Starting phenix.real_space_refine on Sat Jun 6 08:25:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9xe7_66784/06_2026/9xe7_66784.cif Found real_map, /net/cci-nas-00/data/ceres_data/9xe7_66784/06_2026/9xe7_66784.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.02 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9xe7_66784/06_2026/9xe7_66784.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9xe7_66784/06_2026/9xe7_66784.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9xe7_66784/06_2026/9xe7_66784.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9xe7_66784/06_2026/9xe7_66784.map" } resolution = 3.02 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= 0.043 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Mn 4 7.51 5 Zn 1 6.06 5 P 46 5.49 5 S 164 5.16 5 C 16598 2.51 5 N 4522 2.21 5 O 5087 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 26422 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 25457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3182, 25457 Classifications: {'peptide': 3182} Link IDs: {'PCIS': 1, 'PTRANS': 96, 'TRANS': 3084} Chain breaks: 21 Chain: "B" Number of atoms: 231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 231 Classifications: {'RNA': 11} Modifications used: {'5*END': 1, 'rna2p_pur': 4, 'rna3p_pur': 3, 'rna3p_pyr': 4} Link IDs: {'rna2p': 3, 'rna3p': 7} Chain: "C" Number of atoms: 258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 258 Classifications: {'RNA': 12} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 6, 'rna3p_pyr': 5} Link IDs: {'rna2p': 1, 'rna3p': 10} Chain: "D" Number of atoms: 191 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 191 Classifications: {'RNA': 9} Modifications used: {'rna3p_pur': 5, 'rna3p_pyr': 4} Link IDs: {'rna3p': 8} Chain: "E" Number of atoms: 170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 170 Classifications: {'RNA': 8} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 4, 'rna3p_pur': 2} Link IDs: {'rna2p': 5, 'rna3p': 2} Chain: "F" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 81 Classifications: {'RNA': 4} Modifications used: {'p5*END': 1, 'rna2p_pyr': 1, 'rna3p_pyr': 3} Link IDs: {'rna2p': 1, 'rna3p': 2} Chain: "A" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 34 Unusual residues: {' MN': 4, ' ZN': 1, '2KH': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 4865 SG CYS A1028 42.606 97.399 96.327 1.00 80.45 S ATOM 4884 SG CYS A1031 45.142 100.174 96.892 1.00 82.56 S ATOM 5127 SG CYS A1062 43.466 98.834 99.894 1.00 81.95 S ATOM 5147 SG CYS A1065 45.919 96.717 98.195 1.00 84.36 S Time building chain proxies: 7.12, per 1000 atoms: 0.27 Number of scatterers: 26422 At special positions: 0 Unit cell: (143.664, 135.78, 138.408, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 Mn 4 24.99 S 164 16.00 P 46 15.00 O 5087 8.00 N 4522 7.00 C 16598 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: 2.48 Conformation dependent library (CDL) restraints added in 1.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A4006 " pdb="ZN ZN A4006 " - pdb=" SG CYS A1031 " pdb="ZN ZN A4006 " - pdb=" SG CYS A1065 " pdb="ZN ZN A4006 " - pdb=" SG CYS A1062 " pdb="ZN ZN A4006 " - pdb=" SG CYS A1028 " Number of angles added : 6 6276 Ramachandran restraints generated. 3138 Oldfield, 0 Emsley, 3138 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6100 Finding SS restraints... Secondary structure from input PDB file: 159 helices and 22 sheets defined 61.3% alpha, 7.1% beta 9 base pairs and 22 stacking pairs defined. Time for finding SS restraints: 4.07 Creating SS restraints... Processing helix chain 'A' and resid 316 through 325 Processing helix chain 'A' and resid 329 through 334 removed outlier: 4.161A pdb=" N HIS A 333 " --> pdb=" O GLY A 329 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N MET A 334 " --> pdb=" O ILE A 330 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 329 through 334' Processing helix chain 'A' and resid 338 through 351 Processing helix chain 'A' and resid 402 through 412 removed outlier: 4.213A pdb=" N THR A 406 " --> pdb=" O LYS A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 425 Processing helix chain 'A' and resid 427 through 436 Processing helix chain 'A' and resid 445 through 459 removed outlier: 3.929A pdb=" N GLY A 449 " --> pdb=" O GLN A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 485 Processing helix chain 'A' and resid 489 through 494 removed outlier: 3.866A pdb=" N GLN A 493 " --> pdb=" O ASP A 489 " (cutoff:3.500A) Processing helix chain 'A' and resid 511 through 523 removed outlier: 3.673A pdb=" N LYS A 523 " --> pdb=" O PHE A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 553 removed outlier: 3.664A pdb=" N VAL A 544 " --> pdb=" O LYS A 540 " (cutoff:3.500A) Processing helix chain 'A' and resid 563 through 581 removed outlier: 3.779A pdb=" N GLN A 567 " --> pdb=" O GLU A 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 586 through 604 removed outlier: 5.159A pdb=" N SER A 596 " --> pdb=" O ASP A 592 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N ASN A 597 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLN A 600 " --> pdb=" O SER A 596 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N LEU A 601 " --> pdb=" O ASN A 597 " (cutoff:3.500A) Processing helix chain 'A' and resid 606 through 622 removed outlier: 3.774A pdb=" N GLU A 612 " --> pdb=" O ASP A 608 " (cutoff:3.500A) Processing helix chain 'A' and resid 625 through 649 removed outlier: 4.044A pdb=" N ARG A 635 " --> pdb=" O LYS A 631 " (cutoff:3.500A) Processing helix chain 'A' and resid 655 through 659 Processing helix chain 'A' and resid 661 through 670 Processing helix chain 'A' and resid 673 through 680 Processing helix chain 'A' and resid 684 through 690 removed outlier: 3.608A pdb=" N LEU A 690 " --> pdb=" O PHE A 687 " (cutoff:3.500A) Processing helix chain 'A' and resid 748 through 761 removed outlier: 3.638A pdb=" N ILE A 752 " --> pdb=" O SER A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 812 through 816 removed outlier: 3.533A pdb=" N LEU A 816 " --> pdb=" O GLU A 813 " (cutoff:3.500A) Processing helix chain 'A' and resid 832 through 843 Processing helix chain 'A' and resid 844 through 854 removed outlier: 3.612A pdb=" N LYS A 848 " --> pdb=" O LYS A 844 " (cutoff:3.500A) Processing helix chain 'A' and resid 869 through 873 removed outlier: 3.997A pdb=" N TRP A 873 " --> pdb=" O PRO A 870 " (cutoff:3.500A) Processing helix chain 'A' and resid 876 through 896 removed outlier: 4.010A pdb=" N VAL A 882 " --> pdb=" O ASP A 878 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N SER A 888 " --> pdb=" O LYS A 884 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N PHE A 889 " --> pdb=" O ASN A 885 " (cutoff:3.500A) Processing helix chain 'A' and resid 899 through 911 Processing helix chain 'A' and resid 912 through 917 Processing helix chain 'A' and resid 930 through 946 removed outlier: 3.551A pdb=" N LYS A 940 " --> pdb=" O GLU A 936 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N GLU A 943 " --> pdb=" O GLU A 939 " (cutoff:3.500A) removed outlier: 5.418A 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: 3.647A pdb=" N LYS A1024 " --> pdb=" O SER A1020 " (cutoff:3.500A) Processing helix chain 'A' and resid 1028 through 1042 Processing helix chain 'A' and resid 1044 through 1055 Processing helix chain 'A' and resid 1057 through 1061 removed outlier: 3.894A 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 removed outlier: 3.572A pdb=" N VAL A1087 " --> pdb=" O LYS A1084 " (cutoff:3.500A) Processing helix chain 'A' and resid 1104 through 1111 removed outlier: 3.811A 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: 3.807A pdb=" N THR A1182 " --> pdb=" O GLU A1178 " (cutoff:3.500A) Processing helix chain 'A' and resid 1196 through 1208 removed outlier: 3.531A pdb=" N LEU A1207 " --> pdb=" O ILE A1203 " (cutoff:3.500A) Processing helix chain 'A' and resid 1221 through 1232 removed outlier: 3.847A pdb=" N LEU A1225 " --> pdb=" O PRO A1221 " (cutoff:3.500A) Processing helix chain 'A' and resid 1237 through 1254 Processing helix chain 'A' and resid 1266 through 1277 removed outlier: 3.547A pdb=" N LEU A1270 " --> pdb=" O SER A1266 " (cutoff:3.500A) removed outlier: 3.638A 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 1328 removed outlier: 3.524A pdb=" N LEU A1323 " --> pdb=" O THR A1319 " (cutoff:3.500A) Processing helix chain 'A' and resid 1330 through 1350 Processing helix chain 'A' and resid 1402 through 1426 removed outlier: 4.064A pdb=" N LEU A1407 " --> pdb=" O ARG A1403 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLY A1408 " --> pdb=" O GLN A1404 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N LEU A1412 " --> pdb=" O GLY A1408 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N TYR A1413 " --> pdb=" O SER A1409 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N GLN A1424 " --> pdb=" O ILE A1420 " (cutoff:3.500A) Processing helix chain 'A' and resid 1428 through 1434 removed outlier: 3.610A 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: 3.582A 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: 3.952A 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 1543 through 1547 Processing helix chain 'A' and resid 1552 through 1571 Processing helix chain 'A' and resid 1572 through 1581 removed outlier: 3.766A 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: 3.907A pdb=" N HIS A1615 " --> pdb=" O TYR A1612 " (cutoff:3.500A) removed outlier: 3.522A 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: 3.596A pdb=" N ARG A1638 " --> pdb=" O GLU A1634 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER A1649 " --> pdb=" O ASP A1645 " (cutoff:3.500A) Processing helix chain 'A' and resid 1659 through 1666 Processing helix chain 'A' and resid 1738 through 1741 removed outlier: 3.871A pdb=" N ASP A1741 " --> pdb=" O PRO A1738 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1738 through 1741' Processing helix chain 'A' and resid 1760 through 1773 Processing helix chain 'A' and resid 1780 through 1791 Processing helix chain 'A' and resid 1792 through 1795 Processing helix chain 'A' and resid 1796 through 1805 Processing helix chain 'A' and resid 1806 through 1810 Processing helix chain 'A' and resid 1812 through 1816 Processing helix chain 'A' and resid 1831 through 1852 Processing helix chain 'A' and resid 1869 through 1877 Processing helix chain 'A' and resid 1883 through 1896 Processing helix chain 'A' and resid 1912 through 1917 Processing helix chain 'A' and resid 1922 through 1944 removed outlier: 3.873A pdb=" N VAL A1936 " --> pdb=" O ILE A1932 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N SER A1939 " --> pdb=" O SER A1935 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N LEU A1940 " --> pdb=" O VAL A1936 " (cutoff:3.500A) Processing helix chain 'A' and resid 1962 through 1977 removed outlier: 3.832A pdb=" N LEU A1969 " --> pdb=" O GLU A1965 " (cutoff:3.500A) Processing helix chain 'A' and resid 1989 through 2002 Processing helix chain 'A' and resid 2005 through 2010 Processing helix chain 'A' and resid 2011 through 2014 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 2080 Processing helix chain 'A' and resid 2081 through 2085 removed outlier: 4.005A pdb=" N CYS A2084 " --> pdb=" O ALA A2081 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LEU A2085 " --> pdb=" O PRO A2082 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2081 through 2085' Processing helix chain 'A' and resid 2117 through 2123 Processing helix chain 'A' and resid 2138 through 2155 Processing helix chain 'A' and resid 2157 through 2163 removed outlier: 3.563A pdb=" N LEU A2163 " --> pdb=" O PHE A2159 " (cutoff:3.500A) Processing helix chain 'A' and resid 2199 through 2209 Processing helix chain 'A' and resid 2212 through 2219 removed outlier: 3.643A pdb=" N THR A2219 " --> pdb=" O CYS A2215 " (cutoff:3.500A) Processing helix chain 'A' and resid 2235 through 2247 Processing helix chain 'A' and resid 2250 through 2260 removed outlier: 3.680A pdb=" N LEU A2260 " --> pdb=" O PHE A2256 " (cutoff:3.500A) Processing helix chain 'A' and resid 2286 through 2305 Processing helix chain 'A' and resid 2316 through 2335 Processing helix chain 'A' and resid 2361 through 2366 removed outlier: 3.802A pdb=" N HIS A2366 " --> pdb=" O TRP A2362 " (cutoff:3.500A) Processing helix chain 'A' and resid 2367 through 2379 Processing helix chain 'A' and resid 2382 through 2397 removed outlier: 3.502A pdb=" N PHE A2388 " --> pdb=" O ASP A2384 " (cutoff:3.500A) Processing helix chain 'A' and resid 2404 through 2421 removed outlier: 3.530A pdb=" N LEU A2415 " --> pdb=" O ILE A2411 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N SER A2421 " --> pdb=" O TYR A2417 " (cutoff:3.500A) Processing helix chain 'A' and resid 2429 through 2440 removed outlier: 3.503A pdb=" N THR A2438 " --> pdb=" O ARG A2434 " (cutoff:3.500A) Processing helix chain 'A' and resid 2441 through 2445 removed outlier: 3.526A pdb=" N ASP A2445 " --> pdb=" O ASP A2442 " (cutoff:3.500A) Processing helix chain 'A' and resid 2447 through 2457 removed outlier: 3.913A pdb=" N LEU A2453 " --> pdb=" O THR A2449 " (cutoff:3.500A) Processing helix chain 'A' and resid 2458 through 2461 removed outlier: 3.564A pdb=" N GLY A2461 " --> pdb=" O ILE A2458 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2458 through 2461' Processing helix chain 'A' and resid 2476 through 2502 removed outlier: 3.995A pdb=" N VAL A2489 " --> pdb=" O SER A2485 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LEU A2490 " --> pdb=" O LEU A2486 " (cutoff:3.500A) Processing helix chain 'A' and resid 2530 through 2558 removed outlier: 4.971A pdb=" N TRP A2542 " --> pdb=" O ASP A2538 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N LYS A2543 " --> pdb=" O GLU A2539 " (cutoff:3.500A) Processing helix chain 'A' and resid 2590 through 2594 removed outlier: 3.607A pdb=" N MET A2594 " --> pdb=" O ILE A2591 " (cutoff:3.500A) Processing helix chain 'A' and resid 2595 through 2600 removed outlier: 3.635A pdb=" N ILE A2599 " --> pdb=" O PHE A2595 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ASN A2600 " --> pdb=" O THR A2596 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2595 through 2600' Processing helix chain 'A' and resid 2605 through 2622 Processing helix chain 'A' and resid 2626 through 2643 removed outlier: 3.544A pdb=" N PHE A2641 " --> pdb=" O ARG A2637 " (cutoff:3.500A) Processing helix chain 'A' and resid 2645 through 2657 removed outlier: 6.535A pdb=" N ILE A2654 " --> pdb=" O ARG A2650 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N LEU A2655 " --> pdb=" O ARG A2651 " (cutoff:3.500A) Processing helix chain 'A' and resid 2660 through 2664 removed outlier: 3.661A pdb=" N GLY A2664 " --> pdb=" O SER A2661 " (cutoff:3.500A) Processing helix chain 'A' and resid 2670 through 2675 Processing helix chain 'A' and resid 2679 through 2697 Processing helix chain 'A' and resid 2753 through 2764 Processing helix chain 'A' and resid 2770 through 2783 Processing helix chain 'A' and resid 2806 through 2816 Processing helix chain 'A' and resid 2816 through 2836 removed outlier: 3.597A pdb=" N SER A2826 " --> pdb=" O ASN A2822 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N VAL A2827 " --> pdb=" O ARG A2823 " (cutoff:3.500A) Processing helix chain 'A' and resid 2869 through 2890 removed outlier: 3.767A pdb=" N GLU A2875 " --> pdb=" O LYS A2871 " (cutoff:3.500A) removed outlier: 3.989A 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: 4.228A pdb=" N GLY A2936 " --> pdb=" O ASN A2932 " (cutoff:3.500A) Processing helix chain 'A' and resid 2944 through 2953 Processing helix chain 'A' and resid 2993 through 3003 Processing helix chain 'A' and resid 3043 through 3060 Processing helix chain 'A' and resid 3062 through 3073 Processing helix chain 'A' and resid 3104 through 3114 removed outlier: 3.503A pdb=" N VAL A3108 " --> pdb=" O ASN A3104 " (cutoff:3.500A) Processing helix chain 'A' and resid 3116 through 3121 Processing helix chain 'A' and resid 3130 through 3140 removed outlier: 3.803A pdb=" N ARG A3135 " --> pdb=" O LEU A3131 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N PHE A3136 " --> pdb=" O LEU A3132 " (cutoff:3.500A) Processing helix chain 'A' and resid 3142 through 3163 Processing helix chain 'A' and resid 3169 through 3187 removed outlier: 3.923A pdb=" N SER A3175 " --> pdb=" O VAL A3171 " (cutoff:3.500A) Processing helix chain 'A' and resid 3209 through 3217 removed outlier: 3.786A pdb=" N VAL A3213 " --> pdb=" O VAL A3209 " (cutoff:3.500A) removed outlier: 4.020A 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 removed outlier: 3.545A pdb=" N ASN A3268 " --> pdb=" O MET A3264 " (cutoff:3.500A) Processing helix chain 'A' and resid 3272 through 3276 removed outlier: 3.618A pdb=" N ILE A3275 " --> pdb=" O ASN A3272 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ARG A3276 " --> pdb=" O MET A3273 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 3272 through 3276' Processing helix chain 'A' and resid 3297 through 3305 Processing helix chain 'A' and resid 3306 through 3309 removed outlier: 3.910A 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 3311 through 3326 Processing helix chain 'A' and resid 3330 through 3335 removed outlier: 4.300A pdb=" N LYS A3334 " --> pdb=" O GLU A3330 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LYS A3335 " --> pdb=" O LEU A3331 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 3330 through 3335' Processing helix chain 'A' and resid 3382 through 3398 Processing helix chain 'A' and resid 3406 through 3416 Processing helix chain 'A' and resid 3419 through 3423 Processing helix chain 'A' and resid 3503 through 3513 Processing helix chain 'A' and resid 3543 through 3555 removed outlier: 3.513A pdb=" N LEU A3547 " --> pdb=" O LEU A3543 " (cutoff:3.500A) Processing helix chain 'A' and resid 3556 through 3569 removed outlier: 3.708A pdb=" N ASP A3560 " --> pdb=" O HIS A3556 " (cutoff:3.500A) Processing helix chain 'A' and resid 3569 through 3578 removed outlier: 3.665A pdb=" N HIS A3573 " --> pdb=" O SER A3569 " (cutoff:3.500A) Processing helix chain 'A' and resid 3587 through 3594 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 Processing helix chain 'A' and resid 3677 through 3687 removed outlier: 3.534A pdb=" N THR A3687 " --> pdb=" O SER A3683 " (cutoff:3.500A) Processing helix chain 'A' and resid 3694 through 3699 removed outlier: 4.115A 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: 3.563A pdb=" N PHE A3737 " --> pdb=" O THR A3733 " (cutoff:3.500A) Processing helix chain 'A' and resid 3740 through 3742 No H-bonds generated for 'chain 'A' and resid 3740 through 3742' Processing helix chain 'A' and resid 3752 through 3760 removed outlier: 3.548A pdb=" N SER A3758 " --> pdb=" O ALA A3755 " (cutoff:3.500A) Processing helix chain 'A' and resid 3792 through 3796 Processing helix chain 'A' and resid 3799 through 3819 Processing helix chain 'A' and resid 3824 through 3831 Processing helix chain 'A' and resid 3851 through 3855 removed outlier: 3.678A 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 3869 through 3888 removed outlier: 7.280A pdb=" N GLU A3875 " --> pdb=" O GLU A3871 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N ALA A3876 " --> pdb=" O LYS A3872 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 437 through 438 Processing sheet with id=AA2, first strand: chain 'A' and resid 694 through 696 removed outlier: 6.540A pdb=" N LEU A 821 " --> pdb=" O SER A 858 " (cutoff:3.500A) removed outlier: 8.056A pdb=" N ILE A 860 " --> pdb=" O LEU A 821 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N LEU A 823 " --> pdb=" O ILE A 860 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N CYS A 862 " --> pdb=" O LEU A 823 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N GLU A 825 " --> pdb=" O CYS A 862 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 728 through 729 removed outlier: 3.657A pdb=" N TYR A1755 " --> pdb=" O VAL A 971 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 947 through 948 removed outlier: 3.753A pdb=" N LEU A 952 " --> pdb=" O ARG A 948 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1003 through 1004 Processing sheet with id=AA6, first strand: chain 'A' and resid 1143 through 1144 Processing sheet with id=AA7, first strand: chain 'A' and resid 1357 through 1358 Processing sheet with id=AA8, first strand: chain 'A' and resid 1357 through 1358 removed outlier: 4.448A pdb=" N LEU A1383 " --> pdb=" O LYS A1373 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N LEU A1386 " --> pdb=" O GLY A1396 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N GLY A1396 " --> pdb=" O LEU A1386 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1732 through 1736 Processing sheet with id=AB1, first strand: chain 'A' and resid 1821 through 1825 removed outlier: 7.022A pdb=" N VAL A2231 " --> pdb=" O ALA A1824 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 2281 through 2285 removed outlier: 7.706A pdb=" N ALA A2268 " --> pdb=" O GLU A2402 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 2507 through 2515 removed outlier: 3.681A pdb=" N GLU A2511 " --> pdb=" O CYS A2522 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 2574 through 2575 Processing sheet with id=AB5, first strand: chain 'A' and resid 2958 through 2959 Processing sheet with id=AB6, first strand: chain 'A' and resid 3006 through 3009 removed outlier: 6.415A pdb=" N SER A3007 " --> pdb=" O VAL A3041 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 3079 through 3081 Processing sheet with id=AB8, first strand: chain 'A' and resid 3086 through 3094 Processing sheet with id=AB9, first strand: chain 'A' and resid 3345 through 3346 removed outlier: 3.538A pdb=" N ILE A3368 " --> pdb=" O HIS A3375 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N LEU A3374 " --> pdb=" O VAL A3456 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N LYS A3458 " --> pdb=" O LEU A3374 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N ILE A3376 " --> pdb=" O LYS A3458 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N ALA A3455 " --> pdb=" O VAL A3435 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL A3435 " --> pdb=" O ALA A3455 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 3466 through 3468 Processing sheet with id=AC2, first strand: chain 'A' and resid 3478 through 3480 removed outlier: 6.640A pdb=" N LEU A3487 " --> pdb=" O ARG A3535 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N ARG A3535 " --> pdb=" O LEU A3487 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N ILE A3489 " --> pdb=" O LEU A3533 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N VAL A3531 " --> pdb=" O TYR A3491 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 3647 through 3650 Processing sheet with id=AC4, first strand: chain 'A' and resid 3765 through 3767 removed outlier: 3.746A pdb=" N ASN A3776 " --> pdb=" O SER A3783 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N SER A3783 " --> pdb=" O ASN A3776 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N PHE A3848 " --> pdb=" O VAL A3786 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N GLN A3843 " --> pdb=" O ASN A3839 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N ASN A3839 " --> pdb=" O GLN A3843 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N CYS A3845 " --> pdb=" O MET A3837 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N MET A3837 " --> pdb=" O CYS A3845 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N GLU A3847 " --> pdb=" O CYS A3835 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N CYS A3835 " --> pdb=" O GLU A3847 " (cutoff:3.500A) 1377 hydrogen bonds defined for protein. 3939 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 22 hydrogen bonds 44 hydrogen bond angles 0 basepair planarities 9 basepair parallelities 22 stacking parallelities Total time for adding SS restraints: 9.02 Time building geometry restraints manager: 3.32 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: 4270 1.30 - 1.43: 6842 1.43 - 1.56: 15515 1.56 - 1.68: 90 1.68 - 1.81: 241 Bond restraints: 26958 Sorted by residual: bond pdb=" C2' 2KH A4001 " pdb=" C3' 2KH A4001 " ideal model delta sigma weight residual 1.548 1.287 0.261 2.00e-02 2.50e+03 1.70e+02 bond pdb=" N3A 2KH A4001 " pdb=" PA 2KH A4001 " ideal model delta sigma weight residual 1.933 1.696 0.237 2.00e-02 2.50e+03 1.41e+02 bond pdb=" O3G 2KH A4001 " pdb=" PG 2KH A4001 " ideal model delta sigma weight residual 1.669 1.467 0.202 2.00e-02 2.50e+03 1.02e+02 bond pdb=" C1' 2KH A4001 " pdb=" N1 2KH A4001 " ideal model delta sigma weight residual 1.502 1.335 0.167 2.00e-02 2.50e+03 6.99e+01 bond pdb=" N3A 2KH A4001 " pdb=" PB 2KH A4001 " ideal model delta sigma weight residual 1.890 1.724 0.166 2.00e-02 2.50e+03 6.91e+01 ... (remaining 26953 not shown) Histogram of bond angle deviations from ideal: 0.00 - 12.28: 36563 12.28 - 24.55: 6 24.55 - 36.83: 0 36.83 - 49.10: 0 49.10 - 61.38: 2 Bond angle restraints: 36571 Sorted by residual: angle pdb=" N3A 2KH A4001 " pdb=" PA 2KH A4001 " pdb=" O2A 2KH A4001 " ideal model delta sigma weight residual 48.17 109.55 -61.38 3.00e+00 1.11e-01 4.19e+02 angle pdb=" O2G 2KH A4001 " pdb=" PG 2KH A4001 " pdb=" O3G 2KH A4001 " ideal model delta sigma weight residual 53.94 109.50 -55.56 3.00e+00 1.11e-01 3.43e+02 angle pdb=" O1A 2KH A4001 " pdb=" PA 2KH A4001 " pdb=" O2A 2KH A4001 " ideal model delta sigma weight residual 130.82 108.71 22.11 3.00e+00 1.11e-01 5.43e+01 angle pdb=" O1B 2KH A4001 " pdb=" PB 2KH A4001 " pdb=" O2B 2KH A4001 " ideal model delta sigma weight residual 130.56 109.49 21.07 3.00e+00 1.11e-01 4.93e+01 angle pdb=" O1G 2KH A4001 " pdb=" PG 2KH A4001 " pdb=" O2G 2KH A4001 " ideal model delta sigma weight residual 130.21 109.58 20.63 3.00e+00 1.11e-01 4.73e+01 ... (remaining 36566 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.61: 16370 35.61 - 71.22: 172 71.22 - 106.83: 16 106.83 - 142.44: 0 142.44 - 178.05: 1 Dihedral angle restraints: 16559 sinusoidal: 7218 harmonic: 9341 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 50.05 -178.05 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 68.00 153.11 -85.11 1 1.70e+01 3.46e-03 3.04e+01 dihedral pdb=" CA ALA A2833 " pdb=" C ALA A2833 " pdb=" N GLY A2834 " pdb=" CA GLY A2834 " ideal model delta harmonic sigma weight residual 180.00 162.48 17.52 0 5.00e+00 4.00e-02 1.23e+01 ... (remaining 16556 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 4024 0.085 - 0.169: 235 0.169 - 0.254: 4 0.254 - 0.338: 1 0.338 - 0.422: 1 Chirality restraints: 4265 Sorted by residual: chirality pdb=" C2' 2KH A4001 " pdb=" C1' 2KH A4001 " pdb=" C3' 2KH A4001 " pdb=" O2' 2KH A4001 " both_signs ideal model delta sigma weight residual False -2.85 -2.42 -0.42 2.00e-01 2.50e+01 4.46e+00 chirality pdb=" CB ILE A1746 " pdb=" CA ILE A1746 " pdb=" CG1 ILE A1746 " pdb=" CG2 ILE A1746 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.26 2.00e-01 2.50e+01 1.70e+00 chirality pdb=" CB ILE A2941 " pdb=" CA ILE A2941 " pdb=" CG1 ILE A2941 " pdb=" CG2 ILE A2941 " both_signs ideal model delta sigma weight residual False 2.64 2.87 -0.22 2.00e-01 2.50e+01 1.22e+00 ... (remaining 4262 not shown) Planarity restraints: 4451 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A2923 " 0.207 9.50e-02 1.11e+02 9.26e-02 5.27e+00 pdb=" NE ARG A2923 " -0.011 2.00e-02 2.50e+03 pdb=" CZ ARG A2923 " -0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG A2923 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG A2923 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A1311 " 0.037 5.00e-02 4.00e+02 5.59e-02 4.99e+00 pdb=" N PRO A1312 " -0.097 5.00e-02 4.00e+02 pdb=" CA PRO A1312 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO A1312 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A1995 " 0.016 2.00e-02 2.50e+03 1.38e-02 4.76e+00 pdb=" CG TRP A1995 " -0.037 2.00e-02 2.50e+03 pdb=" CD1 TRP A1995 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 TRP A1995 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A1995 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A1995 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A1995 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP A1995 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A1995 " 0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP A1995 " 0.001 2.00e-02 2.50e+03 ... (remaining 4448 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.66: 114 2.66 - 3.22: 24515 3.22 - 3.78: 41896 3.78 - 4.34: 58816 4.34 - 4.90: 93971 Nonbonded interactions: 219312 Sorted by model distance: nonbonded pdb=" O2A 2KH A4001 " pdb="MN MN A4004 " model vdw 2.105 2.320 nonbonded pdb=" OD1 ASP A2518 " pdb="MN MN A4004 " model vdw 2.118 2.320 nonbonded pdb=" OD2 ASP A 693 " pdb="MN MN A4002 " model vdw 2.128 2.320 nonbonded pdb=" O1B 2KH A4001 " pdb="MN MN A4005 " model vdw 2.163 2.320 nonbonded pdb=" OD1 ASP A 693 " pdb="MN MN A4003 " model vdw 2.169 2.320 ... (remaining 219307 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: 2.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.500 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 37.310 Find NCS groups from input model: 0.150 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:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7466 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 0.261 26962 Z= 0.231 Angle : 0.794 61.376 36577 Z= 0.358 Chirality : 0.042 0.422 4265 Planarity : 0.005 0.093 4451 Dihedral : 12.184 178.053 10459 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.42 (0.15), residues: 3138 helix: 0.35 (0.12), residues: 1792 sheet: -0.88 (0.32), residues: 256 loop : -1.02 (0.19), residues: 1090 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A2837 TYR 0.021 0.002 TYR A2126 PHE 0.022 0.002 PHE A1966 TRP 0.037 0.002 TRP A1995 HIS 0.006 0.001 HIS A1615 Details of bonding type rmsd/Z covalent geometry : bond 0.00481 / 0.23 (26958) covalent geometry : angle 0.79226 / 0.36 (36571) hydrogen bonds : bond 0.15055 / 10.14 ( 1397) hydrogen bonds : angle 5.91460 / 4.14 ( 3983) metal coordination : bond 0.00939 / 0.46 ( 4) metal coordination : angle 3.95566 / 1.50 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6276 Ramachandran restraints generated. 3138 Oldfield, 0 Emsley, 3138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6276 Ramachandran restraints generated. 3138 Oldfield, 0 Emsley, 3138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 739 residues out of total 2920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 739 time to evaluate : 0.994 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 476 THR cc_start: 0.7431 (p) cc_final: 0.7211 (p) REVERT: A 477 SER cc_start: 0.8146 (m) cc_final: 0.7623 (p) REVERT: A 478 ARG cc_start: 0.8455 (mtt180) cc_final: 0.8014 (mtt-85) REVERT: A 486 LYS cc_start: 0.8490 (mptt) cc_final: 0.8144 (mptt) REVERT: A 678 LEU cc_start: 0.8137 (mt) cc_final: 0.7901 (mm) REVERT: A 808 MET cc_start: 0.7627 (tpt) cc_final: 0.7041 (tpt) REVERT: A 837 ARG cc_start: 0.7383 (mtt-85) cc_final: 0.7157 (mtt-85) REVERT: A 851 GLU cc_start: 0.7724 (tp30) cc_final: 0.7355 (tp30) REVERT: A 859 PHE cc_start: 0.8305 (t80) cc_final: 0.8092 (t80) REVERT: A 930 SER cc_start: 0.8166 (p) cc_final: 0.7945 (t) REVERT: A 943 GLU cc_start: 0.7183 (mm-30) cc_final: 0.6788 (mm-30) REVERT: A 1035 ILE cc_start: 0.7487 (mt) cc_final: 0.7259 (mt) REVERT: A 1040 ASP cc_start: 0.7845 (m-30) cc_final: 0.7559 (m-30) REVERT: A 1117 LYS cc_start: 0.7914 (mmtt) cc_final: 0.7649 (mmtt) REVERT: A 1186 GLU cc_start: 0.7435 (mm-30) cc_final: 0.7161 (mm-30) REVERT: A 1205 ASN cc_start: 0.7491 (p0) cc_final: 0.7206 (p0) REVERT: A 1250 LYS cc_start: 0.7826 (tttm) cc_final: 0.7539 (ttmm) REVERT: A 1292 VAL cc_start: 0.7108 (t) cc_final: 0.6283 (m) REVERT: A 1305 MET cc_start: 0.8541 (mtt) cc_final: 0.8292 (mtp) REVERT: A 1313 TYR cc_start: 0.8234 (m-80) cc_final: 0.7845 (m-80) REVERT: A 1379 LYS cc_start: 0.8544 (mtmt) cc_final: 0.8108 (mtpt) REVERT: A 1401 ASN cc_start: 0.7430 (m-40) cc_final: 0.7134 (m-40) REVERT: A 1467 GLU cc_start: 0.7186 (tp30) cc_final: 0.5727 (mm-30) REVERT: A 1578 LYS cc_start: 0.8058 (tttt) cc_final: 0.7851 (tttm) REVERT: A 1612 TYR cc_start: 0.8487 (m-80) cc_final: 0.8074 (m-80) REVERT: A 1640 MET cc_start: 0.8369 (ttp) cc_final: 0.8162 (ttt) REVERT: A 1740 ASN cc_start: 0.7486 (t0) cc_final: 0.7047 (t0) REVERT: A 1818 GLU cc_start: 0.7721 (mt-10) cc_final: 0.7507 (mt-10) REVERT: A 1837 LYS cc_start: 0.8347 (tttt) cc_final: 0.8112 (tppp) REVERT: A 2291 VAL cc_start: 0.7853 (t) cc_final: 0.7605 (m) REVERT: A 2308 SER cc_start: 0.8458 (p) cc_final: 0.8225 (p) REVERT: A 2515 SER cc_start: 0.8520 (t) cc_final: 0.8317 (p) REVERT: A 2543 LYS cc_start: 0.8231 (tttt) cc_final: 0.7944 (tttt) REVERT: A 2581 MET cc_start: 0.7613 (tmm) cc_final: 0.7397 (tmm) REVERT: A 2633 PHE cc_start: 0.8449 (p90) cc_final: 0.7766 (p90) REVERT: A 2639 GLN cc_start: 0.7149 (tp40) cc_final: 0.6640 (tp-100) REVERT: A 2810 LYS cc_start: 0.8023 (mtmt) cc_final: 0.7648 (mtmt) REVERT: A 2864 MET cc_start: 0.8260 (mmt) cc_final: 0.7946 (mmt) REVERT: A 2896 ASP cc_start: 0.7181 (p0) cc_final: 0.6877 (p0) REVERT: A 2963 PHE cc_start: 0.8477 (m-80) cc_final: 0.8155 (m-80) REVERT: A 3008 ILE cc_start: 0.8105 (mt) cc_final: 0.7840 (tt) REVERT: A 3023 ASN cc_start: 0.8416 (m110) cc_final: 0.8138 (m-40) REVERT: A 3047 LYS cc_start: 0.8555 (tttt) cc_final: 0.8211 (mtpp) REVERT: A 3091 LYS cc_start: 0.8080 (mttt) cc_final: 0.7860 (mttp) REVERT: A 3102 SER cc_start: 0.7973 (m) cc_final: 0.7753 (p) REVERT: A 3113 LEU cc_start: 0.7860 (mp) cc_final: 0.7623 (mt) REVERT: A 3132 LEU cc_start: 0.8554 (mt) cc_final: 0.8317 (mm) REVERT: A 3148 LEU cc_start: 0.7826 (tp) cc_final: 0.7625 (tt) REVERT: A 3155 GLU cc_start: 0.7517 (tp30) cc_final: 0.7157 (tp30) REVERT: A 3159 SER cc_start: 0.7868 (t) cc_final: 0.7620 (p) REVERT: A 3175 SER cc_start: 0.8228 (t) cc_final: 0.8023 (t) REVERT: A 3204 ASN cc_start: 0.8204 (m-40) cc_final: 0.8001 (m-40) REVERT: A 3466 VAL cc_start: 0.7425 (t) cc_final: 0.7149 (m) REVERT: A 3472 PHE cc_start: 0.7897 (t80) cc_final: 0.7602 (t80) REVERT: A 3702 GLU cc_start: 0.7104 (tp30) cc_final: 0.6360 (tp30) REVERT: A 3715 LYS cc_start: 0.8362 (tttt) cc_final: 0.8127 (tttp) REVERT: A 3762 GLU cc_start: 0.7260 (mt-10) cc_final: 0.6955 (mm-30) REVERT: A 3874 ARG cc_start: 0.7918 (ttm110) cc_final: 0.7593 (ttm110) REVERT: A 3882 ASP cc_start: 0.7638 (m-30) cc_final: 0.7028 (m-30) REVERT: A 3886 MET cc_start: 0.7612 (mtp) cc_final: 0.7324 (mtp) outliers start: 0 outliers final: 0 residues processed: 739 average time/residue: 0.2159 time to fit residues: 238.2041 Evaluate side-chains 582 residues out of total 2920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 582 time to evaluate : 1.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 197 optimal weight: 0.8980 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 0.6980 chunk 261 optimal weight: 0.7980 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 0.8980 chunk 155 optimal weight: 7.9990 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 0.8980 chunk 298 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 436 ASN A 559 ASN A 667 GLN A1068 ASN ** A1077 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1758 ASN A2040 HIS ** A2063 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2758 GLN A2961 ASN A2996 HIS A3103 ASN A3244 HIS A3345 ASN A3411 GLN A3497 GLN ** A3740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.160777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.135825 restraints weight = 36127.101| |-----------------------------------------------------------------------------| r_work (start): 0.3691 rms_B_bonded: 1.99 r_work: 0.3571 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3421 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.1699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 26962 Z= 0.138 Angle : 0.525 8.145 36577 Z= 0.272 Chirality : 0.040 0.269 4265 Planarity : 0.004 0.050 4451 Dihedral : 10.191 179.081 4077 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.89 % Favored : 96.08 % Rotamer: Outliers : 1.54 % Allowed : 8.39 % Favored : 90.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.15), residues: 3138 helix: 1.07 (0.12), residues: 1791 sheet: -0.60 (0.33), residues: 247 loop : -0.78 (0.19), residues: 1100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A3025 TYR 0.023 0.001 TYR A 653 PHE 0.020 0.002 PHE A2633 TRP 0.022 0.001 TRP A1995 HIS 0.005 0.001 HIS A3244 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.14 (26958) covalent geometry : angle 0.52319 / 0.27 (36571) hydrogen bonds : bond 0.03801 / 2.55 ( 1397) hydrogen bonds : angle 4.53200 / 3.19 ( 3983) metal coordination : bond 0.00829 / 0.41 ( 4) metal coordination : angle 2.95618 / 1.10 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6276 Ramachandran restraints generated. 3138 Oldfield, 0 Emsley, 3138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6276 Ramachandran restraints generated. 3138 Oldfield, 0 Emsley, 3138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 628 residues out of total 2920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 583 time to evaluate : 1.040 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 471 ASP cc_start: 0.7614 (m-30) cc_final: 0.7219 (m-30) REVERT: A 476 THR cc_start: 0.7407 (p) cc_final: 0.7181 (p) REVERT: A 477 SER cc_start: 0.8050 (m) cc_final: 0.7535 (p) REVERT: A 478 ARG cc_start: 0.8394 (mtt180) cc_final: 0.7956 (mtt-85) REVERT: A 486 LYS cc_start: 0.8483 (mptt) cc_final: 0.8072 (mptt) REVERT: A 599 LYS cc_start: 0.8209 (OUTLIER) cc_final: 0.7737 (mmtm) REVERT: A 631 LYS cc_start: 0.8045 (OUTLIER) cc_final: 0.7827 (mtmt) REVERT: A 678 LEU cc_start: 0.8178 (mt) cc_final: 0.7887 (mm) REVERT: A 759 LEU cc_start: 0.8265 (mt) cc_final: 0.7988 (mt) REVERT: A 797 TYR cc_start: 0.7858 (m-80) cc_final: 0.7654 (m-10) REVERT: A 805 GLU cc_start: 0.8092 (OUTLIER) cc_final: 0.7638 (pp20) REVERT: A 806 ASN cc_start: 0.7436 (p0) cc_final: 0.6931 (p0) REVERT: A 808 MET cc_start: 0.7707 (tpt) cc_final: 0.7058 (tpt) REVERT: A 833 ASP cc_start: 0.8075 (t0) cc_final: 0.7798 (t0) REVERT: A 851 GLU cc_start: 0.7838 (tp30) cc_final: 0.7321 (tp30) REVERT: A 859 PHE cc_start: 0.8375 (t80) cc_final: 0.8142 (t80) REVERT: A 943 GLU cc_start: 0.7434 (mm-30) cc_final: 0.7134 (mm-30) REVERT: A 962 MET cc_start: 0.8343 (OUTLIER) cc_final: 0.8134 (mtm) REVERT: A 1035 ILE cc_start: 0.7462 (mt) cc_final: 0.7255 (mt) REVERT: A 1040 ASP cc_start: 0.7966 (m-30) cc_final: 0.7638 (m-30) REVERT: A 1117 LYS cc_start: 0.7995 (mmtt) cc_final: 0.7743 (mmtt) REVERT: A 1186 GLU cc_start: 0.7727 (mm-30) cc_final: 0.7458 (mm-30) REVERT: A 1292 VAL cc_start: 0.7074 (t) cc_final: 0.6287 (m) REVERT: A 1305 MET cc_start: 0.8627 (mtt) cc_final: 0.8412 (mtp) REVERT: A 1379 LYS cc_start: 0.8368 (mtmt) cc_final: 0.8000 (mtpt) REVERT: A 1380 GLU cc_start: 0.7722 (mt-10) cc_final: 0.7472 (mt-10) REVERT: A 1467 GLU cc_start: 0.7471 (tp30) cc_final: 0.6151 (mm-30) REVERT: A 1515 SER cc_start: 0.8127 (m) cc_final: 0.7921 (t) REVERT: A 1578 LYS cc_start: 0.8221 (tttt) cc_final: 0.8018 (tttp) REVERT: A 1612 TYR cc_start: 0.8542 (m-80) cc_final: 0.8026 (m-80) REVERT: A 1640 MET cc_start: 0.8422 (ttp) cc_final: 0.8184 (ttt) REVERT: A 1740 ASN cc_start: 0.7523 (t0) cc_final: 0.6920 (t0) REVERT: A 1802 LYS cc_start: 0.8615 (ttmt) cc_final: 0.8406 (ttmt) REVERT: A 1818 GLU cc_start: 0.7921 (mt-10) cc_final: 0.7622 (mt-10) REVERT: A 1830 MET cc_start: 0.8186 (ppp) cc_final: 0.7799 (ptm) REVERT: A 1837 LYS cc_start: 0.8391 (tttt) cc_final: 0.8101 (tppp) REVERT: A 1848 VAL cc_start: 0.7615 (t) cc_final: 0.7412 (t) REVERT: A 2044 SER cc_start: 0.8469 (t) cc_final: 0.8053 (p) REVERT: A 2291 VAL cc_start: 0.7843 (t) cc_final: 0.7531 (m) REVERT: A 2308 SER cc_start: 0.8621 (p) cc_final: 0.8363 (p) REVERT: A 2511 GLU cc_start: 0.7781 (OUTLIER) cc_final: 0.7573 (tp30) REVERT: A 2515 SER cc_start: 0.8576 (t) cc_final: 0.8134 (p) REVERT: A 2526 THR cc_start: 0.8448 (m) cc_final: 0.8239 (t) REVERT: A 2543 LYS cc_start: 0.8252 (tttt) cc_final: 0.7979 (tttt) REVERT: A 2581 MET cc_start: 0.7694 (tmm) cc_final: 0.7404 (tmm) REVERT: A 2633 PHE cc_start: 0.8326 (p90) cc_final: 0.7399 (p90) REVERT: A 2639 GLN cc_start: 0.7275 (tp40) cc_final: 0.6647 (tp40) REVERT: A 2786 SER cc_start: 0.8432 (t) cc_final: 0.8217 (p) REVERT: A 2792 ASP cc_start: 0.7356 (t0) cc_final: 0.6961 (t0) REVERT: A 2810 LYS cc_start: 0.7961 (mtmt) cc_final: 0.7448 (mtmt) REVERT: A 2963 PHE cc_start: 0.8481 (m-80) cc_final: 0.8189 (m-80) REVERT: A 3008 ILE cc_start: 0.8190 (mt) cc_final: 0.7934 (tt) REVERT: A 3047 LYS cc_start: 0.8543 (tttt) cc_final: 0.8053 (mtpp) REVERT: A 3091 LYS cc_start: 0.8238 (mttt) cc_final: 0.7991 (mttp) REVERT: A 3120 GLU cc_start: 0.8016 (tt0) cc_final: 0.7809 (tt0) REVERT: A 3150 LYS cc_start: 0.8262 (mtpp) cc_final: 0.8027 (ttpp) REVERT: A 3155 GLU cc_start: 0.7393 (tp30) cc_final: 0.6949 (tp30) REVERT: A 3160 GLU cc_start: 0.7280 (tm-30) cc_final: 0.6901 (tm-30) REVERT: A 3175 SER cc_start: 0.8354 (t) cc_final: 0.8135 (t) REVERT: A 3204 ASN cc_start: 0.8322 (m-40) cc_final: 0.8115 (m-40) REVERT: A 3224 ARG cc_start: 0.7200 (mtp85) cc_final: 0.6932 (mtp85) REVERT: A 3364 GLU cc_start: 0.7708 (mp0) cc_final: 0.7488 (mp0) REVERT: A 3397 MET cc_start: 0.7943 (mmm) cc_final: 0.7577 (mmm) REVERT: A 3451 LYS cc_start: 0.8430 (mttt) cc_final: 0.8153 (mttt) REVERT: A 3461 LYS cc_start: 0.8751 (mttt) cc_final: 0.8517 (mmtt) REVERT: A 3472 PHE cc_start: 0.8036 (t80) cc_final: 0.7717 (t80) REVERT: A 3702 GLU cc_start: 0.7135 (tp30) cc_final: 0.6328 (tp30) REVERT: A 3715 LYS cc_start: 0.8405 (tttt) cc_final: 0.8181 (ttpt) REVERT: A 3760 ILE cc_start: 0.7982 (OUTLIER) cc_final: 0.7748 (mm) REVERT: A 3762 GLU cc_start: 0.7226 (mt-10) cc_final: 0.6960 (mm-30) REVERT: A 3852 LYS cc_start: 0.8449 (tttt) cc_final: 0.7956 (tttt) REVERT: A 3862 LYS cc_start: 0.7939 (tttt) cc_final: 0.7622 (mttt) REVERT: A 3874 ARG cc_start: 0.7858 (ttm110) cc_final: 0.7327 (ttm110) REVERT: A 3877 VAL cc_start: 0.8283 (t) cc_final: 0.8006 (p) outliers start: 45 outliers final: 17 residues processed: 598 average time/residue: 0.2057 time to fit residues: 184.8117 Evaluate side-chains 567 residues out of total 2920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 544 time to evaluate : 0.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 510 ASN Chi-restraints excluded: chain A residue 526 MET Chi-restraints excluded: chain A residue 599 LYS Chi-restraints excluded: chain A residue 631 LYS Chi-restraints excluded: chain A residue 805 GLU Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain A residue 962 MET Chi-restraints excluded: chain A residue 1068 ASN Chi-restraints excluded: chain A residue 1099 SER Chi-restraints excluded: chain A residue 1193 LYS Chi-restraints excluded: chain A residue 1435 VAL Chi-restraints excluded: chain A residue 2248 MET Chi-restraints excluded: chain A residue 2477 HIS Chi-restraints excluded: chain A residue 2511 GLU Chi-restraints excluded: chain A residue 2703 SER Chi-restraints excluded: chain A residue 2754 GLU Chi-restraints excluded: chain A residue 2769 THR Chi-restraints excluded: chain A residue 2933 VAL Chi-restraints excluded: chain A residue 3014 VAL Chi-restraints excluded: chain A residue 3187 GLN Chi-restraints excluded: chain A residue 3261 SER Chi-restraints excluded: chain A residue 3760 ILE Chi-restraints excluded: chain A residue 3851 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 169 optimal weight: 0.6980 chunk 59 optimal weight: 2.9990 chunk 84 optimal weight: 0.0050 chunk 240 optimal weight: 1.9990 chunk 149 optimal weight: 1.9990 chunk 174 optimal weight: 0.9980 chunk 176 optimal weight: 3.9990 chunk 103 optimal weight: 3.9990 chunk 317 optimal weight: 0.7980 chunk 91 optimal weight: 3.9990 chunk 153 optimal weight: 10.0000 overall best weight: 0.8996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 667 GLN A 698 GLN A 960 GLN A1077 ASN A1401 ASN A1404 GLN ** A2063 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2072 ASN ** A2377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2697 ASN A2758 GLN A3103 ASN A3296 GLN A3326 ASN A3411 GLN A3484 HIS ** A3624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.159679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.134481 restraints weight = 36243.630| |-----------------------------------------------------------------------------| r_work (start): 0.3677 rms_B_bonded: 1.99 r_work: 0.3559 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3409 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.2067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 26962 Z= 0.139 Angle : 0.504 7.359 36577 Z= 0.262 Chirality : 0.039 0.246 4265 Planarity : 0.004 0.050 4451 Dihedral : 10.078 179.364 4077 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.79 % Favored : 96.18 % Rotamer: Outliers : 1.85 % Allowed : 10.75 % Favored : 87.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.66 (0.15), residues: 3138 helix: 1.27 (0.12), residues: 1801 sheet: -0.39 (0.35), residues: 229 loop : -0.70 (0.19), residues: 1108 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A3400 TYR 0.013 0.001 TYR A2468 PHE 0.022 0.002 PHE A3553 TRP 0.016 0.001 TRP A1995 HIS 0.004 0.001 HIS A1776 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.14 (26958) covalent geometry : angle 0.50315 / 0.26 (36571) hydrogen bonds : bond 0.03593 / 2.42 ( 1397) hydrogen bonds : angle 4.28553 / 3.02 ( 3983) metal coordination : bond 0.00776 / 0.38 ( 4) metal coordination : angle 2.65839 / 1.05 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6276 Ramachandran restraints generated. 3138 Oldfield, 0 Emsley, 3138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6276 Ramachandran restraints generated. 3138 Oldfield, 0 Emsley, 3138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 612 residues out of total 2920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 558 time to evaluate : 1.155 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 477 SER cc_start: 0.8018 (m) cc_final: 0.7575 (p) REVERT: A 478 ARG cc_start: 0.8361 (mtt180) cc_final: 0.7891 (mtt-85) REVERT: A 486 LYS cc_start: 0.8502 (mptt) cc_final: 0.8101 (mptt) REVERT: A 599 LYS cc_start: 0.8209 (OUTLIER) cc_final: 0.7782 (mmtt) REVERT: A 631 LYS cc_start: 0.8046 (OUTLIER) cc_final: 0.7836 (mtmt) REVERT: A 649 TYR cc_start: 0.7605 (m-80) cc_final: 0.7376 (m-80) REVERT: A 678 LEU cc_start: 0.8152 (mt) cc_final: 0.7816 (mm) REVERT: A 759 LEU cc_start: 0.8288 (mt) cc_final: 0.8029 (mt) REVERT: A 805 GLU cc_start: 0.8077 (OUTLIER) cc_final: 0.7662 (pp20) REVERT: A 806 ASN cc_start: 0.7600 (p0) cc_final: 0.7111 (p0) REVERT: A 808 MET cc_start: 0.7799 (tpt) cc_final: 0.7103 (tpt) REVERT: A 833 ASP cc_start: 0.8070 (t0) cc_final: 0.7778 (t0) REVERT: A 851 GLU cc_start: 0.7817 (tp30) cc_final: 0.7337 (tp30) REVERT: A 877 GLU cc_start: 0.7527 (tt0) cc_final: 0.7292 (tt0) REVERT: A 943 GLU cc_start: 0.7457 (mm-30) cc_final: 0.7152 (mm-30) REVERT: A 1035 ILE cc_start: 0.7460 (mt) cc_final: 0.7259 (mt) REVERT: A 1040 ASP cc_start: 0.7987 (m-30) cc_final: 0.7673 (m-30) REVERT: A 1117 LYS cc_start: 0.8008 (mmtt) cc_final: 0.7754 (mmtt) REVERT: A 1123 ARG cc_start: 0.7813 (ttp-110) cc_final: 0.7476 (ttp-110) REVERT: A 1186 GLU cc_start: 0.7801 (mm-30) cc_final: 0.7517 (mm-30) REVERT: A 1200 ARG cc_start: 0.8536 (mtm-85) cc_final: 0.7956 (ttm110) REVERT: A 1203 ILE cc_start: 0.7575 (OUTLIER) cc_final: 0.7346 (mp) REVERT: A 1292 VAL cc_start: 0.7272 (t) cc_final: 0.6493 (m) REVERT: A 1305 MET cc_start: 0.8645 (mtt) cc_final: 0.8338 (mtp) REVERT: A 1379 LYS cc_start: 0.8339 (mtmt) cc_final: 0.7967 (mtpt) REVERT: A 1380 GLU cc_start: 0.7732 (mt-10) cc_final: 0.7438 (mt-10) REVERT: A 1467 GLU cc_start: 0.7588 (tp30) cc_final: 0.6189 (mm-30) REVERT: A 1515 SER cc_start: 0.8181 (m) cc_final: 0.7942 (t) REVERT: A 1578 LYS cc_start: 0.8280 (tttt) cc_final: 0.8062 (tttp) REVERT: A 1612 TYR cc_start: 0.8586 (m-80) cc_final: 0.8047 (m-80) REVERT: A 1640 MET cc_start: 0.8345 (ttp) cc_final: 0.8099 (ttt) REVERT: A 1740 ASN cc_start: 0.7591 (t0) cc_final: 0.6954 (t0) REVERT: A 1802 LYS cc_start: 0.8604 (ttmt) cc_final: 0.8393 (ttmt) REVERT: A 1818 GLU cc_start: 0.7954 (mt-10) cc_final: 0.7675 (mt-10) REVERT: A 1830 MET cc_start: 0.8175 (ppp) cc_final: 0.7778 (ptm) REVERT: A 1837 LYS cc_start: 0.8397 (tttt) cc_final: 0.8117 (tppp) REVERT: A 2044 SER cc_start: 0.8458 (t) cc_final: 0.8128 (p) REVERT: A 2291 VAL cc_start: 0.7901 (t) cc_final: 0.7579 (m) REVERT: A 2308 SER cc_start: 0.8616 (p) cc_final: 0.8356 (p) REVERT: A 2511 GLU cc_start: 0.7790 (OUTLIER) cc_final: 0.7585 (tp30) REVERT: A 2515 SER cc_start: 0.8594 (t) cc_final: 0.8153 (p) REVERT: A 2543 LYS cc_start: 0.8212 (tttt) cc_final: 0.7933 (tttt) REVERT: A 2581 MET cc_start: 0.7682 (tmm) cc_final: 0.7360 (tmm) REVERT: A 2633 PHE cc_start: 0.8343 (p90) cc_final: 0.7426 (p90) REVERT: A 2639 GLN cc_start: 0.7268 (tp40) cc_final: 0.6620 (tp40) REVERT: A 2792 ASP cc_start: 0.7398 (t0) cc_final: 0.7049 (t0) REVERT: A 2810 LYS cc_start: 0.8011 (mtmt) cc_final: 0.7501 (mtmt) REVERT: A 2963 PHE cc_start: 0.8477 (m-80) cc_final: 0.8196 (m-80) REVERT: A 3008 ILE cc_start: 0.8184 (mt) cc_final: 0.7937 (tt) REVERT: A 3047 LYS cc_start: 0.8546 (tttt) cc_final: 0.8219 (tttt) REVERT: A 3091 LYS cc_start: 0.8252 (mttt) cc_final: 0.7996 (mttp) REVERT: A 3120 GLU cc_start: 0.8112 (tt0) cc_final: 0.7883 (tt0) REVERT: A 3132 LEU cc_start: 0.8749 (mm) cc_final: 0.8516 (mm) REVERT: A 3140 GLN cc_start: 0.8362 (mm-40) cc_final: 0.7965 (mt0) REVERT: A 3155 GLU cc_start: 0.7368 (tp30) cc_final: 0.7019 (tp30) REVERT: A 3160 GLU cc_start: 0.7381 (tm-30) cc_final: 0.6892 (tm-30) REVERT: A 3175 SER cc_start: 0.8357 (t) cc_final: 0.8137 (t) REVERT: A 3204 ASN cc_start: 0.8361 (m-40) cc_final: 0.8066 (m-40) REVERT: A 3224 ARG cc_start: 0.7194 (mtp85) cc_final: 0.6898 (mtp85) REVERT: A 3324 TYR cc_start: 0.8035 (t80) cc_final: 0.6921 (t80) REVERT: A 3390 GLU cc_start: 0.7806 (tt0) cc_final: 0.7558 (pt0) REVERT: A 3397 MET cc_start: 0.7928 (mmm) cc_final: 0.7523 (mmm) REVERT: A 3436 ILE cc_start: 0.8858 (pt) cc_final: 0.8532 (mt) REVERT: A 3451 LYS cc_start: 0.8405 (mttt) cc_final: 0.8171 (mttt) REVERT: A 3461 LYS cc_start: 0.8767 (mttt) cc_final: 0.8522 (mmtt) REVERT: A 3472 PHE cc_start: 0.8066 (t80) cc_final: 0.7726 (t80) REVERT: A 3476 SER cc_start: 0.7622 (m) cc_final: 0.7230 (p) REVERT: A 3539 LYS cc_start: 0.7792 (mmmm) cc_final: 0.7463 (mmmm) REVERT: A 3702 GLU cc_start: 0.7057 (tp30) cc_final: 0.6242 (tp30) REVERT: A 3715 LYS cc_start: 0.8376 (tttt) cc_final: 0.8159 (ttpt) REVERT: A 3760 ILE cc_start: 0.7938 (OUTLIER) cc_final: 0.7735 (mm) REVERT: A 3762 GLU cc_start: 0.7265 (mt-10) cc_final: 0.7059 (mm-30) REVERT: A 3818 MET cc_start: 0.6692 (tmm) cc_final: 0.6484 (ppp) REVERT: A 3852 LYS cc_start: 0.8524 (tttt) cc_final: 0.7961 (tttt) REVERT: A 3862 LYS cc_start: 0.7946 (tttt) cc_final: 0.7651 (mttt) REVERT: A 3874 ARG cc_start: 0.7879 (ttm110) cc_final: 0.7358 (ttm110) REVERT: A 3877 VAL cc_start: 0.8286 (t) cc_final: 0.8000 (p) outliers start: 54 outliers final: 30 residues processed: 581 average time/residue: 0.2102 time to fit residues: 183.3265 Evaluate side-chains 572 residues out of total 2920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 536 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 510 ASN Chi-restraints excluded: chain A residue 526 MET Chi-restraints excluded: chain A residue 599 LYS Chi-restraints excluded: chain A residue 631 LYS Chi-restraints excluded: chain A residue 648 CYS Chi-restraints excluded: chain A residue 747 HIS Chi-restraints excluded: chain A residue 805 GLU Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain A residue 1026 SER Chi-restraints excluded: chain A residue 1193 LYS Chi-restraints excluded: chain A residue 1203 ILE Chi-restraints excluded: chain A residue 1285 LYS Chi-restraints excluded: chain A residue 1435 VAL Chi-restraints excluded: chain A residue 1475 SER Chi-restraints excluded: chain A residue 1564 THR Chi-restraints excluded: chain A residue 1747 THR Chi-restraints excluded: chain A residue 1812 SER Chi-restraints excluded: chain A residue 2248 MET Chi-restraints excluded: chain A residue 2454 VAL Chi-restraints excluded: chain A residue 2477 HIS Chi-restraints excluded: chain A residue 2511 GLU Chi-restraints excluded: chain A residue 2563 ASP Chi-restraints excluded: chain A residue 2754 GLU Chi-restraints excluded: chain A residue 2769 THR Chi-restraints excluded: chain A residue 2933 VAL Chi-restraints excluded: chain A residue 2943 GLU Chi-restraints excluded: chain A residue 3014 VAL Chi-restraints excluded: chain A residue 3113 LEU Chi-restraints excluded: chain A residue 3116 SER Chi-restraints excluded: chain A residue 3187 GLN Chi-restraints excluded: chain A residue 3228 THR Chi-restraints excluded: chain A residue 3247 SER Chi-restraints excluded: chain A residue 3276 ARG Chi-restraints excluded: chain A residue 3459 ILE Chi-restraints excluded: chain A residue 3760 ILE Chi-restraints excluded: chain A residue 3851 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 13 optimal weight: 0.0000 chunk 188 optimal weight: 0.9980 chunk 98 optimal weight: 0.6980 chunk 279 optimal weight: 3.9990 chunk 257 optimal weight: 0.9990 chunk 38 optimal weight: 0.6980 chunk 295 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 220 optimal weight: 0.8980 chunk 82 optimal weight: 0.9980 chunk 253 optimal weight: 0.6980 overall best weight: 0.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 543 ASN A 960 GLN ** A1844 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2316 HIS ** A2377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2607 GLN A2697 ASN ** A3624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3740 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.160180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.135383 restraints weight = 36099.827| |-----------------------------------------------------------------------------| r_work (start): 0.3691 rms_B_bonded: 1.92 r_work: 0.3577 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3431 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 moved from start: 0.2293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 26962 Z= 0.111 Angle : 0.477 7.172 36577 Z= 0.248 Chirality : 0.038 0.259 4265 Planarity : 0.004 0.049 4451 Dihedral : 9.978 179.198 4077 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.76 % Favored : 96.21 % Rotamer: Outliers : 2.40 % Allowed : 11.23 % Favored : 86.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.92 (0.15), residues: 3138 helix: 1.48 (0.12), residues: 1807 sheet: -0.33 (0.35), residues: 229 loop : -0.57 (0.19), residues: 1102 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A3400 TYR 0.014 0.001 TYR A 797 PHE 0.032 0.001 PHE A3553 TRP 0.013 0.001 TRP A1995 HIS 0.006 0.001 HIS A2316 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.11 (26958) covalent geometry : angle 0.47646 / 0.25 (36571) hydrogen bonds : bond 0.03212 / 2.16 ( 1397) hydrogen bonds : angle 4.05690 / 2.86 ( 3983) metal coordination : bond 0.00606 / 0.30 ( 4) metal coordination : angle 2.32261 / 0.93 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6276 Ramachandran restraints generated. 3138 Oldfield, 0 Emsley, 3138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6276 Ramachandran restraints generated. 3138 Oldfield, 0 Emsley, 3138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 633 residues out of total 2920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 563 time to evaluate : 1.000 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 477 SER cc_start: 0.7963 (m) cc_final: 0.7548 (p) REVERT: A 486 LYS cc_start: 0.8506 (mptt) cc_final: 0.8092 (mptt) REVERT: A 599 LYS cc_start: 0.8161 (OUTLIER) cc_final: 0.7712 (mmtt) REVERT: A 631 LYS cc_start: 0.7988 (OUTLIER) cc_final: 0.7774 (mtmt) REVERT: A 678 LEU cc_start: 0.8127 (mt) cc_final: 0.7789 (mm) REVERT: A 759 LEU cc_start: 0.8245 (mt) cc_final: 0.7978 (mt) REVERT: A 805 GLU cc_start: 0.8020 (OUTLIER) cc_final: 0.7736 (pp20) REVERT: A 808 MET cc_start: 0.7793 (tpt) cc_final: 0.7076 (tpt) REVERT: A 833 ASP cc_start: 0.8028 (t0) cc_final: 0.7799 (t0) REVERT: A 851 GLU cc_start: 0.7827 (tp30) cc_final: 0.7281 (tp30) REVERT: A 877 GLU cc_start: 0.7507 (tt0) cc_final: 0.7262 (tt0) REVERT: A 935 LEU cc_start: 0.7973 (mp) cc_final: 0.7751 (mp) REVERT: A 943 GLU cc_start: 0.7453 (mm-30) cc_final: 0.7132 (mm-30) REVERT: A 1040 ASP cc_start: 0.7998 (m-30) cc_final: 0.7681 (m-30) REVERT: A 1117 LYS cc_start: 0.7985 (mmtt) cc_final: 0.7737 (mmtt) REVERT: A 1123 ARG cc_start: 0.7668 (ttp-110) cc_final: 0.7338 (ttp-110) REVERT: A 1186 GLU cc_start: 0.7800 (mm-30) cc_final: 0.7494 (mm-30) REVERT: A 1200 ARG cc_start: 0.8464 (mtm-85) cc_final: 0.7918 (ttm110) REVERT: A 1203 ILE cc_start: 0.7509 (mp) cc_final: 0.7271 (mp) REVERT: A 1305 MET cc_start: 0.8642 (mtt) cc_final: 0.8338 (mtp) REVERT: A 1372 VAL cc_start: 0.8049 (t) cc_final: 0.7656 (p) REVERT: A 1379 LYS cc_start: 0.8292 (mtmt) cc_final: 0.7923 (ptmt) REVERT: A 1467 GLU cc_start: 0.7455 (tp30) cc_final: 0.5953 (mm-30) REVERT: A 1515 SER cc_start: 0.8187 (m) cc_final: 0.7924 (t) REVERT: A 1578 LYS cc_start: 0.8259 (tttt) cc_final: 0.8048 (tttp) REVERT: A 1612 TYR cc_start: 0.8555 (m-80) cc_final: 0.8045 (m-80) REVERT: A 1640 MET cc_start: 0.8317 (ttp) cc_final: 0.8070 (ttt) REVERT: A 1740 ASN cc_start: 0.7544 (t0) cc_final: 0.6883 (t0) REVERT: A 1764 LYS cc_start: 0.8489 (mtpt) cc_final: 0.8137 (mtmm) REVERT: A 1802 LYS cc_start: 0.8554 (ttmt) cc_final: 0.8216 (ttmt) REVERT: A 1818 GLU cc_start: 0.7907 (mt-10) cc_final: 0.7633 (mt-10) REVERT: A 1830 MET cc_start: 0.8136 (ppp) cc_final: 0.7789 (ppp) REVERT: A 1831 MET cc_start: 0.7869 (OUTLIER) cc_final: 0.7500 (mmm) REVERT: A 1837 LYS cc_start: 0.8376 (tttt) cc_final: 0.8107 (tppp) REVERT: A 2039 GLU cc_start: 0.7053 (OUTLIER) cc_final: 0.6824 (mp0) REVERT: A 2044 SER cc_start: 0.8459 (t) cc_final: 0.8094 (p) REVERT: A 2291 VAL cc_start: 0.7832 (t) cc_final: 0.7535 (m) REVERT: A 2308 SER cc_start: 0.8595 (p) cc_final: 0.8337 (p) REVERT: A 2347 VAL cc_start: 0.8441 (p) cc_final: 0.8216 (t) REVERT: A 2375 MET cc_start: 0.8059 (mmm) cc_final: 0.7845 (mmt) REVERT: A 2515 SER cc_start: 0.8582 (t) cc_final: 0.8137 (p) REVERT: A 2543 LYS cc_start: 0.8192 (tttt) cc_final: 0.7917 (tttt) REVERT: A 2581 MET cc_start: 0.7620 (tmm) cc_final: 0.7312 (tmm) REVERT: A 2633 PHE cc_start: 0.8211 (p90) cc_final: 0.7273 (p90) REVERT: A 2639 GLN cc_start: 0.7249 (tp40) cc_final: 0.6669 (tp40) REVERT: A 2792 ASP cc_start: 0.7448 (t0) cc_final: 0.7071 (t0) REVERT: A 2810 LYS cc_start: 0.8015 (mtmt) cc_final: 0.7485 (mtmt) REVERT: A 3008 ILE cc_start: 0.8171 (mt) cc_final: 0.7966 (tt) REVERT: A 3047 LYS cc_start: 0.8456 (tttt) cc_final: 0.8124 (tttt) REVERT: A 3091 LYS cc_start: 0.8197 (mttt) cc_final: 0.7955 (mttp) REVERT: A 3120 GLU cc_start: 0.8092 (tt0) cc_final: 0.7834 (tt0) REVERT: A 3132 LEU cc_start: 0.8747 (mm) cc_final: 0.8530 (mm) REVERT: A 3140 GLN cc_start: 0.8304 (mm-40) cc_final: 0.7920 (mt0) REVERT: A 3155 GLU cc_start: 0.7352 (tp30) cc_final: 0.7012 (tp30) REVERT: A 3160 GLU cc_start: 0.7306 (tm-30) cc_final: 0.6802 (tm-30) REVERT: A 3175 SER cc_start: 0.8374 (t) cc_final: 0.8100 (t) REVERT: A 3199 LYS cc_start: 0.8602 (ptpt) cc_final: 0.8264 (ptpt) REVERT: A 3224 ARG cc_start: 0.7164 (mtp85) cc_final: 0.6873 (mtp85) REVERT: A 3315 ARG cc_start: 0.7707 (OUTLIER) cc_final: 0.7154 (tmm-80) REVERT: A 3364 GLU cc_start: 0.7599 (mp0) cc_final: 0.7352 (mp0) REVERT: A 3397 MET cc_start: 0.7840 (mmm) cc_final: 0.7389 (mmm) REVERT: A 3436 ILE cc_start: 0.8774 (pt) cc_final: 0.8572 (mt) REVERT: A 3451 LYS cc_start: 0.8380 (mttt) cc_final: 0.8138 (mttt) REVERT: A 3461 LYS cc_start: 0.8705 (mttt) cc_final: 0.8456 (mmtt) REVERT: A 3472 PHE cc_start: 0.8046 (t80) cc_final: 0.7724 (t80) REVERT: A 3476 SER cc_start: 0.7623 (m) cc_final: 0.7229 (p) REVERT: A 3539 LYS cc_start: 0.7793 (mmmm) cc_final: 0.7466 (mmmm) REVERT: A 3541 GLU cc_start: 0.7083 (mp0) cc_final: 0.6742 (mp0) REVERT: A 3592 GLU cc_start: 0.7809 (OUTLIER) cc_final: 0.6931 (mp0) REVERT: A 3702 GLU cc_start: 0.6999 (tp30) cc_final: 0.6201 (tp30) REVERT: A 3715 LYS cc_start: 0.8333 (tttt) cc_final: 0.8119 (ttpt) REVERT: A 3818 MET cc_start: 0.6615 (tmm) cc_final: 0.6287 (ppp) REVERT: A 3852 LYS cc_start: 0.8542 (tttt) cc_final: 0.7961 (tttt) REVERT: A 3862 LYS cc_start: 0.7926 (tttt) cc_final: 0.7628 (mttt) REVERT: A 3877 VAL cc_start: 0.8249 (t) cc_final: 0.7954 (p) outliers start: 70 outliers final: 42 residues processed: 589 average time/residue: 0.2058 time to fit residues: 182.4708 Evaluate side-chains 588 residues out of total 2920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 539 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 510 ASN Chi-restraints excluded: chain A residue 526 MET Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 557 SER Chi-restraints excluded: chain A residue 599 LYS Chi-restraints excluded: chain A residue 631 LYS Chi-restraints excluded: chain A residue 648 CYS Chi-restraints excluded: chain A residue 805 GLU Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 900 THR Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain A residue 1026 SER Chi-restraints excluded: chain A residue 1193 LYS Chi-restraints excluded: chain A residue 1285 LYS Chi-restraints excluded: chain A residue 1311 THR Chi-restraints excluded: chain A residue 1435 VAL Chi-restraints excluded: chain A residue 1463 GLU Chi-restraints excluded: chain A residue 1475 SER Chi-restraints excluded: chain A residue 1589 VAL Chi-restraints excluded: chain A residue 1747 THR Chi-restraints excluded: chain A residue 1753 SER Chi-restraints excluded: chain A residue 1812 SER Chi-restraints excluded: chain A residue 1831 MET Chi-restraints excluded: chain A residue 2039 GLU Chi-restraints excluded: chain A residue 2206 MET Chi-restraints excluded: chain A residue 2449 THR Chi-restraints excluded: chain A residue 2477 HIS Chi-restraints excluded: chain A residue 2526 THR Chi-restraints excluded: chain A residue 2563 ASP Chi-restraints excluded: chain A residue 2703 SER Chi-restraints excluded: chain A residue 2754 GLU Chi-restraints excluded: chain A residue 2769 THR Chi-restraints excluded: chain A residue 2933 VAL Chi-restraints excluded: chain A residue 3014 VAL Chi-restraints excluded: chain A residue 3116 SER Chi-restraints excluded: chain A residue 3148 LEU Chi-restraints excluded: chain A residue 3187 GLN Chi-restraints excluded: chain A residue 3228 THR Chi-restraints excluded: chain A residue 3243 LEU Chi-restraints excluded: chain A residue 3247 SER Chi-restraints excluded: chain A residue 3261 SER Chi-restraints excluded: chain A residue 3276 ARG Chi-restraints excluded: chain A residue 3315 ARG Chi-restraints excluded: chain A residue 3504 LEU Chi-restraints excluded: chain A residue 3563 MET Chi-restraints excluded: chain A residue 3592 GLU Chi-restraints excluded: chain A residue 3851 LEU Chi-restraints excluded: chain A residue 3867 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 130 optimal weight: 0.5980 chunk 248 optimal weight: 0.8980 chunk 175 optimal weight: 0.9980 chunk 67 optimal weight: 3.9990 chunk 110 optimal weight: 3.9990 chunk 84 optimal weight: 0.9980 chunk 273 optimal weight: 0.6980 chunk 13 optimal weight: 0.0170 chunk 244 optimal weight: 0.5980 chunk 202 optimal weight: 2.9990 chunk 135 optimal weight: 10.0000 overall best weight: 0.5618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 420 GLN A 960 GLN A1500 ASN A1519 ASN ** A2377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2607 GLN A2697 ASN A2758 GLN A3296 GLN A3421 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.160309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.135466 restraints weight = 36225.236| |-----------------------------------------------------------------------------| r_work (start): 0.3692 rms_B_bonded: 1.93 r_work: 0.3578 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3433 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 moved from start: 0.2487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.062 26962 Z= 0.109 Angle : 0.476 7.306 36577 Z= 0.247 Chirality : 0.038 0.259 4265 Planarity : 0.004 0.049 4451 Dihedral : 9.904 178.980 4077 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.51 % Favored : 96.46 % Rotamer: Outliers : 2.36 % Allowed : 12.57 % Favored : 85.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.15), residues: 3138 helix: 1.53 (0.12), residues: 1813 sheet: -0.20 (0.35), residues: 230 loop : -0.65 (0.19), residues: 1095 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A3400 TYR 0.012 0.001 TYR A 797 PHE 0.035 0.001 PHE A3553 TRP 0.013 0.001 TRP A3482 HIS 0.004 0.001 HIS A2018 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.11 (26958) covalent geometry : angle 0.47485 / 0.25 (36571) hydrogen bonds : bond 0.03144 / 2.11 ( 1397) hydrogen bonds : angle 3.95948 / 2.79 ( 3983) metal coordination : bond 0.00469 / 0.23 ( 4) metal coordination : angle 2.33591 / 0.95 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6276 Ramachandran restraints generated. 3138 Oldfield, 0 Emsley, 3138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6276 Ramachandran restraints generated. 3138 Oldfield, 0 Emsley, 3138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 613 residues out of total 2920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 544 time to evaluate : 0.999 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 477 SER cc_start: 0.7952 (m) cc_final: 0.7510 (p) REVERT: A 486 LYS cc_start: 0.8540 (mptt) cc_final: 0.8109 (mptt) REVERT: A 517 SER cc_start: 0.8099 (t) cc_final: 0.7848 (p) REVERT: A 599 LYS cc_start: 0.8166 (OUTLIER) cc_final: 0.7711 (mmtt) REVERT: A 631 LYS cc_start: 0.7971 (OUTLIER) cc_final: 0.7756 (mttt) REVERT: A 678 LEU cc_start: 0.8112 (mt) cc_final: 0.7780 (mm) REVERT: A 723 GLU cc_start: 0.7613 (tp30) cc_final: 0.7168 (tp30) REVERT: A 808 MET cc_start: 0.7722 (tpt) cc_final: 0.7053 (tpt) REVERT: A 833 ASP cc_start: 0.8045 (t0) cc_final: 0.7803 (t0) REVERT: A 851 GLU cc_start: 0.7869 (tp30) cc_final: 0.7302 (tp30) REVERT: A 877 GLU cc_start: 0.7485 (tt0) cc_final: 0.7192 (tt0) REVERT: A 941 MET cc_start: 0.8207 (mmm) cc_final: 0.7926 (mmt) REVERT: A 943 GLU cc_start: 0.7479 (mm-30) cc_final: 0.7147 (mm-30) REVERT: A 982 ASN cc_start: 0.8049 (m-40) cc_final: 0.7761 (m-40) REVERT: A 1040 ASP cc_start: 0.7985 (m-30) cc_final: 0.7676 (m-30) REVERT: A 1057 GLN cc_start: 0.8559 (OUTLIER) cc_final: 0.7389 (mt0) REVERT: A 1086 GLU cc_start: 0.7504 (mp0) cc_final: 0.7283 (mp0) REVERT: A 1117 LYS cc_start: 0.8019 (mmtt) cc_final: 0.7771 (mmtt) REVERT: A 1123 ARG cc_start: 0.7684 (ttp-110) cc_final: 0.7348 (ttp-110) REVERT: A 1186 GLU cc_start: 0.7823 (mm-30) cc_final: 0.7524 (mm-30) REVERT: A 1200 ARG cc_start: 0.8490 (mtm-85) cc_final: 0.7954 (ttm110) REVERT: A 1203 ILE cc_start: 0.7533 (OUTLIER) cc_final: 0.7290 (mp) REVERT: A 1305 MET cc_start: 0.8652 (mtt) cc_final: 0.8346 (mtp) REVERT: A 1379 LYS cc_start: 0.8278 (mtmt) cc_final: 0.7960 (ptmt) REVERT: A 1402 ARG cc_start: 0.7745 (ttt-90) cc_final: 0.7379 (ttt-90) REVERT: A 1465 ARG cc_start: 0.8004 (mtm180) cc_final: 0.7627 (mtm180) REVERT: A 1467 GLU cc_start: 0.7460 (tp30) cc_final: 0.5997 (mm-30) REVERT: A 1478 ARG cc_start: 0.8223 (mtt-85) cc_final: 0.7926 (mtt90) REVERT: A 1515 SER cc_start: 0.8180 (m) cc_final: 0.7914 (t) REVERT: A 1578 LYS cc_start: 0.8257 (tttt) cc_final: 0.8050 (tttp) REVERT: A 1589 VAL cc_start: 0.8550 (OUTLIER) cc_final: 0.8349 (p) REVERT: A 1740 ASN cc_start: 0.7568 (t0) cc_final: 0.6903 (t0) REVERT: A 1758 ASN cc_start: 0.7824 (m-40) cc_final: 0.7590 (m110) REVERT: A 1764 LYS cc_start: 0.8465 (mtpt) cc_final: 0.8105 (mtmm) REVERT: A 1802 LYS cc_start: 0.8550 (ttmt) cc_final: 0.8142 (ttmt) REVERT: A 1818 GLU cc_start: 0.7892 (mt-10) cc_final: 0.7607 (mt-10) REVERT: A 1830 MET cc_start: 0.8117 (ppp) cc_final: 0.7768 (ppp) REVERT: A 1831 MET cc_start: 0.7874 (mtm) cc_final: 0.7480 (mmm) REVERT: A 1837 LYS cc_start: 0.8377 (tttt) cc_final: 0.8115 (tppp) REVERT: A 2039 GLU cc_start: 0.7044 (OUTLIER) cc_final: 0.6763 (mp0) REVERT: A 2044 SER cc_start: 0.8412 (t) cc_final: 0.8075 (p) REVERT: A 2045 PHE cc_start: 0.8303 (m-80) cc_final: 0.7787 (m-80) REVERT: A 2291 VAL cc_start: 0.7824 (t) cc_final: 0.7537 (m) REVERT: A 2308 SER cc_start: 0.8543 (p) cc_final: 0.8285 (p) REVERT: A 2375 MET cc_start: 0.8076 (mmm) cc_final: 0.7862 (mmt) REVERT: A 2444 TRP cc_start: 0.8254 (m100) cc_final: 0.7716 (m100) REVERT: A 2515 SER cc_start: 0.8608 (t) cc_final: 0.8139 (p) REVERT: A 2543 LYS cc_start: 0.8182 (tttt) cc_final: 0.7912 (tttt) REVERT: A 2581 MET cc_start: 0.7630 (tmm) cc_final: 0.7305 (tmm) REVERT: A 2633 PHE cc_start: 0.8176 (p90) cc_final: 0.7304 (p90) REVERT: A 2639 GLN cc_start: 0.7223 (tp40) cc_final: 0.6656 (tp40) REVERT: A 2792 ASP cc_start: 0.7421 (t0) cc_final: 0.7059 (t0) REVERT: A 2801 ARG cc_start: 0.7944 (mtp85) cc_final: 0.7445 (ttt90) REVERT: A 2810 LYS cc_start: 0.8045 (mtmt) cc_final: 0.7562 (mtmt) REVERT: A 3047 LYS cc_start: 0.8467 (tttt) cc_final: 0.8227 (tttt) REVERT: A 3091 LYS cc_start: 0.8206 (mttt) cc_final: 0.7955 (mttp) REVERT: A 3120 GLU cc_start: 0.8093 (tt0) cc_final: 0.7863 (tt0) REVERT: A 3132 LEU cc_start: 0.8734 (mm) cc_final: 0.8531 (mm) REVERT: A 3140 GLN cc_start: 0.8319 (mm-40) cc_final: 0.7944 (mt0) REVERT: A 3155 GLU cc_start: 0.7350 (tp30) cc_final: 0.7018 (tp30) REVERT: A 3160 GLU cc_start: 0.7352 (tm-30) cc_final: 0.6832 (tm-30) REVERT: A 3175 SER cc_start: 0.8482 (t) cc_final: 0.8270 (t) REVERT: A 3224 ARG cc_start: 0.7163 (mtp85) cc_final: 0.6836 (mtp85) REVERT: A 3364 GLU cc_start: 0.7635 (mp0) cc_final: 0.7353 (mp0) REVERT: A 3390 GLU cc_start: 0.7803 (tt0) cc_final: 0.7475 (pt0) REVERT: A 3397 MET cc_start: 0.7817 (mmm) cc_final: 0.7368 (mmm) REVERT: A 3451 LYS cc_start: 0.8332 (mttt) cc_final: 0.8098 (mttt) REVERT: A 3461 LYS cc_start: 0.8719 (mttt) cc_final: 0.8479 (mmtt) REVERT: A 3472 PHE cc_start: 0.8061 (t80) cc_final: 0.7749 (t80) REVERT: A 3539 LYS cc_start: 0.7741 (mmmm) cc_final: 0.7393 (mmmm) REVERT: A 3541 GLU cc_start: 0.7079 (mp0) cc_final: 0.6610 (mp0) REVERT: A 3702 GLU cc_start: 0.6962 (tp30) cc_final: 0.6185 (tp30) REVERT: A 3715 LYS cc_start: 0.8330 (tttt) cc_final: 0.8114 (ttpt) REVERT: A 3818 MET cc_start: 0.6529 (tmm) cc_final: 0.6243 (ppp) REVERT: A 3862 LYS cc_start: 0.7945 (tttt) cc_final: 0.7651 (mttt) REVERT: A 3877 VAL cc_start: 0.8241 (t) cc_final: 0.7945 (p) outliers start: 69 outliers final: 39 residues processed: 580 average time/residue: 0.2050 time to fit residues: 178.3653 Evaluate side-chains 572 residues out of total 2920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 527 time to evaluate : 0.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 510 ASN Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 557 SER Chi-restraints excluded: chain A residue 599 LYS Chi-restraints excluded: chain A residue 631 LYS Chi-restraints excluded: chain A residue 648 CYS Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain A residue 1026 SER Chi-restraints excluded: chain A residue 1057 GLN Chi-restraints excluded: chain A residue 1153 THR Chi-restraints excluded: chain A residue 1203 ILE Chi-restraints excluded: chain A residue 1285 LYS Chi-restraints excluded: chain A residue 1435 VAL Chi-restraints excluded: chain A residue 1463 GLU Chi-restraints excluded: chain A residue 1475 SER Chi-restraints excluded: chain A residue 1589 VAL Chi-restraints excluded: chain A residue 1747 THR Chi-restraints excluded: chain A residue 1753 SER Chi-restraints excluded: chain A residue 1812 SER Chi-restraints excluded: chain A residue 2039 GLU Chi-restraints excluded: chain A residue 2206 MET Chi-restraints excluded: chain A residue 2260 LEU Chi-restraints excluded: chain A residue 2449 THR Chi-restraints excluded: chain A residue 2477 HIS Chi-restraints excluded: chain A residue 2507 THR Chi-restraints excluded: chain A residue 2526 THR Chi-restraints excluded: chain A residue 2703 SER Chi-restraints excluded: chain A residue 2769 THR Chi-restraints excluded: chain A residue 2933 VAL Chi-restraints excluded: chain A residue 3014 VAL Chi-restraints excluded: chain A residue 3116 SER Chi-restraints excluded: chain A residue 3148 LEU Chi-restraints excluded: chain A residue 3228 THR Chi-restraints excluded: chain A residue 3243 LEU Chi-restraints excluded: chain A residue 3247 SER Chi-restraints excluded: chain A residue 3261 SER Chi-restraints excluded: chain A residue 3459 ILE Chi-restraints excluded: chain A residue 3466 VAL Chi-restraints excluded: chain A residue 3563 MET Chi-restraints excluded: chain A residue 3592 GLU Chi-restraints excluded: chain A residue 3851 LEU Chi-restraints excluded: chain A residue 3867 CYS Chi-restraints excluded: chain A residue 3885 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 220 optimal weight: 0.6980 chunk 147 optimal weight: 5.9990 chunk 275 optimal weight: 3.9990 chunk 125 optimal weight: 1.9990 chunk 165 optimal weight: 0.8980 chunk 313 optimal weight: 1.9990 chunk 71 optimal weight: 0.7980 chunk 294 optimal weight: 6.9990 chunk 174 optimal weight: 0.9980 chunk 286 optimal weight: 2.9990 chunk 57 optimal weight: 0.5980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 960 GLN A1077 ASN A1516 GLN ** A2377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2413 ASN A2692 GLN A2758 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.159510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.134370 restraints weight = 36263.654| |-----------------------------------------------------------------------------| r_work (start): 0.3674 rms_B_bonded: 2.00 r_work: 0.3555 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3406 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.2638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 26962 Z= 0.128 Angle : 0.491 8.427 36577 Z= 0.254 Chirality : 0.039 0.248 4265 Planarity : 0.004 0.045 4451 Dihedral : 9.893 179.290 4077 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.76 % Favored : 96.21 % Rotamer: Outliers : 2.23 % Allowed : 12.84 % Favored : 84.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.15), residues: 3138 helix: 1.53 (0.12), residues: 1816 sheet: -0.23 (0.34), residues: 236 loop : -0.63 (0.19), residues: 1086 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A3400 TYR 0.012 0.001 TYR A1313 PHE 0.038 0.001 PHE A3553 TRP 0.013 0.001 TRP A2362 HIS 0.004 0.001 HIS A3045 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 (26958) covalent geometry : angle 0.49024 / 0.25 (36571) hydrogen bonds : bond 0.03238 / 2.18 ( 1397) hydrogen bonds : angle 3.95172 / 2.79 ( 3983) metal coordination : bond 0.00720 / 0.35 ( 4) metal coordination : angle 2.27572 / 0.93 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6276 Ramachandran restraints generated. 3138 Oldfield, 0 Emsley, 3138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6276 Ramachandran restraints generated. 3138 Oldfield, 0 Emsley, 3138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 603 residues out of total 2920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 538 time to evaluate : 1.010 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 477 SER cc_start: 0.8001 (m) cc_final: 0.7556 (p) REVERT: A 486 LYS cc_start: 0.8528 (mptt) cc_final: 0.8099 (mptt) REVERT: A 517 SER cc_start: 0.8130 (t) cc_final: 0.7830 (p) REVERT: A 599 LYS cc_start: 0.8171 (OUTLIER) cc_final: 0.7739 (mmtt) REVERT: A 631 LYS cc_start: 0.7987 (OUTLIER) cc_final: 0.7786 (mtmt) REVERT: A 678 LEU cc_start: 0.8143 (mt) cc_final: 0.7807 (mm) REVERT: A 808 MET cc_start: 0.7784 (tpt) cc_final: 0.7045 (tpt) REVERT: A 833 ASP cc_start: 0.8058 (t0) cc_final: 0.7812 (t0) REVERT: A 851 GLU cc_start: 0.7879 (tp30) cc_final: 0.7366 (tp30) REVERT: A 877 GLU cc_start: 0.7543 (tt0) cc_final: 0.7288 (tt0) REVERT: A 943 GLU cc_start: 0.7505 (mm-30) cc_final: 0.7179 (mm-30) REVERT: A 982 ASN cc_start: 0.8086 (m-40) cc_final: 0.7819 (m-40) REVERT: A 1040 ASP cc_start: 0.8029 (m-30) cc_final: 0.7710 (m-30) REVERT: A 1057 GLN cc_start: 0.8596 (OUTLIER) cc_final: 0.7372 (mt0) REVERT: A 1117 LYS cc_start: 0.8050 (mmtt) cc_final: 0.7803 (mmtt) REVERT: A 1123 ARG cc_start: 0.7689 (ttp-110) cc_final: 0.7354 (ttp-110) REVERT: A 1200 ARG cc_start: 0.8512 (mtm-85) cc_final: 0.7977 (ttm110) REVERT: A 1203 ILE cc_start: 0.7534 (OUTLIER) cc_final: 0.7313 (mp) REVERT: A 1305 MET cc_start: 0.8657 (mtt) cc_final: 0.8371 (mtp) REVERT: A 1379 LYS cc_start: 0.8313 (mtmt) cc_final: 0.7995 (ptmt) REVERT: A 1515 SER cc_start: 0.8194 (m) cc_final: 0.7914 (t) REVERT: A 1589 VAL cc_start: 0.8499 (OUTLIER) cc_final: 0.8294 (p) REVERT: A 1740 ASN cc_start: 0.7600 (t0) cc_final: 0.6915 (t0) REVERT: A 1764 LYS cc_start: 0.8470 (mtpt) cc_final: 0.8118 (mtmm) REVERT: A 1802 LYS cc_start: 0.8558 (ttmt) cc_final: 0.8209 (ttmt) REVERT: A 1818 GLU cc_start: 0.7891 (mt-10) cc_final: 0.7620 (mt-10) REVERT: A 1837 LYS cc_start: 0.8435 (tttt) cc_final: 0.8184 (tppp) REVERT: A 2039 GLU cc_start: 0.7040 (OUTLIER) cc_final: 0.6819 (mp0) REVERT: A 2044 SER cc_start: 0.8413 (t) cc_final: 0.8083 (p) REVERT: A 2045 PHE cc_start: 0.8322 (m-80) cc_final: 0.7848 (m-80) REVERT: A 2291 VAL cc_start: 0.7878 (t) cc_final: 0.7582 (m) REVERT: A 2308 SER cc_start: 0.8619 (p) cc_final: 0.8356 (p) REVERT: A 2375 MET cc_start: 0.8082 (mmm) cc_final: 0.7864 (mmt) REVERT: A 2444 TRP cc_start: 0.8280 (m100) cc_final: 0.7655 (m100) REVERT: A 2515 SER cc_start: 0.8619 (t) cc_final: 0.8126 (p) REVERT: A 2543 LYS cc_start: 0.8197 (tttt) cc_final: 0.7902 (tttt) REVERT: A 2633 PHE cc_start: 0.8218 (p90) cc_final: 0.7448 (p90) REVERT: A 2639 GLN cc_start: 0.7310 (tp40) cc_final: 0.6679 (tp40) REVERT: A 2764 SER cc_start: 0.8388 (p) cc_final: 0.8090 (t) REVERT: A 2801 ARG cc_start: 0.7976 (mtp85) cc_final: 0.7482 (ttt90) REVERT: A 2810 LYS cc_start: 0.8056 (mtmt) cc_final: 0.7601 (mtmt) REVERT: A 3047 LYS cc_start: 0.8486 (tttt) cc_final: 0.8255 (tttt) REVERT: A 3091 LYS cc_start: 0.8195 (mttt) cc_final: 0.7951 (mttp) REVERT: A 3120 GLU cc_start: 0.8173 (tt0) cc_final: 0.7892 (tt0) REVERT: A 3155 GLU cc_start: 0.7367 (tp30) cc_final: 0.7018 (tp30) REVERT: A 3160 GLU cc_start: 0.7434 (tm-30) cc_final: 0.6897 (tm-30) REVERT: A 3175 SER cc_start: 0.8502 (t) cc_final: 0.8285 (t) REVERT: A 3199 LYS cc_start: 0.8609 (ptpt) cc_final: 0.8331 (ptpt) REVERT: A 3203 MET cc_start: 0.8545 (OUTLIER) cc_final: 0.8335 (mtp) REVERT: A 3224 ARG cc_start: 0.7190 (mtp85) cc_final: 0.6912 (mtp85) REVERT: A 3364 GLU cc_start: 0.7643 (mp0) cc_final: 0.7343 (mp0) REVERT: A 3390 GLU cc_start: 0.7854 (tt0) cc_final: 0.7532 (pt0) REVERT: A 3397 MET cc_start: 0.7818 (mmm) cc_final: 0.7389 (mmm) REVERT: A 3457 VAL cc_start: 0.7811 (t) cc_final: 0.7552 (m) REVERT: A 3461 LYS cc_start: 0.8739 (mttt) cc_final: 0.8506 (mmtt) REVERT: A 3472 PHE cc_start: 0.8095 (t80) cc_final: 0.7732 (t80) REVERT: A 3539 LYS cc_start: 0.7781 (mmmm) cc_final: 0.7481 (mmmm) REVERT: A 3702 GLU cc_start: 0.7059 (tp30) cc_final: 0.6242 (tp30) REVERT: A 3715 LYS cc_start: 0.8381 (tttt) cc_final: 0.8180 (ttpt) REVERT: A 3852 LYS cc_start: 0.8521 (tttt) cc_final: 0.8028 (tttt) REVERT: A 3862 LYS cc_start: 0.7934 (tttt) cc_final: 0.7623 (mttt) REVERT: A 3873 LYS cc_start: 0.7585 (mttt) cc_final: 0.7258 (mttt) REVERT: A 3877 VAL cc_start: 0.8242 (t) cc_final: 0.7945 (p) outliers start: 65 outliers final: 43 residues processed: 570 average time/residue: 0.2040 time to fit residues: 175.7421 Evaluate side-chains 576 residues out of total 2920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 526 time to evaluate : 1.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 510 ASN Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 557 SER Chi-restraints excluded: chain A residue 599 LYS Chi-restraints excluded: chain A residue 631 LYS Chi-restraints excluded: chain A residue 648 CYS Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 876 THR Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain A residue 1026 SER Chi-restraints excluded: chain A residue 1057 GLN Chi-restraints excluded: chain A residue 1153 THR Chi-restraints excluded: chain A residue 1203 ILE Chi-restraints excluded: chain A residue 1285 LYS Chi-restraints excluded: chain A residue 1400 LEU Chi-restraints excluded: chain A residue 1420 ILE Chi-restraints excluded: chain A residue 1435 VAL Chi-restraints excluded: chain A residue 1475 SER Chi-restraints excluded: chain A residue 1589 VAL Chi-restraints excluded: chain A residue 1621 MET Chi-restraints excluded: chain A residue 1753 SER Chi-restraints excluded: chain A residue 1812 SER Chi-restraints excluded: chain A residue 2039 GLU Chi-restraints excluded: chain A residue 2206 MET Chi-restraints excluded: chain A residue 2260 LEU Chi-restraints excluded: chain A residue 2449 THR Chi-restraints excluded: chain A residue 2477 HIS Chi-restraints excluded: chain A residue 2526 THR Chi-restraints excluded: chain A residue 2703 SER Chi-restraints excluded: chain A residue 2769 THR Chi-restraints excluded: chain A residue 2933 VAL Chi-restraints excluded: chain A residue 3014 VAL Chi-restraints excluded: chain A residue 3116 SER Chi-restraints excluded: chain A residue 3118 ILE Chi-restraints excluded: chain A residue 3148 LEU Chi-restraints excluded: chain A residue 3171 VAL Chi-restraints excluded: chain A residue 3203 MET Chi-restraints excluded: chain A residue 3228 THR Chi-restraints excluded: chain A residue 3243 LEU Chi-restraints excluded: chain A residue 3247 SER Chi-restraints excluded: chain A residue 3261 SER Chi-restraints excluded: chain A residue 3338 LEU Chi-restraints excluded: chain A residue 3459 ILE Chi-restraints excluded: chain A residue 3466 VAL Chi-restraints excluded: chain A residue 3502 GLU Chi-restraints excluded: chain A residue 3563 MET Chi-restraints excluded: chain A residue 3592 GLU Chi-restraints excluded: chain A residue 3867 CYS Chi-restraints excluded: chain A residue 3885 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 313 optimal weight: 6.9990 chunk 231 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 171 optimal weight: 2.9990 chunk 41 optimal weight: 0.6980 chunk 314 optimal weight: 7.9990 chunk 3 optimal weight: 30.0000 chunk 251 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 273 optimal weight: 4.9990 chunk 259 optimal weight: 7.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 960 GLN ** A1077 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1154 HIS ** A2377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2476 HIS A2692 GLN A2758 GLN A3375 HIS A3556 HIS A3653 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.153333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.127979 restraints weight = 36183.816| |-----------------------------------------------------------------------------| r_work (start): 0.3611 rms_B_bonded: 1.98 r_work: 0.3494 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3342 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.2943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.108 26962 Z= 0.268 Angle : 0.603 12.022 36577 Z= 0.311 Chirality : 0.044 0.274 4265 Planarity : 0.004 0.047 4451 Dihedral : 10.129 178.976 4077 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.14 % Favored : 95.83 % Rotamer: Outliers : 2.40 % Allowed : 13.84 % Favored : 83.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.60 (0.15), residues: 3138 helix: 1.20 (0.12), residues: 1807 sheet: -0.44 (0.33), residues: 243 loop : -0.66 (0.20), residues: 1088 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A1805 TYR 0.019 0.002 TYR A2468 PHE 0.032 0.002 PHE A3553 TRP 0.015 0.002 TRP A2362 HIS 0.006 0.001 HIS A3244 Details of bonding type rmsd/Z covalent geometry : bond 0.00623 / 0.27 (26958) covalent geometry : angle 0.60185 / 0.31 (36571) hydrogen bonds : bond 0.04207 / 2.83 ( 1397) hydrogen bonds : angle 4.29412 / 3.03 ( 3983) metal coordination : bond 0.01487 / 0.74 ( 4) metal coordination : angle 3.26578 / 1.50 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6276 Ramachandran restraints generated. 3138 Oldfield, 0 Emsley, 3138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6276 Ramachandran restraints generated. 3138 Oldfield, 0 Emsley, 3138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 657 residues out of total 2920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 587 time to evaluate : 1.020 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 477 SER cc_start: 0.7967 (m) cc_final: 0.7591 (p) REVERT: A 486 LYS cc_start: 0.8536 (mptt) cc_final: 0.8058 (mptt) REVERT: A 599 LYS cc_start: 0.8163 (OUTLIER) cc_final: 0.7773 (mmtt) REVERT: A 649 TYR cc_start: 0.7818 (m-80) cc_final: 0.7550 (m-80) REVERT: A 653 TYR cc_start: 0.7809 (t80) cc_final: 0.7608 (t80) REVERT: A 656 GLU cc_start: 0.7884 (tp30) cc_final: 0.7484 (tp30) REVERT: A 678 LEU cc_start: 0.8148 (mt) cc_final: 0.7794 (mm) REVERT: A 732 GLU cc_start: 0.8131 (mt-10) cc_final: 0.7898 (mt-10) REVERT: A 745 GLU cc_start: 0.7964 (mt-10) cc_final: 0.7643 (mt-10) REVERT: A 753 MET cc_start: 0.7702 (OUTLIER) cc_final: 0.7473 (mtp) REVERT: A 807 HIS cc_start: 0.7977 (m90) cc_final: 0.7759 (m90) REVERT: A 808 MET cc_start: 0.7882 (tpt) cc_final: 0.7222 (tpt) REVERT: A 833 ASP cc_start: 0.8115 (t0) cc_final: 0.7839 (t0) REVERT: A 851 GLU cc_start: 0.7899 (tp30) cc_final: 0.7317 (tp30) REVERT: A 877 GLU cc_start: 0.7554 (tt0) cc_final: 0.7349 (tt0) REVERT: A 1040 ASP cc_start: 0.8150 (m-30) cc_final: 0.7708 (m-30) REVERT: A 1057 GLN cc_start: 0.8647 (OUTLIER) cc_final: 0.7425 (mt0) REVERT: A 1073 SER cc_start: 0.8758 (t) cc_final: 0.8450 (m) REVERT: A 1096 PHE cc_start: 0.8063 (m-10) cc_final: 0.7664 (m-10) REVERT: A 1117 LYS cc_start: 0.8135 (mmtt) cc_final: 0.7862 (mmtt) REVERT: A 1200 ARG cc_start: 0.8522 (mtm-85) cc_final: 0.7985 (ttm110) REVERT: A 1203 ILE cc_start: 0.7586 (OUTLIER) cc_final: 0.7343 (mp) REVERT: A 1217 LYS cc_start: 0.8192 (OUTLIER) cc_final: 0.7970 (ttmm) REVERT: A 1254 GLU cc_start: 0.7809 (pt0) cc_final: 0.7572 (pt0) REVERT: A 1305 MET cc_start: 0.8755 (mtt) cc_final: 0.8545 (mtp) REVERT: A 1353 PHE cc_start: 0.7631 (m-10) cc_final: 0.7318 (m-80) REVERT: A 1379 LYS cc_start: 0.8343 (mtmt) cc_final: 0.8022 (mtpt) REVERT: A 1402 ARG cc_start: 0.7834 (ttt-90) cc_final: 0.7492 (ttt-90) REVERT: A 1515 SER cc_start: 0.8188 (m) cc_final: 0.7987 (t) REVERT: A 1605 ARG cc_start: 0.8129 (tpp80) cc_final: 0.7889 (ttt90) REVERT: A 1740 ASN cc_start: 0.7688 (t0) cc_final: 0.6941 (t0) REVERT: A 1808 LYS cc_start: 0.8451 (mmtp) cc_final: 0.8217 (mmmt) REVERT: A 1818 GLU cc_start: 0.7884 (mt-10) cc_final: 0.7668 (mt-10) REVERT: A 1830 MET cc_start: 0.8123 (ppp) cc_final: 0.7921 (ppp) REVERT: A 1837 LYS cc_start: 0.8463 (tttt) cc_final: 0.8230 (tppp) REVERT: A 2039 GLU cc_start: 0.7091 (OUTLIER) cc_final: 0.6884 (mp0) REVERT: A 2044 SER cc_start: 0.8439 (t) cc_final: 0.8078 (p) REVERT: A 2045 PHE cc_start: 0.8367 (m-80) cc_final: 0.8075 (m-80) REVERT: A 2291 VAL cc_start: 0.8064 (t) cc_final: 0.7637 (m) REVERT: A 2308 SER cc_start: 0.8670 (p) cc_final: 0.8442 (m) REVERT: A 2515 SER cc_start: 0.8576 (t) cc_final: 0.8084 (p) REVERT: A 2543 LYS cc_start: 0.8206 (tttt) cc_final: 0.7925 (tttt) REVERT: A 2581 MET cc_start: 0.7612 (tmm) cc_final: 0.7396 (tmm) REVERT: A 2608 SER cc_start: 0.7741 (m) cc_final: 0.7454 (p) REVERT: A 2639 GLN cc_start: 0.7382 (tp40) cc_final: 0.6795 (tp40) REVERT: A 2764 SER cc_start: 0.8565 (p) cc_final: 0.8291 (t) REVERT: A 2810 LYS cc_start: 0.8029 (mtmt) cc_final: 0.7567 (mtmt) REVERT: A 2929 THR cc_start: 0.8244 (m) cc_final: 0.7846 (p) REVERT: A 3047 LYS cc_start: 0.8566 (tttt) cc_final: 0.8353 (tttt) REVERT: A 3074 ARG cc_start: 0.7994 (ptp-110) cc_final: 0.7737 (ptp-170) REVERT: A 3091 LYS cc_start: 0.8253 (mttt) cc_final: 0.8034 (mttm) REVERT: A 3120 GLU cc_start: 0.8190 (tt0) cc_final: 0.7890 (tt0) REVERT: A 3140 GLN cc_start: 0.8422 (mm-40) cc_final: 0.8016 (mt0) REVERT: A 3160 GLU cc_start: 0.7480 (tm-30) cc_final: 0.6959 (tm-30) REVERT: A 3175 SER cc_start: 0.8449 (t) cc_final: 0.8230 (t) REVERT: A 3199 LYS cc_start: 0.8655 (ptpt) cc_final: 0.8285 (ptpt) REVERT: A 3203 MET cc_start: 0.8572 (ttm) cc_final: 0.8364 (mtp) REVERT: A 3224 ARG cc_start: 0.7243 (mtp85) cc_final: 0.6927 (mtp85) REVERT: A 3324 TYR cc_start: 0.8063 (t80) cc_final: 0.7790 (t80) REVERT: A 3358 TYR cc_start: 0.7443 (t80) cc_final: 0.7170 (t80) REVERT: A 3390 GLU cc_start: 0.7858 (tt0) cc_final: 0.7551 (pt0) REVERT: A 3397 MET cc_start: 0.7783 (mmm) cc_final: 0.7473 (mmm) REVERT: A 3451 LYS cc_start: 0.8537 (mttt) cc_final: 0.8229 (mttt) REVERT: A 3461 LYS cc_start: 0.8703 (mttt) cc_final: 0.8465 (mmtt) REVERT: A 3472 PHE cc_start: 0.8087 (t80) cc_final: 0.7673 (t80) REVERT: A 3539 LYS cc_start: 0.7858 (mmmm) cc_final: 0.7627 (mmmm) REVERT: A 3702 GLU cc_start: 0.7203 (tp30) cc_final: 0.6411 (tp30) REVERT: A 3852 LYS cc_start: 0.8613 (tttt) cc_final: 0.8217 (tttt) REVERT: A 3862 LYS cc_start: 0.7997 (tttt) cc_final: 0.7698 (mttt) REVERT: A 3873 LYS cc_start: 0.7623 (mttt) cc_final: 0.7352 (mttt) outliers start: 70 outliers final: 47 residues processed: 622 average time/residue: 0.2066 time to fit residues: 193.2051 Evaluate side-chains 612 residues out of total 2920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 559 time to evaluate : 0.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 510 ASN Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 557 SER Chi-restraints excluded: chain A residue 599 LYS Chi-restraints excluded: chain A residue 753 MET Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 876 THR Chi-restraints excluded: chain A residue 900 THR Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain A residue 1026 SER Chi-restraints excluded: chain A residue 1057 GLN Chi-restraints excluded: chain A residue 1203 ILE Chi-restraints excluded: chain A residue 1217 LYS Chi-restraints excluded: chain A residue 1285 LYS Chi-restraints excluded: chain A residue 1328 THR Chi-restraints excluded: chain A residue 1376 SER Chi-restraints excluded: chain A residue 1400 LEU Chi-restraints excluded: chain A residue 1420 ILE Chi-restraints excluded: chain A residue 1435 VAL Chi-restraints excluded: chain A residue 1475 SER Chi-restraints excluded: chain A residue 1640 MET Chi-restraints excluded: chain A residue 1658 THR Chi-restraints excluded: chain A residue 1753 SER Chi-restraints excluded: chain A residue 1812 SER Chi-restraints excluded: chain A residue 2039 GLU Chi-restraints excluded: chain A residue 2206 MET Chi-restraints excluded: chain A residue 2260 LEU Chi-restraints excluded: chain A residue 2407 SER Chi-restraints excluded: chain A residue 2441 LEU Chi-restraints excluded: chain A residue 2449 THR Chi-restraints excluded: chain A residue 2477 HIS Chi-restraints excluded: chain A residue 2507 THR Chi-restraints excluded: chain A residue 2526 THR Chi-restraints excluded: chain A residue 2703 SER Chi-restraints excluded: chain A residue 2769 THR Chi-restraints excluded: chain A residue 2933 VAL Chi-restraints excluded: chain A residue 3014 VAL Chi-restraints excluded: chain A residue 3116 SER Chi-restraints excluded: chain A residue 3118 ILE Chi-restraints excluded: chain A residue 3171 VAL Chi-restraints excluded: chain A residue 3228 THR Chi-restraints excluded: chain A residue 3243 LEU Chi-restraints excluded: chain A residue 3247 SER Chi-restraints excluded: chain A residue 3261 SER Chi-restraints excluded: chain A residue 3338 LEU Chi-restraints excluded: chain A residue 3466 VAL Chi-restraints excluded: chain A residue 3502 GLU Chi-restraints excluded: chain A residue 3504 LEU Chi-restraints excluded: chain A residue 3563 MET Chi-restraints excluded: chain A residue 3592 GLU Chi-restraints excluded: chain A residue 3851 LEU Chi-restraints excluded: chain A residue 3867 CYS Chi-restraints excluded: chain A residue 3885 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 153 optimal weight: 6.9990 chunk 51 optimal weight: 0.7980 chunk 304 optimal weight: 0.0370 chunk 52 optimal weight: 0.2980 chunk 81 optimal weight: 1.9990 chunk 219 optimal weight: 1.9990 chunk 318 optimal weight: 3.9990 chunk 222 optimal weight: 8.9990 chunk 38 optimal weight: 2.9990 chunk 291 optimal weight: 1.9990 chunk 98 optimal weight: 0.7980 overall best weight: 0.7860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 473 ASN A 960 GLN A1055 ASN ** A1844 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2470 HIS A2692 GLN A2758 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.157524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.132706 restraints weight = 36255.372| |-----------------------------------------------------------------------------| r_work (start): 0.3652 rms_B_bonded: 1.93 r_work: 0.3538 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3391 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.2967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.100 26962 Z= 0.134 Angle : 0.532 14.334 36577 Z= 0.272 Chirality : 0.040 0.211 4265 Planarity : 0.004 0.048 4451 Dihedral : 10.042 179.949 4077 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.73 % Favored : 96.24 % Rotamer: Outliers : 2.09 % Allowed : 14.66 % Favored : 83.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.15), residues: 3138 helix: 1.37 (0.12), residues: 1806 sheet: -0.24 (0.35), residues: 225 loop : -0.66 (0.20), residues: 1107 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A1805 TYR 0.012 0.001 TYR A1503 PHE 0.033 0.001 PHE A3553 TRP 0.013 0.001 TRP A2542 HIS 0.006 0.001 HIS A2018 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.13 (26958) covalent geometry : angle 0.53095 / 0.27 (36571) hydrogen bonds : bond 0.03465 / 2.32 ( 1397) hydrogen bonds : angle 4.05515 / 2.86 ( 3983) metal coordination : bond 0.00701 / 0.34 ( 4) metal coordination : angle 2.53134 / 1.17 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6276 Ramachandran restraints generated. 3138 Oldfield, 0 Emsley, 3138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6276 Ramachandran restraints generated. 3138 Oldfield, 0 Emsley, 3138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 609 residues out of total 2920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 548 time to evaluate : 1.092 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 477 SER cc_start: 0.8042 (m) cc_final: 0.7620 (p) REVERT: A 486 LYS cc_start: 0.8533 (mptt) cc_final: 0.8118 (mptt) REVERT: A 517 SER cc_start: 0.8235 (t) cc_final: 0.7926 (p) REVERT: A 599 LYS cc_start: 0.8153 (OUTLIER) cc_final: 0.7739 (mmtt) REVERT: A 649 TYR cc_start: 0.7710 (m-80) cc_final: 0.7413 (m-80) REVERT: A 678 LEU cc_start: 0.8108 (mt) cc_final: 0.7766 (mm) REVERT: A 745 GLU cc_start: 0.7905 (mt-10) cc_final: 0.7561 (mt-10) REVERT: A 753 MET cc_start: 0.7584 (OUTLIER) cc_final: 0.6954 (mtp) REVERT: A 808 MET cc_start: 0.7828 (tpt) cc_final: 0.7131 (tpt) REVERT: A 851 GLU cc_start: 0.7886 (tp30) cc_final: 0.7295 (tp30) REVERT: A 860 ILE cc_start: 0.8839 (pt) cc_final: 0.8616 (pt) REVERT: A 877 GLU cc_start: 0.7495 (tt0) cc_final: 0.7257 (tt0) REVERT: A 1040 ASP cc_start: 0.8112 (m-30) cc_final: 0.7771 (m-30) REVERT: A 1057 GLN cc_start: 0.8557 (OUTLIER) cc_final: 0.7382 (mt0) REVERT: A 1073 SER cc_start: 0.8716 (t) cc_final: 0.8434 (m) REVERT: A 1117 LYS cc_start: 0.8058 (mmtt) cc_final: 0.7795 (mmtt) REVERT: A 1123 ARG cc_start: 0.7697 (ttp-110) cc_final: 0.7350 (ttp-110) REVERT: A 1125 LYS cc_start: 0.6581 (mttt) cc_final: 0.6276 (mttt) REVERT: A 1200 ARG cc_start: 0.8499 (mtm-85) cc_final: 0.7971 (ttm110) REVERT: A 1203 ILE cc_start: 0.7500 (OUTLIER) cc_final: 0.7277 (mp) REVERT: A 1217 LYS cc_start: 0.8255 (OUTLIER) cc_final: 0.7989 (ttmm) REVERT: A 1254 GLU cc_start: 0.7747 (pt0) cc_final: 0.7502 (pt0) REVERT: A 1305 MET cc_start: 0.8688 (mtt) cc_final: 0.8478 (mtp) REVERT: A 1379 LYS cc_start: 0.8239 (mtmt) cc_final: 0.7896 (mtpt) REVERT: A 1515 SER cc_start: 0.8167 (m) cc_final: 0.7912 (t) REVERT: A 1740 ASN cc_start: 0.7639 (t0) cc_final: 0.6919 (t0) REVERT: A 1808 LYS cc_start: 0.8387 (mmtp) cc_final: 0.8160 (mmmt) REVERT: A 1818 GLU cc_start: 0.7874 (mt-10) cc_final: 0.7633 (mt-10) REVERT: A 1837 LYS cc_start: 0.8375 (tttt) cc_final: 0.8125 (tppp) REVERT: A 2039 GLU cc_start: 0.7000 (OUTLIER) cc_final: 0.6795 (mp0) REVERT: A 2044 SER cc_start: 0.8442 (t) cc_final: 0.8110 (p) REVERT: A 2045 PHE cc_start: 0.8370 (m-80) cc_final: 0.8002 (m-80) REVERT: A 2291 VAL cc_start: 0.7915 (t) cc_final: 0.7549 (m) REVERT: A 2308 SER cc_start: 0.8600 (p) cc_final: 0.8369 (m) REVERT: A 2470 HIS cc_start: 0.7525 (OUTLIER) cc_final: 0.7145 (t70) REVERT: A 2515 SER cc_start: 0.8571 (t) cc_final: 0.8084 (p) REVERT: A 2543 LYS cc_start: 0.8150 (tttt) cc_final: 0.7846 (tttt) REVERT: A 2581 MET cc_start: 0.7593 (tmm) cc_final: 0.6690 (tmm) REVERT: A 2633 PHE cc_start: 0.8249 (p90) cc_final: 0.7374 (p90) REVERT: A 2639 GLN cc_start: 0.7287 (tp40) cc_final: 0.6679 (tp40) REVERT: A 2764 SER cc_start: 0.8519 (p) cc_final: 0.8243 (t) REVERT: A 2810 LYS cc_start: 0.8003 (mtmt) cc_final: 0.7588 (mtmt) REVERT: A 3047 LYS cc_start: 0.8421 (tttt) cc_final: 0.8089 (tttt) REVERT: A 3091 LYS cc_start: 0.8252 (mttt) cc_final: 0.7991 (mttp) REVERT: A 3120 GLU cc_start: 0.8109 (tt0) cc_final: 0.7816 (tt0) REVERT: A 3140 GLN cc_start: 0.8396 (mm-40) cc_final: 0.7948 (mm-40) REVERT: A 3160 GLU cc_start: 0.7422 (tm-30) cc_final: 0.6904 (tm-30) REVERT: A 3175 SER cc_start: 0.8436 (t) cc_final: 0.8224 (t) REVERT: A 3199 LYS cc_start: 0.8611 (ptpt) cc_final: 0.8264 (ptpt) REVERT: A 3203 MET cc_start: 0.8553 (ttm) cc_final: 0.8344 (mtp) REVERT: A 3224 ARG cc_start: 0.7214 (mtp85) cc_final: 0.6886 (mtp85) REVERT: A 3390 GLU cc_start: 0.7801 (tt0) cc_final: 0.7501 (pt0) REVERT: A 3397 MET cc_start: 0.7768 (mmm) cc_final: 0.7441 (mmm) REVERT: A 3451 LYS cc_start: 0.8460 (mttt) cc_final: 0.8151 (mttt) REVERT: A 3461 LYS cc_start: 0.8741 (mttt) cc_final: 0.8480 (mmtt) REVERT: A 3476 SER cc_start: 0.7587 (m) cc_final: 0.7236 (p) REVERT: A 3539 LYS cc_start: 0.7729 (mmmm) cc_final: 0.7510 (mmmm) REVERT: A 3702 GLU cc_start: 0.7066 (tp30) cc_final: 0.6247 (tp30) REVERT: A 3852 LYS cc_start: 0.8589 (tttt) cc_final: 0.8113 (tttt) REVERT: A 3862 LYS cc_start: 0.7990 (tttt) cc_final: 0.7683 (mttt) REVERT: A 3873 LYS cc_start: 0.7545 (mttt) cc_final: 0.7248 (mttt) outliers start: 61 outliers final: 47 residues processed: 582 average time/residue: 0.2099 time to fit residues: 182.8605 Evaluate side-chains 588 residues out of total 2920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 534 time to evaluate : 1.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 510 ASN Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 557 SER Chi-restraints excluded: chain A residue 599 LYS Chi-restraints excluded: chain A residue 753 MET Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 876 THR Chi-restraints excluded: chain A residue 900 THR Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain A residue 954 LEU Chi-restraints excluded: chain A residue 1026 SER Chi-restraints excluded: chain A residue 1057 GLN Chi-restraints excluded: chain A residue 1193 LYS Chi-restraints excluded: chain A residue 1203 ILE Chi-restraints excluded: chain A residue 1217 LYS Chi-restraints excluded: chain A residue 1285 LYS Chi-restraints excluded: chain A residue 1420 ILE Chi-restraints excluded: chain A residue 1435 VAL Chi-restraints excluded: chain A residue 1475 SER Chi-restraints excluded: chain A residue 1621 MET Chi-restraints excluded: chain A residue 1753 SER Chi-restraints excluded: chain A residue 1812 SER Chi-restraints excluded: chain A residue 2039 GLU Chi-restraints excluded: chain A residue 2206 MET Chi-restraints excluded: chain A residue 2260 LEU Chi-restraints excluded: chain A residue 2441 LEU Chi-restraints excluded: chain A residue 2449 THR Chi-restraints excluded: chain A residue 2470 HIS Chi-restraints excluded: chain A residue 2477 HIS Chi-restraints excluded: chain A residue 2507 THR Chi-restraints excluded: chain A residue 2526 THR Chi-restraints excluded: chain A residue 2675 VAL Chi-restraints excluded: chain A residue 2703 SER Chi-restraints excluded: chain A residue 2769 THR Chi-restraints excluded: chain A residue 2933 VAL Chi-restraints excluded: chain A residue 3014 VAL Chi-restraints excluded: chain A residue 3116 SER Chi-restraints excluded: chain A residue 3118 ILE Chi-restraints excluded: chain A residue 3148 LEU Chi-restraints excluded: chain A residue 3228 THR Chi-restraints excluded: chain A residue 3243 LEU Chi-restraints excluded: chain A residue 3247 SER Chi-restraints excluded: chain A residue 3261 SER Chi-restraints excluded: chain A residue 3307 SER Chi-restraints excluded: chain A residue 3338 LEU Chi-restraints excluded: chain A residue 3459 ILE Chi-restraints excluded: chain A residue 3466 VAL Chi-restraints excluded: chain A residue 3502 GLU Chi-restraints excluded: chain A residue 3563 MET Chi-restraints excluded: chain A residue 3592 GLU Chi-restraints excluded: chain A residue 3851 LEU Chi-restraints excluded: chain A residue 3867 CYS Chi-restraints excluded: chain A residue 3885 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 86 optimal weight: 0.9980 chunk 143 optimal weight: 6.9990 chunk 191 optimal weight: 0.8980 chunk 76 optimal weight: 0.0770 chunk 53 optimal weight: 0.9980 chunk 222 optimal weight: 7.9990 chunk 250 optimal weight: 0.8980 chunk 87 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 chunk 54 optimal weight: 0.6980 chunk 159 optimal weight: 9.9990 overall best weight: 0.7138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2470 HIS A2692 GLN A2758 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.158076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.133197 restraints weight = 36129.622| |-----------------------------------------------------------------------------| r_work (start): 0.3659 rms_B_bonded: 1.93 r_work: 0.3545 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3398 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.3023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 26962 Z= 0.127 Angle : 0.529 13.418 36577 Z= 0.270 Chirality : 0.039 0.201 4265 Planarity : 0.004 0.052 4451 Dihedral : 10.005 179.580 4077 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.86 % Favored : 96.11 % Rotamer: Outliers : 1.92 % Allowed : 15.27 % Favored : 82.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.16), residues: 3138 helix: 1.44 (0.12), residues: 1812 sheet: -0.12 (0.35), residues: 238 loop : -0.65 (0.20), residues: 1088 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A2969 TYR 0.018 0.001 TYR A 653 PHE 0.033 0.001 PHE A3553 TRP 0.014 0.001 TRP A2542 HIS 0.005 0.001 HIS A3045 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 (26958) covalent geometry : angle 0.52845 / 0.27 (36571) hydrogen bonds : bond 0.03322 / 2.23 ( 1397) hydrogen bonds : angle 3.98567 / 2.81 ( 3983) metal coordination : bond 0.00700 / 0.34 ( 4) metal coordination : angle 2.40886 / 1.08 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6276 Ramachandran restraints generated. 3138 Oldfield, 0 Emsley, 3138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6276 Ramachandran restraints generated. 3138 Oldfield, 0 Emsley, 3138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 591 residues out of total 2920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 535 time to evaluate : 1.016 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 477 SER cc_start: 0.8041 (m) cc_final: 0.7604 (p) REVERT: A 486 LYS cc_start: 0.8457 (mptt) cc_final: 0.8005 (mptt) REVERT: A 517 SER cc_start: 0.8180 (t) cc_final: 0.7928 (p) REVERT: A 599 LYS cc_start: 0.8153 (OUTLIER) cc_final: 0.7693 (mmtt) REVERT: A 649 TYR cc_start: 0.7609 (m-80) cc_final: 0.7247 (m-80) REVERT: A 668 THR cc_start: 0.8554 (m) cc_final: 0.8299 (m) REVERT: A 723 GLU cc_start: 0.7556 (tp30) cc_final: 0.7338 (tp30) REVERT: A 745 GLU cc_start: 0.7897 (mt-10) cc_final: 0.7540 (mt-10) REVERT: A 808 MET cc_start: 0.7796 (tpt) cc_final: 0.7099 (tpt) REVERT: A 851 GLU cc_start: 0.7891 (tp30) cc_final: 0.7298 (tp30) REVERT: A 860 ILE cc_start: 0.8833 (pt) cc_final: 0.8610 (pt) REVERT: A 877 GLU cc_start: 0.7526 (tt0) cc_final: 0.7297 (tt0) REVERT: A 941 MET cc_start: 0.8261 (mmm) cc_final: 0.8012 (mmt) REVERT: A 1040 ASP cc_start: 0.8061 (m-30) cc_final: 0.7735 (m-30) REVERT: A 1057 GLN cc_start: 0.8522 (OUTLIER) cc_final: 0.7404 (mt0) REVERT: A 1073 SER cc_start: 0.8735 (t) cc_final: 0.8443 (m) REVERT: A 1086 GLU cc_start: 0.7663 (mp0) cc_final: 0.7458 (mp0) REVERT: A 1117 LYS cc_start: 0.8050 (mmtt) cc_final: 0.7796 (mmtt) REVERT: A 1123 ARG cc_start: 0.7645 (ttp-110) cc_final: 0.7293 (ttp-110) REVERT: A 1200 ARG cc_start: 0.8507 (mtm-85) cc_final: 0.7970 (ttm110) REVERT: A 1203 ILE cc_start: 0.7494 (OUTLIER) cc_final: 0.7255 (mp) REVERT: A 1217 LYS cc_start: 0.8282 (OUTLIER) cc_final: 0.8029 (ttmm) REVERT: A 1254 GLU cc_start: 0.7717 (pt0) cc_final: 0.7471 (pt0) REVERT: A 1379 LYS cc_start: 0.8229 (mtmt) cc_final: 0.7888 (mtpt) REVERT: A 1515 SER cc_start: 0.8136 (m) cc_final: 0.7882 (t) REVERT: A 1620 GLU cc_start: 0.8106 (pp20) cc_final: 0.7530 (pp20) REVERT: A 1740 ASN cc_start: 0.7655 (t0) cc_final: 0.6926 (t0) REVERT: A 1758 ASN cc_start: 0.7890 (m-40) cc_final: 0.7643 (m110) REVERT: A 1802 LYS cc_start: 0.8514 (ttmt) cc_final: 0.8124 (ttmt) REVERT: A 1808 LYS cc_start: 0.8374 (mmtp) cc_final: 0.8162 (mmmt) REVERT: A 1818 GLU cc_start: 0.7932 (mt-10) cc_final: 0.7700 (mt-10) REVERT: A 1837 LYS cc_start: 0.8389 (tttt) cc_final: 0.8154 (tppp) REVERT: A 2045 PHE cc_start: 0.8314 (m-80) cc_final: 0.7807 (m-80) REVERT: A 2291 VAL cc_start: 0.7906 (t) cc_final: 0.7560 (m) REVERT: A 2308 SER cc_start: 0.8574 (p) cc_final: 0.8346 (m) REVERT: A 2470 HIS cc_start: 0.7387 (OUTLIER) cc_final: 0.6981 (t70) REVERT: A 2515 SER cc_start: 0.8546 (t) cc_final: 0.8068 (p) REVERT: A 2543 LYS cc_start: 0.8177 (tttt) cc_final: 0.7879 (tttt) REVERT: A 2581 MET cc_start: 0.7577 (tmm) cc_final: 0.6652 (tmm) REVERT: A 2633 PHE cc_start: 0.8183 (p90) cc_final: 0.7325 (p90) REVERT: A 2639 GLN cc_start: 0.7293 (tp40) cc_final: 0.6666 (tp40) REVERT: A 2764 SER cc_start: 0.8491 (p) cc_final: 0.8227 (t) REVERT: A 2801 ARG cc_start: 0.8018 (mtp85) cc_final: 0.7342 (ttt90) REVERT: A 2810 LYS cc_start: 0.8005 (mtmt) cc_final: 0.7584 (mtmt) REVERT: A 2929 THR cc_start: 0.8119 (m) cc_final: 0.7727 (p) REVERT: A 3047 LYS cc_start: 0.8431 (tttt) cc_final: 0.8100 (tttt) REVERT: A 3091 LYS cc_start: 0.8261 (mttt) cc_final: 0.8003 (mttp) REVERT: A 3115 GLU cc_start: 0.7144 (pm20) cc_final: 0.6859 (pm20) REVERT: A 3140 GLN cc_start: 0.8383 (mm-40) cc_final: 0.7938 (mt0) REVERT: A 3160 GLU cc_start: 0.7441 (tm-30) cc_final: 0.6925 (tm-30) REVERT: A 3175 SER cc_start: 0.8469 (t) cc_final: 0.8260 (t) REVERT: A 3199 LYS cc_start: 0.8618 (ptpt) cc_final: 0.8281 (ptpt) REVERT: A 3224 ARG cc_start: 0.7211 (mtp85) cc_final: 0.6888 (mtp85) REVERT: A 3390 GLU cc_start: 0.7794 (tt0) cc_final: 0.7511 (pt0) REVERT: A 3391 ARG cc_start: 0.7974 (mtp85) cc_final: 0.7773 (mtp85) REVERT: A 3397 MET cc_start: 0.7724 (mmm) cc_final: 0.7406 (mmm) REVERT: A 3426 LYS cc_start: 0.7931 (tptt) cc_final: 0.7496 (tptt) REVERT: A 3461 LYS cc_start: 0.8733 (mttt) cc_final: 0.8475 (mmtt) REVERT: A 3472 PHE cc_start: 0.7978 (t80) cc_final: 0.7495 (t80) REVERT: A 3476 SER cc_start: 0.7629 (m) cc_final: 0.7261 (p) REVERT: A 3702 GLU cc_start: 0.7077 (tp30) cc_final: 0.6554 (tp30) REVERT: A 3852 LYS cc_start: 0.8578 (tttt) cc_final: 0.8100 (tttt) REVERT: A 3862 LYS cc_start: 0.7974 (tttt) cc_final: 0.7674 (mttt) outliers start: 56 outliers final: 46 residues processed: 569 average time/residue: 0.2097 time to fit residues: 179.6188 Evaluate side-chains 574 residues out of total 2920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 523 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 510 ASN Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 557 SER Chi-restraints excluded: chain A residue 599 LYS Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 876 THR Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain A residue 954 LEU Chi-restraints excluded: chain A residue 1026 SER Chi-restraints excluded: chain A residue 1057 GLN Chi-restraints excluded: chain A residue 1193 LYS Chi-restraints excluded: chain A residue 1203 ILE Chi-restraints excluded: chain A residue 1217 LYS Chi-restraints excluded: chain A residue 1285 LYS Chi-restraints excluded: chain A residue 1400 LEU Chi-restraints excluded: chain A residue 1420 ILE Chi-restraints excluded: chain A residue 1435 VAL Chi-restraints excluded: chain A residue 1475 SER Chi-restraints excluded: chain A residue 1753 SER Chi-restraints excluded: chain A residue 1812 SER Chi-restraints excluded: chain A residue 2206 MET Chi-restraints excluded: chain A residue 2260 LEU Chi-restraints excluded: chain A residue 2407 SER Chi-restraints excluded: chain A residue 2441 LEU Chi-restraints excluded: chain A residue 2449 THR Chi-restraints excluded: chain A residue 2470 HIS Chi-restraints excluded: chain A residue 2477 HIS Chi-restraints excluded: chain A residue 2507 THR Chi-restraints excluded: chain A residue 2526 THR Chi-restraints excluded: chain A residue 2675 VAL Chi-restraints excluded: chain A residue 2703 SER Chi-restraints excluded: chain A residue 2769 THR Chi-restraints excluded: chain A residue 2933 VAL Chi-restraints excluded: chain A residue 3014 VAL Chi-restraints excluded: chain A residue 3116 SER Chi-restraints excluded: chain A residue 3118 ILE Chi-restraints excluded: chain A residue 3228 THR Chi-restraints excluded: chain A residue 3237 VAL Chi-restraints excluded: chain A residue 3243 LEU Chi-restraints excluded: chain A residue 3247 SER Chi-restraints excluded: chain A residue 3261 SER Chi-restraints excluded: chain A residue 3459 ILE Chi-restraints excluded: chain A residue 3466 VAL Chi-restraints excluded: chain A residue 3502 GLU Chi-restraints excluded: chain A residue 3504 LEU Chi-restraints excluded: chain A residue 3563 MET Chi-restraints excluded: chain A residue 3592 GLU Chi-restraints excluded: chain A residue 3851 LEU Chi-restraints excluded: chain A residue 3867 CYS Chi-restraints excluded: chain A residue 3885 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 143 optimal weight: 6.9990 chunk 4 optimal weight: 0.0670 chunk 51 optimal weight: 0.5980 chunk 238 optimal weight: 0.4980 chunk 290 optimal weight: 7.9990 chunk 139 optimal weight: 6.9990 chunk 314 optimal weight: 5.9990 chunk 271 optimal weight: 4.9990 chunk 164 optimal weight: 1.9990 chunk 56 optimal weight: 0.6980 chunk 198 optimal weight: 0.6980 overall best weight: 0.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1077 ASN ** A2377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2692 GLN A2697 ASN A2758 GLN A3170 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.159228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.134373 restraints weight = 35965.173| |-----------------------------------------------------------------------------| r_work (start): 0.3675 rms_B_bonded: 1.93 r_work: 0.3561 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3414 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.3074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.165 26962 Z= 0.114 Angle : 0.529 15.825 36577 Z= 0.269 Chirality : 0.038 0.191 4265 Planarity : 0.004 0.055 4451 Dihedral : 9.960 179.018 4077 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.79 % Favored : 96.18 % Rotamer: Outliers : 1.71 % Allowed : 15.82 % Favored : 82.47 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.98 (0.16), residues: 3138 helix: 1.52 (0.12), residues: 1814 sheet: -0.15 (0.34), residues: 242 loop : -0.60 (0.20), residues: 1082 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A1805 TYR 0.017 0.001 TYR A 653 PHE 0.031 0.001 PHE A3553 TRP 0.014 0.001 TRP A2542 HIS 0.005 0.001 HIS A3045 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.11 (26958) covalent geometry : angle 0.52842 / 0.27 (36571) hydrogen bonds : bond 0.03173 / 2.12 ( 1397) hydrogen bonds : angle 3.93040 / 2.78 ( 3983) metal coordination : bond 0.00590 / 0.29 ( 4) metal coordination : angle 2.32162 / 1.00 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6276 Ramachandran restraints generated. 3138 Oldfield, 0 Emsley, 3138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6276 Ramachandran restraints generated. 3138 Oldfield, 0 Emsley, 3138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 577 residues out of total 2920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 527 time to evaluate : 0.913 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 477 SER cc_start: 0.8015 (m) cc_final: 0.7584 (p) REVERT: A 486 LYS cc_start: 0.8457 (mptt) cc_final: 0.7998 (mptt) REVERT: A 517 SER cc_start: 0.8133 (t) cc_final: 0.7906 (p) REVERT: A 599 LYS cc_start: 0.8195 (OUTLIER) cc_final: 0.7937 (tppt) REVERT: A 649 TYR cc_start: 0.7555 (m-80) cc_final: 0.7175 (m-80) REVERT: A 668 THR cc_start: 0.8547 (m) cc_final: 0.8287 (m) REVERT: A 723 GLU cc_start: 0.7578 (tp30) cc_final: 0.7314 (tp30) REVERT: A 808 MET cc_start: 0.7739 (tpt) cc_final: 0.7032 (tpt) REVERT: A 851 GLU cc_start: 0.7876 (tp30) cc_final: 0.7315 (tp30) REVERT: A 877 GLU cc_start: 0.7524 (tt0) cc_final: 0.7288 (tt0) REVERT: A 962 MET cc_start: 0.8130 (mtm) cc_final: 0.7927 (ttm) REVERT: A 1040 ASP cc_start: 0.8055 (m-30) cc_final: 0.7719 (m-30) REVERT: A 1057 GLN cc_start: 0.8526 (OUTLIER) cc_final: 0.7444 (mt0) REVERT: A 1073 SER cc_start: 0.8730 (t) cc_final: 0.8431 (m) REVERT: A 1117 LYS cc_start: 0.8035 (mmtt) cc_final: 0.7809 (mmtt) REVERT: A 1123 ARG cc_start: 0.7618 (ttp-110) cc_final: 0.7260 (ttp-110) REVERT: A 1200 ARG cc_start: 0.8484 (mtm-85) cc_final: 0.7941 (ttm110) REVERT: A 1203 ILE cc_start: 0.7463 (OUTLIER) cc_final: 0.7210 (mp) REVERT: A 1217 LYS cc_start: 0.8261 (OUTLIER) cc_final: 0.8005 (ttmm) REVERT: A 1254 GLU cc_start: 0.7724 (pt0) cc_final: 0.7481 (pt0) REVERT: A 1379 LYS cc_start: 0.8229 (mtmt) cc_final: 0.7893 (mtpt) REVERT: A 1515 SER cc_start: 0.8119 (m) cc_final: 0.7853 (t) REVERT: A 1620 GLU cc_start: 0.8055 (pp20) cc_final: 0.7499 (pp20) REVERT: A 1740 ASN cc_start: 0.7654 (t0) cc_final: 0.6923 (t0) REVERT: A 1764 LYS cc_start: 0.8479 (mtpt) cc_final: 0.8148 (mtmm) REVERT: A 1802 LYS cc_start: 0.8486 (ttmt) cc_final: 0.8219 (ttmt) REVERT: A 1808 LYS cc_start: 0.8355 (mmtp) cc_final: 0.8130 (mmmt) REVERT: A 1818 GLU cc_start: 0.7918 (mt-10) cc_final: 0.7672 (mt-10) REVERT: A 1837 LYS cc_start: 0.8380 (tttt) cc_final: 0.8162 (tppp) REVERT: A 2045 PHE cc_start: 0.8277 (m-80) cc_final: 0.7665 (m-80) REVERT: A 2291 VAL cc_start: 0.7871 (t) cc_final: 0.7542 (m) REVERT: A 2308 SER cc_start: 0.8543 (p) cc_final: 0.8255 (p) REVERT: A 2515 SER cc_start: 0.8549 (t) cc_final: 0.8051 (p) REVERT: A 2543 LYS cc_start: 0.8189 (tttt) cc_final: 0.7889 (tttt) REVERT: A 2581 MET cc_start: 0.7589 (tmm) cc_final: 0.6670 (tmm) REVERT: A 2593 PHE cc_start: 0.7845 (m-80) cc_final: 0.7472 (m-80) REVERT: A 2633 PHE cc_start: 0.8106 (p90) cc_final: 0.7274 (p90) REVERT: A 2639 GLN cc_start: 0.7272 (tp40) cc_final: 0.6642 (tp40) REVERT: A 2801 ARG cc_start: 0.7983 (mtp85) cc_final: 0.7501 (ttt90) REVERT: A 2810 LYS cc_start: 0.8018 (mtmt) cc_final: 0.7604 (mtmt) REVERT: A 2901 GLN cc_start: 0.7868 (mt0) cc_final: 0.7638 (mt0) REVERT: A 2929 THR cc_start: 0.8207 (m) cc_final: 0.7882 (p) REVERT: A 3047 LYS cc_start: 0.8435 (tttt) cc_final: 0.8104 (tttt) REVERT: A 3091 LYS cc_start: 0.8234 (mttt) cc_final: 0.8007 (mttm) REVERT: A 3140 GLN cc_start: 0.8377 (mm-40) cc_final: 0.7927 (mt0) REVERT: A 3160 GLU cc_start: 0.7442 (tm-30) cc_final: 0.6919 (tm-30) REVERT: A 3175 SER cc_start: 0.8461 (t) cc_final: 0.8246 (t) REVERT: A 3199 LYS cc_start: 0.8611 (ptpt) cc_final: 0.8300 (ptpt) REVERT: A 3224 ARG cc_start: 0.7216 (mtp85) cc_final: 0.7005 (mtp85) REVERT: A 3390 GLU cc_start: 0.7785 (tt0) cc_final: 0.7516 (pt0) REVERT: A 3397 MET cc_start: 0.7720 (mmm) cc_final: 0.7400 (mmm) REVERT: A 3426 LYS cc_start: 0.7879 (tptt) cc_final: 0.7473 (tptt) REVERT: A 3461 LYS cc_start: 0.8704 (mttt) cc_final: 0.8440 (mmtt) REVERT: A 3472 PHE cc_start: 0.7937 (t80) cc_final: 0.7462 (t80) REVERT: A 3629 SER cc_start: 0.7581 (p) cc_final: 0.7329 (m) REVERT: A 3702 GLU cc_start: 0.7049 (tp30) cc_final: 0.6554 (tp30) REVERT: A 3852 LYS cc_start: 0.8572 (tttt) cc_final: 0.8117 (tttt) REVERT: A 3862 LYS cc_start: 0.7956 (tttt) cc_final: 0.7656 (mttt) REVERT: A 3873 LYS cc_start: 0.7515 (mttt) cc_final: 0.7180 (mttt) outliers start: 50 outliers final: 45 residues processed: 555 average time/residue: 0.1932 time to fit residues: 161.9109 Evaluate side-chains 565 residues out of total 2920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 516 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 510 ASN Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 557 SER Chi-restraints excluded: chain A residue 599 LYS Chi-restraints excluded: chain A residue 876 THR Chi-restraints excluded: chain A residue 900 THR Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain A residue 954 LEU Chi-restraints excluded: chain A residue 1026 SER Chi-restraints excluded: chain A residue 1057 GLN Chi-restraints excluded: chain A residue 1193 LYS Chi-restraints excluded: chain A residue 1203 ILE Chi-restraints excluded: chain A residue 1217 LYS Chi-restraints excluded: chain A residue 1285 LYS Chi-restraints excluded: chain A residue 1400 LEU Chi-restraints excluded: chain A residue 1420 ILE Chi-restraints excluded: chain A residue 1435 VAL Chi-restraints excluded: chain A residue 1475 SER Chi-restraints excluded: chain A residue 1753 SER Chi-restraints excluded: chain A residue 1812 SER Chi-restraints excluded: chain A residue 2206 MET Chi-restraints excluded: chain A residue 2260 LEU Chi-restraints excluded: chain A residue 2407 SER Chi-restraints excluded: chain A residue 2439 ASP Chi-restraints excluded: chain A residue 2441 LEU Chi-restraints excluded: chain A residue 2449 THR Chi-restraints excluded: chain A residue 2477 HIS Chi-restraints excluded: chain A residue 2507 THR Chi-restraints excluded: chain A residue 2526 THR Chi-restraints excluded: chain A residue 2675 VAL Chi-restraints excluded: chain A residue 2703 SER Chi-restraints excluded: chain A residue 2769 THR Chi-restraints excluded: chain A residue 2933 VAL Chi-restraints excluded: chain A residue 3014 VAL Chi-restraints excluded: chain A residue 3116 SER Chi-restraints excluded: chain A residue 3118 ILE Chi-restraints excluded: chain A residue 3228 THR Chi-restraints excluded: chain A residue 3237 VAL Chi-restraints excluded: chain A residue 3247 SER Chi-restraints excluded: chain A residue 3261 SER Chi-restraints excluded: chain A residue 3459 ILE Chi-restraints excluded: chain A residue 3466 VAL Chi-restraints excluded: chain A residue 3502 GLU Chi-restraints excluded: chain A residue 3504 LEU Chi-restraints excluded: chain A residue 3563 MET Chi-restraints excluded: chain A residue 3592 GLU Chi-restraints excluded: chain A residue 3867 CYS Chi-restraints excluded: chain A residue 3885 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 275 optimal weight: 0.7980 chunk 279 optimal weight: 0.9980 chunk 292 optimal weight: 0.0470 chunk 183 optimal weight: 0.7980 chunk 103 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 316 optimal weight: 1.9990 chunk 304 optimal weight: 0.8980 chunk 177 optimal weight: 1.9990 chunk 37 optimal weight: 0.0970 chunk 151 optimal weight: 5.9990 overall best weight: 0.5276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 543 ASN A1077 ASN ** A2377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2470 HIS A2692 GLN A2697 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.159466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.134674 restraints weight = 35938.498| |-----------------------------------------------------------------------------| r_work (start): 0.3680 rms_B_bonded: 1.92 r_work: 0.3566 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3419 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.3127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.161 26962 Z= 0.113 Angle : 0.519 15.663 36577 Z= 0.264 Chirality : 0.038 0.183 4265 Planarity : 0.004 0.056 4451 Dihedral : 9.916 178.756 4077 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.76 % Favored : 96.21 % Rotamer: Outliers : 1.78 % Allowed : 15.62 % Favored : 82.60 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.04 (0.16), residues: 3138 helix: 1.62 (0.12), residues: 1810 sheet: -0.19 (0.34), residues: 240 loop : -0.63 (0.20), residues: 1088 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A1805 TYR 0.018 0.001 TYR A 653 PHE 0.029 0.001 PHE A3553 TRP 0.014 0.001 TRP A2542 HIS 0.005 0.001 HIS A3045 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.11 (26958) covalent geometry : angle 0.51820 / 0.26 (36571) hydrogen bonds : bond 0.03116 / 2.09 ( 1397) hydrogen bonds : angle 3.88516 / 2.75 ( 3983) metal coordination : bond 0.00603 / 0.30 ( 4) metal coordination : angle 2.28650 / 0.97 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8279.74 seconds wall clock time: 142 minutes 7.94 seconds (8527.94 seconds total)