Starting phenix.real_space_refine on Tue Aug 26 12:14:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jw1_61848/08_2025/9jw1_61848_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jw1_61848/08_2025/9jw1_61848.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.46 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9jw1_61848/08_2025/9jw1_61848_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jw1_61848/08_2025/9jw1_61848_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9jw1_61848/08_2025/9jw1_61848.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jw1_61848/08_2025/9jw1_61848.map" } resolution = 3.46 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.043 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: 6 Type Number sf(0) Gaussians P 3 5.49 5 Mg 1 5.21 5 S 218 5.16 5 C 22904 2.51 5 N 6208 2.21 5 O 6603 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 35937 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 35905 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4471, 35905 Classifications: {'peptide': 4471} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 183, 'TRANS': 4287} Chain breaks: 15 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 7.70, per 1000 atoms: 0.21 Number of scatterers: 35937 At special positions: 0 Unit cell: (132.93, 159.305, 234.21, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 218 16.00 P 3 15.00 Mg 1 11.99 O 6603 8.00 N 6208 7.00 C 22904 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: 2.52 Conformation dependent library (CDL) restraints added in 1.6 seconds Enol-peptide restraints added in 953.7 nanoseconds 8878 Ramachandran restraints generated. 4439 Oldfield, 0 Emsley, 4439 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8566 Finding SS restraints... Secondary structure from input PDB file: 211 helices and 18 sheets defined 60.0% alpha, 4.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.91 Creating SS restraints... Processing helix chain 'A' and resid 523 through 541 Processing helix chain 'A' and resid 549 through 564 removed outlier: 3.542A pdb=" N GLN A 558 " --> pdb=" O THR A 554 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU A 563 " --> pdb=" O PHE A 559 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N GLN A 564 " --> pdb=" O CYS A 560 " (cutoff:3.500A) Processing helix chain 'A' and resid 583 through 599 Processing helix chain 'A' and resid 618 through 633 removed outlier: 3.566A pdb=" N THR A 622 " --> pdb=" O SER A 618 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N LEU A 624 " --> pdb=" O LEU A 620 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ILE A 633 " --> pdb=" O VAL A 629 " (cutoff:3.500A) Processing helix chain 'A' and resid 640 through 649 removed outlier: 4.217A pdb=" N LEU A 644 " --> pdb=" O SER A 640 " (cutoff:3.500A) Processing helix chain 'A' and resid 654 through 663 removed outlier: 4.088A pdb=" N LEU A 662 " --> pdb=" O PHE A 658 " (cutoff:3.500A) Processing helix chain 'A' and resid 671 through 686 removed outlier: 3.829A pdb=" N TYR A 675 " --> pdb=" O SER A 671 " (cutoff:3.500A) Processing helix chain 'A' and resid 689 through 693 Processing helix chain 'A' and resid 694 through 702 Processing helix chain 'A' and resid 715 through 720 Processing helix chain 'A' and resid 737 through 746 removed outlier: 3.791A pdb=" N GLU A 746 " --> pdb=" O GLN A 742 " (cutoff:3.500A) Processing helix chain 'A' and resid 747 through 752 Processing helix chain 'A' and resid 754 through 764 removed outlier: 4.184A pdb=" N PHE A 758 " --> pdb=" O ASP A 754 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N ARG A 759 " --> pdb=" O GLU A 755 " (cutoff:3.500A) Processing helix chain 'A' and resid 769 through 777 removed outlier: 3.708A pdb=" N TYR A 773 " --> pdb=" O HIS A 769 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N MET A 774 " --> pdb=" O LEU A 770 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N GLU A 775 " --> pdb=" O VAL A 771 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N PHE A 777 " --> pdb=" O TYR A 773 " (cutoff:3.500A) Processing helix chain 'A' and resid 777 through 784 Processing helix chain 'A' and resid 786 through 798 removed outlier: 4.493A pdb=" N ASP A 790 " --> pdb=" O ALA A 786 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LEU A 792 " --> pdb=" O ILE A 788 " (cutoff:3.500A) Processing helix chain 'A' and resid 798 through 807 Processing helix chain 'A' and resid 810 through 830 removed outlier: 3.715A pdb=" N VAL A 817 " --> pdb=" O ASP A 813 " (cutoff:3.500A) Processing helix chain 'A' and resid 843 through 856 removed outlier: 3.569A pdb=" N VAL A 847 " --> pdb=" O SER A 843 " (cutoff:3.500A) Processing helix chain 'A' and resid 865 through 887 removed outlier: 3.549A pdb=" N ALA A 869 " --> pdb=" O TYR A 865 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LEU A 884 " --> pdb=" O ARG A 880 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N VAL A 885 " --> pdb=" O LEU A 881 " (cutoff:3.500A) Processing helix chain 'A' and resid 895 through 918 Processing helix chain 'A' and resid 934 through 944 Processing helix chain 'A' and resid 952 through 966 removed outlier: 3.628A pdb=" N LEU A 957 " --> pdb=" O TRP A 953 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N MET A 961 " --> pdb=" O LEU A 957 " (cutoff:3.500A) Processing helix chain 'A' and resid 969 through 978 Processing helix chain 'A' and resid 989 through 1008 Processing helix chain 'A' and resid 1021 through 1037 removed outlier: 3.531A pdb=" N PHE A1025 " --> pdb=" O ASP A1021 " (cutoff:3.500A) Processing helix chain 'A' and resid 1043 through 1054 removed outlier: 3.625A pdb=" N ILE A1047 " --> pdb=" O ASN A1043 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU A1054 " --> pdb=" O HIS A1050 " (cutoff:3.500A) Processing helix chain 'A' and resid 1054 through 1067 removed outlier: 4.157A pdb=" N LYS A1058 " --> pdb=" O LEU A1054 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASP A1067 " --> pdb=" O LEU A1063 " (cutoff:3.500A) Processing helix chain 'A' and resid 1068 through 1074 Processing helix chain 'A' and resid 1075 through 1099 removed outlier: 3.514A pdb=" N LEU A1081 " --> pdb=" O ASP A1077 " (cutoff:3.500A) Processing helix chain 'A' and resid 1102 through 1112 Processing helix chain 'A' and resid 1112 through 1127 Processing helix chain 'A' and resid 1135 through 1166 Processing helix chain 'A' and resid 1176 through 1184 Processing helix chain 'A' and resid 1190 through 1195 removed outlier: 3.642A pdb=" N THR A1194 " --> pdb=" O ARG A1190 " (cutoff:3.500A) Processing helix chain 'A' and resid 1214 through 1226 removed outlier: 3.517A pdb=" N GLN A1218 " --> pdb=" O SER A1214 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N GLU A1219 " --> pdb=" O SER A1215 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N MET A1220 " --> pdb=" O GLN A1216 " (cutoff:3.500A) Processing helix chain 'A' and resid 1230 through 1245 Proline residue: A1243 - end of helix Processing helix chain 'A' and resid 1270 through 1277 removed outlier: 3.873A pdb=" N TYR A1277 " --> pdb=" O GLU A1273 " (cutoff:3.500A) Processing helix chain 'A' and resid 1280 through 1296 Processing helix chain 'A' and resid 1301 through 1307 Processing helix chain 'A' and resid 1313 through 1326 removed outlier: 3.730A pdb=" N LEU A1317 " --> pdb=" O LYS A1313 " (cutoff:3.500A) Processing helix chain 'A' and resid 1335 through 1367 removed outlier: 4.060A pdb=" N GLU A1341 " --> pdb=" O LYS A1337 " (cutoff:3.500A) Processing helix chain 'A' and resid 1374 through 1384 removed outlier: 4.098A pdb=" N LEU A1378 " --> pdb=" O VAL A1374 " (cutoff:3.500A) Processing helix chain 'A' and resid 1409 through 1411 No H-bonds generated for 'chain 'A' and resid 1409 through 1411' Processing helix chain 'A' and resid 1412 through 1421 removed outlier: 3.826A pdb=" N LEU A1421 " --> pdb=" O GLY A1417 " (cutoff:3.500A) Processing helix chain 'A' and resid 1425 through 1434 Processing helix chain 'A' and resid 1438 through 1453 removed outlier: 4.233A pdb=" N LYS A1442 " --> pdb=" O ILE A1438 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N VAL A1443 " --> pdb=" O ASN A1439 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ILE A1450 " --> pdb=" O ASP A1446 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N SER A1451 " --> pdb=" O LEU A1447 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N GLY A1453 " --> pdb=" O SER A1449 " (cutoff:3.500A) Processing helix chain 'A' and resid 1460 through 1471 removed outlier: 3.691A pdb=" N HIS A1466 " --> pdb=" O VAL A1462 " (cutoff:3.500A) Processing helix chain 'A' and resid 1472 through 1477 removed outlier: 3.716A pdb=" N PHE A1477 " --> pdb=" O ALA A1473 " (cutoff:3.500A) Processing helix chain 'A' and resid 1484 through 1493 removed outlier: 3.655A pdb=" N LYS A1493 " --> pdb=" O MET A1489 " (cutoff:3.500A) Processing helix chain 'A' and resid 1504 through 1515 removed outlier: 3.583A pdb=" N ARG A1514 " --> pdb=" O CYS A1510 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ASN A1515 " --> pdb=" O ASP A1511 " (cutoff:3.500A) Processing helix chain 'A' and resid 1515 through 1520 removed outlier: 3.852A pdb=" N LYS A1520 " --> pdb=" O LEU A1516 " (cutoff:3.500A) Processing helix chain 'A' and resid 1535 through 1543 Processing helix chain 'A' and resid 1558 through 1562 Processing helix chain 'A' and resid 1581 through 1595 removed outlier: 3.556A pdb=" N LEU A1588 " --> pdb=" O GLU A1584 " (cutoff:3.500A) Processing helix chain 'A' and resid 1604 through 1630 removed outlier: 3.765A pdb=" N PHE A1609 " --> pdb=" O GLU A1605 " (cutoff:3.500A) Processing helix chain 'A' and resid 1632 through 1636 removed outlier: 4.452A pdb=" N THR A1636 " --> pdb=" O LEU A1633 " (cutoff:3.500A) Processing helix chain 'A' and resid 1668 through 1698 Processing helix chain 'A' and resid 1705 through 1716 removed outlier: 3.766A pdb=" N VAL A1710 " --> pdb=" O ALA A1706 " (cutoff:3.500A) Processing helix chain 'A' and resid 1722 through 1730 Processing helix chain 'A' and resid 1737 through 1745 Processing helix chain 'A' and resid 1750 through 1771 removed outlier: 3.851A pdb=" N ARG A1754 " --> pdb=" O SER A1750 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N TYR A1755 " --> pdb=" O GLU A1751 " (cutoff:3.500A) Proline residue: A1765 - end of helix Processing helix chain 'A' and resid 1773 through 1789 Processing helix chain 'A' and resid 1790 through 1792 No H-bonds generated for 'chain 'A' and resid 1790 through 1792' Processing helix chain 'A' and resid 1798 through 1812 removed outlier: 3.628A pdb=" N MET A1812 " --> pdb=" O HIS A1808 " (cutoff:3.500A) Processing helix chain 'A' and resid 1836 through 1840 Processing helix chain 'A' and resid 1841 through 1849 removed outlier: 3.627A pdb=" N LEU A1845 " --> pdb=" O LEU A1841 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ALA A1846 " --> pdb=" O PRO A1842 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N VAL A1847 " --> pdb=" O ALA A1843 " (cutoff:3.500A) Processing helix chain 'A' and resid 1870 through 1882 removed outlier: 3.912A pdb=" N VAL A1874 " --> pdb=" O THR A1870 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N LEU A1877 " --> pdb=" O GLU A1873 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ARG A1880 " --> pdb=" O LEU A1876 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU A1882 " --> pdb=" O LEU A1878 " (cutoff:3.500A) Processing helix chain 'A' and resid 1897 through 1900 Processing helix chain 'A' and resid 1901 through 1917 Processing helix chain 'A' and resid 1933 through 1935 No H-bonds generated for 'chain 'A' and resid 1933 through 1935' Processing helix chain 'A' and resid 1937 through 1944 Processing helix chain 'A' and resid 1945 through 1947 No H-bonds generated for 'chain 'A' and resid 1945 through 1947' Processing helix chain 'A' and resid 1955 through 1968 Processing helix chain 'A' and resid 1975 through 1979 removed outlier: 3.808A pdb=" N ALA A1978 " --> pdb=" O SER A1975 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N VAL A1979 " --> pdb=" O ALA A1976 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1975 through 1979' Processing helix chain 'A' and resid 1980 through 1984 removed outlier: 3.878A pdb=" N ARG A1983 " --> pdb=" O PHE A1980 " (cutoff:3.500A) Processing helix chain 'A' and resid 2003 through 2014 removed outlier: 3.972A pdb=" N MET A2011 " --> pdb=" O ASP A2007 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLN A2012 " --> pdb=" O LYS A2008 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ASN A2014 " --> pdb=" O LYS A2010 " (cutoff:3.500A) Processing helix chain 'A' and resid 2031 through 2040 removed outlier: 3.870A pdb=" N VAL A2035 " --> pdb=" O ASP A2031 " (cutoff:3.500A) Processing helix chain 'A' and resid 2041 through 2043 No H-bonds generated for 'chain 'A' and resid 2041 through 2043' Processing helix chain 'A' and resid 2044 through 2049 removed outlier: 4.331A pdb=" N LYS A2049 " --> pdb=" O GLN A2046 " (cutoff:3.500A) Processing helix chain 'A' and resid 2065 through 2074 Processing helix chain 'A' and resid 2136 through 2142 Processing helix chain 'A' and resid 2165 through 2173 removed outlier: 3.981A pdb=" N GLN A2169 " --> pdb=" O GLN A2165 " (cutoff:3.500A) Processing helix chain 'A' and resid 2196 through 2204 removed outlier: 3.731A pdb=" N LEU A2202 " --> pdb=" O LEU A2198 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N HIS A2204 " --> pdb=" O HIS A2200 " (cutoff:3.500A) Processing helix chain 'A' and resid 2211 through 2230 removed outlier: 5.521A pdb=" N ASN A2217 " --> pdb=" O SER A2213 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N PHE A2218 " --> pdb=" O GLU A2214 " (cutoff:3.500A) Processing helix chain 'A' and resid 2246 through 2264 removed outlier: 4.043A pdb=" N ARG A2260 " --> pdb=" O ILE A2256 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N ASP A2261 " --> pdb=" O PHE A2257 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N PHE A2262 " --> pdb=" O MET A2258 " (cutoff:3.500A) Processing helix chain 'A' and resid 2348 through 2357 Processing helix chain 'A' and resid 2369 through 2382 Processing helix chain 'A' and resid 2396 through 2413 removed outlier: 3.716A pdb=" N ILE A2403 " --> pdb=" O ASN A2399 " (cutoff:3.500A) Processing helix chain 'A' and resid 2425 through 2439 Processing helix chain 'A' and resid 2456 through 2477 removed outlier: 3.561A pdb=" N ILE A2460 " --> pdb=" O THR A2456 " (cutoff:3.500A) Processing helix chain 'A' and resid 2495 through 2503 Processing helix chain 'A' and resid 2531 through 2540 Processing helix chain 'A' and resid 2562 through 2564 No H-bonds generated for 'chain 'A' and resid 2562 through 2564' Processing helix chain 'A' and resid 2586 through 2600 Processing helix chain 'A' and resid 2601 through 2606 Processing helix chain 'A' and resid 2608 through 2629 Processing helix chain 'A' and resid 2637 through 2639 No H-bonds generated for 'chain 'A' and resid 2637 through 2639' Processing helix chain 'A' and resid 2640 through 2669 removed outlier: 3.863A pdb=" N LYS A2646 " --> pdb=" O GLU A2642 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N ALA A2656 " --> pdb=" O HIS A2652 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N MET A2657 " --> pdb=" O GLU A2653 " (cutoff:3.500A) Processing helix chain 'A' and resid 2679 through 2693 removed outlier: 3.655A pdb=" N LEU A2687 " --> pdb=" O TRP A2683 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLY A2690 " --> pdb=" O MET A2686 " (cutoff:3.500A) Processing helix chain 'A' and resid 2699 through 2708 Processing helix chain 'A' and resid 2709 through 2711 No H-bonds generated for 'chain 'A' and resid 2709 through 2711' Processing helix chain 'A' and resid 2712 through 2716 removed outlier: 3.833A pdb=" N ASP A2716 " --> pdb=" O LYS A2713 " (cutoff:3.500A) Processing helix chain 'A' and resid 2717 through 2734 Processing helix chain 'A' and resid 2745 through 2761 Processing helix chain 'A' and resid 2774 through 2787 removed outlier: 4.155A pdb=" N GLN A2787 " --> pdb=" O ALA A2783 " (cutoff:3.500A) Processing helix chain 'A' and resid 2793 through 2798 removed outlier: 3.764A pdb=" N SER A2798 " --> pdb=" O ASP A2794 " (cutoff:3.500A) Processing helix chain 'A' and resid 2814 through 2830 removed outlier: 3.851A pdb=" N ILE A2818 " --> pdb=" O THR A2814 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N PHE A2828 " --> pdb=" O GLN A2824 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLN A2829 " --> pdb=" O CYS A2825 " (cutoff:3.500A) Processing helix chain 'A' and resid 2846 through 2850 removed outlier: 3.918A pdb=" N ALA A2849 " --> pdb=" O VAL A2846 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLU A2850 " --> pdb=" O GLY A2847 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2846 through 2850' Processing helix chain 'A' and resid 2859 through 2867 removed outlier: 3.691A pdb=" N GLU A2865 " --> pdb=" O HIS A2861 " (cutoff:3.500A) Processing helix chain 'A' and resid 2907 through 2918 Processing helix chain 'A' and resid 2923 through 2928 Processing helix chain 'A' and resid 2934 through 2947 removed outlier: 3.541A pdb=" N ASP A2947 " --> pdb=" O CYS A2943 " (cutoff:3.500A) Processing helix chain 'A' and resid 2953 through 2968 removed outlier: 3.808A pdb=" N TYR A2957 " --> pdb=" O LEU A2953 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LEU A2959 " --> pdb=" O ASP A2955 " (cutoff:3.500A) Processing helix chain 'A' and resid 2978 through 2985 removed outlier: 3.611A pdb=" N ALA A2982 " --> pdb=" O ASP A2978 " (cutoff:3.500A) Processing helix chain 'A' and resid 2994 through 3003 removed outlier: 3.787A pdb=" N ASN A3002 " --> pdb=" O ILE A2998 " (cutoff:3.500A) Processing helix chain 'A' and resid 3015 through 3023 removed outlier: 3.988A pdb=" N LYS A3019 " --> pdb=" O MET A3015 " (cutoff:3.500A) Processing helix chain 'A' and resid 3050 through 3058 Processing helix chain 'A' and resid 3078 through 3097 removed outlier: 3.610A pdb=" N ARG A3085 " --> pdb=" O THR A3081 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ARG A3089 " --> pdb=" O ARG A3085 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N VAL A3090 " --> pdb=" O ASN A3086 " (cutoff:3.500A) Processing helix chain 'A' and resid 3154 through 3161 removed outlier: 3.713A pdb=" N PHE A3161 " --> pdb=" O VAL A3157 " (cutoff:3.500A) Processing helix chain 'A' and resid 3162 through 3169 Processing helix chain 'A' and resid 3181 through 3200 removed outlier: 4.082A pdb=" N ILE A3187 " --> pdb=" O TRP A3183 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N VAL A3188 " --> pdb=" O GLN A3184 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLU A3189 " --> pdb=" O LYS A3185 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLU A3196 " --> pdb=" O CYS A3192 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ASN A3200 " --> pdb=" O GLU A3196 " (cutoff:3.500A) Processing helix chain 'A' and resid 3213 through 3218 removed outlier: 3.630A pdb=" N VAL A3217 " --> pdb=" O SER A3213 " (cutoff:3.500A) Processing helix chain 'A' and resid 3224 through 3238 Processing helix chain 'A' and resid 3243 through 3259 removed outlier: 3.539A pdb=" N HIS A3247 " --> pdb=" O THR A3243 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLN A3248 " --> pdb=" O GLU A3244 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N SER A3251 " --> pdb=" O HIS A3247 " (cutoff:3.500A) Processing helix chain 'A' and resid 3260 through 3262 No H-bonds generated for 'chain 'A' and resid 3260 through 3262' Processing helix chain 'A' and resid 3263 through 3274 removed outlier: 3.594A pdb=" N VAL A3267 " --> pdb=" O THR A3263 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N VAL A3268 " --> pdb=" O PRO A3264 " (cutoff:3.500A) Processing helix chain 'A' and resid 3277 through 3290 removed outlier: 3.581A pdb=" N ARG A3290 " --> pdb=" O GLU A3286 " (cutoff:3.500A) Processing helix chain 'A' and resid 3295 through 3305 removed outlier: 3.520A pdb=" N HIS A3305 " --> pdb=" O GLN A3301 " (cutoff:3.500A) Processing helix chain 'A' and resid 3326 through 3338 removed outlier: 3.528A pdb=" N GLU A3336 " --> pdb=" O ILE A3332 " (cutoff:3.500A) Processing helix chain 'A' and resid 3354 through 3367 Processing helix chain 'A' and resid 3386 through 3405 removed outlier: 3.605A pdb=" N LEU A3390 " --> pdb=" O ARG A3386 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE A3399 " --> pdb=" O LYS A3395 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLU A3401 " --> pdb=" O SER A3397 " (cutoff:3.500A) Processing helix chain 'A' and resid 3454 through 3460 removed outlier: 3.885A pdb=" N HIS A3460 " --> pdb=" O ARG A3457 " (cutoff:3.500A) Processing helix chain 'A' and resid 3463 through 3468 removed outlier: 4.139A pdb=" N PHE A3467 " --> pdb=" O ILE A3463 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA A3468 " --> pdb=" O SER A3464 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 3463 through 3468' Processing helix chain 'A' and resid 3531 through 3538 Processing helix chain 'A' and resid 3539 through 3544 Processing helix chain 'A' and resid 3555 through 3568 removed outlier: 4.287A pdb=" N ARG A3559 " --> pdb=" O THR A3555 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL A3561 " --> pdb=" O ASN A3557 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N VAL A3562 " --> pdb=" O MET A3558 " (cutoff:3.500A) Processing helix chain 'A' and resid 3572 through 3595 removed outlier: 3.900A pdb=" N GLU A3595 " --> pdb=" O LYS A3591 " (cutoff:3.500A) Processing helix chain 'A' and resid 3602 through 3610 Processing helix chain 'A' and resid 3610 through 3616 removed outlier: 3.572A pdb=" N GLU A3616 " --> pdb=" O ASP A3612 " (cutoff:3.500A) Processing helix chain 'A' and resid 3619 through 3629 Processing helix chain 'A' and resid 3632 through 3641 Processing helix chain 'A' and resid 3648 through 3652 Processing helix chain 'A' and resid 3658 through 3671 removed outlier: 3.555A pdb=" N ARG A3662 " --> pdb=" O PRO A3658 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ASP A3671 " --> pdb=" O PHE A3667 " (cutoff:3.500A) Processing helix chain 'A' and resid 3711 through 3730 Processing helix chain 'A' and resid 3734 through 3746 removed outlier: 3.888A pdb=" N VAL A3740 " --> pdb=" O PRO A3736 " (cutoff:3.500A) Processing helix chain 'A' and resid 3746 through 3755 Processing helix chain 'A' and resid 3757 through 3776 removed outlier: 3.713A pdb=" N ILE A3772 " --> pdb=" O LEU A3768 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LEU A3773 " --> pdb=" O LYS A3769 " (cutoff:3.500A) Processing helix chain 'A' and resid 3780 through 3801 Processing helix chain 'A' and resid 3810 through 3821 removed outlier: 4.284A pdb=" N VAL A3814 " --> pdb=" O SER A3810 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N HIS A3815 " --> pdb=" O LEU A3811 " (cutoff:3.500A) Processing helix chain 'A' and resid 3821 through 3835 Processing helix chain 'A' and resid 3837 through 3849 removed outlier: 4.434A pdb=" N SER A3841 " --> pdb=" O GLN A3837 " (cutoff:3.500A) Processing helix chain 'A' and resid 3857 through 3873 Processing helix chain 'A' and resid 3878 through 3898 removed outlier: 4.352A pdb=" N MET A3891 " --> pdb=" O LYS A3887 " (cutoff:3.500A) Proline residue: A3892 - end of helix Processing helix chain 'A' and resid 3899 through 3902 Processing helix chain 'A' and resid 3906 through 3933 removed outlier: 3.871A pdb=" N ARG A3914 " --> pdb=" O GLN A3910 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLU A3915 " --> pdb=" O ALA A3911 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N HIS A3932 " --> pdb=" O LEU A3928 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL A3933 " --> pdb=" O PHE A3929 " (cutoff:3.500A) Processing helix chain 'A' and resid 3934 through 3939 Processing helix chain 'A' and resid 3944 through 3959 removed outlier: 3.612A pdb=" N VAL A3952 " --> pdb=" O VAL A3948 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N PHE A3953 " --> pdb=" O THR A3949 " (cutoff:3.500A) Processing helix chain 'A' and resid 3967 through 3986 removed outlier: 3.789A pdb=" N SER A3986 " --> pdb=" O LYS A3982 " (cutoff:3.500A) Processing helix chain 'A' and resid 4018 through 4026 removed outlier: 3.881A pdb=" N ALA A4023 " --> pdb=" O ARG A4019 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N TRP A4024 " --> pdb=" O CYS A4020 " (cutoff:3.500A) Processing helix chain 'A' and resid 4048 through 4078 removed outlier: 3.647A pdb=" N HIS A4058 " --> pdb=" O ALA A4054 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N GLN A4063 " --> pdb=" O ALA A4059 " (cutoff:3.500A) Processing helix chain 'A' and resid 4085 through 4097 removed outlier: 3.951A pdb=" N ILE A4089 " --> pdb=" O GLU A4085 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N PHE A4097 " --> pdb=" O LEU A4093 " (cutoff:3.500A) Processing helix chain 'A' and resid 4146 through 4159 Processing helix chain 'A' and resid 4167 through 4187 removed outlier: 3.915A pdb=" N LEU A4173 " --> pdb=" O GLU A4169 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N SER A4187 " --> pdb=" O LEU A4183 " (cutoff:3.500A) Processing helix chain 'A' and resid 4190 through 4207 Processing helix chain 'A' and resid 4222 through 4244 Processing helix chain 'A' and resid 4252 through 4271 removed outlier: 3.663A pdb=" N LYS A4256 " --> pdb=" O MET A4252 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N CYS A4258 " --> pdb=" O LYS A4254 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N GLU A4271 " --> pdb=" O CYS A4267 " (cutoff:3.500A) Processing helix chain 'A' and resid 4273 through 4288 Processing helix chain 'A' and resid 4288 through 4296 removed outlier: 3.563A pdb=" N VAL A4292 " --> pdb=" O GLY A4288 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N SER A4296 " --> pdb=" O VAL A4292 " (cutoff:3.500A) Processing helix chain 'A' and resid 4308 through 4316 Processing helix chain 'A' and resid 4331 through 4347 removed outlier: 3.776A pdb=" N LYS A4335 " --> pdb=" O GLY A4331 " (cutoff:3.500A) Processing helix chain 'A' and resid 4350 through 4359 removed outlier: 3.752A pdb=" N ALA A4356 " --> pdb=" O GLY A4352 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ALA A4359 " --> pdb=" O THR A4355 " (cutoff:3.500A) Processing helix chain 'A' and resid 4363 through 4385 removed outlier: 4.173A pdb=" N ILE A4381 " --> pdb=" O ARG A4377 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N SER A4385 " --> pdb=" O ILE A4381 " (cutoff:3.500A) Processing helix chain 'A' and resid 4393 through 4407 Processing helix chain 'A' and resid 4412 through 4424 Processing helix chain 'A' and resid 4439 through 4457 Processing helix chain 'A' and resid 4462 through 4471 removed outlier: 3.534A pdb=" N LYS A4466 " --> pdb=" O LEU A4462 " (cutoff:3.500A) Processing helix chain 'A' and resid 4575 through 4597 Processing helix chain 'A' and resid 4597 through 4605 removed outlier: 4.226A pdb=" N LEU A4601 " --> pdb=" O SER A4597 " (cutoff:3.500A) Processing helix chain 'A' and resid 4615 through 4632 Processing helix chain 'A' and resid 4634 through 4651 removed outlier: 3.780A pdb=" N LEU A4649 " --> pdb=" O VAL A4645 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LEU A4650 " --> pdb=" O LEU A4646 " (cutoff:3.500A) Processing helix chain 'A' and resid 4670 through 4691 removed outlier: 3.947A pdb=" N VAL A4684 " --> pdb=" O GLU A4680 " (cutoff:3.500A) Proline residue: A4687 - end of helix Processing helix chain 'A' and resid 4691 through 4706 removed outlier: 3.889A pdb=" N THR A4695 " --> pdb=" O HIS A4691 " (cutoff:3.500A) Proline residue: A4697 - end of helix Processing helix chain 'A' and resid 4707 through 4711 Processing helix chain 'A' and resid 4712 through 4719 removed outlier: 3.778A pdb=" N ILE A4718 " --> pdb=" O VAL A4714 " (cutoff:3.500A) Processing helix chain 'A' and resid 4721 through 4725 Processing helix chain 'A' and resid 4748 through 4760 Processing helix chain 'A' and resid 4765 through 4774 removed outlier: 3.965A pdb=" N LYS A4774 " --> pdb=" O HIS A4770 " (cutoff:3.500A) Processing helix chain 'A' and resid 4774 through 4779 Processing helix chain 'A' and resid 4780 through 4782 No H-bonds generated for 'chain 'A' and resid 4780 through 4782' Processing helix chain 'A' and resid 4783 through 4796 removed outlier: 3.502A pdb=" N ILE A4787 " --> pdb=" O PHE A4783 " (cutoff:3.500A) Processing helix chain 'A' and resid 4808 through 4816 Processing helix chain 'A' and resid 4818 through 4847 removed outlier: 3.835A pdb=" N LEU A4839 " --> pdb=" O THR A4835 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N ARG A4841 " --> pdb=" O ASN A4837 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N SER A4842 " --> pdb=" O LYS A4838 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N THR A4845 " --> pdb=" O ARG A4841 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLY A4847 " --> pdb=" O LEU A4843 " (cutoff:3.500A) Processing helix chain 'A' and resid 4854 through 4858 removed outlier: 3.527A pdb=" N SER A4857 " --> pdb=" O ASP A4854 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N THR A4858 " --> pdb=" O TYR A4855 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 4854 through 4858' Processing helix chain 'A' and resid 4865 through 4869 Processing helix chain 'A' and resid 4876 through 4900 removed outlier: 4.255A pdb=" N ALA A4880 " --> pdb=" O LEU A4876 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLU A4893 " --> pdb=" O ARG A4889 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ILE A4894 " --> pdb=" O LEU A4890 " (cutoff:3.500A) Processing helix chain 'A' and resid 4929 through 4934 Processing helix chain 'A' and resid 4952 through 4964 Processing helix chain 'A' and resid 4986 through 4998 removed outlier: 3.906A pdb=" N LEU A4990 " --> pdb=" O ASN A4986 " (cutoff:3.500A) Processing helix chain 'A' and resid 5004 through 5015 Processing helix chain 'A' and resid 5017 through 5038 Processing helix chain 'A' and resid 5045 through 5053 removed outlier: 3.513A pdb=" N GLN A5051 " --> pdb=" O ASN A5047 " (cutoff:3.500A) Processing helix chain 'A' and resid 5060 through 5068 removed outlier: 3.862A pdb=" N LEU A5064 " --> pdb=" O THR A5060 " (cutoff:3.500A) Processing helix chain 'A' and resid 5074 through 5093 removed outlier: 3.661A pdb=" N ALA A5084 " --> pdb=" O GLN A5080 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N SER A5087 " --> pdb=" O SER A5083 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LEU A5090 " --> pdb=" O LYS A5086 " (cutoff:3.500A) Processing helix chain 'A' and resid 5102 through 5106 Processing helix chain 'A' and resid 5110 through 5124 removed outlier: 3.789A pdb=" N THR A5119 " --> pdb=" O LYS A5115 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N PHE A5120 " --> pdb=" O LEU A5116 " (cutoff:3.500A) Processing helix chain 'A' and resid 5127 through 5140 Processing helix chain 'A' and resid 5148 through 5153 removed outlier: 4.096A pdb=" N PHE A5152 " --> pdb=" O THR A5148 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ARG A5153 " --> pdb=" O GLU A5149 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 5148 through 5153' Processing helix chain 'A' and resid 5158 through 5170 Processing helix chain 'A' and resid 5174 through 5181 removed outlier: 3.756A pdb=" N ALA A5178 " --> pdb=" O LEU A5174 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N PHE A5181 " --> pdb=" O MET A5177 " (cutoff:3.500A) Processing helix chain 'A' and resid 5190 through 5203 removed outlier: 3.666A pdb=" N LEU A5200 " --> pdb=" O THR A5196 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N LYS A5201 " --> pdb=" O ALA A5197 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 1579 through 1580 removed outlier: 3.713A pdb=" N VAL A1547 " --> pdb=" O HIS A1564 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE A1548 " --> pdb=" O ALA A1639 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 1830 through 1835 removed outlier: 6.607A pdb=" N LEU A1863 " --> pdb=" O LEU A1895 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 2020 through 2025 removed outlier: 6.119A pdb=" N LYS A2021 " --> pdb=" O HIS A2055 " (cutoff:3.500A) removed outlier: 7.309A pdb=" N ASP A2057 " --> pdb=" O LYS A2021 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N ILE A2023 " --> pdb=" O ASP A2057 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N PHE A2054 " --> pdb=" O ILE A2096 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N GLU A2098 " --> pdb=" O PHE A2054 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N LEU A2056 " --> pdb=" O GLU A2098 " (cutoff:3.500A) removed outlier: 8.309A pdb=" N LEU A2100 " --> pdb=" O LEU A2056 " (cutoff:3.500A) removed outlier: 8.181A pdb=" N VAL A2058 " --> pdb=" O LEU A2100 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N GLY A1987 " --> pdb=" O VAL A2097 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N ILE A2099 " --> pdb=" O GLY A1987 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N VAL A1989 " --> pdb=" O ILE A2099 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N ILE A1988 " --> pdb=" O VAL A2130 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 2078 through 2079 Processing sheet with id=AA5, first strand: chain 'A' and resid 2306 through 2307 Processing sheet with id=AA6, first strand: chain 'A' and resid 2323 through 2324 removed outlier: 6.322A pdb=" N VAL A2330 " --> pdb=" O ASP A2344 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ASP A2344 " --> pdb=" O VAL A2330 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LYS A2342 " --> pdb=" O ALA A2332 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 2446 through 2450 removed outlier: 3.726A pdb=" N PHE A2485 " --> pdb=" O LYS A2447 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N LEU A2484 " --> pdb=" O ILE A2521 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N ALA A2523 " --> pdb=" O LEU A2484 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N PHE A2486 " --> pdb=" O ALA A2523 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N VAL A2416 " --> pdb=" O ALA A2522 " (cutoff:3.500A) removed outlier: 8.168A pdb=" N CYS A2524 " --> pdb=" O VAL A2416 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ILE A2418 " --> pdb=" O CYS A2524 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 2506 through 2507 Processing sheet with id=AA9, first strand: chain 'A' and resid 2555 through 2556 removed outlier: 3.612A pdb=" N ILE A2559 " --> pdb=" O LEU A2556 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 2801 through 2808 removed outlier: 8.514A pdb=" N GLY A2880 " --> pdb=" O TYR A2837 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N SER A2839 " --> pdb=" O GLY A2880 " (cutoff:3.500A) removed outlier: 8.022A pdb=" N VAL A2882 " --> pdb=" O SER A2839 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N VAL A2841 " --> pdb=" O VAL A2882 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N ILE A2884 " --> pdb=" O VAL A2841 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N LEU A2843 " --> pdb=" O ILE A2884 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N LEU A2765 " --> pdb=" O GLY A2883 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N SER A2885 " --> pdb=" O LEU A2765 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N LEU A2767 " --> pdb=" O SER A2885 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 3067 through 3069 Processing sheet with id=AB3, first strand: chain 'A' and resid 3121 through 3123 removed outlier: 4.450A pdb=" N LYS A3127 " --> pdb=" O VAL A3142 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 3345 through 3348 removed outlier: 6.120A pdb=" N THR A3345 " --> pdb=" O ILE A3376 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N GLN A3378 " --> pdb=" O THR A3345 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N LEU A3347 " --> pdb=" O GLN A3378 " (cutoff:3.500A) removed outlier: 8.196A pdb=" N ASP A3380 " --> pdb=" O LEU A3347 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N LYS A3373 " --> pdb=" O PHE A3413 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N TYR A3415 " --> pdb=" O LYS A3373 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N LEU A3375 " --> pdb=" O TYR A3415 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N ILE A3417 " --> pdb=" O LEU A3375 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N PHE A3377 " --> pdb=" O ILE A3417 " (cutoff:3.500A) removed outlier: 8.020A pdb=" N LYS A3419 " --> pdb=" O PHE A3377 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N THR A3379 " --> pdb=" O LYS A3419 " (cutoff:3.500A) removed outlier: 8.594A pdb=" N VAL A3440 " --> pdb=" O PHE A3315 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N GLU A3317 " --> pdb=" O VAL A3440 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 3547 through 3549 Processing sheet with id=AB6, first strand: chain 'A' and resid 4007 through 4009 Processing sheet with id=AB7, first strand: chain 'A' and resid 4503 through 4504 Processing sheet with id=AB8, first strand: chain 'A' and resid 4910 through 4911 removed outlier: 6.505A pdb=" N VAL A4910 " --> pdb=" O LEU A4971 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'A' and resid 4940 through 4941 1741 hydrogen bonds defined for protein. 5106 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 11.81 Time building geometry restraints manager: 3.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 5960 1.30 - 1.43: 9232 1.43 - 1.56: 21174 1.56 - 1.69: 7 1.69 - 1.82: 317 Bond restraints: 36690 Sorted by residual: bond pdb=" CA PRO A2134 " pdb=" C PRO A2134 " ideal model delta sigma weight residual 1.517 1.405 0.112 9.30e-03 1.16e+04 1.44e+02 bond pdb=" C4 ATP A5301 " pdb=" C5 ATP A5301 " ideal model delta sigma weight residual 1.388 1.451 -0.063 1.00e-02 1.00e+04 3.93e+01 bond pdb=" CA HIS A1920 " pdb=" C HIS A1920 " ideal model delta sigma weight residual 1.522 1.451 0.071 1.20e-02 6.94e+03 3.52e+01 bond pdb=" C4 ATP A5301 " pdb=" N9 ATP A5301 " ideal model delta sigma weight residual 1.374 1.315 0.059 1.00e-02 1.00e+04 3.45e+01 bond pdb=" CA VAL A2002 " pdb=" CB VAL A2002 " ideal model delta sigma weight residual 1.545 1.467 0.077 1.45e-02 4.76e+03 2.85e+01 ... (remaining 36685 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.81: 49465 4.81 - 9.63: 169 9.63 - 14.44: 22 14.44 - 19.25: 2 19.25 - 24.07: 4 Bond angle restraints: 49662 Sorted by residual: angle pdb=" PB ATP A5301 " pdb=" O3B ATP A5301 " pdb=" PG ATP A5301 " ideal model delta sigma weight residual 139.87 117.38 22.49 1.00e+00 1.00e+00 5.06e+02 angle pdb=" PA ATP A5301 " pdb=" O3A ATP A5301 " pdb=" PB ATP A5301 " ideal model delta sigma weight residual 136.83 117.11 19.72 1.00e+00 1.00e+00 3.89e+02 angle pdb=" O PRO A4969 " pdb=" C PRO A4969 " pdb=" N ARG A4970 " ideal model delta sigma weight residual 122.64 145.41 -22.77 1.35e+00 5.49e-01 2.84e+02 angle pdb=" N LEU A2000 " pdb=" CA LEU A2000 " pdb=" C LEU A2000 " ideal model delta sigma weight residual 112.59 96.18 16.41 1.22e+00 6.72e-01 1.81e+02 angle pdb=" CA PRO A4969 " pdb=" C PRO A4969 " pdb=" O PRO A4969 " ideal model delta sigma weight residual 120.60 96.53 24.07 1.82e+00 3.02e-01 1.75e+02 ... (remaining 49657 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 19226 17.93 - 35.86: 2395 35.86 - 53.79: 570 53.79 - 71.73: 91 71.73 - 89.66: 40 Dihedral angle restraints: 22322 sinusoidal: 9185 harmonic: 13137 Sorted by residual: dihedral pdb=" CA GLY A 895 " pdb=" C GLY A 895 " pdb=" N ASN A 896 " pdb=" CA ASN A 896 " ideal model delta harmonic sigma weight residual 180.00 144.10 35.90 0 5.00e+00 4.00e-02 5.15e+01 dihedral pdb=" CA THR A3058 " pdb=" C THR A3058 " pdb=" N PHE A3059 " pdb=" CA PHE A3059 " ideal model delta harmonic sigma weight residual -180.00 -147.20 -32.80 0 5.00e+00 4.00e-02 4.30e+01 dihedral pdb=" CA GLN A1719 " pdb=" C GLN A1719 " pdb=" N PRO A1720 " pdb=" CA PRO A1720 " ideal model delta harmonic sigma weight residual -180.00 -149.61 -30.39 0 5.00e+00 4.00e-02 3.69e+01 ... (remaining 22319 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 4808 0.060 - 0.121: 729 0.121 - 0.181: 60 0.181 - 0.242: 14 0.242 - 0.302: 7 Chirality restraints: 5618 Sorted by residual: chirality pdb=" CG LEU A1161 " pdb=" CB LEU A1161 " pdb=" CD1 LEU A1161 " pdb=" CD2 LEU A1161 " both_signs ideal model delta sigma weight residual False -2.59 -2.29 -0.30 2.00e-01 2.50e+01 2.29e+00 chirality pdb=" CA PRO A2135 " pdb=" N PRO A2135 " pdb=" C PRO A2135 " pdb=" CB PRO A2135 " both_signs ideal model delta sigma weight residual False 2.72 2.42 0.30 2.00e-01 2.50e+01 2.22e+00 chirality pdb=" CA ILE A 540 " pdb=" N ILE A 540 " pdb=" C ILE A 540 " pdb=" CB ILE A 540 " both_signs ideal model delta sigma weight residual False 2.43 2.14 0.30 2.00e-01 2.50e+01 2.20e+00 ... (remaining 5615 not shown) Planarity restraints: 6348 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN A 896 " -0.028 2.00e-02 2.50e+03 5.54e-02 3.06e+01 pdb=" C ASN A 896 " 0.096 2.00e-02 2.50e+03 pdb=" O ASN A 896 " -0.036 2.00e-02 2.50e+03 pdb=" N ASN A 897 " -0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO A4969 " -0.018 2.00e-02 2.50e+03 5.13e-02 2.63e+01 pdb=" C PRO A4969 " 0.088 2.00e-02 2.50e+03 pdb=" O PRO A4969 " -0.035 2.00e-02 2.50e+03 pdb=" N ARG A4970 " -0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 895 " -0.026 2.00e-02 2.50e+03 5.12e-02 2.62e+01 pdb=" C GLY A 895 " 0.089 2.00e-02 2.50e+03 pdb=" O GLY A 895 " -0.033 2.00e-02 2.50e+03 pdb=" N ASN A 896 " -0.030 2.00e-02 2.50e+03 ... (remaining 6345 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 684 2.68 - 3.23: 35791 3.23 - 3.79: 56928 3.79 - 4.34: 74840 4.34 - 4.90: 120937 Nonbonded interactions: 289180 Sorted by model distance: nonbonded pdb=" OG SER A2300 " pdb=" OE1 GLU A2301 " model vdw 2.122 3.040 nonbonded pdb=" OD1 ASN A3557 " pdb=" OG1 THR A5037 " model vdw 2.138 3.040 nonbonded pdb=" O TRP A 719 " pdb=" NH1 ARG A 759 " model vdw 2.147 3.120 nonbonded pdb=" OG SER A4132 " pdb=" O TYR A4939 " model vdw 2.155 3.040 nonbonded pdb=" OE2 GLU A1219 " pdb=" OH TYR A1275 " model vdw 2.160 3.040 ... (remaining 289175 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 11.520 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: 0.060 Extract box with map and model: 0.650 Check model and map are aligned: 0.120 Set scattering table: 0.110 Process input model: 37.240 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.112 36690 Z= 0.226 Angle : 0.822 24.067 49662 Z= 0.465 Chirality : 0.045 0.302 5618 Planarity : 0.005 0.078 6348 Dihedral : 16.659 89.657 13756 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 13.38 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.12 % Favored : 92.75 % Rotamer: Outliers : 0.50 % Allowed : 19.45 % Favored : 80.05 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.55 % Twisted General : 0.05 % 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 aren not related in a simple way. whole: -1.02 (0.13), residues: 4439 helix: 0.08 (0.11), residues: 2489 sheet: 0.35 (0.37), residues: 200 loop : -1.88 (0.15), residues: 1750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A4417 TYR 0.036 0.001 TYR A3835 PHE 0.034 0.002 PHE A3739 TRP 0.065 0.002 TRP A 691 HIS 0.011 0.001 HIS A4983 Details of bonding type rmsd covalent geometry : bond 0.00370 (36690) covalent geometry : angle 0.82239 (49662) hydrogen bonds : bond 0.14964 ( 1741) hydrogen bonds : angle 6.41524 ( 5106) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8878 Ramachandran restraints generated. 4439 Oldfield, 0 Emsley, 4439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8878 Ramachandran restraints generated. 4439 Oldfield, 0 Emsley, 4439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 463 residues out of total 4006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 443 time to evaluate : 1.252 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 734 MET cc_start: 0.4039 (ptm) cc_final: 0.3782 (ptm) REVERT: A 1162 LYS cc_start: 0.8538 (mmtt) cc_final: 0.8206 (ptmm) REVERT: A 1344 LYS cc_start: 0.6788 (mmtm) cc_final: 0.6509 (mmtm) REVERT: A 1455 ASN cc_start: 0.8399 (t0) cc_final: 0.8138 (t0) REVERT: A 1653 MET cc_start: 0.8256 (tpt) cc_final: 0.7907 (tpt) REVERT: A 2156 LEU cc_start: 0.8268 (mm) cc_final: 0.7982 (tp) REVERT: A 2249 LYS cc_start: 0.9067 (mmmm) cc_final: 0.8853 (mtpt) REVERT: A 2721 LEU cc_start: 0.8571 (OUTLIER) cc_final: 0.8310 (mp) REVERT: A 3598 PHE cc_start: 0.7500 (p90) cc_final: 0.6877 (p90) REVERT: A 3818 TYR cc_start: 0.7984 (t80) cc_final: 0.7764 (t80) REVERT: A 4064 MET cc_start: 0.7945 (ppp) cc_final: 0.7597 (ppp) REVERT: A 4266 PHE cc_start: 0.7559 (m-80) cc_final: 0.7344 (m-80) REVERT: A 4581 LEU cc_start: 0.8713 (mm) cc_final: 0.8217 (pp) REVERT: A 4673 MET cc_start: 0.6116 (mtp) cc_final: 0.5885 (tpt) REVERT: A 4777 GLU cc_start: 0.8053 (pt0) cc_final: 0.7697 (pm20) REVERT: A 4829 ILE cc_start: 0.8508 (pt) cc_final: 0.8244 (mt) REVERT: A 5166 MET cc_start: 0.8494 (mpp) cc_final: 0.8211 (mpp) outliers start: 20 outliers final: 8 residues processed: 460 average time/residue: 0.2058 time to fit residues: 155.3198 Evaluate side-chains 354 residues out of total 4006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 345 time to evaluate : 1.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 899 VAL Chi-restraints excluded: chain A residue 2026 ILE Chi-restraints excluded: chain A residue 2721 LEU Chi-restraints excluded: chain A residue 2939 TYR Chi-restraints excluded: chain A residue 3059 PHE Chi-restraints excluded: chain A residue 3161 PHE Chi-restraints excluded: chain A residue 3258 LEU Chi-restraints excluded: chain A residue 3379 THR Chi-restraints excluded: chain A residue 3951 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 432 optimal weight: 1.9990 chunk 197 optimal weight: 2.9990 chunk 388 optimal weight: 20.0000 chunk 215 optimal weight: 0.2980 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 0.0270 chunk 248 optimal weight: 0.0270 chunk 207 optimal weight: 0.6980 chunk 401 optimal weight: 3.9990 chunk 424 optimal weight: 7.9990 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 548 ASN A 565 GLN A 904 GLN A 973 GLN A1043 ASN ** A1210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1602 ASN A1702 ASN A2584 GLN A2787 GLN A3107 ASN A3378 GLN A3682 ASN A3840 HIS A4197 HIS A4262 GLN ** A4275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A4293 GLN A4314 GLN A4563 GLN ** A4619 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4626 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4651 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4653 GLN A4676 ASN A4728 HIS ** A4754 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A4799 GLN ** A4802 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4936 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.138981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.101489 restraints weight = 75726.557| |-----------------------------------------------------------------------------| r_work (start): 0.3596 rms_B_bonded: 3.06 r_work: 0.3347 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.1037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 36690 Z= 0.140 Angle : 0.645 11.629 49662 Z= 0.325 Chirality : 0.041 0.203 5618 Planarity : 0.005 0.071 6348 Dihedral : 5.693 88.283 4874 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.85 % Favored : 93.11 % Rotamer: Outliers : 2.28 % Allowed : 17.40 % Favored : 80.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.55 % Twisted General : 0.02 % 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 aren not related in a simple way. whole: -0.73 (0.13), residues: 4439 helix: 0.39 (0.11), residues: 2494 sheet: -0.05 (0.35), residues: 212 loop : -1.82 (0.15), residues: 1733 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 798 TYR 0.017 0.001 TYR A2939 PHE 0.025 0.001 PHE A1286 TRP 0.026 0.002 TRP A4741 HIS 0.012 0.001 HIS A4983 Details of bonding type rmsd covalent geometry : bond 0.00313 (36690) covalent geometry : angle 0.64520 (49662) hydrogen bonds : bond 0.04380 ( 1741) hydrogen bonds : angle 4.85414 ( 5106) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8878 Ramachandran restraints generated. 4439 Oldfield, 0 Emsley, 4439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8878 Ramachandran restraints generated. 4439 Oldfield, 0 Emsley, 4439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 480 residues out of total 4006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 389 time to evaluate : 1.490 Fit side-chains revert: symmetry clash REVERT: A 548 ASN cc_start: 0.8012 (OUTLIER) cc_final: 0.7173 (t0) REVERT: A 589 TYR cc_start: 0.5893 (OUTLIER) cc_final: 0.5422 (t80) REVERT: A 644 LEU cc_start: 0.8584 (mm) cc_final: 0.8082 (pp) REVERT: A 713 ARG cc_start: 0.8202 (tpp80) cc_final: 0.7944 (mmm160) REVERT: A 771 VAL cc_start: 0.7313 (p) cc_final: 0.6936 (p) REVERT: A 878 MET cc_start: 0.7747 (mtt) cc_final: 0.7069 (mtt) REVERT: A 987 LEU cc_start: 0.7438 (OUTLIER) cc_final: 0.7236 (tt) REVERT: A 1162 LYS cc_start: 0.8609 (mmtt) cc_final: 0.8302 (ptmm) REVERT: A 1455 ASN cc_start: 0.8339 (t0) cc_final: 0.8081 (t0) REVERT: A 1557 ILE cc_start: 0.9284 (OUTLIER) cc_final: 0.8982 (tt) REVERT: A 1653 MET cc_start: 0.8219 (tpt) cc_final: 0.7819 (tpt) REVERT: A 2156 LEU cc_start: 0.8391 (mm) cc_final: 0.8052 (tp) REVERT: A 2346 MET cc_start: 0.7700 (tmm) cc_final: 0.7159 (tmm) REVERT: A 2404 LEU cc_start: 0.9124 (OUTLIER) cc_final: 0.8777 (mm) REVERT: A 2527 TYR cc_start: 0.8147 (m-80) cc_final: 0.7643 (m-80) REVERT: A 2657 MET cc_start: 0.8255 (tmm) cc_final: 0.7976 (tmm) REVERT: A 3104 ASN cc_start: 0.7291 (t0) cc_final: 0.6699 (m110) REVERT: A 3789 MET cc_start: 0.8704 (ttp) cc_final: 0.8480 (ttt) REVERT: A 3839 LEU cc_start: 0.9046 (tp) cc_final: 0.8841 (pt) REVERT: A 3864 MET cc_start: 0.6916 (mmm) cc_final: 0.6575 (mmm) REVERT: A 4064 MET cc_start: 0.7958 (ppp) cc_final: 0.7722 (ppp) REVERT: A 4068 PHE cc_start: 0.6999 (t80) cc_final: 0.6754 (t80) REVERT: A 4069 PHE cc_start: 0.7619 (t80) cc_final: 0.7048 (m-80) REVERT: A 4581 LEU cc_start: 0.8700 (OUTLIER) cc_final: 0.8236 (pp) REVERT: A 4673 MET cc_start: 0.6533 (mtp) cc_final: 0.6132 (tpp) REVERT: A 4777 GLU cc_start: 0.8251 (pt0) cc_final: 0.7836 (pm20) REVERT: A 4791 GLN cc_start: 0.8439 (mm-40) cc_final: 0.8038 (pp30) REVERT: A 4855 TYR cc_start: 0.7178 (m-80) cc_final: 0.6755 (m-80) REVERT: A 4896 TYR cc_start: 0.8269 (t80) cc_final: 0.8057 (t80) REVERT: A 5166 MET cc_start: 0.8575 (mpp) cc_final: 0.8373 (mpp) outliers start: 91 outliers final: 35 residues processed: 452 average time/residue: 0.2190 time to fit residues: 164.2175 Evaluate side-chains 392 residues out of total 4006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 351 time to evaluate : 1.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 548 ASN Chi-restraints excluded: chain A residue 589 TYR Chi-restraints excluded: chain A residue 698 LEU Chi-restraints excluded: chain A residue 899 VAL Chi-restraints excluded: chain A residue 987 LEU Chi-restraints excluded: chain A residue 1279 TYR Chi-restraints excluded: chain A residue 1373 SER Chi-restraints excluded: chain A residue 1557 ILE Chi-restraints excluded: chain A residue 1632 MET Chi-restraints excluded: chain A residue 2026 ILE Chi-restraints excluded: chain A residue 2170 TYR Chi-restraints excluded: chain A residue 2179 ASP Chi-restraints excluded: chain A residue 2190 VAL Chi-restraints excluded: chain A residue 2223 ASN Chi-restraints excluded: chain A residue 2396 THR Chi-restraints excluded: chain A residue 2404 LEU Chi-restraints excluded: chain A residue 2446 ILE Chi-restraints excluded: chain A residue 2476 ASP Chi-restraints excluded: chain A residue 2565 VAL Chi-restraints excluded: chain A residue 2939 TYR Chi-restraints excluded: chain A residue 3059 PHE Chi-restraints excluded: chain A residue 3161 PHE Chi-restraints excluded: chain A residue 3204 HIS Chi-restraints excluded: chain A residue 3258 LEU Chi-restraints excluded: chain A residue 3379 THR Chi-restraints excluded: chain A residue 3451 MET Chi-restraints excluded: chain A residue 3699 MET Chi-restraints excluded: chain A residue 3728 TYR Chi-restraints excluded: chain A residue 3731 ASP Chi-restraints excluded: chain A residue 3838 VAL Chi-restraints excluded: chain A residue 3843 MET Chi-restraints excluded: chain A residue 4096 LEU Chi-restraints excluded: chain A residue 4189 TYR Chi-restraints excluded: chain A residue 4311 VAL Chi-restraints excluded: chain A residue 4581 LEU Chi-restraints excluded: chain A residue 4749 VAL Chi-restraints excluded: chain A residue 4864 THR Chi-restraints excluded: chain A residue 4965 LEU Chi-restraints excluded: chain A residue 5060 THR Chi-restraints excluded: chain A residue 5063 VAL Chi-restraints excluded: chain A residue 5138 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 290 optimal weight: 2.9990 chunk 357 optimal weight: 20.0000 chunk 281 optimal weight: 1.9990 chunk 398 optimal weight: 10.0000 chunk 187 optimal weight: 0.7980 chunk 424 optimal weight: 5.9990 chunk 81 optimal weight: 9.9990 chunk 11 optimal weight: 6.9990 chunk 189 optimal weight: 2.9990 chunk 226 optimal weight: 0.9980 chunk 125 optimal weight: 0.4980 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1946 HIS A2223 ASN A2399 ASN A3117 ASN A3222 HIS A3593 GLN A3629 GLN ** A4275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4619 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A4626 GLN ** A4651 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4754 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4936 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A4940 GLN A5074 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.134845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.094985 restraints weight = 75768.628| |-----------------------------------------------------------------------------| r_work (start): 0.3471 rms_B_bonded: 3.04 r_work: 0.3229 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.1532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 36690 Z= 0.200 Angle : 0.659 11.584 49662 Z= 0.333 Chirality : 0.043 0.240 5618 Planarity : 0.005 0.066 6348 Dihedral : 5.685 88.338 4870 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.23 % Favored : 92.72 % Rotamer: Outliers : 3.23 % Allowed : 17.20 % Favored : 79.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.55 % Twisted General : 0.07 % 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 aren not related in a simple way. whole: -0.74 (0.13), residues: 4439 helix: 0.41 (0.11), residues: 2506 sheet: -0.50 (0.34), residues: 221 loop : -1.83 (0.15), residues: 1712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A2896 TYR 0.020 0.002 TYR A3835 PHE 0.031 0.002 PHE A4266 TRP 0.022 0.002 TRP A4677 HIS 0.011 0.001 HIS A4983 Details of bonding type rmsd covalent geometry : bond 0.00464 (36690) covalent geometry : angle 0.65945 (49662) hydrogen bonds : bond 0.04155 ( 1741) hydrogen bonds : angle 4.71401 ( 5106) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8878 Ramachandran restraints generated. 4439 Oldfield, 0 Emsley, 4439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8878 Ramachandran restraints generated. 4439 Oldfield, 0 Emsley, 4439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 503 residues out of total 4006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 374 time to evaluate : 1.437 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 589 TYR cc_start: 0.6084 (OUTLIER) cc_final: 0.5636 (t80) REVERT: A 682 ARG cc_start: 0.8307 (ttm-80) cc_final: 0.7943 (mtt90) REVERT: A 713 ARG cc_start: 0.8397 (tpp80) cc_final: 0.8137 (mmm160) REVERT: A 878 MET cc_start: 0.8231 (mtt) cc_final: 0.8024 (mtp) REVERT: A 996 GLU cc_start: 0.8106 (OUTLIER) cc_final: 0.7494 (tm-30) REVERT: A 1162 LYS cc_start: 0.8773 (mmtt) cc_final: 0.8339 (ptmm) REVERT: A 1350 HIS cc_start: 0.8160 (OUTLIER) cc_final: 0.7909 (m-70) REVERT: A 1485 PHE cc_start: 0.7479 (t80) cc_final: 0.7243 (t80) REVERT: A 1557 ILE cc_start: 0.9340 (OUTLIER) cc_final: 0.9085 (tt) REVERT: A 1575 GLU cc_start: 0.6688 (OUTLIER) cc_final: 0.6293 (pm20) REVERT: A 2404 LEU cc_start: 0.9165 (OUTLIER) cc_final: 0.8809 (mm) REVERT: A 2896 ARG cc_start: 0.8211 (OUTLIER) cc_final: 0.7818 (mmp-170) REVERT: A 3059 PHE cc_start: 0.7322 (OUTLIER) cc_final: 0.7093 (p90) REVERT: A 3237 GLN cc_start: 0.8456 (mm110) cc_final: 0.8210 (mm110) REVERT: A 3789 MET cc_start: 0.8917 (ttp) cc_final: 0.8689 (ttt) REVERT: A 3832 LEU cc_start: 0.8492 (mp) cc_final: 0.8186 (mp) REVERT: A 3839 LEU cc_start: 0.9134 (tp) cc_final: 0.8922 (pt) REVERT: A 3869 MET cc_start: 0.8915 (ppp) cc_final: 0.8484 (ppp) REVERT: A 3872 ARG cc_start: 0.8593 (mtm180) cc_final: 0.8290 (mtm180) REVERT: A 3883 LEU cc_start: 0.8066 (tp) cc_final: 0.7599 (tp) REVERT: A 4064 MET cc_start: 0.8142 (ppp) cc_final: 0.7926 (ppp) REVERT: A 4069 PHE cc_start: 0.7647 (t80) cc_final: 0.7138 (m-80) REVERT: A 4483 MET cc_start: 0.5687 (tpp) cc_final: 0.5408 (tpp) REVERT: A 4581 LEU cc_start: 0.8720 (mm) cc_final: 0.8271 (pp) REVERT: A 4777 GLU cc_start: 0.8215 (pt0) cc_final: 0.7772 (pm20) REVERT: A 4791 GLN cc_start: 0.8398 (mm-40) cc_final: 0.7938 (pp30) REVERT: A 4855 TYR cc_start: 0.7164 (m-80) cc_final: 0.6705 (m-80) REVERT: A 5096 GLU cc_start: 0.7838 (pm20) cc_final: 0.7453 (pm20) outliers start: 129 outliers final: 65 residues processed: 462 average time/residue: 0.2129 time to fit residues: 162.4752 Evaluate side-chains 406 residues out of total 4006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 333 time to evaluate : 1.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 589 TYR Chi-restraints excluded: chain A residue 698 LEU Chi-restraints excluded: chain A residue 774 MET Chi-restraints excluded: chain A residue 795 ILE Chi-restraints excluded: chain A residue 802 LEU Chi-restraints excluded: chain A residue 876 CYS Chi-restraints excluded: chain A residue 899 VAL Chi-restraints excluded: chain A residue 996 GLU Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain A residue 1117 LEU Chi-restraints excluded: chain A residue 1173 VAL Chi-restraints excluded: chain A residue 1279 TYR Chi-restraints excluded: chain A residue 1350 HIS Chi-restraints excluded: chain A residue 1353 VAL Chi-restraints excluded: chain A residue 1373 SER Chi-restraints excluded: chain A residue 1557 ILE Chi-restraints excluded: chain A residue 1575 GLU Chi-restraints excluded: chain A residue 1594 LEU Chi-restraints excluded: chain A residue 1632 MET Chi-restraints excluded: chain A residue 1649 VAL Chi-restraints excluded: chain A residue 1812 MET Chi-restraints excluded: chain A residue 1845 LEU Chi-restraints excluded: chain A residue 2026 ILE Chi-restraints excluded: chain A residue 2168 TYR Chi-restraints excluded: chain A residue 2170 TYR Chi-restraints excluded: chain A residue 2190 VAL Chi-restraints excluded: chain A residue 2223 ASN Chi-restraints excluded: chain A residue 2255 MET Chi-restraints excluded: chain A residue 2396 THR Chi-restraints excluded: chain A residue 2404 LEU Chi-restraints excluded: chain A residue 2446 ILE Chi-restraints excluded: chain A residue 2476 ASP Chi-restraints excluded: chain A residue 2506 MET Chi-restraints excluded: chain A residue 2565 VAL Chi-restraints excluded: chain A residue 2658 LEU Chi-restraints excluded: chain A residue 2686 MET Chi-restraints excluded: chain A residue 2691 VAL Chi-restraints excluded: chain A residue 2782 VAL Chi-restraints excluded: chain A residue 2814 THR Chi-restraints excluded: chain A residue 2896 ARG Chi-restraints excluded: chain A residue 2939 TYR Chi-restraints excluded: chain A residue 3012 VAL Chi-restraints excluded: chain A residue 3059 PHE Chi-restraints excluded: chain A residue 3077 ASP Chi-restraints excluded: chain A residue 3161 PHE Chi-restraints excluded: chain A residue 3204 HIS Chi-restraints excluded: chain A residue 3219 ILE Chi-restraints excluded: chain A residue 3258 LEU Chi-restraints excluded: chain A residue 3261 CYS Chi-restraints excluded: chain A residue 3379 THR Chi-restraints excluded: chain A residue 3451 MET Chi-restraints excluded: chain A residue 3728 TYR Chi-restraints excluded: chain A residue 3774 LEU Chi-restraints excluded: chain A residue 3838 VAL Chi-restraints excluded: chain A residue 3843 MET Chi-restraints excluded: chain A residue 3893 LEU Chi-restraints excluded: chain A residue 3951 HIS Chi-restraints excluded: chain A residue 4096 LEU Chi-restraints excluded: chain A residue 4189 TYR Chi-restraints excluded: chain A residue 4289 MET Chi-restraints excluded: chain A residue 4311 VAL Chi-restraints excluded: chain A residue 4512 SER Chi-restraints excluded: chain A residue 4567 VAL Chi-restraints excluded: chain A residue 4590 LEU Chi-restraints excluded: chain A residue 4749 VAL Chi-restraints excluded: chain A residue 4781 VAL Chi-restraints excluded: chain A residue 4825 LEU Chi-restraints excluded: chain A residue 4864 THR Chi-restraints excluded: chain A residue 4870 LEU Chi-restraints excluded: chain A residue 4932 LEU Chi-restraints excluded: chain A residue 5060 THR Chi-restraints excluded: chain A residue 5063 VAL Chi-restraints excluded: chain A residue 5138 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 126 optimal weight: 7.9990 chunk 79 optimal weight: 1.9990 chunk 403 optimal weight: 4.9990 chunk 267 optimal weight: 0.5980 chunk 134 optimal weight: 0.7980 chunk 385 optimal weight: 1.9990 chunk 279 optimal weight: 0.9980 chunk 334 optimal weight: 5.9990 chunk 102 optimal weight: 0.8980 chunk 34 optimal weight: 0.0970 chunk 98 optimal weight: 3.9990 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1564 HIS A2223 ASN ** A4066 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4619 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4754 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4936 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.137125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.099042 restraints weight = 74989.054| |-----------------------------------------------------------------------------| r_work (start): 0.3549 rms_B_bonded: 2.85 r_work: 0.3341 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.1687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 36690 Z= 0.131 Angle : 0.623 11.317 49662 Z= 0.311 Chirality : 0.041 0.291 5618 Planarity : 0.004 0.070 6348 Dihedral : 5.537 87.377 4870 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.69 % Favored : 93.26 % Rotamer: Outliers : 2.63 % Allowed : 18.55 % Favored : 78.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.55 % Twisted General : 0.02 % 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 aren not related in a simple way. whole: -0.62 (0.13), residues: 4439 helix: 0.52 (0.11), residues: 2512 sheet: -0.53 (0.34), residues: 221 loop : -1.78 (0.15), residues: 1706 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A4970 TYR 0.021 0.001 TYR A3835 PHE 0.025 0.001 PHE A1286 TRP 0.024 0.001 TRP A 691 HIS 0.011 0.001 HIS A4983 Details of bonding type rmsd covalent geometry : bond 0.00295 (36690) covalent geometry : angle 0.62275 (49662) hydrogen bonds : bond 0.03736 ( 1741) hydrogen bonds : angle 4.55335 ( 5106) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8878 Ramachandran restraints generated. 4439 Oldfield, 0 Emsley, 4439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8878 Ramachandran restraints generated. 4439 Oldfield, 0 Emsley, 4439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 480 residues out of total 4006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 375 time to evaluate : 1.449 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 589 TYR cc_start: 0.5972 (OUTLIER) cc_final: 0.5447 (t80) REVERT: A 682 ARG cc_start: 0.8243 (ttm-80) cc_final: 0.7872 (mtt90) REVERT: A 698 LEU cc_start: 0.7790 (OUTLIER) cc_final: 0.7315 (mt) REVERT: A 987 LEU cc_start: 0.7455 (OUTLIER) cc_final: 0.7246 (tt) REVERT: A 996 GLU cc_start: 0.8034 (OUTLIER) cc_final: 0.7453 (tm-30) REVERT: A 1162 LYS cc_start: 0.8554 (mmtt) cc_final: 0.8276 (ptmm) REVERT: A 1220 MET cc_start: 0.7663 (OUTLIER) cc_final: 0.7354 (ttp) REVERT: A 1375 LEU cc_start: 0.7745 (mt) cc_final: 0.7529 (mt) REVERT: A 1557 ILE cc_start: 0.9244 (OUTLIER) cc_final: 0.8947 (tt) REVERT: A 1575 GLU cc_start: 0.6691 (OUTLIER) cc_final: 0.6444 (pm20) REVERT: A 2162 GLU cc_start: 0.8703 (OUTLIER) cc_final: 0.7352 (mt-10) REVERT: A 2404 LEU cc_start: 0.9047 (OUTLIER) cc_final: 0.8680 (mm) REVERT: A 2686 MET cc_start: 0.8645 (OUTLIER) cc_final: 0.8324 (mtp) REVERT: A 2896 ARG cc_start: 0.7837 (OUTLIER) cc_final: 0.7416 (mmp-170) REVERT: A 3237 GLN cc_start: 0.8135 (mm110) cc_final: 0.7903 (mm110) REVERT: A 3832 LEU cc_start: 0.8373 (mp) cc_final: 0.8107 (mp) REVERT: A 3869 MET cc_start: 0.8955 (ppp) cc_final: 0.8657 (ppp) REVERT: A 3872 ARG cc_start: 0.8630 (mtm180) cc_final: 0.8345 (mtm180) REVERT: A 3883 LEU cc_start: 0.8105 (tp) cc_final: 0.7657 (tp) REVERT: A 3891 MET cc_start: 0.8622 (mmm) cc_final: 0.8296 (tpt) REVERT: A 4064 MET cc_start: 0.8104 (ppp) cc_final: 0.7796 (ppp) REVERT: A 4069 PHE cc_start: 0.7587 (t80) cc_final: 0.7133 (m-80) REVERT: A 4192 ASN cc_start: 0.8858 (t0) cc_final: 0.8475 (p0) REVERT: A 4483 MET cc_start: 0.5554 (tpp) cc_final: 0.5199 (tpp) REVERT: A 4581 LEU cc_start: 0.8672 (mm) cc_final: 0.8342 (pp) REVERT: A 4777 GLU cc_start: 0.8202 (pt0) cc_final: 0.7807 (pm20) REVERT: A 4791 GLN cc_start: 0.8421 (mm-40) cc_final: 0.8083 (pp30) REVERT: A 4855 TYR cc_start: 0.7110 (m-80) cc_final: 0.6711 (m-80) REVERT: A 5035 LEU cc_start: 0.8634 (tt) cc_final: 0.8381 (mt) REVERT: A 5096 GLU cc_start: 0.7751 (pm20) cc_final: 0.7352 (pm20) outliers start: 105 outliers final: 58 residues processed: 451 average time/residue: 0.2188 time to fit residues: 164.8328 Evaluate side-chains 403 residues out of total 4006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 334 time to evaluate : 1.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 589 TYR Chi-restraints excluded: chain A residue 698 LEU Chi-restraints excluded: chain A residue 774 MET Chi-restraints excluded: chain A residue 802 LEU Chi-restraints excluded: chain A residue 823 MET Chi-restraints excluded: chain A residue 876 CYS Chi-restraints excluded: chain A residue 899 VAL Chi-restraints excluded: chain A residue 987 LEU Chi-restraints excluded: chain A residue 996 GLU Chi-restraints excluded: chain A residue 1033 ILE Chi-restraints excluded: chain A residue 1173 VAL Chi-restraints excluded: chain A residue 1220 MET Chi-restraints excluded: chain A residue 1266 ARG Chi-restraints excluded: chain A residue 1279 TYR Chi-restraints excluded: chain A residue 1353 VAL Chi-restraints excluded: chain A residue 1373 SER Chi-restraints excluded: chain A residue 1557 ILE Chi-restraints excluded: chain A residue 1575 GLU Chi-restraints excluded: chain A residue 1594 LEU Chi-restraints excluded: chain A residue 1632 MET Chi-restraints excluded: chain A residue 1649 VAL Chi-restraints excluded: chain A residue 1781 ILE Chi-restraints excluded: chain A residue 1812 MET Chi-restraints excluded: chain A residue 1823 ARG Chi-restraints excluded: chain A residue 2026 ILE Chi-restraints excluded: chain A residue 2162 GLU Chi-restraints excluded: chain A residue 2168 TYR Chi-restraints excluded: chain A residue 2170 TYR Chi-restraints excluded: chain A residue 2190 VAL Chi-restraints excluded: chain A residue 2396 THR Chi-restraints excluded: chain A residue 2404 LEU Chi-restraints excluded: chain A residue 2427 THR Chi-restraints excluded: chain A residue 2446 ILE Chi-restraints excluded: chain A residue 2476 ASP Chi-restraints excluded: chain A residue 2658 LEU Chi-restraints excluded: chain A residue 2686 MET Chi-restraints excluded: chain A residue 2814 THR Chi-restraints excluded: chain A residue 2896 ARG Chi-restraints excluded: chain A residue 2923 LEU Chi-restraints excluded: chain A residue 2939 TYR Chi-restraints excluded: chain A residue 3161 PHE Chi-restraints excluded: chain A residue 3204 HIS Chi-restraints excluded: chain A residue 3205 HIS Chi-restraints excluded: chain A residue 3219 ILE Chi-restraints excluded: chain A residue 3261 CYS Chi-restraints excluded: chain A residue 3379 THR Chi-restraints excluded: chain A residue 3451 MET Chi-restraints excluded: chain A residue 3619 THR Chi-restraints excluded: chain A residue 3699 MET Chi-restraints excluded: chain A residue 3728 TYR Chi-restraints excluded: chain A residue 3774 LEU Chi-restraints excluded: chain A residue 3784 LEU Chi-restraints excluded: chain A residue 3838 VAL Chi-restraints excluded: chain A residue 3843 MET Chi-restraints excluded: chain A residue 3951 HIS Chi-restraints excluded: chain A residue 4096 LEU Chi-restraints excluded: chain A residue 4189 TYR Chi-restraints excluded: chain A residue 4289 MET Chi-restraints excluded: chain A residue 4311 VAL Chi-restraints excluded: chain A residue 4512 SER Chi-restraints excluded: chain A residue 4567 VAL Chi-restraints excluded: chain A residue 4749 VAL Chi-restraints excluded: chain A residue 4781 VAL Chi-restraints excluded: chain A residue 4825 LEU Chi-restraints excluded: chain A residue 4864 THR Chi-restraints excluded: chain A residue 4870 LEU Chi-restraints excluded: chain A residue 5060 THR Chi-restraints excluded: chain A residue 5103 SER Chi-restraints excluded: chain A residue 5138 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 25 optimal weight: 1.9990 chunk 151 optimal weight: 2.9990 chunk 13 optimal weight: 7.9990 chunk 354 optimal weight: 30.0000 chunk 373 optimal weight: 9.9990 chunk 400 optimal weight: 2.9990 chunk 434 optimal weight: 3.9990 chunk 116 optimal weight: 3.9990 chunk 212 optimal weight: 0.9980 chunk 406 optimal weight: 0.0670 chunk 45 optimal weight: 0.2980 overall best weight: 1.2722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2399 ASN A3002 ASN ** A3884 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4063 GLN ** A4066 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A4275 HIS A4314 GLN ** A4366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4619 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4626 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4936 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.135416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.096481 restraints weight = 75286.616| |-----------------------------------------------------------------------------| r_work (start): 0.3502 rms_B_bonded: 3.02 r_work: 0.3282 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.1952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 36690 Z= 0.178 Angle : 0.654 11.070 49662 Z= 0.326 Chirality : 0.042 0.295 5618 Planarity : 0.004 0.073 6348 Dihedral : 5.450 85.410 4866 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.48 % Favored : 92.48 % Rotamer: Outliers : 3.23 % Allowed : 19.23 % Favored : 77.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.55 % Twisted General : 0.05 % 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 aren not related in a simple way. whole: -0.65 (0.13), residues: 4439 helix: 0.51 (0.11), residues: 2520 sheet: -0.84 (0.34), residues: 221 loop : -1.79 (0.15), residues: 1698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A4970 TYR 0.019 0.002 TYR A3767 PHE 0.026 0.002 PHE A 658 TRP 0.022 0.001 TRP A4677 HIS 0.010 0.001 HIS A4983 Details of bonding type rmsd covalent geometry : bond 0.00414 (36690) covalent geometry : angle 0.65424 (49662) hydrogen bonds : bond 0.03843 ( 1741) hydrogen bonds : angle 4.57929 ( 5106) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8878 Ramachandran restraints generated. 4439 Oldfield, 0 Emsley, 4439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8878 Ramachandran restraints generated. 4439 Oldfield, 0 Emsley, 4439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 478 residues out of total 4006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 349 time to evaluate : 1.399 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 589 TYR cc_start: 0.6029 (OUTLIER) cc_final: 0.5485 (t80) REVERT: A 682 ARG cc_start: 0.8354 (ttm-80) cc_final: 0.8008 (mtt90) REVERT: A 698 LEU cc_start: 0.7809 (OUTLIER) cc_final: 0.7210 (mt) REVERT: A 713 ARG cc_start: 0.8549 (mmm160) cc_final: 0.8269 (tpp80) REVERT: A 734 MET cc_start: 0.4182 (ptm) cc_final: 0.3759 (ptm) REVERT: A 823 MET cc_start: 0.6815 (OUTLIER) cc_final: 0.6534 (ttp) REVERT: A 878 MET cc_start: 0.8094 (mtp) cc_final: 0.7236 (mtp) REVERT: A 996 GLU cc_start: 0.8114 (OUTLIER) cc_final: 0.7517 (tm-30) REVERT: A 1037 TRP cc_start: 0.7219 (OUTLIER) cc_final: 0.6986 (m100) REVERT: A 1162 LYS cc_start: 0.8689 (mmtt) cc_final: 0.8315 (ptmm) REVERT: A 1220 MET cc_start: 0.7542 (ttp) cc_final: 0.7101 (ttp) REVERT: A 1350 HIS cc_start: 0.8102 (OUTLIER) cc_final: 0.7859 (m-70) REVERT: A 1557 ILE cc_start: 0.9275 (OUTLIER) cc_final: 0.8988 (tt) REVERT: A 1575 GLU cc_start: 0.6691 (OUTLIER) cc_final: 0.6387 (pm20) REVERT: A 2162 GLU cc_start: 0.8722 (OUTLIER) cc_final: 0.7629 (mt-10) REVERT: A 2404 LEU cc_start: 0.9093 (OUTLIER) cc_final: 0.8739 (mm) REVERT: A 2527 TYR cc_start: 0.8116 (m-80) cc_final: 0.7822 (m-80) REVERT: A 2534 MET cc_start: 0.8430 (OUTLIER) cc_final: 0.8077 (ttt) REVERT: A 2896 ARG cc_start: 0.8048 (OUTLIER) cc_final: 0.7599 (mmp-170) REVERT: A 3104 ASN cc_start: 0.7627 (t0) cc_final: 0.7115 (m110) REVERT: A 3237 GLN cc_start: 0.8276 (mm110) cc_final: 0.8024 (mm110) REVERT: A 3832 LEU cc_start: 0.8301 (mp) cc_final: 0.8045 (mp) REVERT: A 3869 MET cc_start: 0.9022 (ppp) cc_final: 0.8796 (ppp) REVERT: A 3872 ARG cc_start: 0.8635 (mtm180) cc_final: 0.8348 (mtm180) REVERT: A 3883 LEU cc_start: 0.8115 (tp) cc_final: 0.7654 (tp) REVERT: A 3887 LYS cc_start: 0.8394 (mttp) cc_final: 0.8085 (mttp) REVERT: A 4064 MET cc_start: 0.8214 (ppp) cc_final: 0.7892 (ppp) REVERT: A 4069 PHE cc_start: 0.7705 (t80) cc_final: 0.7218 (m-80) REVERT: A 4192 ASN cc_start: 0.8782 (t0) cc_final: 0.8480 (p0) REVERT: A 4483 MET cc_start: 0.5676 (tpp) cc_final: 0.5221 (tpp) REVERT: A 4581 LEU cc_start: 0.8797 (mm) cc_final: 0.8408 (pp) REVERT: A 4764 ARG cc_start: 0.7665 (mmm160) cc_final: 0.7253 (tpm170) REVERT: A 4777 GLU cc_start: 0.8254 (pt0) cc_final: 0.7881 (pm20) REVERT: A 4791 GLN cc_start: 0.8417 (mm-40) cc_final: 0.8024 (pp30) REVERT: A 4855 TYR cc_start: 0.7151 (m-80) cc_final: 0.6681 (m-80) REVERT: A 5096 GLU cc_start: 0.7808 (pm20) cc_final: 0.7368 (pm20) REVERT: A 5155 GLN cc_start: 0.8871 (mm110) cc_final: 0.8520 (tp40) outliers start: 129 outliers final: 78 residues processed: 443 average time/residue: 0.2087 time to fit residues: 154.5428 Evaluate side-chains 418 residues out of total 4006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 328 time to evaluate : 1.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 589 TYR Chi-restraints excluded: chain A residue 599 VAL Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 698 LEU Chi-restraints excluded: chain A residue 774 MET Chi-restraints excluded: chain A residue 795 ILE Chi-restraints excluded: chain A residue 802 LEU Chi-restraints excluded: chain A residue 823 MET Chi-restraints excluded: chain A residue 876 CYS Chi-restraints excluded: chain A residue 899 VAL Chi-restraints excluded: chain A residue 996 GLU Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain A residue 1007 CYS Chi-restraints excluded: chain A residue 1033 ILE Chi-restraints excluded: chain A residue 1037 TRP Chi-restraints excluded: chain A residue 1096 LEU Chi-restraints excluded: chain A residue 1117 LEU Chi-restraints excluded: chain A residue 1173 VAL Chi-restraints excluded: chain A residue 1266 ARG Chi-restraints excluded: chain A residue 1279 TYR Chi-restraints excluded: chain A residue 1350 HIS Chi-restraints excluded: chain A residue 1353 VAL Chi-restraints excluded: chain A residue 1373 SER Chi-restraints excluded: chain A residue 1557 ILE Chi-restraints excluded: chain A residue 1575 GLU Chi-restraints excluded: chain A residue 1594 LEU Chi-restraints excluded: chain A residue 1632 MET Chi-restraints excluded: chain A residue 1649 VAL Chi-restraints excluded: chain A residue 1812 MET Chi-restraints excluded: chain A residue 2026 ILE Chi-restraints excluded: chain A residue 2150 THR Chi-restraints excluded: chain A residue 2162 GLU Chi-restraints excluded: chain A residue 2168 TYR Chi-restraints excluded: chain A residue 2170 TYR Chi-restraints excluded: chain A residue 2181 ASP Chi-restraints excluded: chain A residue 2190 VAL Chi-restraints excluded: chain A residue 2223 ASN Chi-restraints excluded: chain A residue 2255 MET Chi-restraints excluded: chain A residue 2396 THR Chi-restraints excluded: chain A residue 2404 LEU Chi-restraints excluded: chain A residue 2427 THR Chi-restraints excluded: chain A residue 2446 ILE Chi-restraints excluded: chain A residue 2476 ASP Chi-restraints excluded: chain A residue 2492 THR Chi-restraints excluded: chain A residue 2506 MET Chi-restraints excluded: chain A residue 2534 MET Chi-restraints excluded: chain A residue 2565 VAL Chi-restraints excluded: chain A residue 2645 VAL Chi-restraints excluded: chain A residue 2658 LEU Chi-restraints excluded: chain A residue 2686 MET Chi-restraints excluded: chain A residue 2691 VAL Chi-restraints excluded: chain A residue 2814 THR Chi-restraints excluded: chain A residue 2896 ARG Chi-restraints excluded: chain A residue 2923 LEU Chi-restraints excluded: chain A residue 2939 TYR Chi-restraints excluded: chain A residue 2999 PHE Chi-restraints excluded: chain A residue 3012 VAL Chi-restraints excluded: chain A residue 3077 ASP Chi-restraints excluded: chain A residue 3161 PHE Chi-restraints excluded: chain A residue 3204 HIS Chi-restraints excluded: chain A residue 3205 HIS Chi-restraints excluded: chain A residue 3219 ILE Chi-restraints excluded: chain A residue 3261 CYS Chi-restraints excluded: chain A residue 3379 THR Chi-restraints excluded: chain A residue 3451 MET Chi-restraints excluded: chain A residue 3619 THR Chi-restraints excluded: chain A residue 3699 MET Chi-restraints excluded: chain A residue 3728 TYR Chi-restraints excluded: chain A residue 3774 LEU Chi-restraints excluded: chain A residue 3838 VAL Chi-restraints excluded: chain A residue 3843 MET Chi-restraints excluded: chain A residue 3951 HIS Chi-restraints excluded: chain A residue 4096 LEU Chi-restraints excluded: chain A residue 4138 LEU Chi-restraints excluded: chain A residue 4189 TYR Chi-restraints excluded: chain A residue 4289 MET Chi-restraints excluded: chain A residue 4311 VAL Chi-restraints excluded: chain A residue 4512 SER Chi-restraints excluded: chain A residue 4524 ILE Chi-restraints excluded: chain A residue 4567 VAL Chi-restraints excluded: chain A residue 4578 VAL Chi-restraints excluded: chain A residue 4749 VAL Chi-restraints excluded: chain A residue 4781 VAL Chi-restraints excluded: chain A residue 4798 PHE Chi-restraints excluded: chain A residue 4864 THR Chi-restraints excluded: chain A residue 4870 LEU Chi-restraints excluded: chain A residue 5060 THR Chi-restraints excluded: chain A residue 5063 VAL Chi-restraints excluded: chain A residue 5103 SER Chi-restraints excluded: chain A residue 5138 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 377 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 106 optimal weight: 0.8980 chunk 409 optimal weight: 0.8980 chunk 446 optimal weight: 1.9990 chunk 215 optimal weight: 0.3980 chunk 335 optimal weight: 0.8980 chunk 51 optimal weight: 4.9990 chunk 188 optimal weight: 0.3980 chunk 191 optimal weight: 0.3980 chunk 323 optimal weight: 2.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 852 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3597 GLN ** A3884 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4066 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4619 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4626 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4936 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.137072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.097360 restraints weight = 75239.579| |-----------------------------------------------------------------------------| r_work (start): 0.3517 rms_B_bonded: 2.92 r_work: 0.3329 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.2027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 36690 Z= 0.124 Angle : 0.626 11.958 49662 Z= 0.308 Chirality : 0.041 0.288 5618 Planarity : 0.004 0.075 6348 Dihedral : 5.302 85.021 4866 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.65 % Favored : 93.31 % Rotamer: Outliers : 2.55 % Allowed : 20.41 % Favored : 77.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.55 % Twisted General : 0.02 % 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 aren not related in a simple way. whole: -0.52 (0.13), residues: 4439 helix: 0.62 (0.11), residues: 2520 sheet: -0.76 (0.34), residues: 221 loop : -1.75 (0.15), residues: 1698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A4970 TYR 0.020 0.001 TYR A3767 PHE 0.026 0.001 PHE A1286 TRP 0.025 0.001 TRP A 691 HIS 0.009 0.001 HIS A4983 Details of bonding type rmsd covalent geometry : bond 0.00279 (36690) covalent geometry : angle 0.62599 (49662) hydrogen bonds : bond 0.03579 ( 1741) hydrogen bonds : angle 4.45197 ( 5106) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8878 Ramachandran restraints generated. 4439 Oldfield, 0 Emsley, 4439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8878 Ramachandran restraints generated. 4439 Oldfield, 0 Emsley, 4439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 464 residues out of total 4006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 362 time to evaluate : 1.283 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 589 TYR cc_start: 0.6016 (OUTLIER) cc_final: 0.5526 (t80) REVERT: A 682 ARG cc_start: 0.8118 (ttm-80) cc_final: 0.7707 (mtt90) REVERT: A 734 MET cc_start: 0.3856 (ptm) cc_final: 0.3462 (ptm) REVERT: A 878 MET cc_start: 0.8174 (mtp) cc_final: 0.7971 (mtp) REVERT: A 996 GLU cc_start: 0.8063 (OUTLIER) cc_final: 0.7476 (tm-30) REVERT: A 1162 LYS cc_start: 0.8621 (mmtt) cc_final: 0.8283 (ptmm) REVERT: A 1220 MET cc_start: 0.7661 (OUTLIER) cc_final: 0.7212 (ttp) REVERT: A 1287 ILE cc_start: 0.8776 (mm) cc_final: 0.8570 (mm) REVERT: A 1350 HIS cc_start: 0.8045 (OUTLIER) cc_final: 0.7810 (m-70) REVERT: A 1557 ILE cc_start: 0.9213 (OUTLIER) cc_final: 0.8921 (tt) REVERT: A 1575 GLU cc_start: 0.6763 (OUTLIER) cc_final: 0.6519 (pm20) REVERT: A 1782 MET cc_start: 0.8387 (ttm) cc_final: 0.7882 (ttm) REVERT: A 2162 GLU cc_start: 0.8661 (OUTLIER) cc_final: 0.7573 (mt-10) REVERT: A 2168 TYR cc_start: 0.7922 (OUTLIER) cc_final: 0.7310 (t80) REVERT: A 2185 TYR cc_start: 0.8186 (OUTLIER) cc_final: 0.7790 (m-80) REVERT: A 2404 LEU cc_start: 0.9049 (OUTLIER) cc_final: 0.8687 (mm) REVERT: A 2686 MET cc_start: 0.8659 (OUTLIER) cc_final: 0.8377 (mtp) REVERT: A 2896 ARG cc_start: 0.7849 (OUTLIER) cc_final: 0.7400 (mmp-170) REVERT: A 3237 GLN cc_start: 0.8198 (mm110) cc_final: 0.7960 (mm110) REVERT: A 3832 LEU cc_start: 0.8288 (mp) cc_final: 0.8079 (mp) REVERT: A 3872 ARG cc_start: 0.8629 (mtm180) cc_final: 0.8338 (mtm180) REVERT: A 3883 LEU cc_start: 0.8199 (tp) cc_final: 0.7883 (tp) REVERT: A 3887 LYS cc_start: 0.8329 (mttp) cc_final: 0.8028 (mttp) REVERT: A 3891 MET cc_start: 0.8654 (mmm) cc_final: 0.8279 (tpt) REVERT: A 4064 MET cc_start: 0.8168 (ppp) cc_final: 0.7879 (ppp) REVERT: A 4069 PHE cc_start: 0.7559 (t80) cc_final: 0.7033 (m-80) REVERT: A 4192 ASN cc_start: 0.8791 (t0) cc_final: 0.8498 (p0) REVERT: A 4483 MET cc_start: 0.5483 (tpp) cc_final: 0.4961 (tpp) REVERT: A 4764 ARG cc_start: 0.7605 (mmm160) cc_final: 0.7219 (tpm170) REVERT: A 4777 GLU cc_start: 0.8253 (pt0) cc_final: 0.7898 (pm20) REVERT: A 4791 GLN cc_start: 0.8383 (mm-40) cc_final: 0.8060 (pp30) REVERT: A 4855 TYR cc_start: 0.7132 (m-80) cc_final: 0.6656 (m-80) REVERT: A 5035 LEU cc_start: 0.8665 (tt) cc_final: 0.8383 (mt) REVERT: A 5096 GLU cc_start: 0.7764 (pm20) cc_final: 0.7323 (pm20) outliers start: 102 outliers final: 67 residues processed: 436 average time/residue: 0.2210 time to fit residues: 159.7689 Evaluate side-chains 411 residues out of total 4006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 332 time to evaluate : 1.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 589 TYR Chi-restraints excluded: chain A residue 698 LEU Chi-restraints excluded: chain A residue 774 MET Chi-restraints excluded: chain A residue 802 LEU Chi-restraints excluded: chain A residue 823 MET Chi-restraints excluded: chain A residue 876 CYS Chi-restraints excluded: chain A residue 996 GLU Chi-restraints excluded: chain A residue 1033 ILE Chi-restraints excluded: chain A residue 1117 LEU Chi-restraints excluded: chain A residue 1173 VAL Chi-restraints excluded: chain A residue 1220 MET Chi-restraints excluded: chain A residue 1266 ARG Chi-restraints excluded: chain A residue 1279 TYR Chi-restraints excluded: chain A residue 1350 HIS Chi-restraints excluded: chain A residue 1353 VAL Chi-restraints excluded: chain A residue 1373 SER Chi-restraints excluded: chain A residue 1547 VAL Chi-restraints excluded: chain A residue 1557 ILE Chi-restraints excluded: chain A residue 1575 GLU Chi-restraints excluded: chain A residue 1594 LEU Chi-restraints excluded: chain A residue 1632 MET Chi-restraints excluded: chain A residue 1764 LEU Chi-restraints excluded: chain A residue 1812 MET Chi-restraints excluded: chain A residue 1823 ARG Chi-restraints excluded: chain A residue 1966 HIS Chi-restraints excluded: chain A residue 2026 ILE Chi-restraints excluded: chain A residue 2150 THR Chi-restraints excluded: chain A residue 2162 GLU Chi-restraints excluded: chain A residue 2168 TYR Chi-restraints excluded: chain A residue 2170 TYR Chi-restraints excluded: chain A residue 2185 TYR Chi-restraints excluded: chain A residue 2190 VAL Chi-restraints excluded: chain A residue 2223 ASN Chi-restraints excluded: chain A residue 2255 MET Chi-restraints excluded: chain A residue 2396 THR Chi-restraints excluded: chain A residue 2404 LEU Chi-restraints excluded: chain A residue 2427 THR Chi-restraints excluded: chain A residue 2446 ILE Chi-restraints excluded: chain A residue 2476 ASP Chi-restraints excluded: chain A residue 2615 ILE Chi-restraints excluded: chain A residue 2658 LEU Chi-restraints excluded: chain A residue 2686 MET Chi-restraints excluded: chain A residue 2782 VAL Chi-restraints excluded: chain A residue 2814 THR Chi-restraints excluded: chain A residue 2896 ARG Chi-restraints excluded: chain A residue 2939 TYR Chi-restraints excluded: chain A residue 3012 VAL Chi-restraints excluded: chain A residue 3161 PHE Chi-restraints excluded: chain A residue 3204 HIS Chi-restraints excluded: chain A residue 3219 ILE Chi-restraints excluded: chain A residue 3261 CYS Chi-restraints excluded: chain A residue 3379 THR Chi-restraints excluded: chain A residue 3451 MET Chi-restraints excluded: chain A residue 3619 THR Chi-restraints excluded: chain A residue 3699 MET Chi-restraints excluded: chain A residue 3728 TYR Chi-restraints excluded: chain A residue 3763 LEU Chi-restraints excluded: chain A residue 3774 LEU Chi-restraints excluded: chain A residue 3784 LEU Chi-restraints excluded: chain A residue 3842 LEU Chi-restraints excluded: chain A residue 3843 MET Chi-restraints excluded: chain A residue 3951 HIS Chi-restraints excluded: chain A residue 4008 VAL Chi-restraints excluded: chain A residue 4096 LEU Chi-restraints excluded: chain A residue 4138 LEU Chi-restraints excluded: chain A residue 4189 TYR Chi-restraints excluded: chain A residue 4311 VAL Chi-restraints excluded: chain A residue 4567 VAL Chi-restraints excluded: chain A residue 4621 LEU Chi-restraints excluded: chain A residue 4749 VAL Chi-restraints excluded: chain A residue 4781 VAL Chi-restraints excluded: chain A residue 4798 PHE Chi-restraints excluded: chain A residue 4825 LEU Chi-restraints excluded: chain A residue 4864 THR Chi-restraints excluded: chain A residue 4870 LEU Chi-restraints excluded: chain A residue 4932 LEU Chi-restraints excluded: chain A residue 5060 THR Chi-restraints excluded: chain A residue 5103 SER Chi-restraints excluded: chain A residue 5138 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 155 optimal weight: 1.9990 chunk 432 optimal weight: 0.9990 chunk 144 optimal weight: 1.9990 chunk 257 optimal weight: 0.7980 chunk 163 optimal weight: 4.9990 chunk 323 optimal weight: 3.9990 chunk 81 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 207 optimal weight: 0.8980 chunk 346 optimal weight: 4.9990 chunk 242 optimal weight: 0.6980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 593 HIS A1210 HIS A1350 HIS ** A1351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1602 ASN A2399 ASN A3849 HIS ** A3884 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3932 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4066 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4619 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4626 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4936 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.136029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.096628 restraints weight = 75612.244| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 2.77 r_work: 0.3297 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.2170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 36690 Z= 0.159 Angle : 0.649 13.785 49662 Z= 0.321 Chirality : 0.042 0.315 5618 Planarity : 0.004 0.074 6348 Dihedral : 5.308 83.470 4865 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.21 % Favored : 92.75 % Rotamer: Outliers : 2.85 % Allowed : 20.51 % Favored : 76.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.55 % Twisted General : 0.05 % 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 aren not related in a simple way. whole: -0.53 (0.13), residues: 4439 helix: 0.61 (0.11), residues: 2530 sheet: -0.84 (0.34), residues: 221 loop : -1.75 (0.15), residues: 1688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 713 TYR 0.022 0.001 TYR A3767 PHE 0.040 0.001 PHE A4068 TRP 0.019 0.001 TRP A 691 HIS 0.009 0.001 HIS A4983 Details of bonding type rmsd covalent geometry : bond 0.00368 (36690) covalent geometry : angle 0.64922 (49662) hydrogen bonds : bond 0.03677 ( 1741) hydrogen bonds : angle 4.48133 ( 5106) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8878 Ramachandran restraints generated. 4439 Oldfield, 0 Emsley, 4439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8878 Ramachandran restraints generated. 4439 Oldfield, 0 Emsley, 4439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 455 residues out of total 4006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 341 time to evaluate : 1.124 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 589 TYR cc_start: 0.6058 (OUTLIER) cc_final: 0.5504 (t80) REVERT: A 682 ARG cc_start: 0.8256 (ttm-80) cc_final: 0.7884 (mtt90) REVERT: A 878 MET cc_start: 0.8286 (mtp) cc_final: 0.8008 (mtp) REVERT: A 996 GLU cc_start: 0.8123 (OUTLIER) cc_final: 0.7531 (tm-30) REVERT: A 1162 LYS cc_start: 0.8728 (mmtt) cc_final: 0.8329 (ptmm) REVERT: A 1220 MET cc_start: 0.7632 (ttp) cc_final: 0.7084 (ttp) REVERT: A 1287 ILE cc_start: 0.8783 (mm) cc_final: 0.8572 (mm) REVERT: A 1350 HIS cc_start: 0.7753 (OUTLIER) cc_final: 0.7511 (m90) REVERT: A 1557 ILE cc_start: 0.9234 (OUTLIER) cc_final: 0.8942 (tt) REVERT: A 1575 GLU cc_start: 0.6679 (OUTLIER) cc_final: 0.6429 (pm20) REVERT: A 1653 MET cc_start: 0.7777 (OUTLIER) cc_final: 0.7212 (tpt) REVERT: A 1849 MET cc_start: 0.8226 (ttp) cc_final: 0.7967 (ttm) REVERT: A 2162 GLU cc_start: 0.8680 (OUTLIER) cc_final: 0.7354 (mt-10) REVERT: A 2168 TYR cc_start: 0.7958 (OUTLIER) cc_final: 0.7375 (t80) REVERT: A 2185 TYR cc_start: 0.8209 (OUTLIER) cc_final: 0.7681 (m-80) REVERT: A 2404 LEU cc_start: 0.9080 (OUTLIER) cc_final: 0.8708 (mm) REVERT: A 2452 HIS cc_start: 0.7130 (OUTLIER) cc_final: 0.6854 (m-70) REVERT: A 2527 TYR cc_start: 0.8075 (m-80) cc_final: 0.7814 (m-80) REVERT: A 2896 ARG cc_start: 0.7905 (OUTLIER) cc_final: 0.7459 (mmp-170) REVERT: A 3237 GLN cc_start: 0.8184 (mm110) cc_final: 0.7947 (mm110) REVERT: A 3454 ASP cc_start: 0.7663 (p0) cc_final: 0.7343 (p0) REVERT: A 3463 ILE cc_start: 0.9267 (OUTLIER) cc_final: 0.9011 (mt) REVERT: A 3832 LEU cc_start: 0.8302 (mp) cc_final: 0.8096 (mp) REVERT: A 3869 MET cc_start: 0.8945 (ppp) cc_final: 0.8519 (ppp) REVERT: A 3872 ARG cc_start: 0.8638 (mtm180) cc_final: 0.8370 (mtm180) REVERT: A 3883 LEU cc_start: 0.8215 (tp) cc_final: 0.7664 (tp) REVERT: A 3887 LYS cc_start: 0.8385 (mttp) cc_final: 0.7996 (mttp) REVERT: A 4069 PHE cc_start: 0.7645 (t80) cc_final: 0.7163 (m-80) REVERT: A 4192 ASN cc_start: 0.8835 (t0) cc_final: 0.8537 (p0) REVERT: A 4483 MET cc_start: 0.5522 (tpp) cc_final: 0.4993 (tpp) REVERT: A 4777 GLU cc_start: 0.8260 (pt0) cc_final: 0.7885 (pm20) REVERT: A 4791 GLN cc_start: 0.8392 (mm-40) cc_final: 0.7989 (pp30) REVERT: A 4855 TYR cc_start: 0.7037 (m-80) cc_final: 0.6717 (m-80) REVERT: A 5035 LEU cc_start: 0.8568 (tt) cc_final: 0.8293 (mt) REVERT: A 5096 GLU cc_start: 0.7813 (pm20) cc_final: 0.7382 (pm20) outliers start: 114 outliers final: 79 residues processed: 426 average time/residue: 0.2280 time to fit residues: 162.7488 Evaluate side-chains 422 residues out of total 4006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 330 time to evaluate : 1.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 589 TYR Chi-restraints excluded: chain A residue 599 VAL Chi-restraints excluded: chain A residue 698 LEU Chi-restraints excluded: chain A residue 774 MET Chi-restraints excluded: chain A residue 802 LEU Chi-restraints excluded: chain A residue 823 MET Chi-restraints excluded: chain A residue 876 CYS Chi-restraints excluded: chain A residue 942 LEU Chi-restraints excluded: chain A residue 996 GLU Chi-restraints excluded: chain A residue 1007 CYS Chi-restraints excluded: chain A residue 1033 ILE Chi-restraints excluded: chain A residue 1096 LEU Chi-restraints excluded: chain A residue 1117 LEU Chi-restraints excluded: chain A residue 1173 VAL Chi-restraints excluded: chain A residue 1266 ARG Chi-restraints excluded: chain A residue 1279 TYR Chi-restraints excluded: chain A residue 1350 HIS Chi-restraints excluded: chain A residue 1373 SER Chi-restraints excluded: chain A residue 1547 VAL Chi-restraints excluded: chain A residue 1557 ILE Chi-restraints excluded: chain A residue 1575 GLU Chi-restraints excluded: chain A residue 1594 LEU Chi-restraints excluded: chain A residue 1632 MET Chi-restraints excluded: chain A residue 1653 MET Chi-restraints excluded: chain A residue 1764 LEU Chi-restraints excluded: chain A residue 1812 MET Chi-restraints excluded: chain A residue 1966 HIS Chi-restraints excluded: chain A residue 2018 VAL Chi-restraints excluded: chain A residue 2026 ILE Chi-restraints excluded: chain A residue 2080 MET Chi-restraints excluded: chain A residue 2150 THR Chi-restraints excluded: chain A residue 2162 GLU Chi-restraints excluded: chain A residue 2168 TYR Chi-restraints excluded: chain A residue 2170 TYR Chi-restraints excluded: chain A residue 2181 ASP Chi-restraints excluded: chain A residue 2185 TYR Chi-restraints excluded: chain A residue 2190 VAL Chi-restraints excluded: chain A residue 2223 ASN Chi-restraints excluded: chain A residue 2255 MET Chi-restraints excluded: chain A residue 2341 ILE Chi-restraints excluded: chain A residue 2396 THR Chi-restraints excluded: chain A residue 2404 LEU Chi-restraints excluded: chain A residue 2427 THR Chi-restraints excluded: chain A residue 2446 ILE Chi-restraints excluded: chain A residue 2452 HIS Chi-restraints excluded: chain A residue 2476 ASP Chi-restraints excluded: chain A residue 2492 THR Chi-restraints excluded: chain A residue 2615 ILE Chi-restraints excluded: chain A residue 2645 VAL Chi-restraints excluded: chain A residue 2658 LEU Chi-restraints excluded: chain A residue 2686 MET Chi-restraints excluded: chain A residue 2782 VAL Chi-restraints excluded: chain A residue 2814 THR Chi-restraints excluded: chain A residue 2896 ARG Chi-restraints excluded: chain A residue 2939 TYR Chi-restraints excluded: chain A residue 2999 PHE Chi-restraints excluded: chain A residue 3012 VAL Chi-restraints excluded: chain A residue 3081 THR Chi-restraints excluded: chain A residue 3105 LEU Chi-restraints excluded: chain A residue 3161 PHE Chi-restraints excluded: chain A residue 3204 HIS Chi-restraints excluded: chain A residue 3219 ILE Chi-restraints excluded: chain A residue 3261 CYS Chi-restraints excluded: chain A residue 3379 THR Chi-restraints excluded: chain A residue 3451 MET Chi-restraints excluded: chain A residue 3463 ILE Chi-restraints excluded: chain A residue 3619 THR Chi-restraints excluded: chain A residue 3728 TYR Chi-restraints excluded: chain A residue 3763 LEU Chi-restraints excluded: chain A residue 3774 LEU Chi-restraints excluded: chain A residue 3842 LEU Chi-restraints excluded: chain A residue 3843 MET Chi-restraints excluded: chain A residue 4008 VAL Chi-restraints excluded: chain A residue 4138 LEU Chi-restraints excluded: chain A residue 4189 TYR Chi-restraints excluded: chain A residue 4311 VAL Chi-restraints excluded: chain A residue 4512 SER Chi-restraints excluded: chain A residue 4567 VAL Chi-restraints excluded: chain A residue 4590 LEU Chi-restraints excluded: chain A residue 4621 LEU Chi-restraints excluded: chain A residue 4749 VAL Chi-restraints excluded: chain A residue 4781 VAL Chi-restraints excluded: chain A residue 4798 PHE Chi-restraints excluded: chain A residue 4825 LEU Chi-restraints excluded: chain A residue 4864 THR Chi-restraints excluded: chain A residue 4870 LEU Chi-restraints excluded: chain A residue 4932 LEU Chi-restraints excluded: chain A residue 4961 VAL Chi-restraints excluded: chain A residue 5060 THR Chi-restraints excluded: chain A residue 5063 VAL Chi-restraints excluded: chain A residue 5103 SER Chi-restraints excluded: chain A residue 5138 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 17 optimal weight: 0.0770 chunk 334 optimal weight: 3.9990 chunk 307 optimal weight: 4.9990 chunk 14 optimal weight: 0.9980 chunk 240 optimal weight: 2.9990 chunk 169 optimal weight: 0.9990 chunk 313 optimal weight: 0.7980 chunk 285 optimal weight: 0.9990 chunk 426 optimal weight: 0.6980 chunk 429 optimal weight: 0.5980 chunk 179 optimal weight: 0.7980 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 593 HIS ** A 852 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1918 GLN A3725 GLN ** A3884 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3919 GLN ** A3932 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4066 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4619 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4626 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4728 HIS ** A4936 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.137148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.098150 restraints weight = 75200.627| |-----------------------------------------------------------------------------| r_work (start): 0.3533 rms_B_bonded: 3.10 r_work: 0.3315 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.2218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 36690 Z= 0.123 Angle : 0.632 12.770 49662 Z= 0.310 Chirality : 0.041 0.318 5618 Planarity : 0.004 0.074 6348 Dihedral : 5.219 83.362 4865 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.58 % Favored : 93.38 % Rotamer: Outliers : 2.60 % Allowed : 20.91 % Favored : 76.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.55 % Twisted General : 0.02 % 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 aren not related in a simple way. whole: -0.44 (0.13), residues: 4439 helix: 0.69 (0.11), residues: 2525 sheet: -0.76 (0.34), residues: 221 loop : -1.73 (0.15), residues: 1693 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 713 TYR 0.024 0.001 TYR A3767 PHE 0.042 0.001 PHE A4068 TRP 0.020 0.001 TRP A 691 HIS 0.029 0.001 HIS A1350 Details of bonding type rmsd covalent geometry : bond 0.00277 (36690) covalent geometry : angle 0.63223 (49662) hydrogen bonds : bond 0.03513 ( 1741) hydrogen bonds : angle 4.38959 ( 5106) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8878 Ramachandran restraints generated. 4439 Oldfield, 0 Emsley, 4439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8878 Ramachandran restraints generated. 4439 Oldfield, 0 Emsley, 4439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 452 residues out of total 4006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 348 time to evaluate : 1.587 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 589 TYR cc_start: 0.5995 (OUTLIER) cc_final: 0.5427 (t80) REVERT: A 682 ARG cc_start: 0.8112 (ttm-80) cc_final: 0.7735 (mtt90) REVERT: A 878 MET cc_start: 0.8322 (mtp) cc_final: 0.8012 (mtp) REVERT: A 996 GLU cc_start: 0.8065 (OUTLIER) cc_final: 0.7458 (tm-30) REVERT: A 1162 LYS cc_start: 0.8642 (mmtt) cc_final: 0.8285 (ptmm) REVERT: A 1286 PHE cc_start: 0.8665 (p90) cc_final: 0.8339 (p90) REVERT: A 1287 ILE cc_start: 0.8761 (mm) cc_final: 0.8524 (mm) REVERT: A 1557 ILE cc_start: 0.9209 (OUTLIER) cc_final: 0.8921 (tt) REVERT: A 1575 GLU cc_start: 0.6770 (OUTLIER) cc_final: 0.6524 (pm20) REVERT: A 1653 MET cc_start: 0.7760 (OUTLIER) cc_final: 0.7120 (tpt) REVERT: A 1782 MET cc_start: 0.8403 (ttm) cc_final: 0.8033 (ttm) REVERT: A 2162 GLU cc_start: 0.8650 (OUTLIER) cc_final: 0.7282 (mt-10) REVERT: A 2168 TYR cc_start: 0.7917 (OUTLIER) cc_final: 0.7320 (t80) REVERT: A 2185 TYR cc_start: 0.8200 (OUTLIER) cc_final: 0.7517 (m-80) REVERT: A 2404 LEU cc_start: 0.9053 (OUTLIER) cc_final: 0.8688 (mm) REVERT: A 2896 ARG cc_start: 0.7825 (OUTLIER) cc_final: 0.7376 (mmp-170) REVERT: A 3237 GLN cc_start: 0.8215 (mm110) cc_final: 0.7982 (mm110) REVERT: A 3463 ILE cc_start: 0.9258 (OUTLIER) cc_final: 0.8984 (mt) REVERT: A 3869 MET cc_start: 0.8967 (ppp) cc_final: 0.8584 (ppp) REVERT: A 3872 ARG cc_start: 0.8607 (mtm180) cc_final: 0.8316 (mtm180) REVERT: A 3883 LEU cc_start: 0.8211 (tp) cc_final: 0.7865 (tp) REVERT: A 3887 LYS cc_start: 0.8355 (mttp) cc_final: 0.7998 (mttp) REVERT: A 4064 MET cc_start: 0.7543 (ppp) cc_final: 0.7317 (ppp) REVERT: A 4069 PHE cc_start: 0.7579 (t80) cc_final: 0.7247 (m-80) REVERT: A 4192 ASN cc_start: 0.8864 (t0) cc_final: 0.8598 (p0) REVERT: A 4375 LEU cc_start: 0.9109 (tp) cc_final: 0.8655 (pp) REVERT: A 4483 MET cc_start: 0.5465 (tpp) cc_final: 0.4928 (tpp) REVERT: A 4581 LEU cc_start: 0.8523 (mt) cc_final: 0.8196 (pp) REVERT: A 4777 GLU cc_start: 0.8267 (pt0) cc_final: 0.7882 (pm20) REVERT: A 4791 GLN cc_start: 0.8328 (mm-40) cc_final: 0.8045 (pp30) REVERT: A 4855 TYR cc_start: 0.7047 (m-80) cc_final: 0.6626 (m-80) REVERT: A 4896 TYR cc_start: 0.8462 (OUTLIER) cc_final: 0.7822 (m-80) REVERT: A 5035 LEU cc_start: 0.8525 (tt) cc_final: 0.8270 (mt) REVERT: A 5096 GLU cc_start: 0.7793 (pm20) cc_final: 0.7388 (pm20) REVERT: A 5166 MET cc_start: 0.8411 (mpp) cc_final: 0.8045 (mpp) outliers start: 104 outliers final: 72 residues processed: 425 average time/residue: 0.2377 time to fit residues: 168.2858 Evaluate side-chains 414 residues out of total 4006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 330 time to evaluate : 1.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 589 TYR Chi-restraints excluded: chain A residue 599 VAL Chi-restraints excluded: chain A residue 698 LEU Chi-restraints excluded: chain A residue 802 LEU Chi-restraints excluded: chain A residue 823 MET Chi-restraints excluded: chain A residue 876 CYS Chi-restraints excluded: chain A residue 942 LEU Chi-restraints excluded: chain A residue 996 GLU Chi-restraints excluded: chain A residue 1007 CYS Chi-restraints excluded: chain A residue 1033 ILE Chi-restraints excluded: chain A residue 1117 LEU Chi-restraints excluded: chain A residue 1173 VAL Chi-restraints excluded: chain A residue 1266 ARG Chi-restraints excluded: chain A residue 1279 TYR Chi-restraints excluded: chain A residue 1349 LEU Chi-restraints excluded: chain A residue 1350 HIS Chi-restraints excluded: chain A residue 1353 VAL Chi-restraints excluded: chain A residue 1373 SER Chi-restraints excluded: chain A residue 1547 VAL Chi-restraints excluded: chain A residue 1557 ILE Chi-restraints excluded: chain A residue 1575 GLU Chi-restraints excluded: chain A residue 1594 LEU Chi-restraints excluded: chain A residue 1632 MET Chi-restraints excluded: chain A residue 1653 MET Chi-restraints excluded: chain A residue 1764 LEU Chi-restraints excluded: chain A residue 1812 MET Chi-restraints excluded: chain A residue 1966 HIS Chi-restraints excluded: chain A residue 2018 VAL Chi-restraints excluded: chain A residue 2026 ILE Chi-restraints excluded: chain A residue 2080 MET Chi-restraints excluded: chain A residue 2162 GLU Chi-restraints excluded: chain A residue 2168 TYR Chi-restraints excluded: chain A residue 2170 TYR Chi-restraints excluded: chain A residue 2185 TYR Chi-restraints excluded: chain A residue 2190 VAL Chi-restraints excluded: chain A residue 2223 ASN Chi-restraints excluded: chain A residue 2255 MET Chi-restraints excluded: chain A residue 2341 ILE Chi-restraints excluded: chain A residue 2396 THR Chi-restraints excluded: chain A residue 2404 LEU Chi-restraints excluded: chain A residue 2427 THR Chi-restraints excluded: chain A residue 2446 ILE Chi-restraints excluded: chain A residue 2476 ASP Chi-restraints excluded: chain A residue 2492 THR Chi-restraints excluded: chain A residue 2615 ILE Chi-restraints excluded: chain A residue 2658 LEU Chi-restraints excluded: chain A residue 2686 MET Chi-restraints excluded: chain A residue 2814 THR Chi-restraints excluded: chain A residue 2896 ARG Chi-restraints excluded: chain A residue 2939 TYR Chi-restraints excluded: chain A residue 3012 VAL Chi-restraints excluded: chain A residue 3077 ASP Chi-restraints excluded: chain A residue 3105 LEU Chi-restraints excluded: chain A residue 3161 PHE Chi-restraints excluded: chain A residue 3204 HIS Chi-restraints excluded: chain A residue 3219 ILE Chi-restraints excluded: chain A residue 3261 CYS Chi-restraints excluded: chain A residue 3319 THR Chi-restraints excluded: chain A residue 3451 MET Chi-restraints excluded: chain A residue 3463 ILE Chi-restraints excluded: chain A residue 3619 THR Chi-restraints excluded: chain A residue 3728 TYR Chi-restraints excluded: chain A residue 3763 LEU Chi-restraints excluded: chain A residue 3774 LEU Chi-restraints excluded: chain A residue 3842 LEU Chi-restraints excluded: chain A residue 3843 MET Chi-restraints excluded: chain A residue 4008 VAL Chi-restraints excluded: chain A residue 4138 LEU Chi-restraints excluded: chain A residue 4189 TYR Chi-restraints excluded: chain A residue 4311 VAL Chi-restraints excluded: chain A residue 4512 SER Chi-restraints excluded: chain A residue 4567 VAL Chi-restraints excluded: chain A residue 4590 LEU Chi-restraints excluded: chain A residue 4621 LEU Chi-restraints excluded: chain A residue 4781 VAL Chi-restraints excluded: chain A residue 4798 PHE Chi-restraints excluded: chain A residue 4816 HIS Chi-restraints excluded: chain A residue 4864 THR Chi-restraints excluded: chain A residue 4870 LEU Chi-restraints excluded: chain A residue 4896 TYR Chi-restraints excluded: chain A residue 4932 LEU Chi-restraints excluded: chain A residue 5060 THR Chi-restraints excluded: chain A residue 5103 SER Chi-restraints excluded: chain A residue 5138 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 204 optimal weight: 2.9990 chunk 344 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 155 optimal weight: 0.9990 chunk 139 optimal weight: 0.8980 chunk 232 optimal weight: 0.9980 chunk 224 optimal weight: 0.7980 chunk 446 optimal weight: 0.9990 chunk 249 optimal weight: 0.5980 chunk 81 optimal weight: 6.9990 chunk 145 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 593 HIS ** A 852 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1350 HIS ** A1351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2399 ASN ** A3884 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3932 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4066 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4619 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4626 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4936 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.136491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.097607 restraints weight = 75467.798| |-----------------------------------------------------------------------------| r_work (start): 0.3532 rms_B_bonded: 2.79 r_work: 0.3354 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3216 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.2320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 36690 Z= 0.140 Angle : 0.644 12.596 49662 Z= 0.315 Chirality : 0.041 0.317 5618 Planarity : 0.004 0.074 6348 Dihedral : 5.196 82.182 4864 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.12 % Favored : 92.84 % Rotamer: Outliers : 2.38 % Allowed : 21.41 % Favored : 76.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.55 % Twisted General : 0.05 % 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 aren not related in a simple way. whole: -0.43 (0.13), residues: 4439 helix: 0.69 (0.11), residues: 2531 sheet: -0.79 (0.34), residues: 221 loop : -1.71 (0.15), residues: 1687 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.000 ARG A2358 TYR 0.030 0.001 TYR A3767 PHE 0.039 0.001 PHE A4068 TRP 0.021 0.001 TRP A 591 HIS 0.009 0.001 HIS A4983 Details of bonding type rmsd covalent geometry : bond 0.00322 (36690) covalent geometry : angle 0.64375 (49662) hydrogen bonds : bond 0.03559 ( 1741) hydrogen bonds : angle 4.39907 ( 5106) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8878 Ramachandran restraints generated. 4439 Oldfield, 0 Emsley, 4439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8878 Ramachandran restraints generated. 4439 Oldfield, 0 Emsley, 4439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 436 residues out of total 4006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 341 time to evaluate : 1.218 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 589 TYR cc_start: 0.5963 (OUTLIER) cc_final: 0.5401 (t80) REVERT: A 682 ARG cc_start: 0.8200 (ttm-80) cc_final: 0.7825 (mtt90) REVERT: A 878 MET cc_start: 0.8452 (mtp) cc_final: 0.8096 (mtp) REVERT: A 996 GLU cc_start: 0.8199 (OUTLIER) cc_final: 0.7608 (tm-30) REVERT: A 1162 LYS cc_start: 0.8692 (mmtt) cc_final: 0.8337 (ptmm) REVERT: A 1286 PHE cc_start: 0.8673 (p90) cc_final: 0.8345 (p90) REVERT: A 1287 ILE cc_start: 0.8791 (mm) cc_final: 0.8543 (mm) REVERT: A 1557 ILE cc_start: 0.9221 (OUTLIER) cc_final: 0.8933 (tt) REVERT: A 1575 GLU cc_start: 0.6765 (OUTLIER) cc_final: 0.6485 (pm20) REVERT: A 1653 MET cc_start: 0.8000 (OUTLIER) cc_final: 0.7497 (tpt) REVERT: A 1782 MET cc_start: 0.8501 (ttm) cc_final: 0.8160 (ttm) REVERT: A 2162 GLU cc_start: 0.8661 (OUTLIER) cc_final: 0.7988 (mt-10) REVERT: A 2168 TYR cc_start: 0.8039 (OUTLIER) cc_final: 0.7426 (t80) REVERT: A 2185 TYR cc_start: 0.8296 (OUTLIER) cc_final: 0.7506 (m-80) REVERT: A 2404 LEU cc_start: 0.9119 (OUTLIER) cc_final: 0.8744 (mm) REVERT: A 2527 TYR cc_start: 0.8144 (m-80) cc_final: 0.7877 (m-80) REVERT: A 2896 ARG cc_start: 0.7952 (OUTLIER) cc_final: 0.7479 (mmp-170) REVERT: A 3237 GLN cc_start: 0.8449 (mm110) cc_final: 0.8206 (mm110) REVERT: A 3463 ILE cc_start: 0.9317 (OUTLIER) cc_final: 0.9046 (mt) REVERT: A 3869 MET cc_start: 0.8958 (ppp) cc_final: 0.8603 (ppp) REVERT: A 3872 ARG cc_start: 0.8580 (mtm180) cc_final: 0.8287 (mtm180) REVERT: A 3883 LEU cc_start: 0.8214 (tp) cc_final: 0.7788 (tp) REVERT: A 3887 LYS cc_start: 0.8388 (mttp) cc_final: 0.7953 (mttp) REVERT: A 4069 PHE cc_start: 0.7386 (t80) cc_final: 0.6880 (m-80) REVERT: A 4192 ASN cc_start: 0.8885 (t0) cc_final: 0.8642 (p0) REVERT: A 4326 ARG cc_start: 0.8258 (mtm110) cc_final: 0.7459 (ttp-170) REVERT: A 4375 LEU cc_start: 0.9118 (tp) cc_final: 0.8669 (pp) REVERT: A 4483 MET cc_start: 0.5506 (tpp) cc_final: 0.4953 (tpp) REVERT: A 4581 LEU cc_start: 0.8520 (mt) cc_final: 0.8220 (pp) REVERT: A 4777 GLU cc_start: 0.8367 (pt0) cc_final: 0.7973 (pm20) REVERT: A 4791 GLN cc_start: 0.8430 (mm-40) cc_final: 0.7998 (pp30) REVERT: A 4855 TYR cc_start: 0.7112 (m-80) cc_final: 0.6663 (m-80) REVERT: A 4970 ARG cc_start: 0.7160 (ttm110) cc_final: 0.6833 (ttm110) REVERT: A 5035 LEU cc_start: 0.8646 (tt) cc_final: 0.8330 (mt) REVERT: A 5096 GLU cc_start: 0.7861 (pm20) cc_final: 0.7430 (pm20) REVERT: A 5166 MET cc_start: 0.8724 (mpp) cc_final: 0.8397 (mpp) outliers start: 95 outliers final: 73 residues processed: 410 average time/residue: 0.2052 time to fit residues: 140.9170 Evaluate side-chains 412 residues out of total 4006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 328 time to evaluate : 1.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 589 TYR Chi-restraints excluded: chain A residue 599 VAL Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 698 LEU Chi-restraints excluded: chain A residue 802 LEU Chi-restraints excluded: chain A residue 823 MET Chi-restraints excluded: chain A residue 876 CYS Chi-restraints excluded: chain A residue 942 LEU Chi-restraints excluded: chain A residue 996 GLU Chi-restraints excluded: chain A residue 1007 CYS Chi-restraints excluded: chain A residue 1033 ILE Chi-restraints excluded: chain A residue 1117 LEU Chi-restraints excluded: chain A residue 1173 VAL Chi-restraints excluded: chain A residue 1266 ARG Chi-restraints excluded: chain A residue 1279 TYR Chi-restraints excluded: chain A residue 1353 VAL Chi-restraints excluded: chain A residue 1373 SER Chi-restraints excluded: chain A residue 1547 VAL Chi-restraints excluded: chain A residue 1557 ILE Chi-restraints excluded: chain A residue 1575 GLU Chi-restraints excluded: chain A residue 1594 LEU Chi-restraints excluded: chain A residue 1632 MET Chi-restraints excluded: chain A residue 1653 MET Chi-restraints excluded: chain A residue 1764 LEU Chi-restraints excluded: chain A residue 1812 MET Chi-restraints excluded: chain A residue 1966 HIS Chi-restraints excluded: chain A residue 2018 VAL Chi-restraints excluded: chain A residue 2026 ILE Chi-restraints excluded: chain A residue 2080 MET Chi-restraints excluded: chain A residue 2150 THR Chi-restraints excluded: chain A residue 2162 GLU Chi-restraints excluded: chain A residue 2168 TYR Chi-restraints excluded: chain A residue 2170 TYR Chi-restraints excluded: chain A residue 2185 TYR Chi-restraints excluded: chain A residue 2190 VAL Chi-restraints excluded: chain A residue 2223 ASN Chi-restraints excluded: chain A residue 2255 MET Chi-restraints excluded: chain A residue 2341 ILE Chi-restraints excluded: chain A residue 2396 THR Chi-restraints excluded: chain A residue 2404 LEU Chi-restraints excluded: chain A residue 2427 THR Chi-restraints excluded: chain A residue 2446 ILE Chi-restraints excluded: chain A residue 2476 ASP Chi-restraints excluded: chain A residue 2492 THR Chi-restraints excluded: chain A residue 2615 ILE Chi-restraints excluded: chain A residue 2645 VAL Chi-restraints excluded: chain A residue 2658 LEU Chi-restraints excluded: chain A residue 2814 THR Chi-restraints excluded: chain A residue 2896 ARG Chi-restraints excluded: chain A residue 2939 TYR Chi-restraints excluded: chain A residue 3012 VAL Chi-restraints excluded: chain A residue 3077 ASP Chi-restraints excluded: chain A residue 3105 LEU Chi-restraints excluded: chain A residue 3161 PHE Chi-restraints excluded: chain A residue 3204 HIS Chi-restraints excluded: chain A residue 3219 ILE Chi-restraints excluded: chain A residue 3261 CYS Chi-restraints excluded: chain A residue 3319 THR Chi-restraints excluded: chain A residue 3451 MET Chi-restraints excluded: chain A residue 3463 ILE Chi-restraints excluded: chain A residue 3619 THR Chi-restraints excluded: chain A residue 3728 TYR Chi-restraints excluded: chain A residue 3763 LEU Chi-restraints excluded: chain A residue 3774 LEU Chi-restraints excluded: chain A residue 3842 LEU Chi-restraints excluded: chain A residue 3843 MET Chi-restraints excluded: chain A residue 4008 VAL Chi-restraints excluded: chain A residue 4138 LEU Chi-restraints excluded: chain A residue 4189 TYR Chi-restraints excluded: chain A residue 4311 VAL Chi-restraints excluded: chain A residue 4512 SER Chi-restraints excluded: chain A residue 4567 VAL Chi-restraints excluded: chain A residue 4590 LEU Chi-restraints excluded: chain A residue 4621 LEU Chi-restraints excluded: chain A residue 4781 VAL Chi-restraints excluded: chain A residue 4798 PHE Chi-restraints excluded: chain A residue 4816 HIS Chi-restraints excluded: chain A residue 4864 THR Chi-restraints excluded: chain A residue 4870 LEU Chi-restraints excluded: chain A residue 4932 LEU Chi-restraints excluded: chain A residue 5060 THR Chi-restraints excluded: chain A residue 5063 VAL Chi-restraints excluded: chain A residue 5103 SER Chi-restraints excluded: chain A residue 5138 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 411 optimal weight: 2.9990 chunk 253 optimal weight: 0.9980 chunk 42 optimal weight: 0.4980 chunk 14 optimal weight: 3.9990 chunk 127 optimal weight: 0.5980 chunk 172 optimal weight: 1.9990 chunk 304 optimal weight: 0.8980 chunk 28 optimal weight: 0.0040 chunk 2 optimal weight: 7.9990 chunk 282 optimal weight: 2.9990 chunk 397 optimal weight: 8.9990 overall best weight: 0.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 593 HIS ** A 852 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2399 ASN ** A3884 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4066 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4619 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4626 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4936 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.137340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.098762 restraints weight = 75104.829| |-----------------------------------------------------------------------------| r_work (start): 0.3553 rms_B_bonded: 2.76 r_work: 0.3372 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3234 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.2361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 36690 Z= 0.124 Angle : 0.639 12.572 49662 Z= 0.312 Chirality : 0.041 0.323 5618 Planarity : 0.004 0.074 6348 Dihedral : 5.138 82.729 4864 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.40 % Favored : 93.56 % Rotamer: Outliers : 2.23 % Allowed : 21.66 % Favored : 76.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.55 % Twisted General : 0.02 % 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 aren not related in a simple way. whole: -0.39 (0.13), residues: 4439 helix: 0.73 (0.11), residues: 2530 sheet: -0.75 (0.34), residues: 221 loop : -1.70 (0.15), residues: 1688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A2358 TYR 0.030 0.001 TYR A3767 PHE 0.032 0.001 PHE A4068 TRP 0.032 0.001 TRP A 691 HIS 0.019 0.001 HIS A3932 Details of bonding type rmsd covalent geometry : bond 0.00280 (36690) covalent geometry : angle 0.63920 (49662) hydrogen bonds : bond 0.03480 ( 1741) hydrogen bonds : angle 4.36358 ( 5106) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8878 Ramachandran restraints generated. 4439 Oldfield, 0 Emsley, 4439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8878 Ramachandran restraints generated. 4439 Oldfield, 0 Emsley, 4439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 4006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 338 time to evaluate : 1.425 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 589 TYR cc_start: 0.5971 (OUTLIER) cc_final: 0.5400 (t80) REVERT: A 682 ARG cc_start: 0.8118 (ttm-80) cc_final: 0.7755 (mtt90) REVERT: A 878 MET cc_start: 0.8450 (mtp) cc_final: 0.8093 (mtp) REVERT: A 996 GLU cc_start: 0.8171 (OUTLIER) cc_final: 0.7579 (tm-30) REVERT: A 1162 LYS cc_start: 0.8672 (mmtt) cc_final: 0.8311 (ptmm) REVERT: A 1286 PHE cc_start: 0.8662 (p90) cc_final: 0.8305 (p90) REVERT: A 1287 ILE cc_start: 0.8793 (mm) cc_final: 0.8541 (mm) REVERT: A 1557 ILE cc_start: 0.9201 (OUTLIER) cc_final: 0.8917 (tt) REVERT: A 1575 GLU cc_start: 0.6803 (OUTLIER) cc_final: 0.5790 (pm20) REVERT: A 1653 MET cc_start: 0.7929 (OUTLIER) cc_final: 0.7319 (tpt) REVERT: A 2162 GLU cc_start: 0.8652 (OUTLIER) cc_final: 0.7992 (mt-10) REVERT: A 2168 TYR cc_start: 0.8045 (OUTLIER) cc_final: 0.7426 (t80) REVERT: A 2185 TYR cc_start: 0.8285 (OUTLIER) cc_final: 0.7337 (m-80) REVERT: A 2404 LEU cc_start: 0.9102 (OUTLIER) cc_final: 0.8743 (mm) REVERT: A 2896 ARG cc_start: 0.7826 (OUTLIER) cc_final: 0.7320 (mmp-170) REVERT: A 3237 GLN cc_start: 0.8451 (mm110) cc_final: 0.8189 (mm110) REVERT: A 3463 ILE cc_start: 0.9312 (OUTLIER) cc_final: 0.9041 (mt) REVERT: A 3869 MET cc_start: 0.8945 (ppp) cc_final: 0.8575 (ppp) REVERT: A 3872 ARG cc_start: 0.8569 (mtm180) cc_final: 0.8273 (mtm180) REVERT: A 3883 LEU cc_start: 0.8223 (tp) cc_final: 0.7872 (tp) REVERT: A 3887 LYS cc_start: 0.8416 (mttp) cc_final: 0.8064 (mttp) REVERT: A 4069 PHE cc_start: 0.7412 (t80) cc_final: 0.6950 (m-80) REVERT: A 4192 ASN cc_start: 0.8764 (t0) cc_final: 0.8533 (p0) REVERT: A 4375 LEU cc_start: 0.9146 (tp) cc_final: 0.8685 (pp) REVERT: A 4483 MET cc_start: 0.5462 (tpp) cc_final: 0.4905 (tpp) REVERT: A 4581 LEU cc_start: 0.8608 (mt) cc_final: 0.8322 (pp) REVERT: A 4777 GLU cc_start: 0.8360 (pt0) cc_final: 0.7966 (pm20) REVERT: A 4791 GLN cc_start: 0.8409 (mm-40) cc_final: 0.8075 (pp30) REVERT: A 4855 TYR cc_start: 0.7082 (m-80) cc_final: 0.6630 (m-80) REVERT: A 4970 ARG cc_start: 0.7124 (ttm110) cc_final: 0.6797 (ttm110) REVERT: A 5035 LEU cc_start: 0.8625 (tt) cc_final: 0.8356 (mt) REVERT: A 5096 GLU cc_start: 0.7815 (pm20) cc_final: 0.7354 (pm20) REVERT: A 5166 MET cc_start: 0.8638 (mpp) cc_final: 0.8370 (mpp) outliers start: 89 outliers final: 72 residues processed: 403 average time/residue: 0.2348 time to fit residues: 157.6539 Evaluate side-chains 412 residues out of total 4006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 329 time to evaluate : 1.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 589 TYR Chi-restraints excluded: chain A residue 599 VAL Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 698 LEU Chi-restraints excluded: chain A residue 802 LEU Chi-restraints excluded: chain A residue 823 MET Chi-restraints excluded: chain A residue 876 CYS Chi-restraints excluded: chain A residue 942 LEU Chi-restraints excluded: chain A residue 996 GLU Chi-restraints excluded: chain A residue 1007 CYS Chi-restraints excluded: chain A residue 1033 ILE Chi-restraints excluded: chain A residue 1117 LEU Chi-restraints excluded: chain A residue 1173 VAL Chi-restraints excluded: chain A residue 1266 ARG Chi-restraints excluded: chain A residue 1279 TYR Chi-restraints excluded: chain A residue 1353 VAL Chi-restraints excluded: chain A residue 1373 SER Chi-restraints excluded: chain A residue 1547 VAL Chi-restraints excluded: chain A residue 1557 ILE Chi-restraints excluded: chain A residue 1575 GLU Chi-restraints excluded: chain A residue 1594 LEU Chi-restraints excluded: chain A residue 1653 MET Chi-restraints excluded: chain A residue 1764 LEU Chi-restraints excluded: chain A residue 1812 MET Chi-restraints excluded: chain A residue 1966 HIS Chi-restraints excluded: chain A residue 2018 VAL Chi-restraints excluded: chain A residue 2026 ILE Chi-restraints excluded: chain A residue 2080 MET Chi-restraints excluded: chain A residue 2150 THR Chi-restraints excluded: chain A residue 2162 GLU Chi-restraints excluded: chain A residue 2168 TYR Chi-restraints excluded: chain A residue 2170 TYR Chi-restraints excluded: chain A residue 2185 TYR Chi-restraints excluded: chain A residue 2190 VAL Chi-restraints excluded: chain A residue 2223 ASN Chi-restraints excluded: chain A residue 2255 MET Chi-restraints excluded: chain A residue 2341 ILE Chi-restraints excluded: chain A residue 2396 THR Chi-restraints excluded: chain A residue 2404 LEU Chi-restraints excluded: chain A residue 2427 THR Chi-restraints excluded: chain A residue 2446 ILE Chi-restraints excluded: chain A residue 2476 ASP Chi-restraints excluded: chain A residue 2492 THR Chi-restraints excluded: chain A residue 2565 VAL Chi-restraints excluded: chain A residue 2645 VAL Chi-restraints excluded: chain A residue 2658 LEU Chi-restraints excluded: chain A residue 2814 THR Chi-restraints excluded: chain A residue 2896 ARG Chi-restraints excluded: chain A residue 2939 TYR Chi-restraints excluded: chain A residue 3012 VAL Chi-restraints excluded: chain A residue 3077 ASP Chi-restraints excluded: chain A residue 3105 LEU Chi-restraints excluded: chain A residue 3161 PHE Chi-restraints excluded: chain A residue 3204 HIS Chi-restraints excluded: chain A residue 3219 ILE Chi-restraints excluded: chain A residue 3261 CYS Chi-restraints excluded: chain A residue 3319 THR Chi-restraints excluded: chain A residue 3451 MET Chi-restraints excluded: chain A residue 3463 ILE Chi-restraints excluded: chain A residue 3619 THR Chi-restraints excluded: chain A residue 3728 TYR Chi-restraints excluded: chain A residue 3763 LEU Chi-restraints excluded: chain A residue 3774 LEU Chi-restraints excluded: chain A residue 4008 VAL Chi-restraints excluded: chain A residue 4138 LEU Chi-restraints excluded: chain A residue 4189 TYR Chi-restraints excluded: chain A residue 4311 VAL Chi-restraints excluded: chain A residue 4512 SER Chi-restraints excluded: chain A residue 4567 VAL Chi-restraints excluded: chain A residue 4590 LEU Chi-restraints excluded: chain A residue 4621 LEU Chi-restraints excluded: chain A residue 4765 VAL Chi-restraints excluded: chain A residue 4781 VAL Chi-restraints excluded: chain A residue 4798 PHE Chi-restraints excluded: chain A residue 4816 HIS Chi-restraints excluded: chain A residue 4864 THR Chi-restraints excluded: chain A residue 4870 LEU Chi-restraints excluded: chain A residue 4932 LEU Chi-restraints excluded: chain A residue 5060 THR Chi-restraints excluded: chain A residue 5063 VAL Chi-restraints excluded: chain A residue 5103 SER Chi-restraints excluded: chain A residue 5138 ILE Chi-restraints excluded: chain A residue 5173 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 260 optimal weight: 0.8980 chunk 358 optimal weight: 3.9990 chunk 166 optimal weight: 0.0020 chunk 287 optimal weight: 3.9990 chunk 113 optimal weight: 0.9980 chunk 44 optimal weight: 2.9990 chunk 108 optimal weight: 0.6980 chunk 224 optimal weight: 0.5980 chunk 70 optimal weight: 0.8980 chunk 80 optimal weight: 6.9990 chunk 156 optimal weight: 0.2980 overall best weight: 0.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 593 HIS ** A 852 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2303 HIS A3849 HIS ** A3884 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4066 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4619 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4626 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4936 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.137829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.099363 restraints weight = 74924.206| |-----------------------------------------------------------------------------| r_work (start): 0.3562 rms_B_bonded: 2.83 r_work: 0.3379 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3240 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.2421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 36690 Z= 0.119 Angle : 0.646 14.512 49662 Z= 0.313 Chirality : 0.041 0.312 5618 Planarity : 0.004 0.074 6348 Dihedral : 5.087 82.782 4864 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.65 % Favored : 93.31 % Rotamer: Outliers : 2.08 % Allowed : 22.03 % Favored : 75.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.55 % Twisted General : 0.02 % 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 aren not related in a simple way. whole: -0.35 (0.13), residues: 4439 helix: 0.76 (0.11), residues: 2532 sheet: -0.64 (0.35), residues: 219 loop : -1.70 (0.15), residues: 1688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A2358 TYR 0.015 0.001 TYR A 773 PHE 0.029 0.001 PHE A1286 TRP 0.023 0.001 TRP A 591 HIS 0.012 0.001 HIS A3932 Details of bonding type rmsd covalent geometry : bond 0.00268 (36690) covalent geometry : angle 0.64563 (49662) hydrogen bonds : bond 0.03419 ( 1741) hydrogen bonds : angle 4.33354 ( 5106) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10841.34 seconds wall clock time: 186 minutes 22.53 seconds (11182.53 seconds total)