb=" O ASP A2442 " (cutoff:3.500A) Processing helix chain 'A' and resid 2447 through 2457 removed outlier: 3.830A pdb=" N LEU A2453 " --> pdb=" O THR A2449 " (cutoff:3.500A) Processing helix chain 'A' and resid 2458 through 2461 Processing helix chain 'A' and resid 2478 through 2503 removed outlier: 4.045A pdb=" N VAL A2489 " --> pdb=" O SER A2485 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N LEU A2490 " --> pdb=" O LEU A2486 " (cutoff:3.500A) Processing helix chain 'A' and resid 2530 through 2558 removed outlier: 5.038A pdb=" N TRP A2542 " --> pdb=" O ASP A2538 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N LYS A2543 " --> pdb=" O GLU A2539 " (cutoff:3.500A) Processing helix chain 'A' and resid 2590 through 2594 removed outlier: 3.632A pdb=" N MET A2594 " --> pdb=" O ILE A2591 " (cutoff:3.500A) Processing helix chain 'A' and resid 2595 through 2600 removed outlier: 3.805A pdb=" N ILE A2599 " --> pdb=" O PHE A2595 " (cutoff:3.500A) removed outlier: 3.676A 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 2623 Processing helix chain 'A' and resid 2626 through 2643 removed outlier: 3.586A pdb=" N PHE A2641 " --> pdb=" O ARG A2637 " (cutoff:3.500A) Processing helix chain 'A' and resid 2645 through 2657 removed outlier: 6.604A pdb=" N ILE A2654 " --> pdb=" O ARG A2650 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N LEU A2655 " --> pdb=" O ARG A2651 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU A2657 " --> pdb=" O GLY A2653 " (cutoff:3.500A) Processing helix chain 'A' and resid 2660 through 2664 removed outlier: 3.600A pdb=" N GLY A2664 " --> pdb=" O SER A2661 " (cutoff:3.500A) Processing helix chain 'A' and resid 2671 through 2676 removed outlier: 4.132A 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 2814 removed outlier: 3.520A pdb=" N GLY A2812 " --> pdb=" O TRP A2808 " (cutoff:3.500A) Processing helix chain 'A' and resid 2816 through 2836 removed outlier: 3.680A pdb=" N SER A2826 " --> pdb=" O ASN A2822 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N VAL A2827 " --> pdb=" O ARG A2823 " (cutoff:3.500A) Processing helix chain 'A' and resid 2869 through 2890 removed outlier: 3.674A pdb=" N GLU A2875 " --> pdb=" O LYS A2871 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ARG A2878 " --> pdb=" O ARG A2874 " (cutoff:3.500A) Processing helix chain 'A' and resid 2898 through 2908 Processing helix chain 'A' and resid 2916 through 2929 Processing helix chain 'A' and resid 2932 through 2939 removed outlier: 3.649A pdb=" N GLY A2936 " --> pdb=" O ASN A2932 " (cutoff:3.500A) Processing helix chain 'A' and resid 2944 through 2953 removed outlier: 3.830A pdb=" N ILE A2948 " --> pdb=" O LEU A2944 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N MET A2953 " --> pdb=" O TYR A2949 " (cutoff:3.500A) Processing helix chain 'A' and resid 2993 through 3003 Processing helix chain 'A' and resid 3043 through 3060 Processing helix chain 'A' and resid 3062 through 3073 Processing helix chain 'A' and resid 3104 through 3114 Processing helix chain 'A' and resid 3116 through 3121 Processing helix chain 'A' and resid 3127 through 3129 No H-bonds generated for 'chain 'A' and resid 3127 through 3129' Processing helix chain 'A' and resid 3130 through 3141 removed outlier: 3.680A pdb=" N ASP A3134 " --> pdb=" O ASN A3130 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N PHE A3136 " --> pdb=" O LEU A3132 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N MET A3139 " --> pdb=" O ARG A3135 " (cutoff:3.500A) Processing helix chain 'A' and resid 3142 through 3163 removed outlier: 3.680A pdb=" N LEU A3148 " --> pdb=" O SER A3144 " (cutoff:3.500A) Processing helix chain 'A' and resid 3167 through 3187 removed outlier: 3.612A pdb=" N ALA A3172 " --> pdb=" O LEU A3168 " (cutoff:3.500A) Processing helix chain 'A' and resid 3209 through 3217 removed outlier: 3.889A pdb=" N VAL A3213 " --> pdb=" O VAL A3209 " (cutoff:3.500A) removed outlier: 4.055A 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: 3.571A pdb=" N ILE A3275 " --> pdb=" O ASN A3272 " (cutoff:3.500A) Processing helix chain 'A' and resid 3288 through 3293 removed outlier: 4.080A pdb=" N GLU A3292 " --> pdb=" O SER A3288 " (cutoff:3.500A) Processing helix chain 'A' and resid 3297 through 3305 Processing helix chain 'A' and resid 3306 through 3309 removed outlier: 3.808A 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 Processing helix chain 'A' and resid 3327 through 3329 No H-bonds generated for 'chain 'A' and resid 3327 through 3329' Processing helix chain 'A' and resid 3330 through 3335 removed outlier: 3.943A pdb=" N LYS A3334 " --> pdb=" O GLU A3330 " (cutoff:3.500A) Processing helix chain 'A' and resid 3382 through 3398 Processing helix chain 'A' and resid 3406 through 3416 Processing helix chain 'A' and resid 3503 through 3514 removed outlier: 3.620A pdb=" N SER A3514 " --> pdb=" O LEU A3510 " (cutoff:3.500A) Processing helix chain 'A' and resid 3543 through 3556 removed outlier: 3.538A pdb=" N LEU A3547 " --> pdb=" O LEU A3543 " (cutoff:3.500A) Processing helix chain 'A' and resid 3556 through 3565 removed outlier: 3.906A pdb=" N ASP A3560 " --> pdb=" O HIS A3556 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N VAL A3565 " --> pdb=" O ALA A3561 " (cutoff:3.500A) Processing helix chain 'A' and resid 3587 through 3594 removed outlier: 3.667A pdb=" N GLU A3592 " --> pdb=" O VAL A3588 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU A3594 " --> pdb=" O PHE A3590 " (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 3642 removed outlier: 3.668A pdb=" N GLN A3635 " --> pdb=" O TRP A3631 " (cutoff:3.500A) Processing helix chain 'A' and resid 3677 through 3687 removed outlier: 3.671A pdb=" N THR A3687 " --> pdb=" O SER A3683 " (cutoff:3.500A) Processing helix chain 'A' and resid 3694 through 3699 removed outlier: 4.082A pdb=" N LEU A3699 " --> pdb=" O ALA A3696 " (cutoff:3.500A) Processing helix chain 'A' and resid 3700 through 3722 Processing helix chain 'A' and resid 3724 through 3739 removed outlier: 3.632A pdb=" N PHE A3737 " --> pdb=" O THR A3733 " (cutoff:3.500A) Processing helix chain 'A' and resid 3754 through 3760 Processing helix chain 'A' and resid 3792 through 3796 Processing helix chain 'A' and resid 3799 through 3819 removed outlier: 3.662A pdb=" N HIS A3813 " --> pdb=" O ARG A3809 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N PHE A3819 " --> pdb=" O LEU A3815 " (cutoff:3.500A) Processing helix chain 'A' and resid 3824 through 3831 Processing helix chain 'A' and resid 3851 through 3855 removed outlier: 3.890A pdb=" N SER A3855 " --> pdb=" O LYS A3852 " (cutoff:3.500A) Processing helix chain 'A' and resid 3859 through 3866 Processing helix chain 'A' and resid 3873 through 3888 removed outlier: 3.832A pdb=" N VAL A3877 " --> pdb=" O LYS A3873 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 694 through 696 removed outlier: 6.664A pdb=" N LEU A 821 " --> pdb=" O SER A 858 " (cutoff:3.500A) removed outlier: 8.252A pdb=" N ILE A 860 " --> pdb=" O LEU A 821 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N LEU A 823 " --> pdb=" O ILE A 860 " (cutoff:3.500A) removed outlier: 8.179A pdb=" N CYS A 862 " --> pdb=" O LEU A 823 " (cutoff:3.500A) removed outlier: 6.590A 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: 6.649A pdb=" N GLY A 969 " --> pdb=" O SER A1753 " (cutoff:3.500A) removed outlier: 7.962A pdb=" N TYR A1755 " --> pdb=" O GLY A 969 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N VAL A 971 " --> pdb=" O TYR A1755 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1003 through 1004 Processing sheet with id=AA4, first strand: chain 'A' and resid 1357 through 1362 removed outlier: 3.626A pdb=" N VAL A1372 " --> pdb=" O LYS A1359 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N LEU A1383 " --> pdb=" O LYS A1373 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N LEU A1386 " --> pdb=" O GLY A1396 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N GLY A1396 " --> pdb=" O LEU A1386 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1821 through 1825 removed outlier: 7.024A pdb=" N VAL A2231 " --> pdb=" O ALA A1824 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 2282 through 2285 removed outlier: 7.701A pdb=" N ALA A2268 " --> pdb=" O GLU A2402 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 2507 through 2515 Processing sheet with id=AA8, first strand: chain 'A' and resid 2574 through 2575 Processing sheet with id=AA9, first strand: chain 'A' and resid 2958 through 2959 Processing sheet with id=AB1, first strand: chain 'A' and resid 3006 through 3009 removed outlier: 6.355A pdb=" N SER A3007 " --> pdb=" O VAL A3041 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 3076 through 3081 removed outlier: 6.788A pdb=" N ARG A3224 " --> pdb=" O GLU A3077 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N GLU A3079 " --> pdb=" O PHE A3222 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N PHE A3222 " --> pdb=" O GLU A3079 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 3086 through 3094 Processing sheet with id=AB4, first strand: chain 'A' and resid 3343 through 3346 removed outlier: 7.225A pdb=" N VAL A3456 " --> pdb=" O LEU A3374 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N ILE A3376 " --> pdb=" O VAL A3456 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N ALA A3455 " --> pdb=" O VAL A3435 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 3466 through 3469 Processing sheet with id=AB6, first strand: chain 'A' and resid 3479 through 3482 removed outlier: 3.921A pdb=" N GLN A3481 " --> pdb=" O SER A3488 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N SER A3488 " --> pdb=" O GLN A3481 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N SER A3534 " --> pdb=" O ILE A3489 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N TYR A3491 " --> pdb=" O VAL A3532 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N VAL A3532 " --> pdb=" O TYR A3491 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 3647 through 3650 Processing sheet with id=AB8, first strand: chain 'A' and resid 3765 through 3767 removed outlier: 3.621A pdb=" N ILE A3771 " --> pdb=" O ILE A3767 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 3765 through 3767 removed outlier: 3.621A pdb=" N ILE A3771 " --> pdb=" O ILE A3767 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE A3788 " --> pdb=" O PHE A3846 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N PHE A3846 " --> pdb=" O ILE A3788 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N THR A3849 " --> pdb=" O ASN A3834 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N ASN A3834 " --> pdb=" O THR A3849 " (cutoff:3.500A) 1338 hydrogen bonds defined for protein. 3816 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 22 hydrogen bonds 44 hydrogen bond angles 0 basepair planarities 9 basepair parallelities 20 stacking parallelities Total time for adding SS restraints: 8.48 Time building geometry restraints manager: 3.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 4142 1.30 - 1.43: 6667 1.43 - 1.56: 14999 1.56 - 1.68: 90 1.68 - 1.81: 233 Bond restraints: 26131 Sorted by residual: bond pdb=" C2' 2KH A4005 " pdb=" C3' 2KH A4005 " ideal model delta sigma weight residual 1.548 1.288 0.260 2.00e-02 2.50e+03 1.70e+02 bond pdb=" N3A 2KH A4005 " pdb=" PA 2KH A4005 " ideal model delta sigma weight residual 1.933 1.695 0.238 2.00e-02 2.50e+03 1.42e+02 bond pdb=" O3G 2KH A4005 " pdb=" PG 2KH A4005 " ideal model delta sigma weight residual 1.669 1.466 0.203 2.00e-02 2.50e+03 1.03e+02 bond pdb=" C1' 2KH A4005 " pdb=" N1 2KH A4005 " ideal model delta sigma weight residual 1.502 1.332 0.170 2.00e-02 2.50e+03 7.24e+01 bond pdb=" N3A 2KH A4005 " pdb=" PB 2KH A4005 " ideal model delta sigma weight residual 1.890 1.724 0.166 2.00e-02 2.50e+03 6.89e+01 ... (remaining 26126 not shown) Histogram of bond angle deviations from ideal: 0.00 - 12.29: 35458 12.29 - 24.58: 6 24.58 - 36.87: 0 36.87 - 49.16: 0 49.16 - 61.44: 2 Bond angle restraints: 35466 Sorted by residual: angle pdb=" N3A 2KH A4005 " pdb=" PA 2KH A4005 " pdb=" O2A 2KH A4005 " ideal model delta sigma weight residual 48.17 109.61 -61.44 3.00e+00 1.11e-01 4.19e+02 angle pdb=" O2G 2KH A4005 " pdb=" PG 2KH A4005 " pdb=" O3G 2KH A4005 " ideal model delta sigma weight residual 53.94 109.68 -55.74 3.00e+00 1.11e-01 3.45e+02 angle pdb=" O1A 2KH A4005 " pdb=" PA 2KH A4005 " pdb=" O2A 2KH A4005 " ideal model delta sigma weight residual 130.82 108.66 22.16 3.00e+00 1.11e-01 5.46e+01 angle pdb=" O1B 2KH A4005 " pdb=" PB 2KH A4005 " pdb=" O2B 2KH A4005 " ideal model delta sigma weight residual 130.56 109.34 21.22 3.00e+00 1.11e-01 5.00e+01 angle pdb=" O1G 2KH A4005 " pdb=" PG 2KH A4005 " pdb=" O2G 2KH A4005 " ideal model delta sigma weight residual 130.21 109.68 20.53 3.00e+00 1.11e-01 4.68e+01 ... (remaining 35461 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.97: 15862 35.97 - 71.94: 187 71.94 - 107.90: 15 107.90 - 143.87: 0 143.87 - 179.84: 1 Dihedral angle restraints: 16065 sinusoidal: 7031 harmonic: 9034 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 51.84 -179.84 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 68.00 150.27 -82.27 1 1.70e+01 3.46e-03 2.87e+01 dihedral pdb=" CA VAL A3237 " pdb=" C VAL A3237 " pdb=" N LYS A3238 " pdb=" CA LYS A3238 " ideal model delta harmonic sigma weight residual -180.00 -160.76 -19.24 0 5.00e+00 4.00e-02 1.48e+01 ... (remaining 16062 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.090: 3937 0.090 - 0.179: 199 0.179 - 0.269: 1 0.269 - 0.359: 0 0.359 - 0.448: 1 Chirality restraints: 4138 Sorted by residual: chirality pdb=" C2' 2KH A4005 " pdb=" C1' 2KH A4005 " pdb=" C3' 2KH A4005 " pdb=" O2' 2KH A4005 " both_signs ideal model delta sigma weight residual False -2.85 -2.40 -0.45 2.00e-01 2.50e+01 5.02e+00 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 2.27 0.20 2.00e-01 2.50e+01 1.01e+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 2.81 -0.16 2.00e-01 2.50e+01 6.74e-01 ... (remaining 4135 not shown) Planarity restraints: 4304 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A2503 " -0.036 5.00e-02 4.00e+02 5.44e-02 4.74e+00 pdb=" N PRO A2504 " 0.094 5.00e-02 4.00e+02 pdb=" CA PRO A2504 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO A2504 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 885 " 0.011 2.00e-02 2.50e+03 2.15e-02 4.62e+00 pdb=" C ASN A 885 " -0.037 2.00e-02 2.50e+03 pdb=" O ASN A 885 " 0.014 2.00e-02 2.50e+03 pdb=" N SER A 886 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A1311 " 0.034 5.00e-02 4.00e+02 5.18e-02 4.30e+00 pdb=" N PRO A1312 " -0.090 5.00e-02 4.00e+02 pdb=" CA PRO A1312 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A1312 " 0.029 5.00e-02 4.00e+02 ... (remaining 4301 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 101 2.66 - 3.22: 23436 3.22 - 3.78: 40239 3.78 - 4.34: 56586 4.34 - 4.90: 90731 Nonbonded interactions: 211093 Sorted by model distance: nonbonded pdb="MN MN A4004 " pdb=" O1B 2KH A4005 " model vdw 2.101 3.060 nonbonded pdb=" OD1 ASP A2358 " pdb="MN MN A4004 " model vdw 2.107 3.060 nonbonded pdb=" OP3 U F 1 " pdb="MN MN A4002 " model vdw 2.122 3.060 nonbonded pdb="MN MN A4003 " pdb=" O2A 2KH A4005 " model vdw 2.129 3.060 nonbonded pdb=" OD1 ASP A2518 " pdb="MN MN A4003 " model vdw 2.139 3.060 ... (remaining 211088 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: 2.760 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: 0.040 Extract box with map and model: 0.600 Check model and map are aligned: 0.100 Set scattering table: 0.100 Process input model: 33.140 Find NCS groups from input model: 0.140 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: 0.000 Load rotamer database and sin/cos tables:8.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.260 26135 Z= 0.241 Angle : 0.782 61.444 35472 Z= 0.367 Chirality : 0.042 0.448 4138 Planarity : 0.004 0.054 4304 Dihedral : 12.261 179.839 10161 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % 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: -0.50 (0.15), residues: 3028 helix: 0.22 (0.12), residues: 1749 sheet: -0.57 (0.36), residues: 228 loop : -1.06 (0.18), residues: 1051 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A3100 TYR 0.027 0.002 TYR A2994 PHE 0.024 0.002 PHE A2633 TRP 0.018 0.002 TRP A2542 HIS 0.008 0.001 HIS A2512 Details of bonding type rmsd/Z covalent geometry : bond 0.00495 / 0.24 (26131) covalent geometry : angle 0.77960 / 0.37 (35466) hydrogen bonds : bond 0.16454 / 10.65 ( 1355) hydrogen bonds : angle 6.08473 / 4.22 ( 3860) metal coordination : bond 0.01003 / 0.49 ( 4) metal coordination : angle 5.17595 / 2.86 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6056 Ramachandran restraints generated. 3028 Oldfield, 0 Emsley, 3028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6056 Ramachandran restraints generated. 3028 Oldfield, 0 Emsley, 3028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 738 residues out of total 2828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 738 time to evaluate : 0.637 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 450 MET cc_start: 0.5373 (ttp) cc_final: 0.5015 (ttp) REVERT: A 454 MET cc_start: 0.5439 (mtt) cc_final: 0.5180 (mtt) REVERT: A 467 ARG cc_start: 0.7578 (ttp-110) cc_final: 0.7209 (ptt90) REVERT: A 471 ASP cc_start: 0.7872 (m-30) cc_final: 0.7620 (m-30) REVERT: A 584 VAL cc_start: 0.8556 (t) cc_final: 0.8328 (p) REVERT: A 805 GLU cc_start: 0.7745 (tt0) cc_final: 0.7399 (tm-30) REVERT: A 844 LYS cc_start: 0.8220 (tttt) cc_final: 0.7812 (ttpt) REVERT: A 982 ASN cc_start: 0.8102 (m-40) cc_final: 0.7835 (m110) REVERT: A 1037 LYS cc_start: 0.8370 (tttt) cc_final: 0.8122 (ttmm) REVERT: A 1097 GLU cc_start: 0.7995 (pt0) cc_final: 0.7605 (pm20) REVERT: A 1123 ARG cc_start: 0.7560 (ttp-110) cc_final: 0.7303 (ttp-110) REVERT: A 1131 LEU cc_start: 0.7707 (tp) cc_final: 0.7432 (tp) REVERT: A 1186 GLU cc_start: 0.7789 (mm-30) cc_final: 0.7279 (mm-30) REVERT: A 1204 SER cc_start: 0.8287 (m) cc_final: 0.8057 (p) REVERT: A 1206 SER cc_start: 0.8037 (m) cc_final: 0.7814 (m) REVERT: A 1250 LYS cc_start: 0.7494 (tttm) cc_final: 0.7182 (tttp) REVERT: A 1254 GLU cc_start: 0.7617 (mt-10) cc_final: 0.7371 (mt-10) REVERT: A 1275 ASP cc_start: 0.7640 (m-30) cc_final: 0.7394 (m-30) REVERT: A 1292 VAL cc_start: 0.7694 (t) cc_final: 0.6415 (m) REVERT: A 1377 ASN cc_start: 0.7923 (t0) cc_final: 0.7671 (t0) REVERT: A 1410 SER cc_start: 0.8066 (m) cc_final: 0.7845 (p) REVERT: A 1467 GLU cc_start: 0.7627 (tp30) cc_final: 0.7284 (mm-30) REVERT: A 1482 ASN cc_start: 0.7758 (p0) cc_final: 0.7534 (p0) REVERT: A 1503 TYR cc_start: 0.7996 (m-80) cc_final: 0.7453 (m-80) REVERT: A 1583 ARG cc_start: 0.8164 (ttm170) cc_final: 0.7615 (ttm170) REVERT: A 1588 GLU cc_start: 0.7459 (mt-10) cc_final: 0.7178 (mt-10) REVERT: A 1831 MET cc_start: 0.7953 (mtt) cc_final: 0.7715 (mmm) REVERT: A 1836 PHE cc_start: 0.8253 (m-80) cc_final: 0.7989 (m-80) REVERT: A 1844 ASN cc_start: 0.7151 (m-40) cc_final: 0.6855 (m-40) REVERT: A 1955 MET cc_start: 0.5599 (tpt) cc_final: 0.5192 (tpt) REVERT: A 2298 MET cc_start: 0.8369 (tpt) cc_final: 0.8083 (tpp) REVERT: A 2327 ASP cc_start: 0.7375 (m-30) cc_final: 0.7165 (m-30) REVERT: A 2555 VAL cc_start: 0.8217 (p) cc_final: 0.8006 (t) REVERT: A 2581 MET cc_start: 0.7462 (tmm) cc_final: 0.7255 (tmm) REVERT: A 2586 VAL cc_start: 0.8068 (t) cc_final: 0.7854 (p) REVERT: A 2639 GLN cc_start: 0.7816 (tp40) cc_final: 0.7317 (tm-30) REVERT: A 2943 GLU cc_start: 0.7588 (mt-10) cc_final: 0.7057 (tm-30) REVERT: A 2956 TYR cc_start: 0.8324 (m-80) cc_final: 0.7890 (m-80) REVERT: A 3020 PHE cc_start: 0.8711 (m-80) cc_final: 0.8458 (m-80) REVERT: A 3077 GLU cc_start: 0.7084 (mt-10) cc_final: 0.6845 (pt0) REVERT: A 3090 THR cc_start: 0.8532 (p) cc_final: 0.8292 (m) REVERT: A 3092 LEU cc_start: 0.8248 (mp) cc_final: 0.7956 (mt) REVERT: A 3286 GLU cc_start: 0.7069 (pt0) cc_final: 0.5446 (pt0) REVERT: A 3323 ASP cc_start: 0.7086 (m-30) cc_final: 0.6766 (m-30) REVERT: A 3508 LYS cc_start: 0.7957 (tttm) cc_final: 0.7662 (tttp) REVERT: A 3532 VAL cc_start: 0.8403 (t) cc_final: 0.8203 (p) REVERT: A 3683 SER cc_start: 0.8409 (t) cc_final: 0.7998 (p) REVERT: A 3715 LYS cc_start: 0.7942 (tttt) cc_final: 0.7714 (tttt) REVERT: A 3731 LEU cc_start: 0.7940 (tp) cc_final: 0.7447 (tp) REVERT: A 3742 GLU cc_start: 0.7271 (mm-30) cc_final: 0.7044 (mm-30) REVERT: A 3772 LEU cc_start: 0.7841 (mt) cc_final: 0.7349 (mm) REVERT: A 3785 LYS cc_start: 0.7675 (tttt) cc_final: 0.7283 (tttt) REVERT: A 3870 MET cc_start: 0.7059 (mmm) cc_final: 0.6321 (mmm) REVERT: A 3888 THR cc_start: 0.8317 (p) cc_final: 0.8117 (m) outliers start: 0 outliers final: 3 residues processed: 738 average time/residue: 0.6709 time to fit residues: 574.7897 Evaluate side-chains 587 residues out of total 2828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 584 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 620 ILE Chi-restraints excluded: chain A residue 1522 LEU Chi-restraints excluded: chain A residue 3551 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 197 optimal weight: 0.9990 chunk 215 optimal weight: 0.7980 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 0.7980 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 0.9990 chunk 298 optimal weight: 0.4980 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 579 GLN A 622 ASN A 820 GLN A1060 ASN A1258 ASN A1381 ASN A1395 GLN A1758 ASN A1768 GLN A2258 GLN A2275 GLN A2316 HIS ** A2413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2607 GLN A2695 GLN A2776 GLN ** A2822 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2996 HIS ** A3045 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3204 ASN A3462 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.166428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.137910 restraints weight = 33288.153| |-----------------------------------------------------------------------------| r_work (start): 0.3732 rms_B_bonded: 1.70 r_work: 0.3615 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3466 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.1559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 26135 Z= 0.148 Angle : 0.544 7.123 35472 Z= 0.283 Chirality : 0.040 0.185 4138 Planarity : 0.004 0.050 4304 Dihedral : 10.750 179.053 3984 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 2.40 % Allowed : 11.07 % Favored : 86.53 % 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: 0.24 (0.15), residues: 3028 helix: 0.89 (0.13), residues: 1761 sheet: -0.51 (0.35), residues: 233 loop : -0.84 (0.19), residues: 1034 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 990 TYR 0.014 0.001 TYR A1617 PHE 0.023 0.002 PHE A2633 TRP 0.017 0.001 TRP A3631 HIS 0.006 0.001 HIS A1615 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.15 (26131) covalent geometry : angle 0.54255 / 0.28 (35466) hydrogen bonds : bond 0.04629 / 3.04 ( 1355) hydrogen bonds : angle 4.70898 / 3.27 ( 3860) metal coordination : bond 0.00646 / 0.32 ( 4) metal coordination : angle 3.48131 / 1.92 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6056 Ramachandran restraints generated. 3028 Oldfield, 0 Emsley, 3028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6056 Ramachandran restraints generated. 3028 Oldfield, 0 Emsley, 3028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 643 residues out of total 2828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 575 time to evaluate : 0.981 Fit side-chains REVERT: A 467 ARG cc_start: 0.7665 (ttp-110) cc_final: 0.7191 (ptt90) REVERT: A 471 ASP cc_start: 0.8007 (m-30) cc_final: 0.7733 (m-30) REVERT: A 563 GLU cc_start: 0.8013 (pt0) cc_final: 0.7719 (pt0) REVERT: A 578 LEU cc_start: 0.8310 (mp) cc_final: 0.8075 (mt) REVERT: A 580 GLU cc_start: 0.7525 (OUTLIER) cc_final: 0.7222 (tm-30) REVERT: A 584 VAL cc_start: 0.8584 (t) cc_final: 0.8316 (p) REVERT: A 631 LYS cc_start: 0.7956 (OUTLIER) cc_final: 0.7745 (tptt) REVERT: A 746 VAL cc_start: 0.8061 (t) cc_final: 0.7847 (p) REVERT: A 805 GLU cc_start: 0.7777 (tt0) cc_final: 0.7407 (tm-30) REVERT: A 844 LYS cc_start: 0.8249 (tttt) cc_final: 0.8013 (ttpt) REVERT: A 982 ASN cc_start: 0.8116 (m-40) cc_final: 0.7884 (m110) REVERT: A 1037 LYS cc_start: 0.8271 (tttt) cc_final: 0.7932 (ttmm) REVERT: A 1097 GLU cc_start: 0.8032 (pt0) cc_final: 0.7517 (pm20) REVERT: A 1123 ARG cc_start: 0.7625 (ttp-110) cc_final: 0.7416 (ttp-110) REVERT: A 1131 LEU cc_start: 0.7620 (tp) cc_final: 0.7411 (tp) REVERT: A 1138 MET cc_start: 0.8585 (ptp) cc_final: 0.8371 (ptp) REVERT: A 1186 GLU cc_start: 0.7741 (mm-30) cc_final: 0.7187 (mm-30) REVERT: A 1204 SER cc_start: 0.8151 (m) cc_final: 0.7940 (p) REVERT: A 1206 SER cc_start: 0.8083 (m) cc_final: 0.7805 (m) REVERT: A 1377 ASN cc_start: 0.7926 (t0) cc_final: 0.7608 (t0) REVERT: A 1410 SER cc_start: 0.8151 (m) cc_final: 0.7868 (p) REVERT: A 1465 ARG cc_start: 0.8309 (OUTLIER) cc_final: 0.7904 (mtm180) REVERT: A 1503 TYR cc_start: 0.8007 (m-80) cc_final: 0.7309 (m-80) REVERT: A 1583 ARG cc_start: 0.8207 (ttm170) cc_final: 0.7560 (ttm170) REVERT: A 1588 GLU cc_start: 0.7676 (mt-10) cc_final: 0.7288 (mt-10) REVERT: A 1595 THR cc_start: 0.8712 (m) cc_final: 0.8277 (m) REVERT: A 1644 LEU cc_start: 0.8418 (mm) cc_final: 0.8104 (mt) REVERT: A 1806 ASP cc_start: 0.7241 (p0) cc_final: 0.6918 (p0) REVERT: A 1831 MET cc_start: 0.7776 (mtt) cc_final: 0.7520 (mmm) REVERT: A 1836 PHE cc_start: 0.8250 (m-80) cc_final: 0.8033 (m-80) REVERT: A 1844 ASN cc_start: 0.6966 (m-40) cc_final: 0.6669 (m-40) REVERT: A 1955 MET cc_start: 0.5610 (tpt) cc_final: 0.5177 (tpt) REVERT: A 2206 MET cc_start: 0.5605 (mmm) cc_final: 0.5249 (mmm) REVERT: A 2344 SER cc_start: 0.8668 (t) cc_final: 0.8432 (m) REVERT: A 2579 GLU cc_start: 0.6829 (mt-10) cc_final: 0.6614 (mt-10) REVERT: A 2581 MET cc_start: 0.7575 (tmm) cc_final: 0.7272 (tmm) REVERT: A 2582 MET cc_start: 0.8227 (mmm) cc_final: 0.7583 (mmm) REVERT: A 2586 VAL cc_start: 0.8241 (t) cc_final: 0.8015 (p) REVERT: A 2639 GLN cc_start: 0.7899 (tp40) cc_final: 0.7426 (tm-30) REVERT: A 2641 PHE cc_start: 0.8433 (m-80) cc_final: 0.7787 (m-80) REVERT: A 2747 GLU cc_start: 0.8182 (OUTLIER) cc_final: 0.7968 (tp30) REVERT: A 2801 ARG cc_start: 0.7766 (ttp80) cc_final: 0.7436 (ttp-170) REVERT: A 2802 MET cc_start: 0.8335 (ttm) cc_final: 0.8110 (ttm) REVERT: A 2953 MET cc_start: 0.7959 (mtp) cc_final: 0.7126 (mtm) REVERT: A 2956 TYR cc_start: 0.8418 (m-80) cc_final: 0.7983 (m-80) REVERT: A 2999 ASP cc_start: 0.7900 (m-30) cc_final: 0.7609 (m-30) REVERT: A 3008 ILE cc_start: 0.8583 (OUTLIER) cc_final: 0.8230 (tt) REVERT: A 3020 PHE cc_start: 0.8751 (m-80) cc_final: 0.8489 (m-80) REVERT: A 3081 GLU cc_start: 0.7404 (mm-30) cc_final: 0.6890 (mm-30) REVERT: A 3092 LEU cc_start: 0.8182 (mp) cc_final: 0.7891 (mt) REVERT: A 3195 PHE cc_start: 0.8315 (p90) cc_final: 0.8055 (p90) REVERT: A 3221 ARG cc_start: 0.7761 (mmt-90) cc_final: 0.7537 (mmt-90) REVERT: A 3259 LYS cc_start: 0.7493 (ttmt) cc_final: 0.7158 (mttt) REVERT: A 3286 GLU cc_start: 0.7359 (pt0) cc_final: 0.5918 (pt0) REVERT: A 3446 LYS cc_start: 0.8062 (tttm) cc_final: 0.7668 (ttpp) REVERT: A 3468 LYS cc_start: 0.7785 (tttt) cc_final: 0.7577 (tttt) REVERT: A 3475 GLU cc_start: 0.7926 (mm-30) cc_final: 0.7624 (mm-30) REVERT: A 3480 LEU cc_start: 0.8212 (mt) cc_final: 0.7990 (mt) REVERT: A 3532 VAL cc_start: 0.8483 (t) cc_final: 0.8237 (p) REVERT: A 3660 LEU cc_start: 0.8449 (OUTLIER) cc_final: 0.8247 (pp) REVERT: A 3683 SER cc_start: 0.8323 (t) cc_final: 0.7960 (p) REVERT: A 3715 LYS cc_start: 0.7990 (tttt) cc_final: 0.7751 (tttt) REVERT: A 3731 LEU cc_start: 0.7643 (tp) cc_final: 0.7364 (tp) REVERT: A 3742 GLU cc_start: 0.7321 (mm-30) cc_final: 0.7024 (mm-30) REVERT: A 3750 ARG cc_start: 0.7709 (mtt-85) cc_final: 0.7505 (mtt-85) REVERT: A 3772 LEU cc_start: 0.7523 (mt) cc_final: 0.7122 (mm) REVERT: A 3785 LYS cc_start: 0.7532 (tttt) cc_final: 0.7119 (tttt) outliers start: 68 outliers final: 23 residues processed: 597 average time/residue: 0.6724 time to fit residues: 462.9279 Evaluate side-chains 564 residues out of total 2828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 535 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 566 SER Chi-restraints excluded: chain A residue 580 GLU Chi-restraints excluded: chain A residue 631 LYS Chi-restraints excluded: chain A residue 752 ILE Chi-restraints excluded: chain A residue 865 CYS Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1072 ILE Chi-restraints excluded: chain A residue 1349 CYS Chi-restraints excluded: chain A residue 1457 GLU Chi-restraints excluded: chain A residue 1459 THR Chi-restraints excluded: chain A residue 1465 ARG Chi-restraints excluded: chain A residue 1631 VAL Chi-restraints excluded: chain A residue 1640 MET Chi-restraints excluded: chain A residue 1812 SER Chi-restraints excluded: chain A residue 2230 SER Chi-restraints excluded: chain A residue 2260 LEU Chi-restraints excluded: chain A residue 2540 THR Chi-restraints excluded: chain A residue 2747 GLU Chi-restraints excluded: chain A residue 3008 ILE Chi-restraints excluded: chain A residue 3013 THR Chi-restraints excluded: chain A residue 3124 THR Chi-restraints excluded: chain A residue 3144 SER Chi-restraints excluded: chain A residue 3184 MET Chi-restraints excluded: chain A residue 3400 ARG Chi-restraints excluded: chain A residue 3420 SER Chi-restraints excluded: chain A residue 3466 VAL Chi-restraints excluded: chain A residue 3498 THR Chi-restraints excluded: chain A residue 3597 VAL Chi-restraints excluded: chain A residue 3660 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 278 optimal weight: 0.8980 chunk 125 optimal weight: 4.9990 chunk 198 optimal weight: 4.9990 chunk 110 optimal weight: 5.9990 chunk 286 optimal weight: 1.9990 chunk 108 optimal weight: 1.9990 chunk 144 optimal weight: 9.9990 chunk 117 optimal weight: 3.9990 chunk 173 optimal weight: 4.9990 chunk 63 optimal weight: 0.6980 chunk 157 optimal weight: 0.8980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 549 HIS A 647 ASN A 820 GLN A1055 ASN A1514 ASN A1768 GLN A1886 GLN A2258 GLN A2316 HIS A2359 ASN ** A2413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2623 ASN A2695 GLN A2776 GLN A2822 ASN A3204 ASN A3268 ASN A3462 GLN A3653 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.164571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.135805 restraints weight = 33231.301| |-----------------------------------------------------------------------------| r_work (start): 0.3703 rms_B_bonded: 1.71 r_work: 0.3586 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3437 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.1905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 26135 Z= 0.177 Angle : 0.531 7.156 35472 Z= 0.276 Chirality : 0.041 0.186 4138 Planarity : 0.004 0.050 4304 Dihedral : 10.623 177.619 3978 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.97 % Allowed : 12.62 % Favored : 84.41 % 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: 0.36 (0.15), residues: 3028 helix: 1.03 (0.13), residues: 1773 sheet: -0.61 (0.35), residues: 229 loop : -0.86 (0.19), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 990 TYR 0.018 0.002 TYR A2994 PHE 0.022 0.002 PHE A2633 TRP 0.024 0.002 TRP A3631 HIS 0.007 0.001 HIS A3045 Details of bonding type rmsd/Z covalent geometry : bond 0.00413 / 0.18 (26131) covalent geometry : angle 0.52912 / 0.28 (35466) hydrogen bonds : bond 0.04183 / 2.74 ( 1355) hydrogen bonds : angle 4.43054 / 3.09 ( 3860) metal coordination : bond 0.00744 / 0.37 ( 4) metal coordination : angle 3.09475 / 1.71 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6056 Ramachandran restraints generated. 3028 Oldfield, 0 Emsley, 3028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6056 Ramachandran restraints generated. 3028 Oldfield, 0 Emsley, 3028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 640 residues out of total 2828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 556 time to evaluate : 1.016 Fit side-chains revert: symmetry clash REVERT: A 467 ARG cc_start: 0.7601 (ttp-110) cc_final: 0.7174 (ptt90) REVERT: A 471 ASP cc_start: 0.8014 (m-30) cc_final: 0.7731 (m-30) REVERT: A 563 GLU cc_start: 0.7999 (pt0) cc_final: 0.7693 (pt0) REVERT: A 580 GLU cc_start: 0.7540 (OUTLIER) cc_final: 0.7206 (tm-30) REVERT: A 584 VAL cc_start: 0.8622 (t) cc_final: 0.8387 (p) REVERT: A 753 MET cc_start: 0.8202 (OUTLIER) cc_final: 0.7645 (mtp) REVERT: A 844 LYS cc_start: 0.8251 (tttt) cc_final: 0.8016 (ttpt) REVERT: A 896 ARG cc_start: 0.8126 (OUTLIER) cc_final: 0.7890 (mtp85) REVERT: A 982 ASN cc_start: 0.8213 (m-40) cc_final: 0.7996 (m110) REVERT: A 1036 LYS cc_start: 0.7455 (tttt) cc_final: 0.7236 (ttmt) REVERT: A 1037 LYS cc_start: 0.8248 (tttt) cc_final: 0.7960 (ttmm) REVERT: A 1097 GLU cc_start: 0.8093 (pt0) cc_final: 0.7531 (pm20) REVERT: A 1131 LEU cc_start: 0.7619 (tp) cc_final: 0.7408 (tp) REVERT: A 1186 GLU cc_start: 0.7765 (mm-30) cc_final: 0.7167 (mm-30) REVERT: A 1204 SER cc_start: 0.8149 (m) cc_final: 0.7923 (p) REVERT: A 1206 SER cc_start: 0.8088 (m) cc_final: 0.7803 (m) REVERT: A 1213 GLN cc_start: 0.7817 (mm-40) cc_final: 0.7511 (mm110) REVERT: A 1254 GLU cc_start: 0.7567 (mt-10) cc_final: 0.7367 (mt-10) REVERT: A 1292 VAL cc_start: 0.7779 (t) cc_final: 0.7577 (p) REVERT: A 1377 ASN cc_start: 0.7917 (t0) cc_final: 0.7598 (t0) REVERT: A 1465 ARG cc_start: 0.8352 (OUTLIER) cc_final: 0.7986 (mtm180) REVERT: A 1503 TYR cc_start: 0.8049 (m-80) cc_final: 0.7328 (m-80) REVERT: A 1583 ARG cc_start: 0.8216 (ttm170) cc_final: 0.7527 (ttm170) REVERT: A 1588 GLU cc_start: 0.7703 (mt-10) cc_final: 0.7316 (mt-10) REVERT: A 1595 THR cc_start: 0.8732 (m) cc_final: 0.8338 (m) REVERT: A 1610 ASP cc_start: 0.7618 (m-30) cc_final: 0.7333 (m-30) REVERT: A 1644 LEU cc_start: 0.8450 (mm) cc_final: 0.8115 (mt) REVERT: A 1806 ASP cc_start: 0.7281 (p0) cc_final: 0.7029 (p0) REVERT: A 1831 MET cc_start: 0.7798 (mtt) cc_final: 0.7553 (mmm) REVERT: A 1836 PHE cc_start: 0.8313 (m-80) cc_final: 0.7998 (m-80) REVERT: A 1837 LYS cc_start: 0.8227 (mtpp) cc_final: 0.7785 (mmmt) REVERT: A 1844 ASN cc_start: 0.6970 (m-40) cc_final: 0.6659 (m-40) REVERT: A 1955 MET cc_start: 0.5679 (tpt) cc_final: 0.5202 (tpt) REVERT: A 2206 MET cc_start: 0.5619 (mmm) cc_final: 0.5193 (mmm) REVERT: A 2239 MET cc_start: 0.8323 (tpp) cc_final: 0.8084 (mpp) REVERT: A 2344 SER cc_start: 0.8713 (t) cc_final: 0.8503 (m) REVERT: A 2418 ARG cc_start: 0.7851 (tpt-90) cc_final: 0.7611 (ttt-90) REVERT: A 2579 GLU cc_start: 0.6875 (mt-10) cc_final: 0.6623 (mt-10) REVERT: A 2581 MET cc_start: 0.7525 (tmm) cc_final: 0.7096 (tmm) REVERT: A 2586 VAL cc_start: 0.8244 (t) cc_final: 0.8025 (p) REVERT: A 2639 GLN cc_start: 0.7926 (tp40) cc_final: 0.7720 (mm-40) REVERT: A 2641 PHE cc_start: 0.8431 (m-80) cc_final: 0.7707 (m-80) REVERT: A 2747 GLU cc_start: 0.8208 (OUTLIER) cc_final: 0.7976 (tp30) REVERT: A 2801 ARG cc_start: 0.7739 (ttp80) cc_final: 0.7450 (ttp-170) REVERT: A 2956 TYR cc_start: 0.8491 (m-80) cc_final: 0.8034 (m-80) REVERT: A 2999 ASP cc_start: 0.7899 (m-30) cc_final: 0.7618 (m-30) REVERT: A 3008 ILE cc_start: 0.8586 (OUTLIER) cc_final: 0.8253 (tt) REVERT: A 3020 PHE cc_start: 0.8817 (m-80) cc_final: 0.8591 (m-80) REVERT: A 3081 GLU cc_start: 0.7426 (mm-30) cc_final: 0.6978 (mm-30) REVERT: A 3092 LEU cc_start: 0.8152 (mp) cc_final: 0.7878 (mt) REVERT: A 3115 GLU cc_start: 0.6870 (pm20) cc_final: 0.6653 (pm20) REVERT: A 3195 PHE cc_start: 0.8315 (p90) cc_final: 0.8069 (p90) REVERT: A 3446 LYS cc_start: 0.8071 (tttm) cc_final: 0.7669 (ttpp) REVERT: A 3475 GLU cc_start: 0.7952 (mm-30) cc_final: 0.7648 (mm-30) REVERT: A 3480 LEU cc_start: 0.8479 (mt) cc_final: 0.8220 (mt) REVERT: A 3532 VAL cc_start: 0.8565 (t) cc_final: 0.8324 (p) REVERT: A 3645 ASN cc_start: 0.8083 (m-40) cc_final: 0.7578 (t160) REVERT: A 3683 SER cc_start: 0.8318 (t) cc_final: 0.7860 (m) REVERT: A 3715 LYS cc_start: 0.8003 (tttt) cc_final: 0.7692 (tttt) REVERT: A 3737 PHE cc_start: 0.7679 (t80) cc_final: 0.7158 (t80) REVERT: A 3785 LYS cc_start: 0.7601 (tttt) cc_final: 0.7227 (tttt) REVERT: A 3870 MET cc_start: 0.7014 (mmm) cc_final: 0.6761 (mmt) REVERT: A 3884 ILE cc_start: 0.8576 (mm) cc_final: 0.8220 (mm) REVERT: A 3888 THR cc_start: 0.8549 (m) cc_final: 0.8305 (p) outliers start: 84 outliers final: 36 residues processed: 591 average time/residue: 0.6790 time to fit residues: 463.6655 Evaluate side-chains 571 residues out of total 2828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 529 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 565 ILE Chi-restraints excluded: chain A residue 566 SER Chi-restraints excluded: chain A residue 580 GLU Chi-restraints excluded: chain A residue 752 ILE Chi-restraints excluded: chain A residue 753 MET Chi-restraints excluded: chain A residue 833 ASP Chi-restraints excluded: chain A residue 865 CYS Chi-restraints excluded: chain A residue 896 ARG Chi-restraints excluded: chain A residue 953 THR Chi-restraints excluded: chain A residue 970 VAL Chi-restraints excluded: chain A residue 1063 SER Chi-restraints excluded: chain A residue 1072 ILE Chi-restraints excluded: chain A residue 1134 LEU Chi-restraints excluded: chain A residue 1257 ARG Chi-restraints excluded: chain A residue 1366 CYS Chi-restraints excluded: chain A residue 1459 THR Chi-restraints excluded: chain A residue 1465 ARG Chi-restraints excluded: chain A residue 1522 LEU Chi-restraints excluded: chain A residue 1573 VAL Chi-restraints excluded: chain A residue 1640 MET Chi-restraints excluded: chain A residue 1812 SER Chi-restraints excluded: chain A residue 2230 SER Chi-restraints excluded: chain A residue 2260 LEU Chi-restraints excluded: chain A residue 2449 THR Chi-restraints excluded: chain A residue 2540 THR Chi-restraints excluded: chain A residue 2568 LEU Chi-restraints excluded: chain A residue 2747 GLU Chi-restraints excluded: chain A residue 2838 SER Chi-restraints excluded: chain A residue 2913 SER Chi-restraints excluded: chain A residue 3008 ILE Chi-restraints excluded: chain A residue 3013 THR Chi-restraints excluded: chain A residue 3059 GLN Chi-restraints excluded: chain A residue 3124 THR Chi-restraints excluded: chain A residue 3184 MET Chi-restraints excluded: chain A residue 3346 THR Chi-restraints excluded: chain A residue 3400 ARG Chi-restraints excluded: chain A residue 3420 SER Chi-restraints excluded: chain A residue 3439 SER Chi-restraints excluded: chain A residue 3461 LYS Chi-restraints excluded: chain A residue 3465 THR Chi-restraints excluded: chain A residue 3498 THR Chi-restraints excluded: chain A residue 3597 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 143 optimal weight: 9.9990 chunk 40 optimal weight: 3.9990 chunk 126 optimal weight: 0.0770 chunk 224 optimal weight: 0.0980 chunk 117 optimal weight: 0.0170 chunk 81 optimal weight: 0.8980 chunk 120 optimal weight: 3.9990 chunk 30 optimal weight: 0.9980 chunk 272 optimal weight: 0.6980 chunk 104 optimal weight: 0.9990 chunk 187 optimal weight: 2.9990 overall best weight: 0.3576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 597 ASN A 820 GLN ** A 987 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1154 HIS A2258 GLN A2316 HIS ** A2413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2692 GLN A2695 GLN A2776 GLN A2787 ASN A2932 ASN A3204 ASN A3411 GLN A3462 GLN A3503 ASN A3740 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.166422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.138222 restraints weight = 33072.403| |-----------------------------------------------------------------------------| r_work (start): 0.3728 rms_B_bonded: 1.87 r_work: 0.3604 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3452 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.2077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 26135 Z= 0.102 Angle : 0.494 12.298 35472 Z= 0.255 Chirality : 0.038 0.191 4138 Planarity : 0.004 0.100 4304 Dihedral : 10.536 178.050 3978 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.69 % Allowed : 13.40 % Favored : 83.91 % 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: 0.63 (0.16), residues: 3028 helix: 1.28 (0.13), residues: 1780 sheet: -0.52 (0.36), residues: 225 loop : -0.84 (0.19), residues: 1023 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 990 TYR 0.016 0.001 TYR A3358 PHE 0.022 0.001 PHE A3739 TRP 0.016 0.001 TRP A3631 HIS 0.006 0.001 HIS A1615 Details of bonding type rmsd/Z covalent geometry : bond 0.00222 / 0.10 (26131) covalent geometry : angle 0.49272 / 0.25 (35466) hydrogen bonds : bond 0.03511 / 2.29 ( 1355) hydrogen bonds : angle 4.19734 / 2.93 ( 3860) metal coordination : bond 0.00376 / 0.18 ( 4) metal coordination : angle 2.52972 / 1.39 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6056 Ramachandran restraints generated. 3028 Oldfield, 0 Emsley, 3028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6056 Ramachandran restraints generated. 3028 Oldfield, 0 Emsley, 3028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 634 residues out of total 2828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 558 time to evaluate : 0.747 Fit side-chains revert: symmetry clash REVERT: A 467 ARG cc_start: 0.7647 (ttp-110) cc_final: 0.7153 (ptt90) REVERT: A 471 ASP cc_start: 0.7985 (m-30) cc_final: 0.7700 (m-30) REVERT: A 563 GLU cc_start: 0.7946 (pt0) cc_final: 0.7587 (pt0) REVERT: A 580 GLU cc_start: 0.7447 (OUTLIER) cc_final: 0.7079 (tm-30) REVERT: A 584 VAL cc_start: 0.8575 (t) cc_final: 0.8322 (p) REVERT: A 755 ASN cc_start: 0.7540 (t0) cc_final: 0.7226 (t0) REVERT: A 844 LYS cc_start: 0.8177 (tttt) cc_final: 0.7914 (ttpt) REVERT: A 982 ASN cc_start: 0.8126 (m-40) cc_final: 0.7904 (m110) REVERT: A 1036 LYS cc_start: 0.7404 (tttt) cc_final: 0.7152 (ttmt) REVERT: A 1037 LYS cc_start: 0.8197 (tttt) cc_final: 0.7806 (ttmm) REVERT: A 1080 LYS cc_start: 0.8296 (mttm) cc_final: 0.8096 (mmtp) REVERT: A 1097 GLU cc_start: 0.8081 (pt0) cc_final: 0.7435 (pm20) REVERT: A 1213 GLN cc_start: 0.7808 (mm-40) cc_final: 0.7456 (mm110) REVERT: A 1233 LYS cc_start: 0.7523 (mtpt) cc_final: 0.7283 (mtmt) REVERT: A 1292 VAL cc_start: 0.7734 (t) cc_final: 0.7523 (p) REVERT: A 1377 ASN cc_start: 0.7914 (t0) cc_final: 0.7550 (t0) REVERT: A 1402 ARG cc_start: 0.7731 (ttm-80) cc_final: 0.7394 (ttp-170) REVERT: A 1403 ARG cc_start: 0.7912 (ttt180) cc_final: 0.7703 (ttt180) REVERT: A 1410 SER cc_start: 0.8170 (m) cc_final: 0.7960 (p) REVERT: A 1465 ARG cc_start: 0.8354 (OUTLIER) cc_final: 0.7970 (mtm180) REVERT: A 1503 TYR cc_start: 0.7955 (m-80) cc_final: 0.7391 (m-80) REVERT: A 1583 ARG cc_start: 0.8164 (ttm170) cc_final: 0.7395 (ttm170) REVERT: A 1588 GLU cc_start: 0.7753 (mt-10) cc_final: 0.7318 (mt-10) REVERT: A 1595 THR cc_start: 0.8734 (m) cc_final: 0.8369 (m) REVERT: A 1610 ASP cc_start: 0.7604 (m-30) cc_final: 0.7308 (m-30) REVERT: A 1644 LEU cc_start: 0.8326 (mm) cc_final: 0.7990 (mt) REVERT: A 1806 ASP cc_start: 0.7351 (p0) cc_final: 0.7150 (p0) REVERT: A 1830 MET cc_start: 0.8362 (OUTLIER) cc_final: 0.7419 (ptm) REVERT: A 1831 MET cc_start: 0.7802 (mtt) cc_final: 0.7558 (mmm) REVERT: A 1836 PHE cc_start: 0.8247 (m-80) cc_final: 0.8003 (m-80) REVERT: A 1844 ASN cc_start: 0.6890 (m-40) cc_final: 0.6568 (m-40) REVERT: A 1955 MET cc_start: 0.5261 (tpt) cc_final: 0.4827 (tpt) REVERT: A 2206 MET cc_start: 0.5596 (mmm) cc_final: 0.5186 (mmm) REVERT: A 2239 MET cc_start: 0.8291 (tpp) cc_final: 0.8047 (tpp) REVERT: A 2318 LYS cc_start: 0.8031 (mtpp) cc_final: 0.7712 (ttmm) REVERT: A 2344 SER cc_start: 0.8732 (t) cc_final: 0.8491 (m) REVERT: A 2581 MET cc_start: 0.7599 (tmm) cc_final: 0.7232 (tmm) REVERT: A 2586 VAL cc_start: 0.8285 (t) cc_final: 0.8041 (p) REVERT: A 2639 GLN cc_start: 0.7887 (tp40) cc_final: 0.7351 (tm-30) REVERT: A 2641 PHE cc_start: 0.8418 (m-80) cc_final: 0.7742 (m-80) REVERT: A 2747 GLU cc_start: 0.8223 (OUTLIER) cc_final: 0.7968 (tp30) REVERT: A 2956 TYR cc_start: 0.8472 (m-80) cc_final: 0.8012 (m-80) REVERT: A 3008 ILE cc_start: 0.8524 (OUTLIER) cc_final: 0.8195 (tt) REVERT: A 3020 PHE cc_start: 0.8773 (m-80) cc_final: 0.8481 (m-80) REVERT: A 3081 GLU cc_start: 0.7450 (mm-30) cc_final: 0.7104 (mm-30) REVERT: A 3092 LEU cc_start: 0.8058 (mp) cc_final: 0.7794 (mt) REVERT: A 3115 GLU cc_start: 0.6854 (pm20) cc_final: 0.6555 (pm20) REVERT: A 3116 SER cc_start: 0.7421 (m) cc_final: 0.6722 (p) REVERT: A 3120 GLU cc_start: 0.7526 (mp0) cc_final: 0.7277 (mp0) REVERT: A 3192 VAL cc_start: 0.7869 (OUTLIER) cc_final: 0.7597 (p) REVERT: A 3195 PHE cc_start: 0.8316 (p90) cc_final: 0.8041 (p90) REVERT: A 3221 ARG cc_start: 0.8103 (mmt-90) cc_final: 0.7870 (mmm160) REVERT: A 3396 TRP cc_start: 0.8130 (t60) cc_final: 0.7706 (t60) REVERT: A 3446 LYS cc_start: 0.8037 (tttm) cc_final: 0.7630 (ttpp) REVERT: A 3475 GLU cc_start: 0.7940 (mm-30) cc_final: 0.7640 (mm-30) REVERT: A 3480 LEU cc_start: 0.8464 (mt) cc_final: 0.8166 (mt) REVERT: A 3532 VAL cc_start: 0.8561 (t) cc_final: 0.8311 (p) REVERT: A 3645 ASN cc_start: 0.8084 (m-40) cc_final: 0.7566 (t160) REVERT: A 3660 LEU cc_start: 0.8428 (pp) cc_final: 0.8206 (pp) REVERT: A 3683 SER cc_start: 0.8224 (t) cc_final: 0.7741 (p) REVERT: A 3695 LEU cc_start: 0.8009 (mt) cc_final: 0.7808 (mm) REVERT: A 3715 LYS cc_start: 0.8034 (tttt) cc_final: 0.7703 (tttt) REVERT: A 3742 GLU cc_start: 0.7386 (mm-30) cc_final: 0.6976 (mm-30) REVERT: A 3750 ARG cc_start: 0.7719 (mtt-85) cc_final: 0.7505 (mtt-85) REVERT: A 3785 LYS cc_start: 0.7512 (tttt) cc_final: 0.7111 (tttt) REVERT: A 3870 MET cc_start: 0.6977 (mmm) cc_final: 0.6736 (mmt) REVERT: A 3884 ILE cc_start: 0.8422 (mm) cc_final: 0.8081 (mm) REVERT: A 3888 THR cc_start: 0.8493 (m) cc_final: 0.8231 (p) outliers start: 76 outliers final: 31 residues processed: 591 average time/residue: 0.6776 time to fit residues: 460.9809 Evaluate side-chains 574 residues out of total 2828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 537 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 580 GLU Chi-restraints excluded: chain A residue 598 MET Chi-restraints excluded: chain A residue 752 ILE Chi-restraints excluded: chain A residue 833 ASP Chi-restraints excluded: chain A residue 858 SER Chi-restraints excluded: chain A residue 865 CYS Chi-restraints excluded: chain A residue 953 THR Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1051 LEU Chi-restraints excluded: chain A residue 1072 ILE Chi-restraints excluded: chain A residue 1134 LEU Chi-restraints excluded: chain A residue 1366 CYS Chi-restraints excluded: chain A residue 1382 MET Chi-restraints excluded: chain A residue 1459 THR Chi-restraints excluded: chain A residue 1465 ARG Chi-restraints excluded: chain A residue 1522 LEU Chi-restraints excluded: chain A residue 1573 VAL Chi-restraints excluded: chain A residue 1640 MET Chi-restraints excluded: chain A residue 1812 SER Chi-restraints excluded: chain A residue 1830 MET Chi-restraints excluded: chain A residue 2260 LEU Chi-restraints excluded: chain A residue 2449 THR Chi-restraints excluded: chain A residue 2540 THR Chi-restraints excluded: chain A residue 2747 GLU Chi-restraints excluded: chain A residue 2818 LEU Chi-restraints excluded: chain A residue 2838 SER Chi-restraints excluded: chain A residue 3008 ILE Chi-restraints excluded: chain A residue 3013 THR Chi-restraints excluded: chain A residue 3059 GLN Chi-restraints excluded: chain A residue 3124 THR Chi-restraints excluded: chain A residue 3184 MET Chi-restraints excluded: chain A residue 3192 VAL Chi-restraints excluded: chain A residue 3400 ARG Chi-restraints excluded: chain A residue 3420 SER Chi-restraints excluded: chain A residue 3461 LYS Chi-restraints excluded: chain A residue 3498 THR Chi-restraints excluded: chain A residue 3597 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 130 optimal weight: 9.9990 chunk 27 optimal weight: 9.9990 chunk 3 optimal weight: 1.9990 chunk 232 optimal weight: 0.5980 chunk 68 optimal weight: 2.9990 chunk 136 optimal weight: 7.9990 chunk 2 optimal weight: 20.0000 chunk 11 optimal weight: 3.9990 chunk 288 optimal weight: 0.9990 chunk 98 optimal weight: 0.7980 chunk 206 optimal weight: 0.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 466 HIS A 820 GLN A1093 ASN A1277 GLN ** A1369 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2258 GLN A2275 GLN ** A2413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2692 GLN A2776 GLN A2787 ASN A2822 ASN A2935 HIS A2961 ASN A3204 ASN A3462 GLN A3740 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.165037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.136109 restraints weight = 33171.302| |-----------------------------------------------------------------------------| r_work (start): 0.3704 rms_B_bonded: 1.71 r_work: 0.3583 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3433 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.2212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 26135 Z= 0.154 Angle : 0.511 10.840 35472 Z= 0.264 Chirality : 0.040 0.187 4138 Planarity : 0.004 0.052 4304 Dihedral : 10.519 178.031 3978 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.69 % Allowed : 14.85 % Favored : 82.46 % 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: 0.66 (0.16), residues: 3028 helix: 1.31 (0.13), residues: 1786 sheet: -0.47 (0.36), residues: 221 loop : -0.84 (0.19), residues: 1021 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A1805 TYR 0.014 0.001 TYR A 653 PHE 0.021 0.002 PHE A2633 TRP 0.014 0.001 TRP A2542 HIS 0.006 0.001 HIS A3045 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.15 (26131) covalent geometry : angle 0.50967 / 0.26 (35466) hydrogen bonds : bond 0.03721 / 2.43 ( 1355) hydrogen bonds : angle 4.16719 / 2.91 ( 3860) metal coordination : bond 0.00624 / 0.31 ( 4) metal coordination : angle 2.49889 / 1.38 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6056 Ramachandran restraints generated. 3028 Oldfield, 0 Emsley, 3028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6056 Ramachandran restraints generated. 3028 Oldfield, 0 Emsley, 3028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 637 residues out of total 2828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 561 time to evaluate : 1.031 Fit side-chains revert: symmetry clash REVERT: A 467 ARG cc_start: 0.7604 (ttp-110) cc_final: 0.7171 (ptt90) REVERT: A 471 ASP cc_start: 0.7994 (m-30) cc_final: 0.7679 (m-30) REVERT: A 493 GLN cc_start: 0.6731 (mp10) cc_final: 0.6522 (mp10) REVERT: A 563 GLU cc_start: 0.7924 (pt0) cc_final: 0.7648 (pt0) REVERT: A 580 GLU cc_start: 0.7609 (OUTLIER) cc_final: 0.7203 (tm-30) REVERT: A 584 VAL cc_start: 0.8613 (t) cc_final: 0.8363 (p) REVERT: A 755 ASN cc_start: 0.7526 (t0) cc_final: 0.7215 (t0) REVERT: A 844 LYS cc_start: 0.8181 (tttt) cc_final: 0.7934 (ttpt) REVERT: A 929 VAL cc_start: 0.7890 (m) cc_final: 0.7594 (t) REVERT: A 960 GLN cc_start: 0.8161 (OUTLIER) cc_final: 0.7680 (mt0) REVERT: A 982 ASN cc_start: 0.8174 (m-40) cc_final: 0.7945 (m110) REVERT: A 990 ARG cc_start: 0.8289 (ttp80) cc_final: 0.8079 (ttm110) REVERT: A 1036 LYS cc_start: 0.7464 (tttt) cc_final: 0.7231 (ttmt) REVERT: A 1037 LYS cc_start: 0.8243 (tttt) cc_final: 0.7927 (ttmm) REVERT: A 1086 GLU cc_start: 0.8122 (mm-30) cc_final: 0.7922 (mm-30) REVERT: A 1097 GLU cc_start: 0.8124 (pt0) cc_final: 0.7549 (pm20) REVERT: A 1213 GLN cc_start: 0.7829 (mm-40) cc_final: 0.7439 (mm110) REVERT: A 1233 LYS cc_start: 0.7570 (mtpt) cc_final: 0.7354 (mtmt) REVERT: A 1377 ASN cc_start: 0.7936 (t0) cc_final: 0.7619 (t0) REVERT: A 1402 ARG cc_start: 0.7795 (ttm-80) cc_final: 0.7429 (ttp-170) REVERT: A 1465 ARG cc_start: 0.8372 (OUTLIER) cc_final: 0.7985 (mtm180) REVERT: A 1503 TYR cc_start: 0.8025 (m-80) cc_final: 0.7404 (m-80) REVERT: A 1583 ARG cc_start: 0.8165 (ttm170) cc_final: 0.7421 (ttm170) REVERT: A 1588 GLU cc_start: 0.7703 (mt-10) cc_final: 0.7299 (mt-10) REVERT: A 1595 THR cc_start: 0.8736 (m) cc_final: 0.8386 (m) REVERT: A 1610 ASP cc_start: 0.7626 (m-30) cc_final: 0.7346 (m-30) REVERT: A 1644 LEU cc_start: 0.8343 (mm) cc_final: 0.7998 (mt) REVERT: A 1831 MET cc_start: 0.7794 (mtt) cc_final: 0.7571 (mmm) REVERT: A 1836 PHE cc_start: 0.8322 (m-80) cc_final: 0.8003 (m-80) REVERT: A 1837 LYS cc_start: 0.8198 (mtpp) cc_final: 0.7792 (mmmt) REVERT: A 1844 ASN cc_start: 0.6994 (m-40) cc_final: 0.6661 (m-40) REVERT: A 1955 MET cc_start: 0.5274 (tpt) cc_final: 0.4818 (tpt) REVERT: A 2206 MET cc_start: 0.5578 (mmm) cc_final: 0.5162 (mmm) REVERT: A 2239 MET cc_start: 0.8302 (tpp) cc_final: 0.8058 (tpp) REVERT: A 2418 ARG cc_start: 0.7843 (ttt90) cc_final: 0.7575 (ttm-80) REVERT: A 2579 GLU cc_start: 0.6864 (mt-10) cc_final: 0.6566 (mt-10) REVERT: A 2581 MET cc_start: 0.7554 (tmm) cc_final: 0.7188 (tmm) REVERT: A 2586 VAL cc_start: 0.8234 (t) cc_final: 0.8031 (p) REVERT: A 2639 GLN cc_start: 0.7948 (tp40) cc_final: 0.7454 (tm-30) REVERT: A 2641 PHE cc_start: 0.8430 (m-80) cc_final: 0.7740 (m-80) REVERT: A 2661 SER cc_start: 0.8752 (t) cc_final: 0.8443 (m) REVERT: A 2747 GLU cc_start: 0.8263 (OUTLIER) cc_final: 0.8016 (tp30) REVERT: A 2956 TYR cc_start: 0.8514 (m-80) cc_final: 0.8067 (m-80) REVERT: A 2999 ASP cc_start: 0.7855 (m-30) cc_final: 0.7603 (m-30) REVERT: A 3008 ILE cc_start: 0.8541 (OUTLIER) cc_final: 0.8219 (tt) REVERT: A 3020 PHE cc_start: 0.8823 (m-80) cc_final: 0.8543 (m-80) REVERT: A 3081 GLU cc_start: 0.7516 (OUTLIER) cc_final: 0.7201 (mm-30) REVERT: A 3092 LEU cc_start: 0.8082 (mp) cc_final: 0.7864 (mt) REVERT: A 3115 GLU cc_start: 0.6791 (pm20) cc_final: 0.6520 (pm20) REVERT: A 3116 SER cc_start: 0.7580 (m) cc_final: 0.6981 (p) REVERT: A 3192 VAL cc_start: 0.7910 (OUTLIER) cc_final: 0.7658 (p) REVERT: A 3195 PHE cc_start: 0.8291 (p90) cc_final: 0.7995 (p90) REVERT: A 3446 LYS cc_start: 0.8084 (tttm) cc_final: 0.7710 (ttpp) REVERT: A 3475 GLU cc_start: 0.7941 (mm-30) cc_final: 0.7648 (mm-30) REVERT: A 3480 LEU cc_start: 0.8556 (mt) cc_final: 0.8254 (mt) REVERT: A 3532 VAL cc_start: 0.8552 (t) cc_final: 0.8316 (p) REVERT: A 3660 LEU cc_start: 0.8463 (pp) cc_final: 0.8242 (pp) REVERT: A 3683 SER cc_start: 0.8282 (t) cc_final: 0.7502 (m) REVERT: A 3715 LYS cc_start: 0.7961 (tttt) cc_final: 0.7686 (tttt) REVERT: A 3742 GLU cc_start: 0.7398 (mm-30) cc_final: 0.7005 (mm-30) REVERT: A 3750 ARG cc_start: 0.7766 (mtt-85) cc_final: 0.7539 (mtt-85) REVERT: A 3785 LYS cc_start: 0.7566 (tttt) cc_final: 0.7179 (tttt) REVERT: A 3870 MET cc_start: 0.6996 (mmm) cc_final: 0.6521 (mmm) REVERT: A 3884 ILE cc_start: 0.8507 (mm) cc_final: 0.8204 (mm) REVERT: A 3888 THR cc_start: 0.8499 (m) cc_final: 0.8248 (p) outliers start: 76 outliers final: 41 residues processed: 591 average time/residue: 0.6669 time to fit residues: 457.2800 Evaluate side-chains 590 residues out of total 2828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 542 time to evaluate : 0.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 572 ILE Chi-restraints excluded: chain A residue 580 GLU Chi-restraints excluded: chain A residue 598 MET Chi-restraints excluded: chain A residue 752 ILE Chi-restraints excluded: chain A residue 833 ASP Chi-restraints excluded: chain A residue 858 SER Chi-restraints excluded: chain A residue 860 ILE Chi-restraints excluded: chain A residue 865 CYS Chi-restraints excluded: chain A residue 876 THR Chi-restraints excluded: chain A residue 953 THR Chi-restraints excluded: chain A residue 960 GLN Chi-restraints excluded: chain A residue 970 VAL Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1051 LEU Chi-restraints excluded: chain A residue 1063 SER Chi-restraints excluded: chain A residue 1072 ILE Chi-restraints excluded: chain A residue 1228 VAL Chi-restraints excluded: chain A residue 1366 CYS Chi-restraints excluded: chain A residue 1382 MET Chi-restraints excluded: chain A residue 1459 THR Chi-restraints excluded: chain A residue 1465 ARG Chi-restraints excluded: chain A residue 1522 LEU Chi-restraints excluded: chain A residue 1573 VAL Chi-restraints excluded: chain A residue 1812 SER Chi-restraints excluded: chain A residue 2230 SER Chi-restraints excluded: chain A residue 2260 LEU Chi-restraints excluded: chain A residue 2287 THR Chi-restraints excluded: chain A residue 2449 THR Chi-restraints excluded: chain A residue 2540 THR Chi-restraints excluded: chain A residue 2543 LYS Chi-restraints excluded: chain A residue 2747 GLU Chi-restraints excluded: chain A residue 2769 THR Chi-restraints excluded: chain A residue 2818 LEU Chi-restraints excluded: chain A residue 2838 SER Chi-restraints excluded: chain A residue 3008 ILE Chi-restraints excluded: chain A residue 3013 THR Chi-restraints excluded: chain A residue 3059 GLN Chi-restraints excluded: chain A residue 3081 GLU Chi-restraints excluded: chain A residue 3124 THR Chi-restraints excluded: chain A residue 3184 MET Chi-restraints excluded: chain A residue 3192 VAL Chi-restraints excluded: chain A residue 3420 SER Chi-restraints excluded: chain A residue 3439 SER Chi-restraints excluded: chain A residue 3461 LYS Chi-restraints excluded: chain A residue 3465 THR Chi-restraints excluded: chain A residue 3498 THR Chi-restraints excluded: chain A residue 3597 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 252 optimal weight: 1.9990 chunk 236 optimal weight: 0.5980 chunk 188 optimal weight: 2.9990 chunk 24 optimal weight: 0.5980 chunk 277 optimal weight: 0.1980 chunk 17 optimal weight: 0.6980 chunk 295 optimal weight: 1.9990 chunk 28 optimal weight: 5.9990 chunk 210 optimal weight: 1.9990 chunk 278 optimal weight: 10.0000 chunk 179 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 820 GLN A 960 GLN ** A 987 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1093 ASN A1277 GLN A2258 GLN ** A2413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2776 GLN A2787 ASN A2961 ASN ** A3045 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3204 ASN A3462 GLN A3740 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.165449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.136514 restraints weight = 33253.445| |-----------------------------------------------------------------------------| r_work (start): 0.3703 rms_B_bonded: 1.88 r_work: 0.3584 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3431 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.2312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 26135 Z= 0.128 Angle : 0.503 10.316 35472 Z= 0.258 Chirality : 0.039 0.238 4138 Planarity : 0.004 0.076 4304 Dihedral : 10.498 178.336 3978 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 2.90 % Allowed : 15.84 % Favored : 81.26 % 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: 0.74 (0.16), residues: 3028 helix: 1.38 (0.13), residues: 1787 sheet: -0.48 (0.36), residues: 221 loop : -0.82 (0.19), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.000 ARG A1805 TYR 0.018 0.001 TYR A 576 PHE 0.026 0.001 PHE A1230 TRP 0.015 0.001 TRP A2542 HIS 0.006 0.001 HIS A3045 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 (26131) covalent geometry : angle 0.50231 / 0.26 (35466) hydrogen bonds : bond 0.03542 / 2.32 ( 1355) hydrogen bonds : angle 4.07754 / 2.84 ( 3860) metal coordination : bond 0.00501 / 0.25 ( 4) metal coordination : angle 2.22761 / 1.23 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6056 Ramachandran restraints generated. 3028 Oldfield, 0 Emsley, 3028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6056 Ramachandran restraints generated. 3028 Oldfield, 0 Emsley, 3028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 640 residues out of total 2828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 558 time to evaluate : 0.838 Fit side-chains revert: symmetry clash REVERT: A 454 MET cc_start: 0.5503 (mtt) cc_final: 0.5300 (mtt) REVERT: A 467 ARG cc_start: 0.7643 (ttp-110) cc_final: 0.7133 (ptt90) REVERT: A 471 ASP cc_start: 0.7976 (m-30) cc_final: 0.7643 (m-30) REVERT: A 493 GLN cc_start: 0.6766 (mp10) cc_final: 0.6540 (mp10) REVERT: A 563 GLU cc_start: 0.7921 (pt0) cc_final: 0.7645 (pt0) REVERT: A 584 VAL cc_start: 0.8585 (t) cc_final: 0.8327 (p) REVERT: A 755 ASN cc_start: 0.7535 (t0) cc_final: 0.7208 (t0) REVERT: A 844 LYS cc_start: 0.8238 (tttt) cc_final: 0.7959 (ttpt) REVERT: A 929 VAL cc_start: 0.7883 (m) cc_final: 0.7600 (t) REVERT: A 982 ASN cc_start: 0.8122 (m-40) cc_final: 0.7905 (m110) REVERT: A 1036 LYS cc_start: 0.7436 (tttt) cc_final: 0.7181 (ttmt) REVERT: A 1037 LYS cc_start: 0.8227 (tttt) cc_final: 0.7863 (ttmm) REVERT: A 1059 THR cc_start: 0.7819 (p) cc_final: 0.7495 (t) REVERT: A 1097 GLU cc_start: 0.8110 (pt0) cc_final: 0.7463 (pm20) REVERT: A 1213 GLN cc_start: 0.7813 (mm-40) cc_final: 0.7416 (mm110) REVERT: A 1233 LYS cc_start: 0.7543 (mtpt) cc_final: 0.7308 (mtmt) REVERT: A 1292 VAL cc_start: 0.7758 (t) cc_final: 0.7554 (p) REVERT: A 1377 ASN cc_start: 0.7982 (t0) cc_final: 0.7641 (t0) REVERT: A 1402 ARG cc_start: 0.7755 (ttm-80) cc_final: 0.7507 (ttm-80) REVERT: A 1403 ARG cc_start: 0.7944 (ttt-90) cc_final: 0.7652 (ttt180) REVERT: A 1463 GLU cc_start: 0.7699 (OUTLIER) cc_final: 0.7405 (mt-10) REVERT: A 1465 ARG cc_start: 0.8401 (OUTLIER) cc_final: 0.8012 (mtm180) REVERT: A 1503 TYR cc_start: 0.8002 (m-80) cc_final: 0.7353 (m-80) REVERT: A 1544 LYS cc_start: 0.8404 (mtpm) cc_final: 0.8204 (mttm) REVERT: A 1583 ARG cc_start: 0.8148 (ttm170) cc_final: 0.7449 (ttm170) REVERT: A 1588 GLU cc_start: 0.7782 (mt-10) cc_final: 0.7382 (mt-10) REVERT: A 1595 THR cc_start: 0.8753 (m) cc_final: 0.8382 (m) REVERT: A 1610 ASP cc_start: 0.7648 (m-30) cc_final: 0.7356 (m-30) REVERT: A 1644 LEU cc_start: 0.8269 (mm) cc_final: 0.7932 (mt) REVERT: A 1831 MET cc_start: 0.7814 (mtt) cc_final: 0.7557 (mmm) REVERT: A 1836 PHE cc_start: 0.8314 (m-80) cc_final: 0.7975 (m-80) REVERT: A 1837 LYS cc_start: 0.8153 (mtpp) cc_final: 0.7716 (mmmt) REVERT: A 1844 ASN cc_start: 0.6925 (m-40) cc_final: 0.6599 (m-40) REVERT: A 1955 MET cc_start: 0.5280 (tpt) cc_final: 0.4817 (tpt) REVERT: A 2206 MET cc_start: 0.5570 (mmm) cc_final: 0.5148 (mmm) REVERT: A 2328 CYS cc_start: 0.8060 (m) cc_final: 0.7828 (m) REVERT: A 2418 ARG cc_start: 0.7827 (ttt90) cc_final: 0.7560 (ttm-80) REVERT: A 2579 GLU cc_start: 0.6937 (mt-10) cc_final: 0.6552 (mt-10) REVERT: A 2581 MET cc_start: 0.7571 (tmm) cc_final: 0.7172 (tmm) REVERT: A 2586 VAL cc_start: 0.8298 (t) cc_final: 0.8039 (p) REVERT: A 2639 GLN cc_start: 0.7952 (tp40) cc_final: 0.7385 (tm-30) REVERT: A 2641 PHE cc_start: 0.8403 (m-80) cc_final: 0.7709 (m-80) REVERT: A 2661 SER cc_start: 0.8734 (t) cc_final: 0.8434 (m) REVERT: A 2747 GLU cc_start: 0.8268 (OUTLIER) cc_final: 0.8004 (tp30) REVERT: A 2956 TYR cc_start: 0.8506 (m-80) cc_final: 0.8039 (m-80) REVERT: A 3008 ILE cc_start: 0.8493 (OUTLIER) cc_final: 0.8198 (tt) REVERT: A 3020 PHE cc_start: 0.8836 (m-80) cc_final: 0.8542 (m-80) REVERT: A 3081 GLU cc_start: 0.7580 (OUTLIER) cc_final: 0.7302 (mm-30) REVERT: A 3090 THR cc_start: 0.8484 (m) cc_final: 0.8246 (p) REVERT: A 3115 GLU cc_start: 0.6952 (pm20) cc_final: 0.6651 (pm20) REVERT: A 3154 ASP cc_start: 0.7275 (m-30) cc_final: 0.7020 (m-30) REVERT: A 3192 VAL cc_start: 0.7870 (OUTLIER) cc_final: 0.7653 (p) REVERT: A 3195 PHE cc_start: 0.8279 (p90) cc_final: 0.7981 (p90) REVERT: A 3446 LYS cc_start: 0.8117 (tttm) cc_final: 0.7700 (ttpp) REVERT: A 3475 GLU cc_start: 0.7990 (mm-30) cc_final: 0.7690 (mm-30) REVERT: A 3480 LEU cc_start: 0.8593 (mt) cc_final: 0.8281 (mt) REVERT: A 3532 VAL cc_start: 0.8582 (t) cc_final: 0.8332 (p) REVERT: A 3660 LEU cc_start: 0.8419 (pp) cc_final: 0.8215 (pp) REVERT: A 3683 SER cc_start: 0.8183 (t) cc_final: 0.7461 (m) REVERT: A 3695 LEU cc_start: 0.8034 (mt) cc_final: 0.7830 (mm) REVERT: A 3715 LYS cc_start: 0.8006 (tttt) cc_final: 0.7673 (tttt) REVERT: A 3742 GLU cc_start: 0.7450 (mm-30) cc_final: 0.7028 (mm-30) REVERT: A 3750 ARG cc_start: 0.7828 (mtt-85) cc_final: 0.7620 (mtt-85) REVERT: A 3785 LYS cc_start: 0.7540 (tttt) cc_final: 0.7159 (tttt) REVERT: A 3870 MET cc_start: 0.6964 (mmm) cc_final: 0.6508 (mmm) REVERT: A 3884 ILE cc_start: 0.8429 (mm) cc_final: 0.8129 (mm) REVERT: A 3888 THR cc_start: 0.8492 (m) cc_final: 0.8246 (p) outliers start: 82 outliers final: 49 residues processed: 593 average time/residue: 0.6792 time to fit residues: 466.4907 Evaluate side-chains 597 residues out of total 2828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 542 time to evaluate : 1.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 566 SER Chi-restraints excluded: chain A residue 572 ILE Chi-restraints excluded: chain A residue 598 MET Chi-restraints excluded: chain A residue 608 ASP Chi-restraints excluded: chain A residue 752 ILE Chi-restraints excluded: chain A residue 833 ASP Chi-restraints excluded: chain A residue 858 SER Chi-restraints excluded: chain A residue 865 CYS Chi-restraints excluded: chain A residue 876 THR Chi-restraints excluded: chain A residue 953 THR Chi-restraints excluded: chain A residue 956 THR Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1051 LEU Chi-restraints excluded: chain A residue 1063 SER Chi-restraints excluded: chain A residue 1072 ILE Chi-restraints excluded: chain A residue 1134 LEU Chi-restraints excluded: chain A residue 1228 VAL Chi-restraints excluded: chain A residue 1366 CYS Chi-restraints excluded: chain A residue 1382 MET Chi-restraints excluded: chain A residue 1459 THR Chi-restraints excluded: chain A residue 1463 GLU Chi-restraints excluded: chain A residue 1465 ARG Chi-restraints excluded: chain A residue 1522 LEU Chi-restraints excluded: chain A residue 1570 VAL Chi-restraints excluded: chain A residue 1573 VAL Chi-restraints excluded: chain A residue 1812 SER Chi-restraints excluded: chain A residue 1916 VAL Chi-restraints excluded: chain A residue 2230 SER Chi-restraints excluded: chain A residue 2260 LEU Chi-restraints excluded: chain A residue 2287 THR Chi-restraints excluded: chain A residue 2449 THR Chi-restraints excluded: chain A residue 2540 THR Chi-restraints excluded: chain A residue 2543 LYS Chi-restraints excluded: chain A residue 2587 THR Chi-restraints excluded: chain A residue 2610 MET Chi-restraints excluded: chain A residue 2747 GLU Chi-restraints excluded: chain A residue 2769 THR Chi-restraints excluded: chain A residue 2817 ASN Chi-restraints excluded: chain A residue 2818 LEU Chi-restraints excluded: chain A residue 2838 SER Chi-restraints excluded: chain A residue 3008 ILE Chi-restraints excluded: chain A residue 3013 THR Chi-restraints excluded: chain A residue 3059 GLN Chi-restraints excluded: chain A residue 3081 GLU Chi-restraints excluded: chain A residue 3124 THR Chi-restraints excluded: chain A residue 3132 LEU Chi-restraints excluded: chain A residue 3184 MET Chi-restraints excluded: chain A residue 3192 VAL Chi-restraints excluded: chain A residue 3346 THR Chi-restraints excluded: chain A residue 3420 SER Chi-restraints excluded: chain A residue 3461 LYS Chi-restraints excluded: chain A residue 3465 THR Chi-restraints excluded: chain A residue 3498 THR Chi-restraints excluded: chain A residue 3597 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 54 optimal weight: 8.9990 chunk 253 optimal weight: 4.9990 chunk 248 optimal weight: 0.8980 chunk 146 optimal weight: 10.0000 chunk 133 optimal weight: 0.0970 chunk 34 optimal weight: 0.6980 chunk 119 optimal weight: 0.0270 chunk 258 optimal weight: 2.9990 chunk 3 optimal weight: 0.6980 chunk 252 optimal weight: 0.6980 chunk 197 optimal weight: 3.9990 overall best weight: 0.4436 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 820 GLN A 960 GLN A1093 ASN A1277 GLN A1648 ASN A2258 GLN ** A2413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2614 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2776 GLN A2787 ASN ** A2822 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2961 ASN ** A3045 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3204 ASN A3462 GLN A3740 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.165828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.136776 restraints weight = 33073.329| |-----------------------------------------------------------------------------| r_work (start): 0.3713 rms_B_bonded: 1.85 r_work: 0.3584 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3429 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.2389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 26135 Z= 0.107 Angle : 0.496 9.845 35472 Z= 0.256 Chirality : 0.038 0.190 4138 Planarity : 0.004 0.082 4304 Dihedral : 10.457 178.202 3978 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.93 % Allowed : 16.23 % Favored : 80.83 % 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: 0.86 (0.16), residues: 3028 helix: 1.49 (0.13), residues: 1784 sheet: -0.48 (0.35), residues: 221 loop : -0.77 (0.19), residues: 1023 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.000 ARG A1805 TYR 0.019 0.001 TYR A 576 PHE 0.019 0.001 PHE A2633 TRP 0.016 0.001 TRP A2542 HIS 0.005 0.001 HIS A1615 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.11 (26131) covalent geometry : angle 0.49580 / 0.26 (35466) hydrogen bonds : bond 0.03372 / 2.20 ( 1355) hydrogen bonds : angle 4.00728 / 2.79 ( 3860) metal coordination : bond 0.00375 / 0.18 ( 4) metal coordination : angle 2.07868 / 1.14 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6056 Ramachandran restraints generated. 3028 Oldfield, 0 Emsley, 3028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6056 Ramachandran restraints generated. 3028 Oldfield, 0 Emsley, 3028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 637 residues out of total 2828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 554 time to evaluate : 1.022 Fit side-chains revert: symmetry clash REVERT: A 454 MET cc_start: 0.5539 (mtt) cc_final: 0.5314 (mtt) REVERT: A 467 ARG cc_start: 0.7645 (ttp-110) cc_final: 0.7169 (ptt90) REVERT: A 471 ASP cc_start: 0.8043 (m-30) cc_final: 0.7721 (m-30) REVERT: A 493 GLN cc_start: 0.6743 (mp10) cc_final: 0.6542 (mp10) REVERT: A 563 GLU cc_start: 0.7914 (pt0) cc_final: 0.7679 (pt0) REVERT: A 584 VAL cc_start: 0.8598 (t) cc_final: 0.8350 (p) REVERT: A 619 ASP cc_start: 0.7694 (m-30) cc_final: 0.7471 (m-30) REVERT: A 631 LYS cc_start: 0.7876 (tptp) cc_final: 0.7667 (tptp) REVERT: A 755 ASN cc_start: 0.7493 (t0) cc_final: 0.7205 (t0) REVERT: A 844 LYS cc_start: 0.8200 (tttt) cc_final: 0.7946 (ttpt) REVERT: A 982 ASN cc_start: 0.8119 (m-40) cc_final: 0.7905 (m110) REVERT: A 1036 LYS cc_start: 0.7494 (tttt) cc_final: 0.7248 (ttmt) REVERT: A 1037 LYS cc_start: 0.8259 (tttt) cc_final: 0.7925 (ttmm) REVERT: A 1059 THR cc_start: 0.7813 (p) cc_final: 0.7505 (t) REVERT: A 1097 GLU cc_start: 0.8116 (pt0) cc_final: 0.7530 (pm20) REVERT: A 1213 GLN cc_start: 0.7800 (mm-40) cc_final: 0.7414 (mm110) REVERT: A 1233 LYS cc_start: 0.7551 (mtpt) cc_final: 0.7337 (mtmt) REVERT: A 1282 LYS cc_start: 0.8691 (mttt) cc_final: 0.8474 (mtmm) REVERT: A 1377 ASN cc_start: 0.7964 (t0) cc_final: 0.7653 (t0) REVERT: A 1402 ARG cc_start: 0.7784 (ttm-80) cc_final: 0.7536 (ttm-80) REVERT: A 1463 GLU cc_start: 0.7688 (OUTLIER) cc_final: 0.7416 (mt-10) REVERT: A 1465 ARG cc_start: 0.8391 (OUTLIER) cc_final: 0.8017 (mtm180) REVERT: A 1583 ARG cc_start: 0.8169 (ttm170) cc_final: 0.7496 (ttm170) REVERT: A 1588 GLU cc_start: 0.7754 (mt-10) cc_final: 0.7374 (mt-10) REVERT: A 1595 THR cc_start: 0.8728 (m) cc_final: 0.8511 (m) REVERT: A 1610 ASP cc_start: 0.7637 (m-30) cc_final: 0.7363 (m-30) REVERT: A 1644 LEU cc_start: 0.8273 (mm) cc_final: 0.7979 (mt) REVERT: A 1830 MET cc_start: 0.8334 (OUTLIER) cc_final: 0.7285 (ptm) REVERT: A 1831 MET cc_start: 0.7827 (mtt) cc_final: 0.7593 (mmm) REVERT: A 1836 PHE cc_start: 0.8365 (m-80) cc_final: 0.8022 (m-80) REVERT: A 1837 LYS cc_start: 0.8213 (mtpp) cc_final: 0.7803 (mmmt) REVERT: A 1844 ASN cc_start: 0.7063 (m-40) cc_final: 0.6724 (m-40) REVERT: A 1955 MET cc_start: 0.5270 (tpt) cc_final: 0.4805 (tpt) REVERT: A 2206 MET cc_start: 0.5563 (mmm) cc_final: 0.5142 (mmm) REVERT: A 2328 CYS cc_start: 0.8081 (m) cc_final: 0.7873 (m) REVERT: A 2418 ARG cc_start: 0.7861 (ttt90) cc_final: 0.7632 (ttm-80) REVERT: A 2579 GLU cc_start: 0.6936 (mt-10) cc_final: 0.6633 (mt-10) REVERT: A 2581 MET cc_start: 0.7576 (tmm) cc_final: 0.7197 (tmm) REVERT: A 2586 VAL cc_start: 0.8258 (t) cc_final: 0.8019 (p) REVERT: A 2639 GLN cc_start: 0.7940 (tp40) cc_final: 0.7436 (tm-30) REVERT: A 2641 PHE cc_start: 0.8422 (m-80) cc_final: 0.7756 (m-80) REVERT: A 2661 SER cc_start: 0.8648 (t) cc_final: 0.8405 (m) REVERT: A 2747 GLU cc_start: 0.8247 (OUTLIER) cc_final: 0.7987 (tp30) REVERT: A 2956 TYR cc_start: 0.8495 (m-80) cc_final: 0.8050 (m-80) REVERT: A 3008 ILE cc_start: 0.8536 (OUTLIER) cc_final: 0.8257 (tt) REVERT: A 3020 PHE cc_start: 0.8815 (m-80) cc_final: 0.8533 (m-80) REVERT: A 3081 GLU cc_start: 0.7620 (OUTLIER) cc_final: 0.7367 (mm-30) REVERT: A 3092 LEU cc_start: 0.8084 (OUTLIER) cc_final: 0.7818 (mt) REVERT: A 3115 GLU cc_start: 0.6940 (pm20) cc_final: 0.6698 (pm20) REVERT: A 3154 ASP cc_start: 0.7269 (m-30) cc_final: 0.7028 (m-30) REVERT: A 3195 PHE cc_start: 0.8271 (p90) cc_final: 0.8052 (p90) REVERT: A 3315 ARG cc_start: 0.8060 (ttp80) cc_final: 0.7481 (ttp80) REVERT: A 3396 TRP cc_start: 0.8183 (t60) cc_final: 0.7781 (t60) REVERT: A 3446 LYS cc_start: 0.8112 (tttm) cc_final: 0.7745 (ttpp) REVERT: A 3475 GLU cc_start: 0.7992 (mm-30) cc_final: 0.7711 (mm-30) REVERT: A 3480 LEU cc_start: 0.8595 (mt) cc_final: 0.8306 (mt) REVERT: A 3532 VAL cc_start: 0.8574 (t) cc_final: 0.8349 (p) REVERT: A 3683 SER cc_start: 0.8214 (t) cc_final: 0.7765 (p) REVERT: A 3715 LYS cc_start: 0.8032 (tttt) cc_final: 0.7689 (tttt) REVERT: A 3742 GLU cc_start: 0.7435 (mm-30) cc_final: 0.7033 (mm-30) REVERT: A 3785 LYS cc_start: 0.7541 (tttt) cc_final: 0.7163 (tttt) REVERT: A 3870 MET cc_start: 0.6968 (mmm) cc_final: 0.6493 (mmm) REVERT: A 3884 ILE cc_start: 0.8518 (mm) cc_final: 0.8234 (mm) REVERT: A 3888 THR cc_start: 0.8486 (m) cc_final: 0.8263 (p) outliers start: 83 outliers final: 49 residues processed: 591 average time/residue: 0.6504 time to fit residues: 443.9803 Evaluate side-chains 596 residues out of total 2828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 540 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 566 SER Chi-restraints excluded: chain A residue 572 ILE Chi-restraints excluded: chain A residue 598 MET Chi-restraints excluded: chain A residue 608 ASP Chi-restraints excluded: chain A residue 752 ILE Chi-restraints excluded: chain A residue 833 ASP Chi-restraints excluded: chain A residue 858 SER Chi-restraints excluded: chain A residue 865 CYS Chi-restraints excluded: chain A residue 953 THR Chi-restraints excluded: chain A residue 956 THR Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1051 LEU Chi-restraints excluded: chain A residue 1063 SER Chi-restraints excluded: chain A residue 1072 ILE Chi-restraints excluded: chain A residue 1228 VAL Chi-restraints excluded: chain A residue 1272 LYS Chi-restraints excluded: chain A residue 1366 CYS Chi-restraints excluded: chain A residue 1382 MET Chi-restraints excluded: chain A residue 1459 THR Chi-restraints excluded: chain A residue 1463 GLU Chi-restraints excluded: chain A residue 1465 ARG Chi-restraints excluded: chain A residue 1522 LEU Chi-restraints excluded: chain A residue 1525 LEU Chi-restraints excluded: chain A residue 1570 VAL Chi-restraints excluded: chain A residue 1573 VAL Chi-restraints excluded: chain A residue 1812 SER Chi-restraints excluded: chain A residue 1830 MET Chi-restraints excluded: chain A residue 1916 VAL Chi-restraints excluded: chain A residue 2230 SER Chi-restraints excluded: chain A residue 2260 LEU Chi-restraints excluded: chain A residue 2287 THR Chi-restraints excluded: chain A residue 2449 THR Chi-restraints excluded: chain A residue 2540 THR Chi-restraints excluded: chain A residue 2587 THR Chi-restraints excluded: chain A residue 2610 MET Chi-restraints excluded: chain A residue 2747 GLU Chi-restraints excluded: chain A residue 2769 THR Chi-restraints excluded: chain A residue 2817 ASN Chi-restraints excluded: chain A residue 2818 LEU Chi-restraints excluded: chain A residue 2838 SER Chi-restraints excluded: chain A residue 3008 ILE Chi-restraints excluded: chain A residue 3013 THR Chi-restraints excluded: chain A residue 3059 GLN Chi-restraints excluded: chain A residue 3081 GLU Chi-restraints excluded: chain A residue 3092 LEU Chi-restraints excluded: chain A residue 3124 THR Chi-restraints excluded: chain A residue 3184 MET Chi-restraints excluded: chain A residue 3228 THR Chi-restraints excluded: chain A residue 3346 THR Chi-restraints excluded: chain A residue 3420 SER Chi-restraints excluded: chain A residue 3461 LYS Chi-restraints excluded: chain A residue 3465 THR Chi-restraints excluded: chain A residue 3498 THR Chi-restraints excluded: chain A residue 3597 VAL Chi-restraints excluded: chain A residue 3751 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 14 optimal weight: 0.9990 chunk 236 optimal weight: 0.0570 chunk 230 optimal weight: 5.9990 chunk 166 optimal weight: 0.8980 chunk 78 optimal weight: 1.9990 chunk 265 optimal weight: 6.9990 chunk 64 optimal weight: 0.4980 chunk 129 optimal weight: 20.0000 chunk 30 optimal weight: 0.2980 chunk 248 optimal weight: 0.7980 chunk 31 optimal weight: 4.9990 overall best weight: 0.5098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 820 GLN A 960 GLN A1093 ASN A1277 GLN A1648 ASN A2258 GLN ** A2413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2614 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2776 GLN A2787 ASN A2822 ASN ** A3045 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3204 ASN A3462 GLN A3740 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.166006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.137271 restraints weight = 33144.962| |-----------------------------------------------------------------------------| r_work (start): 0.3720 rms_B_bonded: 1.72 r_work: 0.3600 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3448 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.2461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 26135 Z= 0.109 Angle : 0.505 11.536 35472 Z= 0.259 Chirality : 0.038 0.188 4138 Planarity : 0.004 0.095 4304 Dihedral : 10.412 178.037 3978 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 2.69 % Allowed : 16.62 % Favored : 80.69 % 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: 0.94 (0.16), residues: 3028 helix: 1.55 (0.13), residues: 1777 sheet: -0.47 (0.35), residues: 221 loop : -0.73 (0.19), residues: 1030 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG A 990 TYR 0.016 0.001 TYR A1755 PHE 0.018 0.001 PHE A2633 TRP 0.015 0.001 TRP A2542 HIS 0.005 0.001 HIS A1615 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.11 (26131) covalent geometry : angle 0.50392 / 0.26 (35466) hydrogen bonds : bond 0.03328 / 2.16 ( 1355) hydrogen bonds : angle 3.97295 / 2.76 ( 3860) metal coordination : bond 0.00376 / 0.18 ( 4) metal coordination : angle 2.00567 / 1.10 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6056 Ramachandran restraints generated. 3028 Oldfield, 0 Emsley, 3028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6056 Ramachandran restraints generated. 3028 Oldfield, 0 Emsley, 3028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 620 residues out of total 2828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 544 time to evaluate : 1.023 Fit side-chains revert: symmetry clash REVERT: A 454 MET cc_start: 0.5559 (mtt) cc_final: 0.5347 (mtt) REVERT: A 467 ARG cc_start: 0.7641 (ttp-110) cc_final: 0.7118 (ptt90) REVERT: A 471 ASP cc_start: 0.8015 (m-30) cc_final: 0.7696 (m-30) REVERT: A 493 GLN cc_start: 0.6714 (mp10) cc_final: 0.6493 (mp10) REVERT: A 545 LEU cc_start: 0.7800 (OUTLIER) cc_final: 0.7566 (mp) REVERT: A 563 GLU cc_start: 0.7859 (pt0) cc_final: 0.7622 (pt0) REVERT: A 584 VAL cc_start: 0.8612 (t) cc_final: 0.8377 (p) REVERT: A 619 ASP cc_start: 0.7659 (m-30) cc_final: 0.7424 (m-30) REVERT: A 755 ASN cc_start: 0.7446 (t0) cc_final: 0.7171 (t0) REVERT: A 844 LYS cc_start: 0.8186 (tttt) cc_final: 0.7933 (ttpt) REVERT: A 982 ASN cc_start: 0.8082 (m-40) cc_final: 0.7861 (m110) REVERT: A 1036 LYS cc_start: 0.7485 (tttt) cc_final: 0.7248 (ttmt) REVERT: A 1037 LYS cc_start: 0.8236 (tttt) cc_final: 0.7920 (ttmm) REVERT: A 1059 THR cc_start: 0.7807 (p) cc_final: 0.7513 (t) REVERT: A 1097 GLU cc_start: 0.8100 (pt0) cc_final: 0.7538 (pm20) REVERT: A 1133 LYS cc_start: 0.7981 (mptt) cc_final: 0.7743 (mptp) REVERT: A 1213 GLN cc_start: 0.7754 (mm-40) cc_final: 0.7375 (mm110) REVERT: A 1233 LYS cc_start: 0.7542 (mtpt) cc_final: 0.7328 (mtmt) REVERT: A 1377 ASN cc_start: 0.7912 (t0) cc_final: 0.7510 (t0) REVERT: A 1402 ARG cc_start: 0.7732 (ttm-80) cc_final: 0.7482 (ttm-80) REVERT: A 1463 GLU cc_start: 0.7678 (OUTLIER) cc_final: 0.7403 (mt-10) REVERT: A 1465 ARG cc_start: 0.8359 (OUTLIER) cc_final: 0.7959 (mtm180) REVERT: A 1583 ARG cc_start: 0.8161 (ttm170) cc_final: 0.7468 (ttm170) REVERT: A 1588 GLU cc_start: 0.7698 (mt-10) cc_final: 0.7317 (mt-10) REVERT: A 1610 ASP cc_start: 0.7579 (m-30) cc_final: 0.7310 (m-30) REVERT: A 1644 LEU cc_start: 0.8245 (mm) cc_final: 0.7924 (mt) REVERT: A 1831 MET cc_start: 0.7764 (mtt) cc_final: 0.7527 (mmm) REVERT: A 1836 PHE cc_start: 0.8358 (m-80) cc_final: 0.8061 (m-80) REVERT: A 1837 LYS cc_start: 0.8202 (mtpp) cc_final: 0.7792 (mmmt) REVERT: A 1844 ASN cc_start: 0.7030 (m-40) cc_final: 0.6703 (m-40) REVERT: A 1955 MET cc_start: 0.5214 (tpt) cc_final: 0.4768 (tpt) REVERT: A 2206 MET cc_start: 0.5517 (mmm) cc_final: 0.5092 (mmm) REVERT: A 2239 MET cc_start: 0.8313 (tpp) cc_final: 0.8101 (tpp) REVERT: A 2318 LYS cc_start: 0.7958 (mtpp) cc_final: 0.7469 (mtpp) REVERT: A 2328 CYS cc_start: 0.8014 (m) cc_final: 0.7813 (m) REVERT: A 2418 ARG cc_start: 0.7858 (ttt90) cc_final: 0.7609 (ttm-80) REVERT: A 2579 GLU cc_start: 0.6908 (mt-10) cc_final: 0.6377 (mt-10) REVERT: A 2581 MET cc_start: 0.7540 (tmm) cc_final: 0.7175 (tmm) REVERT: A 2586 VAL cc_start: 0.8236 (t) cc_final: 0.7994 (p) REVERT: A 2639 GLN cc_start: 0.7914 (tp40) cc_final: 0.7419 (tm-30) REVERT: A 2641 PHE cc_start: 0.8423 (m-80) cc_final: 0.7763 (m-80) REVERT: A 2747 GLU cc_start: 0.8209 (OUTLIER) cc_final: 0.7940 (tp30) REVERT: A 2943 GLU cc_start: 0.7699 (OUTLIER) cc_final: 0.7442 (pt0) REVERT: A 2956 TYR cc_start: 0.8480 (m-80) cc_final: 0.8049 (m-80) REVERT: A 3008 ILE cc_start: 0.8531 (OUTLIER) cc_final: 0.8259 (tt) REVERT: A 3020 PHE cc_start: 0.8802 (m-80) cc_final: 0.8470 (m-80) REVERT: A 3081 GLU cc_start: 0.7512 (OUTLIER) cc_final: 0.7201 (mm-30) REVERT: A 3092 LEU cc_start: 0.8079 (mp) cc_final: 0.7810 (mt) REVERT: A 3115 GLU cc_start: 0.7002 (pm20) cc_final: 0.6759 (pm20) REVERT: A 3154 ASP cc_start: 0.7247 (m-30) cc_final: 0.6996 (m-30) REVERT: A 3195 PHE cc_start: 0.8225 (p90) cc_final: 0.7964 (p90) REVERT: A 3306 LEU cc_start: 0.8087 (tt) cc_final: 0.7612 (tt) REVERT: A 3315 ARG cc_start: 0.8032 (ttp80) cc_final: 0.7388 (ttp80) REVERT: A 3396 TRP cc_start: 0.8158 (t60) cc_final: 0.7723 (t60) REVERT: A 3446 LYS cc_start: 0.8088 (tttm) cc_final: 0.7749 (ttpp) REVERT: A 3475 GLU cc_start: 0.7969 (mm-30) cc_final: 0.7687 (mm-30) REVERT: A 3480 LEU cc_start: 0.8601 (mt) cc_final: 0.8327 (mt) REVERT: A 3532 VAL cc_start: 0.8579 (t) cc_final: 0.8365 (p) REVERT: A 3660 LEU cc_start: 0.8394 (pp) cc_final: 0.8131 (pp) REVERT: A 3683 SER cc_start: 0.8198 (t) cc_final: 0.7713 (p) REVERT: A 3715 LYS cc_start: 0.7915 (tttt) cc_final: 0.7623 (tttt) REVERT: A 3731 LEU cc_start: 0.7892 (tp) cc_final: 0.7598 (tt) REVERT: A 3742 GLU cc_start: 0.7362 (mm-30) cc_final: 0.7011 (mm-30) REVERT: A 3870 MET cc_start: 0.6962 (mmm) cc_final: 0.6481 (mmm) REVERT: A 3888 THR cc_start: 0.8526 (m) cc_final: 0.8285 (p) outliers start: 76 outliers final: 45 residues processed: 577 average time/residue: 0.6551 time to fit residues: 436.0113 Evaluate side-chains 580 residues out of total 2828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 528 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 572 ILE Chi-restraints excluded: chain A residue 598 MET Chi-restraints excluded: chain A residue 752 ILE Chi-restraints excluded: chain A residue 833 ASP Chi-restraints excluded: chain A residue 858 SER Chi-restraints excluded: chain A residue 865 CYS Chi-restraints excluded: chain A residue 876 THR Chi-restraints excluded: chain A residue 953 THR Chi-restraints excluded: chain A residue 956 THR Chi-restraints excluded: chain A residue 970 VAL Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1051 LEU Chi-restraints excluded: chain A residue 1063 SER Chi-restraints excluded: chain A residue 1228 VAL Chi-restraints excluded: chain A residue 1272 LYS Chi-restraints excluded: chain A residue 1366 CYS Chi-restraints excluded: chain A residue 1382 MET Chi-restraints excluded: chain A residue 1459 THR Chi-restraints excluded: chain A residue 1463 GLU Chi-restraints excluded: chain A residue 1465 ARG Chi-restraints excluded: chain A residue 1522 LEU Chi-restraints excluded: chain A residue 1570 VAL Chi-restraints excluded: chain A residue 1573 VAL Chi-restraints excluded: chain A residue 1812 SER Chi-restraints excluded: chain A residue 1916 VAL Chi-restraints excluded: chain A residue 2230 SER Chi-restraints excluded: chain A residue 2260 LEU Chi-restraints excluded: chain A residue 2287 THR Chi-restraints excluded: chain A residue 2449 THR Chi-restraints excluded: chain A residue 2540 THR Chi-restraints excluded: chain A residue 2587 THR Chi-restraints excluded: chain A residue 2610 MET Chi-restraints excluded: chain A residue 2747 GLU Chi-restraints excluded: chain A residue 2769 THR Chi-restraints excluded: chain A residue 2817 ASN Chi-restraints excluded: chain A residue 2838 SER Chi-restraints excluded: chain A residue 2943 GLU Chi-restraints excluded: chain A residue 3008 ILE Chi-restraints excluded: chain A residue 3013 THR Chi-restraints excluded: chain A residue 3081 GLU Chi-restraints excluded: chain A residue 3124 THR Chi-restraints excluded: chain A residue 3125 LYS Chi-restraints excluded: chain A residue 3184 MET Chi-restraints excluded: chain A residue 3228 THR Chi-restraints excluded: chain A residue 3346 THR Chi-restraints excluded: chain A residue 3420 SER Chi-restraints excluded: chain A residue 3461 LYS Chi-restraints excluded: chain A residue 3465 THR Chi-restraints excluded: chain A residue 3498 THR Chi-restraints excluded: chain A residue 3597 VAL Chi-restraints excluded: chain A residue 3751 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 128 optimal weight: 0.4980 chunk 261 optimal weight: 3.9990 chunk 192 optimal weight: 0.8980 chunk 245 optimal weight: 0.9990 chunk 98 optimal weight: 0.8980 chunk 117 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 chunk 146 optimal weight: 50.0000 chunk 303 optimal weight: 6.9990 chunk 89 optimal weight: 0.5980 chunk 73 optimal weight: 5.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 820 GLN A1093 ASN A1277 GLN A1648 ASN A2258 GLN A2359 ASN ** A2413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2614 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2776 GLN A2787 ASN ** A3045 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3204 ASN A3462 GLN A3484 HIS A3740 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.165764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.136783 restraints weight = 33192.754| |-----------------------------------------------------------------------------| r_work (start): 0.3710 rms_B_bonded: 1.73 r_work: 0.3589 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3438 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.2529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 26135 Z= 0.130 Angle : 0.528 11.415 35472 Z= 0.269 Chirality : 0.039 0.190 4138 Planarity : 0.004 0.071 4304 Dihedral : 10.380 178.004 3978 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 2.30 % Allowed : 17.68 % Favored : 80.02 % 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: 0.86 (0.16), residues: 3028 helix: 1.52 (0.13), residues: 1782 sheet: -0.45 (0.36), residues: 221 loop : -0.84 (0.19), residues: 1025 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG A2969 TYR 0.015 0.001 TYR A1503 PHE 0.025 0.001 PHE A3136 TRP 0.016 0.001 TRP A 874 HIS 0.005 0.001 HIS A3045 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 (26131) covalent geometry : angle 0.52762 / 0.27 (35466) hydrogen bonds : bond 0.03409 / 2.22 ( 1355) hydrogen bonds : angle 3.97857 / 2.76 ( 3860) metal coordination : bond 0.00491 / 0.24 ( 4) metal coordination : angle 2.12818 / 1.17 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6056 Ramachandran restraints generated. 3028 Oldfield, 0 Emsley, 3028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6056 Ramachandran restraints generated. 3028 Oldfield, 0 Emsley, 3028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 598 residues out of total 2828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 533 time to evaluate : 0.970 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 454 MET cc_start: 0.5553 (mtt) cc_final: 0.5335 (mtt) REVERT: A 467 ARG cc_start: 0.7626 (ttp-110) cc_final: 0.7103 (ptt90) REVERT: A 471 ASP cc_start: 0.7992 (m-30) cc_final: 0.7666 (m-30) REVERT: A 493 GLN cc_start: 0.6703 (mp10) cc_final: 0.6490 (mp10) REVERT: A 563 GLU cc_start: 0.7826 (pt0) cc_final: 0.7624 (pt0) REVERT: A 584 VAL cc_start: 0.8616 (t) cc_final: 0.8392 (p) REVERT: A 619 ASP cc_start: 0.7685 (m-30) cc_final: 0.7438 (m-30) REVERT: A 755 ASN cc_start: 0.7470 (t0) cc_final: 0.7169 (t0) REVERT: A 844 LYS cc_start: 0.8182 (tttt) cc_final: 0.7929 (ttpt) REVERT: A 929 VAL cc_start: 0.7873 (m) cc_final: 0.7534 (t) REVERT: A 982 ASN cc_start: 0.8098 (m-40) cc_final: 0.7885 (m110) REVERT: A 1036 LYS cc_start: 0.7491 (tttt) cc_final: 0.7251 (ttmt) REVERT: A 1037 LYS cc_start: 0.8234 (tttt) cc_final: 0.7931 (ttmm) REVERT: A 1059 THR cc_start: 0.7819 (p) cc_final: 0.7537 (t) REVERT: A 1097 GLU cc_start: 0.8132 (pt0) cc_final: 0.7574 (pm20) REVERT: A 1133 LYS cc_start: 0.7993 (mptt) cc_final: 0.7761 (mptp) REVERT: A 1233 LYS cc_start: 0.7558 (mtpt) cc_final: 0.7340 (mtmt) REVERT: A 1250 LYS cc_start: 0.7490 (ttpt) cc_final: 0.7243 (tttp) REVERT: A 1380 GLU cc_start: 0.7348 (pt0) cc_final: 0.7052 (pt0) REVERT: A 1402 ARG cc_start: 0.7746 (ttm-80) cc_final: 0.7502 (ttm-80) REVERT: A 1465 ARG cc_start: 0.8361 (OUTLIER) cc_final: 0.7996 (mtm180) REVERT: A 1583 ARG cc_start: 0.8174 (ttm170) cc_final: 0.7477 (ttm170) REVERT: A 1588 GLU cc_start: 0.7704 (mt-10) cc_final: 0.7327 (mt-10) REVERT: A 1644 LEU cc_start: 0.8240 (mm) cc_final: 0.7899 (mt) REVERT: A 1830 MET cc_start: 0.8294 (OUTLIER) cc_final: 0.8055 (ppp) REVERT: A 1831 MET cc_start: 0.7720 (mtt) cc_final: 0.7520 (mmm) REVERT: A 1836 PHE cc_start: 0.8356 (m-80) cc_final: 0.8052 (m-80) REVERT: A 1837 LYS cc_start: 0.8202 (mtpp) cc_final: 0.7795 (mmmt) REVERT: A 1844 ASN cc_start: 0.7025 (m-40) cc_final: 0.6700 (m-40) REVERT: A 1955 MET cc_start: 0.5301 (tpt) cc_final: 0.4818 (tpt) REVERT: A 2206 MET cc_start: 0.5527 (mmm) cc_final: 0.5134 (mmm) REVERT: A 2418 ARG cc_start: 0.7858 (ttt90) cc_final: 0.7610 (ttm-80) REVERT: A 2581 MET cc_start: 0.7538 (tmm) cc_final: 0.7174 (tmm) REVERT: A 2586 VAL cc_start: 0.8236 (t) cc_final: 0.7997 (p) REVERT: A 2639 GLN cc_start: 0.7943 (tp40) cc_final: 0.7709 (mm-40) REVERT: A 2641 PHE cc_start: 0.8423 (m-80) cc_final: 0.7760 (m-80) REVERT: A 2747 GLU cc_start: 0.8246 (OUTLIER) cc_final: 0.7985 (tp30) REVERT: A 2943 GLU cc_start: 0.7722 (mt-10) cc_final: 0.7468 (pt0) REVERT: A 2956 TYR cc_start: 0.8497 (m-80) cc_final: 0.8055 (m-80) REVERT: A 2999 ASP cc_start: 0.7671 (m-30) cc_final: 0.7402 (m-30) REVERT: A 3008 ILE cc_start: 0.8564 (OUTLIER) cc_final: 0.8260 (tt) REVERT: A 3020 PHE cc_start: 0.8832 (m-80) cc_final: 0.8598 (m-80) REVERT: A 3081 GLU cc_start: 0.7508 (OUTLIER) cc_final: 0.7193 (mm-30) REVERT: A 3115 GLU cc_start: 0.6918 (pm20) cc_final: 0.6682 (pm20) REVERT: A 3195 PHE cc_start: 0.8183 (p90) cc_final: 0.7900 (p90) REVERT: A 3306 LEU cc_start: 0.8085 (tt) cc_final: 0.7596 (tt) REVERT: A 3315 ARG cc_start: 0.8034 (ttp80) cc_final: 0.7375 (ttp80) REVERT: A 3396 TRP cc_start: 0.8198 (t60) cc_final: 0.7748 (t60) REVERT: A 3446 LYS cc_start: 0.8077 (tttm) cc_final: 0.7745 (ttpp) REVERT: A 3475 GLU cc_start: 0.7953 (mm-30) cc_final: 0.7673 (mm-30) REVERT: A 3480 LEU cc_start: 0.8637 (mt) cc_final: 0.8389 (mt) REVERT: A 3532 VAL cc_start: 0.8592 (t) cc_final: 0.8386 (p) REVERT: A 3660 LEU cc_start: 0.8400 (pp) cc_final: 0.8127 (pp) REVERT: A 3683 SER cc_start: 0.8178 (t) cc_final: 0.7663 (p) REVERT: A 3715 LYS cc_start: 0.8000 (tttt) cc_final: 0.7667 (tttt) REVERT: A 3742 GLU cc_start: 0.7451 (mm-30) cc_final: 0.7051 (mm-30) REVERT: A 3751 CYS cc_start: 0.7856 (OUTLIER) cc_final: 0.7642 (t) REVERT: A 3870 MET cc_start: 0.6966 (mmm) cc_final: 0.6495 (mmm) REVERT: A 3888 THR cc_start: 0.8553 (m) cc_final: 0.8304 (p) outliers start: 65 outliers final: 44 residues processed: 561 average time/residue: 0.6860 time to fit residues: 444.1455 Evaluate side-chains 569 residues out of total 2828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 519 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 572 ILE Chi-restraints excluded: chain A residue 608 ASP Chi-restraints excluded: chain A residue 752 ILE Chi-restraints excluded: chain A residue 833 ASP Chi-restraints excluded: chain A residue 858 SER Chi-restraints excluded: chain A residue 865 CYS Chi-restraints excluded: chain A residue 876 THR Chi-restraints excluded: chain A residue 953 THR Chi-restraints excluded: chain A residue 954 LEU Chi-restraints excluded: chain A residue 970 VAL Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1051 LEU Chi-restraints excluded: chain A residue 1063 SER Chi-restraints excluded: chain A residue 1072 ILE Chi-restraints excluded: chain A residue 1228 VAL Chi-restraints excluded: chain A residue 1272 LYS Chi-restraints excluded: chain A residue 1366 CYS Chi-restraints excluded: chain A residue 1382 MET Chi-restraints excluded: chain A residue 1459 THR Chi-restraints excluded: chain A residue 1465 ARG Chi-restraints excluded: chain A residue 1522 LEU Chi-restraints excluded: chain A residue 1570 VAL Chi-restraints excluded: chain A residue 1573 VAL Chi-restraints excluded: chain A residue 1812 SER Chi-restraints excluded: chain A residue 1830 MET Chi-restraints excluded: chain A residue 1916 VAL Chi-restraints excluded: chain A residue 2230 SER Chi-restraints excluded: chain A residue 2260 LEU Chi-restraints excluded: chain A residue 2287 THR Chi-restraints excluded: chain A residue 2449 THR Chi-restraints excluded: chain A residue 2540 THR Chi-restraints excluded: chain A residue 2587 THR Chi-restraints excluded: chain A residue 2610 MET Chi-restraints excluded: chain A residue 2747 GLU Chi-restraints excluded: chain A residue 2769 THR Chi-restraints excluded: chain A residue 2838 SER Chi-restraints excluded: chain A residue 3008 ILE Chi-restraints excluded: chain A residue 3013 THR Chi-restraints excluded: chain A residue 3081 GLU Chi-restraints excluded: chain A residue 3124 THR Chi-restraints excluded: chain A residue 3184 MET Chi-restraints excluded: chain A residue 3228 THR Chi-restraints excluded: chain A residue 3346 THR Chi-restraints excluded: chain A residue 3420 SER Chi-restraints excluded: chain A residue 3461 LYS Chi-restraints excluded: chain A residue 3465 THR Chi-restraints excluded: chain A residue 3498 THR Chi-restraints excluded: chain A residue 3597 VAL Chi-restraints excluded: chain A residue 3751 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 221 optimal weight: 2.9990 chunk 73 optimal weight: 5.9990 chunk 169 optimal weight: 3.9990 chunk 256 optimal weight: 0.7980 chunk 100 optimal weight: 0.8980 chunk 294 optimal weight: 6.9990 chunk 127 optimal weight: 2.9990 chunk 259 optimal weight: 3.9990 chunk 260 optimal weight: 2.9990 chunk 171 optimal weight: 1.9990 chunk 196 optimal weight: 0.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 820 GLN A 960 GLN A1093 ASN A1277 GLN A1648 ASN ** A2258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2359 ASN ** A2413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2614 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2776 GLN A2787 ASN A2817 ASN ** A2822 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2866 GLN ** A3045 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3204 ASN A3462 GLN A3740 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.163790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.134664 restraints weight = 33118.173| |-----------------------------------------------------------------------------| r_work (start): 0.3679 rms_B_bonded: 1.86 r_work: 0.3553 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3398 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.2592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 26135 Z= 0.201 Angle : 0.575 12.347 35472 Z= 0.293 Chirality : 0.042 0.185 4138 Planarity : 0.004 0.072 4304 Dihedral : 10.407 178.172 3978 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 2.30 % Allowed : 18.14 % Favored : 79.56 % 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: 0.69 (0.15), residues: 3028 helix: 1.36 (0.12), residues: 1784 sheet: -0.47 (0.35), residues: 221 loop : -0.89 (0.19), residues: 1023 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG A2969 TYR 0.018 0.002 TYR A 576 PHE 0.022 0.002 PHE A2633 TRP 0.023 0.002 TRP A 874 HIS 0.008 0.001 HIS A1776 Details of bonding type rmsd/Z covalent geometry : bond 0.00476 / 0.20 (26131) covalent geometry : angle 0.57401 / 0.29 (35466) hydrogen bonds : bond 0.03827 / 2.51 ( 1355) hydrogen bonds : angle 4.07530 / 2.83 ( 3860) metal coordination : bond 0.00787 / 0.39 ( 4) metal coordination : angle 2.41714 / 1.34 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6056 Ramachandran restraints generated. 3028 Oldfield, 0 Emsley, 3028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6056 Ramachandran restraints generated. 3028 Oldfield, 0 Emsley, 3028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 605 residues out of total 2828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 540 time to evaluate : 0.977 Fit side-chains REVERT: A 454 MET cc_start: 0.5506 (mtt) cc_final: 0.5296 (mtt) REVERT: A 467 ARG cc_start: 0.7713 (ttp-110) cc_final: 0.7162 (ptt90) REVERT: A 471 ASP cc_start: 0.8011 (m-30) cc_final: 0.7689 (m-30) REVERT: A 493 GLN cc_start: 0.6800 (mp10) cc_final: 0.6578 (mp10) REVERT: A 563 GLU cc_start: 0.7888 (pt0) cc_final: 0.7639 (pt0) REVERT: A 584 VAL cc_start: 0.8624 (t) cc_final: 0.8393 (p) REVERT: A 755 ASN cc_start: 0.7577 (t0) cc_final: 0.7240 (t0) REVERT: A 844 LYS cc_start: 0.8264 (tttt) cc_final: 0.8018 (ttpt) REVERT: A 929 VAL cc_start: 0.7893 (m) cc_final: 0.7623 (t) REVERT: A 1037 LYS cc_start: 0.8205 (tttt) cc_final: 0.7882 (ttmm) REVERT: A 1059 THR cc_start: 0.7842 (p) cc_final: 0.7592 (t) REVERT: A 1097 GLU cc_start: 0.8141 (pt0) cc_final: 0.7502 (pm20) REVERT: A 1133 LYS cc_start: 0.7987 (mptt) cc_final: 0.7746 (mptp) REVERT: A 1206 SER cc_start: 0.8105 (m) cc_final: 0.7822 (m) REVERT: A 1233 LYS cc_start: 0.7548 (mtpt) cc_final: 0.7308 (mtmt) REVERT: A 1380 GLU cc_start: 0.7332 (pt0) cc_final: 0.7053 (pt0) REVERT: A 1402 ARG cc_start: 0.7770 (ttm-80) cc_final: 0.7516 (ttm-80) REVERT: A 1465 ARG cc_start: 0.8429 (OUTLIER) cc_final: 0.8076 (mtm180) REVERT: A 1583 ARG cc_start: 0.8176 (ttm170) cc_final: 0.7491 (ttm170) REVERT: A 1588 GLU cc_start: 0.7840 (mt-10) cc_final: 0.7447 (mt-10) REVERT: A 1644 LEU cc_start: 0.8172 (mm) cc_final: 0.7867 (mt) REVERT: A 1831 MET cc_start: 0.7773 (mtt) cc_final: 0.7524 (mmm) REVERT: A 1836 PHE cc_start: 0.8334 (m-80) cc_final: 0.7992 (m-80) REVERT: A 1837 LYS cc_start: 0.8176 (mtpp) cc_final: 0.7750 (mmmt) REVERT: A 1844 ASN cc_start: 0.6949 (m-40) cc_final: 0.6624 (m-40) REVERT: A 1955 MET cc_start: 0.5316 (tpt) cc_final: 0.4824 (tpt) REVERT: A 2206 MET cc_start: 0.5542 (mmm) cc_final: 0.5149 (mmm) REVERT: A 2418 ARG cc_start: 0.7865 (ttt90) cc_final: 0.7609 (ttm-80) REVERT: A 2581 MET cc_start: 0.7599 (tmm) cc_final: 0.7129 (tmm) REVERT: A 2586 VAL cc_start: 0.8294 (t) cc_final: 0.8034 (p) REVERT: A 2639 GLN cc_start: 0.8034 (tp40) cc_final: 0.7777 (mm-40) REVERT: A 2747 GLU cc_start: 0.8294 (OUTLIER) cc_final: 0.7987 (tp30) REVERT: A 2943 GLU cc_start: 0.7849 (OUTLIER) cc_final: 0.7548 (pt0) REVERT: A 2956 TYR cc_start: 0.8548 (m-80) cc_final: 0.8074 (m-80) REVERT: A 2999 ASP cc_start: 0.7733 (m-30) cc_final: 0.7423 (m-30) REVERT: A 3008 ILE cc_start: 0.8554 (OUTLIER) cc_final: 0.8204 (tt) REVERT: A 3020 PHE cc_start: 0.8885 (m-80) cc_final: 0.8636 (m-80) REVERT: A 3081 GLU cc_start: 0.7570 (OUTLIER) cc_final: 0.7221 (mm-30) REVERT: A 3092 LEU cc_start: 0.8153 (mp) cc_final: 0.7889 (mt) REVERT: A 3115 GLU cc_start: 0.6919 (pm20) cc_final: 0.6652 (pm20) REVERT: A 3195 PHE cc_start: 0.8245 (p90) cc_final: 0.7915 (p90) REVERT: A 3315 ARG cc_start: 0.7991 (ttp80) cc_final: 0.7371 (ttp80) REVERT: A 3396 TRP cc_start: 0.8298 (t60) cc_final: 0.7764 (t60) REVERT: A 3446 LYS cc_start: 0.8073 (tttm) cc_final: 0.7684 (ttpp) REVERT: A 3475 GLU cc_start: 0.7951 (mm-30) cc_final: 0.7630 (mm-30) REVERT: A 3480 LEU cc_start: 0.8661 (mt) cc_final: 0.8417 (mt) REVERT: A 3532 VAL cc_start: 0.8615 (t) cc_final: 0.8406 (p) REVERT: A 3660 LEU cc_start: 0.8387 (pp) cc_final: 0.8125 (pp) REVERT: A 3683 SER cc_start: 0.8150 (t) cc_final: 0.7478 (m) REVERT: A 3715 LYS cc_start: 0.7987 (tttt) cc_final: 0.7655 (tttt) REVERT: A 3751 CYS cc_start: 0.7904 (OUTLIER) cc_final: 0.7624 (t) REVERT: A 3870 MET cc_start: 0.6959 (mmm) cc_final: 0.6543 (mmm) outliers start: 65 outliers final: 41 residues processed: 569 average time/residue: 0.6631 time to fit residues: 436.6874 Evaluate side-chains 580 residues out of total 2828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 533 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 572 ILE Chi-restraints excluded: chain A residue 752 ILE Chi-restraints excluded: chain A residue 833 ASP Chi-restraints excluded: chain A residue 858 SER Chi-restraints excluded: chain A residue 876 THR Chi-restraints excluded: chain A residue 953 THR Chi-restraints excluded: chain A residue 970 VAL Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1051 LEU Chi-restraints excluded: chain A residue 1063 SER Chi-restraints excluded: chain A residue 1228 VAL Chi-restraints excluded: chain A residue 1272 LYS Chi-restraints excluded: chain A residue 1366 CYS Chi-restraints excluded: chain A residue 1382 MET Chi-restraints excluded: chain A residue 1459 THR Chi-restraints excluded: chain A residue 1465 ARG Chi-restraints excluded: chain A residue 1522 LEU Chi-restraints excluded: chain A residue 1570 VAL Chi-restraints excluded: chain A residue 1573 VAL Chi-restraints excluded: chain A residue 1812 SER Chi-restraints excluded: chain A residue 1916 VAL Chi-restraints excluded: chain A residue 2230 SER Chi-restraints excluded: chain A residue 2260 LEU Chi-restraints excluded: chain A residue 2287 THR Chi-restraints excluded: chain A residue 2449 THR Chi-restraints excluded: chain A residue 2540 THR Chi-restraints excluded: chain A residue 2587 THR Chi-restraints excluded: chain A residue 2610 MET Chi-restraints excluded: chain A residue 2747 GLU Chi-restraints excluded: chain A residue 2769 THR Chi-restraints excluded: chain A residue 2817 ASN Chi-restraints excluded: chain A residue 2838 SER Chi-restraints excluded: chain A residue 2943 GLU Chi-restraints excluded: chain A residue 3008 ILE Chi-restraints excluded: chain A residue 3013 THR Chi-restraints excluded: chain A residue 3081 GLU Chi-restraints excluded: chain A residue 3124 THR Chi-restraints excluded: chain A residue 3184 MET Chi-restraints excluded: chain A residue 3228 THR Chi-restraints excluded: chain A residue 3420 SER Chi-restraints excluded: chain A residue 3461 LYS Chi-restraints excluded: chain A residue 3465 THR Chi-restraints excluded: chain A residue 3498 THR Chi-restraints excluded: chain A residue 3597 VAL Chi-restraints excluded: chain A residue 3705 MET Chi-restraints excluded: chain A residue 3751 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 267 optimal weight: 2.9990 chunk 194 optimal weight: 2.9990 chunk 164 optimal weight: 2.9990 chunk 189 optimal weight: 4.9990 chunk 231 optimal weight: 0.9980 chunk 297 optimal weight: 30.0000 chunk 15 optimal weight: 0.6980 chunk 250 optimal weight: 0.6980 chunk 146 optimal weight: 50.0000 chunk 283 optimal weight: 0.9980 chunk 217 optimal weight: 1.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 820 GLN A 960 GLN A1093 ASN A1277 GLN A1648 ASN ** A2258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2396 ASN ** A2413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2476 HIS ** A2614 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2776 GLN A2787 ASN A2817 ASN ** A2822 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3045 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3051 ASN ** A3140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3204 ASN A3462 GLN A3740 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.164141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.135273 restraints weight = 33096.599| |-----------------------------------------------------------------------------| r_work (start): 0.3685 rms_B_bonded: 1.79 r_work: 0.3562 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3409 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.2620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.241 26135 Z= 0.227 Angle : 0.705 59.182 35472 Z= 0.388 Chirality : 0.046 1.320 4138 Planarity : 0.004 0.068 4304 Dihedral : 10.407 178.169 3978 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 2.02 % Allowed : 19.13 % Favored : 78.85 % Cbeta Deviations : 0.03 % 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: 0.68 (0.15), residues: 3028 helix: 1.35 (0.12), residues: 1784 sheet: -0.47 (0.35), residues: 221 loop : -0.89 (0.19), residues: 1023 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A2969 TYR 0.016 0.002 TYR A1503 PHE 0.022 0.002 PHE A2633 TRP 0.020 0.002 TRP A 874 HIS 0.007 0.001 HIS A1776 Details of bonding type rmsd/Z covalent geometry : bond 0.00513 / 0.23 (26131) covalent geometry : angle 0.70480 / 0.39 (35466) hydrogen bonds : bond 0.03805 / 2.50 ( 1355) hydrogen bonds : angle 4.07585 / 2.83 ( 3860) metal coordination : bond 0.00738 / 0.36 ( 4) metal coordination : angle 2.40641 / 1.34 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11386.39 seconds wall clock time: 209 minutes 4.45 seconds (12544.45 seconds total)