Starting phenix.real_space_refine on Tue Aug 26 16:36:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9g09_50914/08_2025/9g09_50914.cif Found real_map, /net/cci-nas-00/data/ceres_data/9g09_50914/08_2025/9g09_50914.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9g09_50914/08_2025/9g09_50914.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9g09_50914/08_2025/9g09_50914.map" model { file = "/net/cci-nas-00/data/ceres_data/9g09_50914/08_2025/9g09_50914.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9g09_50914/08_2025/9g09_50914.cif" } resolution = 3.4 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= 0.006 sd= 0.081 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 3 6.06 5 P 3 5.49 5 Mg 1 5.21 5 S 227 5.16 5 C 24539 2.51 5 N 6618 2.21 5 O 7044 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 360 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: 38435 Number of models: 1 Model: "" Number of chains: 3 Chain: "B" Number of atoms: 1886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1886 Classifications: {'peptide': 237} Link IDs: {'PTRANS': 23, 'TRANS': 213} Chain: "A" Number of atoms: 36514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4529, 36514 Classifications: {'peptide': 4529} Modifications used: {'COO': 1} Link IDs: {'PCIS': 4, 'PTRANS': 181, 'TRANS': 4343} Chain breaks: 24 Chain: "A" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 35 Unusual residues: {' MG': 1, ' ZN': 3, 'ATP': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 33036 SG CYS A4525 70.910 72.948 144.775 1.00 84.37 S ATOM 29297 SG CYS A4000 60.830 32.988 207.331 1.00 97.40 S ATOM 29446 SG CYS A4020 63.306 28.572 208.296 1.00 97.87 S ATOM 29546 SG CYS A4032 54.015 22.506 210.061 1.00100.44 S ATOM 29571 SG CYS A4035 49.510 20.912 211.867 1.00103.12 S Time building chain proxies: 7.15, per 1000 atoms: 0.19 Number of scatterers: 38435 At special positions: 0 Unit cell: (142.312, 159.637, 246.262, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 3 29.99 S 227 16.00 P 3 15.00 Mg 1 11.99 O 7044 8.00 N 6618 7.00 C 24539 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.86 Conformation dependent library (CDL) restraints added in 1.7 seconds Enol-peptide restraints added in 476.8 nanoseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A5303 " pdb="ZN ZN A5303 " - pdb=" ND1 HIS A4509 " pdb="ZN ZN A5303 " - pdb=" SG CYS A4525 " pdb=" ZN A5304 " pdb="ZN ZN A5304 " - pdb=" SG CYS A4020 " pdb="ZN ZN A5304 " - pdb=" SG CYS A4000 " pdb=" ZN A5305 " pdb="ZN ZN A5305 " - pdb=" NE2 HIS A4014 " pdb="ZN ZN A5305 " - pdb=" SG CYS A4035 " pdb="ZN ZN A5305 " - pdb=" SG CYS A4032 " 9428 Ramachandran restraints generated. 4714 Oldfield, 0 Emsley, 4714 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9142 Finding SS restraints... Secondary structure from input PDB file: 235 helices and 22 sheets defined 63.6% alpha, 6.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.24 Creating SS restraints... Processing helix chain 'B' and resid 37 through 51 Processing helix chain 'B' and resid 57 through 72 Processing helix chain 'B' and resid 228 through 233 Processing helix chain 'B' and resid 247 through 260 removed outlier: 3.518A pdb=" N GLY B 260 " --> pdb=" O GLN B 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 444 removed outlier: 4.007A pdb=" N HIS A 443 " --> pdb=" O SER A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 518 through 541 removed outlier: 3.821A pdb=" N ILE A 540 " --> pdb=" O SER A 536 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N LEU A 541 " --> pdb=" O THR A 537 " (cutoff:3.500A) Processing helix chain 'A' and resid 545 through 565 Processing helix chain 'A' and resid 583 through 599 removed outlier: 3.617A pdb=" N TYR A 589 " --> pdb=" O GLU A 585 " (cutoff:3.500A) Processing helix chain 'A' and resid 619 through 633 Processing helix chain 'A' and resid 641 through 648 Processing helix chain 'A' and resid 654 through 667 removed outlier: 3.632A pdb=" N PHE A 658 " --> pdb=" O SER A 654 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N HIS A 664 " --> pdb=" O ARG A 660 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N ILE A 665 " --> pdb=" O ASP A 661 " (cutoff:3.500A) Processing helix chain 'A' and resid 671 through 686 Processing helix chain 'A' and resid 689 through 693 Processing helix chain 'A' and resid 694 through 703 removed outlier: 3.698A pdb=" N LEU A 698 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLU A 703 " --> pdb=" O HIS A 699 " (cutoff:3.500A) Processing helix chain 'A' and resid 710 through 714 Processing helix chain 'A' and resid 715 through 720 Processing helix chain 'A' and resid 726 through 734 removed outlier: 4.371A pdb=" N PHE A 730 " --> pdb=" O SER A 726 " (cutoff:3.500A) Processing helix chain 'A' and resid 736 through 747 removed outlier: 3.654A pdb=" N LEU A 740 " --> pdb=" O ASP A 736 " (cutoff:3.500A) Processing helix chain 'A' and resid 749 through 754 removed outlier: 3.743A pdb=" N ILE A 753 " --> pdb=" O HIS A 749 " (cutoff:3.500A) Processing helix chain 'A' and resid 756 through 765 Processing helix chain 'A' and resid 766 through 777 removed outlier: 4.523A pdb=" N VAL A 771 " --> pdb=" O LEU A 767 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N MET A 772 " --> pdb=" O SER A 768 " (cutoff:3.500A) Processing helix chain 'A' and resid 777 through 784 removed outlier: 3.662A pdb=" N LEU A 781 " --> pdb=" O PHE A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 786 through 808 removed outlier: 3.928A pdb=" N ASP A 790 " --> pdb=" O ALA A 786 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU A 792 " --> pdb=" O ILE A 788 " (cutoff:3.500A) Proline residue: A 800 - end of helix removed outlier: 3.714A pdb=" N THR A 808 " --> pdb=" O GLN A 804 " (cutoff:3.500A) Processing helix chain 'A' and resid 810 through 831 Processing helix chain 'A' and resid 842 through 859 removed outlier: 3.804A pdb=" N THR A 846 " --> pdb=" O PRO A 842 " (cutoff:3.500A) Processing helix chain 'A' and resid 861 through 864 Processing helix chain 'A' and resid 865 through 881 Processing helix chain 'A' and resid 899 through 918 Processing helix chain 'A' and resid 934 through 944 Processing helix chain 'A' and resid 948 through 951 Processing helix chain 'A' and resid 952 through 967 removed outlier: 3.689A pdb=" N SER A 956 " --> pdb=" O GLY A 952 " (cutoff:3.500A) Processing helix chain 'A' and resid 969 through 980 Processing helix chain 'A' and resid 982 through 986 removed outlier: 4.275A pdb=" N LYS A 985 " --> pdb=" O TRP A 982 " (cutoff:3.500A) Processing helix chain 'A' and resid 989 through 1010 removed outlier: 3.540A pdb=" N LYS A 993 " --> pdb=" O ASP A 989 " (cutoff:3.500A) Processing helix chain 'A' and resid 1021 through 1037 Processing helix chain 'A' and resid 1043 through 1054 Processing helix chain 'A' and resid 1055 through 1067 removed outlier: 3.615A pdb=" N HIS A1059 " --> pdb=" O ALA A1055 " (cutoff:3.500A) Processing helix chain 'A' and resid 1068 through 1074 Processing helix chain 'A' and resid 1075 through 1099 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 1167 Processing helix chain 'A' and resid 1168 through 1170 No H-bonds generated for 'chain 'A' and resid 1168 through 1170' Processing helix chain 'A' and resid 1175 through 1184 Processing helix chain 'A' and resid 1185 through 1189 removed outlier: 3.712A pdb=" N SER A1188 " --> pdb=" O ASP A1185 " (cutoff:3.500A) Processing helix chain 'A' and resid 1190 through 1195 Processing helix chain 'A' and resid 1214 through 1227 Processing helix chain 'A' and resid 1230 through 1235 removed outlier: 4.156A pdb=" N LEU A1235 " --> pdb=" O HIS A1231 " (cutoff:3.500A) Processing helix chain 'A' and resid 1270 through 1278 Processing helix chain 'A' and resid 1278 through 1296 Processing helix chain 'A' and resid 1299 through 1307 Processing helix chain 'A' and resid 1313 through 1326 Processing helix chain 'A' and resid 1335 through 1367 Processing helix chain 'A' and resid 1372 through 1374 No H-bonds generated for 'chain 'A' and resid 1372 through 1374' Processing helix chain 'A' and resid 1375 through 1384 Processing helix chain 'A' and resid 1384 through 1389 Processing helix chain 'A' and resid 1398 through 1407 Processing helix chain 'A' and resid 1411 through 1423 removed outlier: 3.620A pdb=" N LEU A1423 " --> pdb=" O GLN A1419 " (cutoff:3.500A) Processing helix chain 'A' and resid 1424 through 1435 Processing helix chain 'A' and resid 1437 through 1452 removed outlier: 3.765A pdb=" N LEU A1441 " --> pdb=" O GLY A1437 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N LYS A1442 " --> pdb=" O ILE A1438 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N VAL A1443 " --> pdb=" O ASN A1439 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE A1450 " --> pdb=" O ASP A1446 " (cutoff:3.500A) Processing helix chain 'A' and resid 1455 through 1472 removed outlier: 4.073A pdb=" N VAL A1462 " --> pdb=" O ASP A1458 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ALA A1463 " --> pdb=" O VAL A1459 " (cutoff:3.500A) Processing helix chain 'A' and resid 1472 through 1477 removed outlier: 3.597A pdb=" N LEU A1476 " --> pdb=" O TYR A1472 " (cutoff:3.500A) Processing helix chain 'A' and resid 1484 through 1502 removed outlier: 3.749A pdb=" N LEU A1495 " --> pdb=" O HIS A1491 " (cutoff:3.500A) Processing helix chain 'A' and resid 1504 through 1515 Processing helix chain 'A' and resid 1515 through 1525 removed outlier: 4.073A pdb=" N ASN A1523 " --> pdb=" O LEU A1519 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N GLU A1524 " --> pdb=" O LYS A1520 " (cutoff:3.500A) Processing helix chain 'A' and resid 1532 through 1543 removed outlier: 3.660A pdb=" N LEU A1536 " --> pdb=" O SER A1532 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ALA A1537 " --> pdb=" O SER A1533 " (cutoff:3.500A) Processing helix chain 'A' and resid 1558 through 1562 Processing helix chain 'A' and resid 1582 through 1596 Processing helix chain 'A' and resid 1602 through 1630 removed outlier: 3.541A pdb=" N GLY A1630 " --> pdb=" O LEU A1626 " (cutoff:3.500A) Processing helix chain 'A' and resid 1632 through 1636 removed outlier: 3.964A pdb=" N THR A1636 " --> pdb=" O LEU A1633 " (cutoff:3.500A) Processing helix chain 'A' and resid 1668 through 1698 removed outlier: 3.528A pdb=" N LEU A1672 " --> pdb=" O ASP A1668 " (cutoff:3.500A) Processing helix chain 'A' and resid 1699 through 1704 Processing helix chain 'A' and resid 1705 through 1717 removed outlier: 4.229A pdb=" N ARG A1717 " --> pdb=" O SER A1713 " (cutoff:3.500A) Processing helix chain 'A' and resid 1722 through 1731 removed outlier: 3.805A pdb=" N PHE A1731 " --> pdb=" O THR A1727 " (cutoff:3.500A) Processing helix chain 'A' and resid 1737 through 1746 removed outlier: 3.623A pdb=" N VAL A1746 " --> pdb=" O LEU A1742 " (cutoff:3.500A) Processing helix chain 'A' and resid 1750 through 1771 removed outlier: 3.655A pdb=" N ARG A1754 " --> pdb=" O SER A1750 " (cutoff:3.500A) Proline residue: A1765 - end of helix Processing helix chain 'A' and resid 1773 through 1788 Processing helix chain 'A' and resid 1798 through 1813 Processing helix chain 'A' and resid 1836 through 1850 removed outlier: 4.400A pdb=" N LEU A1841 " --> pdb=" O HIS A1837 " (cutoff:3.500A) Proline residue: A1842 - end of helix removed outlier: 3.535A pdb=" N TYR A1848 " --> pdb=" O ALA A1844 " (cutoff:3.500A) Processing helix chain 'A' and resid 1870 through 1883 removed outlier: 3.752A pdb=" N VAL A1874 " --> pdb=" O THR A1870 " (cutoff:3.500A) Processing helix chain 'A' and resid 1896 through 1900 Processing helix chain 'A' and resid 1901 through 1918 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 1943 Processing helix chain 'A' and resid 1944 through 1947 Processing helix chain 'A' and resid 1955 through 1968 Processing helix chain 'A' and resid 1975 through 1980 removed outlier: 3.545A pdb=" N ALA A1978 " --> pdb=" O SER A1975 " (cutoff:3.500A) Processing helix chain 'A' and resid 1997 through 2013 Processing helix chain 'A' and resid 2031 through 2040 removed outlier: 3.628A pdb=" N VAL A2035 " --> pdb=" O ASP A2031 " (cutoff:3.500A) Processing helix chain 'A' and resid 2041 through 2050 removed outlier: 3.878A pdb=" N ASP A2044 " --> pdb=" O PRO A2041 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N ALA A2045 " --> pdb=" O PHE A2042 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N GLN A2046 " --> pdb=" O LEU A2043 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N LYS A2049 " --> pdb=" O GLN A2046 " (cutoff:3.500A) Processing helix chain 'A' and resid 2065 through 2075 Processing helix chain 'A' and resid 2122 through 2127 Processing helix chain 'A' and resid 2134 through 2142 Processing helix chain 'A' and resid 2155 through 2160 Processing helix chain 'A' and resid 2161 through 2176 Proline residue: A2167 - end of helix removed outlier: 3.735A pdb=" N GLN A2176 " --> pdb=" O ARG A2172 " (cutoff:3.500A) Processing helix chain 'A' and resid 2193 through 2206 removed outlier: 4.362A pdb=" N GLY A2206 " --> pdb=" O LEU A2202 " (cutoff:3.500A) Processing helix chain 'A' and resid 2211 through 2232 Processing helix chain 'A' and resid 2246 through 2264 removed outlier: 4.040A pdb=" N ARG A2260 " --> pdb=" O ILE A2256 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N ASP A2261 " --> pdb=" O PHE A2257 " (cutoff:3.500A) removed outlier: 4.099A 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 2364 through 2368 Processing helix chain 'A' and resid 2369 through 2382 Processing helix chain 'A' and resid 2396 through 2413 Processing helix chain 'A' and resid 2425 through 2439 Processing helix chain 'A' and resid 2456 through 2478 Processing helix chain 'A' and resid 2488 through 2493 removed outlier: 5.132A pdb=" N GLU A2493 " --> pdb=" O ASN A2490 " (cutoff:3.500A) Processing helix chain 'A' and resid 2494 through 2503 Processing helix chain 'A' and resid 2531 through 2541 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 2606 Processing helix chain 'A' and resid 2608 through 2629 Processing helix chain 'A' and resid 2638 through 2669 removed outlier: 4.333A pdb=" N ALA A2656 " --> pdb=" O HIS A2652 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N MET A2657 " --> pdb=" O GLU A2653 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA A2660 " --> pdb=" O ALA A2656 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N SER A2669 " --> pdb=" O PHE A2665 " (cutoff:3.500A) Processing helix chain 'A' and resid 2679 through 2693 Processing helix chain 'A' and resid 2699 through 2709 removed outlier: 3.658A pdb=" N TYR A2703 " --> pdb=" O LYS A2699 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ARG A2709 " --> pdb=" O LYS A2705 " (cutoff:3.500A) Processing helix chain 'A' and resid 2717 through 2734 Processing helix chain 'A' and resid 2745 through 2762 Processing helix chain 'A' and resid 2774 through 2786 Processing helix chain 'A' and resid 2793 through 2799 Processing helix chain 'A' and resid 2814 through 2830 removed outlier: 3.810A pdb=" N ILE A2818 " --> pdb=" O THR A2814 " (cutoff:3.500A) Processing helix chain 'A' and resid 2846 through 2850 Processing helix chain 'A' and resid 2855 through 2858 removed outlier: 3.511A pdb=" N LYS A2858 " --> pdb=" O MET A2855 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2855 through 2858' Processing helix chain 'A' and resid 2859 through 2866 Processing helix chain 'A' and resid 2874 through 2878 Processing helix chain 'A' and resid 2890 through 2895 removed outlier: 3.832A pdb=" N ASN A2895 " --> pdb=" O ALA A2892 " (cutoff:3.500A) Processing helix chain 'A' and resid 2906 through 2919 Processing helix chain 'A' and resid 2922 through 2946 removed outlier: 4.292A pdb=" N GLY A2930 " --> pdb=" O ASP A2926 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N TYR A2931 " --> pdb=" O ARG A2927 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ALA A2933 " --> pdb=" O GLN A2929 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N SER A2934 " --> pdb=" O GLY A2930 " (cutoff:3.500A) Processing helix chain 'A' and resid 2952 through 2971 removed outlier: 3.588A pdb=" N TYR A2956 " --> pdb=" O GLY A2952 " (cutoff:3.500A) Processing helix chain 'A' and resid 2975 through 2988 Processing helix chain 'A' and resid 2994 through 3002 Processing helix chain 'A' and resid 3003 through 3008 removed outlier: 4.297A pdb=" N ALA A3006 " --> pdb=" O LEU A3003 " (cutoff:3.500A) Processing helix chain 'A' and resid 3013 through 3023 Processing helix chain 'A' and resid 3050 through 3059 removed outlier: 3.748A pdb=" N ILE A3054 " --> pdb=" O VAL A3050 " (cutoff:3.500A) Processing helix chain 'A' and resid 3079 through 3097 Processing helix chain 'A' and resid 3105 through 3107 No H-bonds generated for 'chain 'A' and resid 3105 through 3107' Processing helix chain 'A' and resid 3108 through 3118 removed outlier: 5.770A pdb=" N ASP A3114 " --> pdb=" O GLU A3110 " (cutoff:3.500A) removed outlier: 5.667A pdb=" N ALA A3115 " --> pdb=" O SER A3111 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ASN A3117 " --> pdb=" O TYR A3113 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLN A3118 " --> pdb=" O ASP A3114 " (cutoff:3.500A) Processing helix chain 'A' and resid 3154 through 3160 Processing helix chain 'A' and resid 3162 through 3169 Processing helix chain 'A' and resid 3175 through 3180 removed outlier: 3.515A pdb=" N VAL A3179 " --> pdb=" O ASP A3175 " (cutoff:3.500A) Processing helix chain 'A' and resid 3181 through 3201 Processing helix chain 'A' and resid 3213 through 3218 Processing helix chain 'A' and resid 3224 through 3238 Processing helix chain 'A' and resid 3243 through 3261 removed outlier: 3.657A pdb=" N CYS A3261 " --> pdb=" O ILE A3257 " (cutoff:3.500A) Processing helix chain 'A' and resid 3263 through 3274 Processing helix chain 'A' and resid 3277 through 3289 Processing helix chain 'A' and resid 3295 through 3307 removed outlier: 3.546A pdb=" N PHE A3299 " --> pdb=" O SER A3295 " (cutoff:3.500A) Processing helix chain 'A' and resid 3326 through 3338 Processing helix chain 'A' and resid 3350 through 3352 No H-bonds generated for 'chain 'A' and resid 3350 through 3352' Processing helix chain 'A' and resid 3354 through 3367 removed outlier: 3.512A pdb=" N PHE A3358 " --> pdb=" O THR A3354 " (cutoff:3.500A) Processing helix chain 'A' and resid 3387 through 3405 Processing helix chain 'A' and resid 3457 through 3461 Processing helix chain 'A' and resid 3462 through 3467 removed outlier: 3.930A pdb=" N PHE A3467 " --> pdb=" O ILE A3463 " (cutoff:3.500A) Processing helix chain 'A' and resid 3531 through 3546 removed outlier: 4.692A pdb=" N GLN A3541 " --> pdb=" O ARG A3537 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N SER A3542 " --> pdb=" O SER A3538 " (cutoff:3.500A) Processing helix chain 'A' and resid 3555 through 3568 removed outlier: 3.678A pdb=" N ARG A3559 " --> pdb=" O THR A3555 " (cutoff:3.500A) Processing helix chain 'A' and resid 3572 through 3595 Processing helix chain 'A' and resid 3599 through 3601 No H-bonds generated for 'chain 'A' and resid 3599 through 3601' Processing helix chain 'A' and resid 3602 through 3609 Processing helix chain 'A' and resid 3610 through 3618 Processing helix chain 'A' and resid 3619 through 3644 Proline residue: A3634 - end of helix Processing helix chain 'A' and resid 3648 through 3654 removed outlier: 4.107A pdb=" N LEU A3652 " --> pdb=" O ASN A3648 " (cutoff:3.500A) Processing helix chain 'A' and resid 3658 through 3671 removed outlier: 3.573A pdb=" N ARG A3662 " --> pdb=" O PRO A3658 " (cutoff:3.500A) Processing helix chain 'A' and resid 3711 through 3730 Processing helix chain 'A' and resid 3734 through 3746 Processing helix chain 'A' and resid 3746 through 3755 Processing helix chain 'A' and resid 3757 through 3776 removed outlier: 3.589A pdb=" N GLN A3761 " --> pdb=" O GLY A3757 " (cutoff:3.500A) Processing helix chain 'A' and resid 3780 through 3801 Processing helix chain 'A' and resid 3811 through 3821 removed outlier: 3.826A 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 3843 removed outlier: 3.639A pdb=" N SER A3841 " --> pdb=" O GLN A3837 " (cutoff:3.500A) Processing helix chain 'A' and resid 3857 through 3872 Processing helix chain 'A' and resid 3878 through 3897 removed outlier: 4.117A pdb=" N MET A3891 " --> pdb=" O LYS A3887 " (cutoff:3.500A) Proline residue: A3892 - end of helix Processing helix chain 'A' and resid 3906 through 3941 removed outlier: 4.257A pdb=" N LEU A3935 " --> pdb=" O GLU A3931 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N GLY A3936 " --> pdb=" O HIS A3932 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N SER A3939 " --> pdb=" O LEU A3935 " (cutoff:3.500A) Processing helix chain 'A' and resid 3944 through 3960 removed outlier: 3.526A pdb=" N PHE A3953 " --> pdb=" O THR A3949 " (cutoff:3.500A) Processing helix chain 'A' and resid 3967 through 3990 removed outlier: 3.668A pdb=" N PHE A3971 " --> pdb=" O THR A3967 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N SER A3990 " --> pdb=" O SER A3986 " (cutoff:3.500A) Processing helix chain 'A' and resid 4018 through 4025 Processing helix chain 'A' and resid 4048 through 4076 Processing helix chain 'A' and resid 4085 through 4096 Processing helix chain 'A' and resid 4132 through 4140 Processing helix chain 'A' and resid 4142 through 4158 removed outlier: 5.611A pdb=" N ASP A4148 " --> pdb=" O HIS A4144 " (cutoff:3.500A) removed outlier: 5.228A pdb=" N TYR A4149 " --> pdb=" O ASP A4145 " (cutoff:3.500A) Processing helix chain 'A' and resid 4167 through 4187 Processing helix chain 'A' and resid 4190 through 4208 Processing helix chain 'A' and resid 4222 through 4245 Processing helix chain 'A' and resid 4253 through 4271 removed outlier: 3.695A pdb=" N GLU A4271 " --> pdb=" O CYS A4267 " (cutoff:3.500A) Processing helix chain 'A' and resid 4273 through 4287 Processing helix chain 'A' and resid 4288 through 4297 removed outlier: 3.658A pdb=" N VAL A4292 " --> pdb=" O GLY A4288 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LYS A4297 " --> pdb=" O GLN A4293 " (cutoff:3.500A) Processing helix chain 'A' and resid 4302 through 4306 Processing helix chain 'A' and resid 4307 through 4314 removed outlier: 4.436A pdb=" N VAL A4311 " --> pdb=" O PRO A4307 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N LYS A4312 " --> pdb=" O LYS A4308 " (cutoff:3.500A) Processing helix chain 'A' and resid 4325 through 4330 Processing helix chain 'A' and resid 4331 through 4348 Processing helix chain 'A' and resid 4351 through 4360 Processing helix chain 'A' and resid 4363 through 4384 removed outlier: 4.142A pdb=" N ILE A4381 " --> pdb=" O ARG A4377 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ARG A4384 " --> pdb=" O ALA A4380 " (cutoff:3.500A) Processing helix chain 'A' and resid 4387 through 4391 Processing helix chain 'A' and resid 4393 through 4407 Processing helix chain 'A' and resid 4412 through 4424 Processing helix chain 'A' and resid 4441 through 4457 Processing helix chain 'A' and resid 4459 through 4461 No H-bonds generated for 'chain 'A' and resid 4459 through 4461' Processing helix chain 'A' and resid 4462 through 4471 Processing helix chain 'A' and resid 4472 through 4478 removed outlier: 4.305A pdb=" N HIS A4477 " --> pdb=" O THR A4474 " (cutoff:3.500A) Processing helix chain 'A' and resid 4486 through 4492 removed outlier: 3.901A pdb=" N ARG A4492 " --> pdb=" O LEU A4488 " (cutoff:3.500A) Processing helix chain 'A' and resid 4561 through 4565 Processing helix chain 'A' and resid 4575 through 4597 Processing helix chain 'A' and resid 4597 through 4605 removed outlier: 3.838A pdb=" N LEU A4601 " --> pdb=" O SER A4597 " (cutoff:3.500A) Processing helix chain 'A' and resid 4611 through 4632 Processing helix chain 'A' and resid 4634 through 4652 Processing helix chain 'A' and resid 4670 through 4690 removed outlier: 3.607A pdb=" N ARG A4674 " --> pdb=" O THR A4670 " (cutoff:3.500A) Proline residue: A4687 - end of helix removed outlier: 3.678A pdb=" N GLU A4690 " --> pdb=" O SER A4686 " (cutoff:3.500A) Processing helix chain 'A' and resid 4691 through 4705 Proline residue: A4697 - end of helix Processing helix chain 'A' and resid 4706 through 4711 removed outlier: 4.119A pdb=" N SER A4711 " --> pdb=" O LYS A4707 " (cutoff:3.500A) Processing helix chain 'A' and resid 4712 through 4720 Processing helix chain 'A' and resid 4721 through 4725 Processing helix chain 'A' and resid 4733 through 4737 Processing helix chain 'A' and resid 4748 through 4759 Processing helix chain 'A' and resid 4760 through 4765 Processing helix chain 'A' and resid 4765 through 4779 removed outlier: 5.098A pdb=" N ALA A4776 " --> pdb=" O LEU A4772 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N GLU A4777 " --> pdb=" O GLN A4773 " (cutoff:3.500A) 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 4799 Processing helix chain 'A' and resid 4808 through 4816 Processing helix chain 'A' and resid 4818 through 4844 removed outlier: 5.114A pdb=" N ARG A4841 " --> pdb=" O ASN A4837 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N SER A4842 " --> pdb=" O LYS A4838 " (cutoff:3.500A) Processing helix chain 'A' and resid 4852 through 4858 removed outlier: 3.921A pdb=" N CYS A4856 " --> pdb=" O PRO A4852 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N THR A4858 " --> pdb=" O ASP A4854 " (cutoff:3.500A) Processing helix chain 'A' and resid 4865 through 4870 removed outlier: 3.581A pdb=" N ILE A4868 " --> pdb=" O GLU A4865 " (cutoff:3.500A) Processing helix chain 'A' and resid 4876 through 4903 removed outlier: 4.256A pdb=" N ALA A4880 " --> pdb=" O LEU A4876 " (cutoff:3.500A) Processing helix chain 'A' and resid 4928 through 4936 Processing helix chain 'A' and resid 4952 through 4965 removed outlier: 3.570A pdb=" N LEU A4965 " --> pdb=" O VAL A4961 " (cutoff:3.500A) Processing helix chain 'A' and resid 4981 through 4985 Processing helix chain 'A' and resid 4986 through 4998 removed outlier: 3.644A 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 Processing helix chain 'A' and resid 5062 through 5068 removed outlier: 3.510A pdb=" N ALA A5066 " --> pdb=" O HIS A5062 " (cutoff:3.500A) Processing helix chain 'A' and resid 5071 through 5073 No H-bonds generated for 'chain 'A' and resid 5071 through 5073' Processing helix chain 'A' and resid 5074 through 5093 Processing helix chain 'A' and resid 5102 through 5106 Processing helix chain 'A' and resid 5110 through 5123 Processing helix chain 'A' and resid 5125 through 5143 removed outlier: 3.583A pdb=" N LYS A5142 " --> pdb=" O ILE A5138 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ASN A5143 " --> pdb=" O LEU A5139 " (cutoff:3.500A) Processing helix chain 'A' and resid 5143 through 5149 Processing helix chain 'A' and resid 5157 through 5169 Processing helix chain 'A' and resid 5174 through 5180 removed outlier: 4.267A pdb=" N ALA A5178 " --> pdb=" O LEU A5174 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N SER A5179 " --> pdb=" O PRO A5175 " (cutoff:3.500A) Processing helix chain 'A' and resid 5189 through 5207 Processing sheet with id=AA1, first strand: chain 'B' and resid 95 through 97 removed outlier: 6.464A pdb=" N ILE B 116 " --> pdb=" O ASN B 137 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N LEU B 136 " --> pdb=" O ARG B 157 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 175 through 177 removed outlier: 6.350A pdb=" N LEU B 176 " --> pdb=" O ALA B 197 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ASN B 240 " --> pdb=" O ALA B 216 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N VAL B 239 " --> pdb=" O PHE B 269 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 460 through 462 removed outlier: 4.721A pdb=" N VAL A 400 " --> pdb=" O LEU A 420 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N GLU A 419 " --> pdb=" O ILE A 436 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N ILE A 436 " --> pdb=" O GLU A 419 " (cutoff:3.500A) removed outlier: 10.972A pdb=" N THR A 380 " --> pdb=" O HIS A 493 " (cutoff:3.500A) removed outlier: 10.613A pdb=" N TYR A 495 " --> pdb=" O THR A 380 " (cutoff:3.500A) removed outlier: 9.654A pdb=" N PHE A 382 " --> pdb=" O TYR A 495 " (cutoff:3.500A) removed outlier: 8.826A pdb=" N ASP A 497 " --> pdb=" O PHE A 382 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N HIS A 384 " --> pdb=" O ASP A 497 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N VAL A 499 " --> pdb=" O HIS A 384 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N ILE A 386 " --> pdb=" O VAL A 499 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 460 through 462 removed outlier: 3.759A pdb=" N ASN A 477 " --> pdb=" O TYR A 569 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N CYS A 479 " --> pdb=" O MET A 567 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N MET A 567 " --> pdb=" O CYS A 479 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1578 through 1581 removed outlier: 5.599A pdb=" N SER A1650 " --> pdb=" O TYR A1642 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N GLU A1665 " --> pdb=" O SER A1650 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N GLN A1652 " --> pdb=" O LEU A1663 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N LEU A1663 " --> pdb=" O GLN A1652 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1830 through 1835 removed outlier: 6.552A pdb=" N LEU A1863 " --> pdb=" O LEU A1895 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 2020 through 2025 removed outlier: 6.430A pdb=" N LYS A2021 " --> pdb=" O HIS A2055 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N ASP A2057 " --> pdb=" O LYS A2021 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ILE A2023 " --> pdb=" O ASP A2057 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N VAL A2052 " --> pdb=" O LEU A2094 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N ILE A2096 " --> pdb=" O VAL A2052 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N PHE A2054 " --> pdb=" O ILE A2096 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N GLU A2098 " --> pdb=" O PHE A2054 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N LEU A2056 " --> pdb=" O GLU A2098 " (cutoff:3.500A) removed outlier: 8.359A pdb=" N LEU A2100 " --> pdb=" O LEU A2056 " (cutoff:3.500A) removed outlier: 8.247A pdb=" N VAL A2058 " --> pdb=" O LEU A2100 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N SER A1991 " --> pdb=" O ILE A2099 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 2078 through 2080 Processing sheet with id=AA9, first strand: chain 'A' and resid 2305 through 2308 Processing sheet with id=AB1, first strand: chain 'A' and resid 2321 through 2324 removed outlier: 7.492A pdb=" N VAL A2330 " --> pdb=" O ARG A2343 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N ARG A2343 " --> pdb=" O VAL A2330 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N ALA A2332 " --> pdb=" O ILE A2341 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 2446 through 2450 removed outlier: 6.320A pdb=" N THR A2482 " --> pdb=" O HIS A2519 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N ILE A2521 " --> pdb=" O THR A2482 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N LEU A2484 " --> pdb=" O ILE A2521 " (cutoff:3.500A) removed outlier: 7.864A pdb=" N ALA A2523 " --> pdb=" O LEU A2484 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N PHE A2486 " --> pdb=" O ALA A2523 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N VAL A2416 " --> pdb=" O ALA A2522 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N CYS A2524 " --> pdb=" O VAL A2416 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N ILE A2418 " --> pdb=" O CYS A2524 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 2506 through 2507 Processing sheet with id=AB4, first strand: chain 'A' and resid 2555 through 2556 Processing sheet with id=AB5, first strand: chain 'A' and resid 2801 through 2808 removed outlier: 5.956A pdb=" N GLN A2801 " --> pdb=" O VAL A2838 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N VAL A2840 " --> pdb=" O GLN A2801 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N HIS A2803 " --> pdb=" O VAL A2840 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N VAL A2842 " --> pdb=" O HIS A2803 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N VAL A2805 " --> pdb=" O VAL A2842 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N ASP A2844 " --> pdb=" O VAL A2805 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N PHE A2807 " --> pdb=" O ASP A2844 " (cutoff:3.500A) removed outlier: 8.546A pdb=" N GLY A2880 " --> pdb=" O TYR A2837 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N SER A2839 " --> pdb=" O GLY A2880 " (cutoff:3.500A) removed outlier: 8.145A pdb=" N VAL A2882 " --> pdb=" O SER A2839 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N VAL A2841 " --> pdb=" O VAL A2882 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N ILE A2884 " --> pdb=" O VAL A2841 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N LEU A2843 " --> pdb=" O ILE A2884 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N PHE A2766 " --> pdb=" O VAL A2900 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 3067 through 3069 Processing sheet with id=AB7, first strand: chain 'A' and resid 3121 through 3123 removed outlier: 4.805A pdb=" N LYS A3127 " --> pdb=" O VAL A3142 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N HIS A3136 " --> pdb=" O LEU A3133 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 3345 through 3348 removed outlier: 6.013A pdb=" N THR A3345 " --> pdb=" O ILE A3376 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N GLN A3378 " --> pdb=" O THR A3345 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N LEU A3347 " --> pdb=" O GLN A3378 " (cutoff:3.500A) removed outlier: 8.623A pdb=" N ASP A3380 " --> pdb=" O LEU A3347 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N LYS A3373 " --> pdb=" O PHE A3413 " (cutoff:3.500A) removed outlier: 7.890A pdb=" N TYR A3415 " --> pdb=" O LYS A3373 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N LEU A3375 " --> pdb=" O TYR A3415 " (cutoff:3.500A) removed outlier: 7.760A pdb=" N ILE A3417 " --> pdb=" O LEU A3375 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N PHE A3377 " --> pdb=" O ILE A3417 " (cutoff:3.500A) removed outlier: 7.945A pdb=" N LYS A3419 " --> pdb=" O PHE A3377 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N THR A3379 " --> pdb=" O LYS A3419 " (cutoff:3.500A) removed outlier: 8.547A pdb=" N VAL A3440 " --> pdb=" O PHE A3315 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N GLU A3317 " --> pdb=" O VAL A3440 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 3547 through 3549 Processing sheet with id=AC1, first strand: chain 'A' and resid 4007 through 4008 Processing sheet with id=AC2, first strand: chain 'A' and resid 4097 through 4098 Processing sheet with id=AC3, first strand: chain 'A' and resid 4130 through 4131 removed outlier: 6.757A pdb=" N GLN A4938 " --> pdb=" O GLN A4949 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N GLN A4949 " --> pdb=" O GLN A4938 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N GLN A4940 " --> pdb=" O THR A4947 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N THR A4947 " --> pdb=" O GLN A4940 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N GLU A4942 " --> pdb=" O ARG A4945 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 4503 through 4504 2111 hydrogen bonds defined for protein. 6090 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: 14.04 Time building geometry restraints manager: 3.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 10557 1.33 - 1.45: 6685 1.45 - 1.57: 21670 1.57 - 1.69: 5 1.69 - 1.81: 332 Bond restraints: 39249 Sorted by residual: bond pdb=" C4 ATP A5301 " pdb=" C5 ATP A5301 " ideal model delta sigma weight residual 1.388 1.462 -0.074 1.00e-02 1.00e+04 5.45e+01 bond pdb=" C5 ATP A5301 " pdb=" C6 ATP A5301 " ideal model delta sigma weight residual 1.409 1.470 -0.061 1.00e-02 1.00e+04 3.77e+01 bond pdb=" C4 ATP A5301 " pdb=" N9 ATP A5301 " ideal model delta sigma weight residual 1.374 1.322 0.052 1.00e-02 1.00e+04 2.71e+01 bond pdb=" C8 ATP A5301 " pdb=" N7 ATP A5301 " ideal model delta sigma weight residual 1.310 1.357 -0.047 1.00e-02 1.00e+04 2.17e+01 bond pdb=" C5 ATP A5301 " pdb=" N7 ATP A5301 " ideal model delta sigma weight residual 1.387 1.342 0.045 1.00e-02 1.00e+04 2.02e+01 ... (remaining 39244 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.80: 53055 4.80 - 9.61: 50 9.61 - 14.41: 16 14.41 - 19.21: 3 19.21 - 24.01: 3 Bond angle restraints: 53127 Sorted by residual: angle pdb=" PB ATP A5301 " pdb=" O3B ATP A5301 " pdb=" PG ATP A5301 " ideal model delta sigma weight residual 139.87 120.54 19.33 1.00e+00 1.00e+00 3.74e+02 angle pdb=" PA ATP A5301 " pdb=" O3A ATP A5301 " pdb=" PB ATP A5301 " ideal model delta sigma weight residual 136.83 119.79 17.04 1.00e+00 1.00e+00 2.91e+02 angle pdb=" CD1 LEU A4971 " pdb=" CG LEU A4971 " pdb=" CD2 LEU A4971 " ideal model delta sigma weight residual 110.80 134.81 -24.01 2.20e+00 2.07e-01 1.19e+02 angle pdb=" CD1 LEU A4918 " pdb=" CG LEU A4918 " pdb=" CD2 LEU A4918 " ideal model delta sigma weight residual 110.80 134.05 -23.25 2.20e+00 2.07e-01 1.12e+02 angle pdb=" C5 ATP A5301 " pdb=" C4 ATP A5301 " pdb=" N3 ATP A5301 " ideal model delta sigma weight residual 126.80 119.48 7.32 1.00e+00 1.00e+00 5.36e+01 ... (remaining 53122 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.01: 21332 18.01 - 36.03: 1924 36.03 - 54.04: 439 54.04 - 72.06: 125 72.06 - 90.07: 53 Dihedral angle restraints: 23873 sinusoidal: 9859 harmonic: 14014 Sorted by residual: dihedral pdb=" CA TYR A4981 " pdb=" C TYR A4981 " pdb=" N ARG A4982 " pdb=" CA ARG A4982 " ideal model delta harmonic sigma weight residual -180.00 -144.96 -35.04 0 5.00e+00 4.00e-02 4.91e+01 dihedral pdb=" CA PRO A2237 " pdb=" C PRO A2237 " pdb=" N SER A2238 " pdb=" CA SER A2238 " ideal model delta harmonic sigma weight residual -180.00 -146.35 -33.65 0 5.00e+00 4.00e-02 4.53e+01 dihedral pdb=" CA PHE B 120 " pdb=" C PHE B 120 " pdb=" N ASN B 121 " pdb=" CA ASN B 121 " ideal model delta harmonic sigma weight residual 180.00 153.30 26.70 0 5.00e+00 4.00e-02 2.85e+01 ... (remaining 23870 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.343: 5990 0.343 - 0.685: 0 0.685 - 1.028: 0 1.028 - 1.371: 2 1.371 - 1.713: 12 Chirality restraints: 6004 Sorted by residual: chirality pdb=" CG LEU B 136 " pdb=" CB LEU B 136 " pdb=" CD1 LEU B 136 " pdb=" CD2 LEU B 136 " both_signs ideal model delta sigma weight residual False -2.59 -0.88 -1.71 2.00e-01 2.50e+01 7.34e+01 chirality pdb=" CG LEU B 168 " pdb=" CB LEU B 168 " pdb=" CD1 LEU B 168 " pdb=" CD2 LEU B 168 " both_signs ideal model delta sigma weight residual False -2.59 -0.88 -1.71 2.00e-01 2.50e+01 7.28e+01 chirality pdb=" CG LEU B 89 " pdb=" CB LEU B 89 " pdb=" CD1 LEU B 89 " pdb=" CD2 LEU B 89 " both_signs ideal model delta sigma weight residual False -2.59 -0.89 -1.70 2.00e-01 2.50e+01 7.20e+01 ... (remaining 6001 not shown) Planarity restraints: 6780 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR A4886 " -0.019 2.00e-02 2.50e+03 3.73e-02 1.39e+01 pdb=" C TYR A4886 " 0.065 2.00e-02 2.50e+03 pdb=" O TYR A4886 " -0.024 2.00e-02 2.50e+03 pdb=" N LEU A4887 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR A1275 " -0.018 2.00e-02 2.50e+03 3.70e-02 1.37e+01 pdb=" C TYR A1275 " 0.064 2.00e-02 2.50e+03 pdb=" O TYR A1275 " -0.024 2.00e-02 2.50e+03 pdb=" N ASP A1276 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A1607 " -0.018 2.00e-02 2.50e+03 3.60e-02 1.30e+01 pdb=" C GLU A1607 " 0.062 2.00e-02 2.50e+03 pdb=" O GLU A1607 " -0.023 2.00e-02 2.50e+03 pdb=" N ARG A1608 " -0.021 2.00e-02 2.50e+03 ... (remaining 6777 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 280 2.54 - 3.13: 32414 3.13 - 3.72: 60679 3.72 - 4.31: 84948 4.31 - 4.90: 141367 Nonbonded interactions: 319688 Sorted by model distance: nonbonded pdb=" O2B ATP A5301 " pdb="MG MG A5302 " model vdw 1.953 2.170 nonbonded pdb=" O SER A4817 " pdb=" NH1 ARG A4822 " model vdw 1.970 3.120 nonbonded pdb=" O ARG A2260 " pdb=" OG1 THR A2264 " model vdw 2.006 3.040 nonbonded pdb=" OE2 GLU A2098 " pdb="MG MG A5302 " model vdw 2.017 2.170 nonbonded pdb=" OD1 ASP A1511 " pdb=" NH2 ARG A1514 " model vdw 2.023 3.120 ... (remaining 319683 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.430 Check model and map are aligned: 0.110 Set scattering table: 0.100 Process input model: 43.620 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: 0.000 Load rotamer database and sin/cos tables:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 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 : 0.009 0.883 39257 Z= 0.536 Angle : 0.722 24.014 53127 Z= 0.423 Chirality : 0.087 1.713 6004 Planarity : 0.010 0.122 6780 Dihedral : 15.513 90.069 14731 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.92 % Favored : 94.97 % Rotamer: Outliers : 2.07 % Allowed : 11.67 % Favored : 86.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.95 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.12 (0.11), residues: 4714 helix: -0.03 (0.09), residues: 2617 sheet: 0.20 (0.27), residues: 340 loop : -1.97 (0.14), residues: 1757 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.030 0.003 ARG B 50 TYR 0.024 0.002 TYR A 773 PHE 0.019 0.002 PHE B 120 TRP 0.019 0.002 TRP A 712 HIS 0.009 0.001 HIS A3951 Details of bonding type rmsd covalent geometry : bond 0.00509 (39249) covalent geometry : angle 0.72221 (53127) hydrogen bonds : bond 0.14684 ( 2109) hydrogen bonds : angle 6.15655 ( 6090) metal coordination : bond 0.40818 ( 7) Misc. bond : bond 0.88309 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9428 Ramachandran restraints generated. 4714 Oldfield, 0 Emsley, 4714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9428 Ramachandran restraints generated. 4714 Oldfield, 0 Emsley, 4714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 731 residues out of total 4292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 642 time to evaluate : 1.502 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 42 LEU cc_start: 0.9011 (OUTLIER) cc_final: 0.8640 (mt) REVERT: B 76 LEU cc_start: 0.8222 (tp) cc_final: 0.7792 (tp) REVERT: B 155 HIS cc_start: 0.7443 (m90) cc_final: 0.6988 (m90) REVERT: B 158 VAL cc_start: 0.8512 (m) cc_final: 0.8226 (t) REVERT: B 193 LEU cc_start: 0.7832 (tp) cc_final: 0.6859 (tp) REVERT: B 196 LEU cc_start: 0.8582 (tp) cc_final: 0.8322 (tt) REVERT: B 272 MET cc_start: -0.0026 (mtm) cc_final: -0.2559 (ptt) REVERT: A 430 ARG cc_start: 0.6918 (mtt90) cc_final: 0.6592 (mtt-85) REVERT: A 441 LYS cc_start: 0.3660 (OUTLIER) cc_final: 0.3050 (mtpt) REVERT: A 442 LYS cc_start: 0.2200 (OUTLIER) cc_final: 0.0728 (mmtt) REVERT: A 446 LYS cc_start: 0.3387 (OUTLIER) cc_final: 0.3032 (ptpp) REVERT: A 450 TYR cc_start: 0.3600 (p90) cc_final: 0.3229 (p90) REVERT: A 453 VAL cc_start: 0.8390 (t) cc_final: 0.8136 (p) REVERT: A 454 ILE cc_start: 0.8624 (mt) cc_final: 0.8390 (mm) REVERT: A 483 LYS cc_start: 0.8564 (tttt) cc_final: 0.8125 (ttmm) REVERT: A 567 MET cc_start: 0.6520 (mmm) cc_final: 0.6099 (mmm) REVERT: A 1346 TYR cc_start: 0.6855 (t80) cc_final: 0.6346 (t80) REVERT: A 1440 GLU cc_start: 0.7705 (OUTLIER) cc_final: 0.7355 (mp0) REVERT: A 1489 MET cc_start: 0.7676 (mmt) cc_final: 0.6953 (mmm) REVERT: A 1616 VAL cc_start: 0.7998 (t) cc_final: 0.7769 (m) REVERT: A 1889 HIS cc_start: 0.7913 (m90) cc_final: 0.7327 (m90) REVERT: A 2626 MET cc_start: 0.8672 (mmm) cc_final: 0.8453 (mmm) REVERT: A 3328 HIS cc_start: 0.7115 (t70) cc_final: 0.6856 (t-170) REVERT: A 3676 ASN cc_start: 0.7556 (t0) cc_final: 0.7247 (p0) REVERT: A 4254 LYS cc_start: 0.4602 (OUTLIER) cc_final: 0.4239 (tptt) REVERT: A 4567 VAL cc_start: 0.8083 (t) cc_final: 0.7857 (m) REVERT: A 4927 ARG cc_start: 0.7606 (mtp-110) cc_final: 0.7361 (ttp-170) outliers start: 89 outliers final: 29 residues processed: 719 average time/residue: 0.2737 time to fit residues: 303.0446 Evaluate side-chains 385 residues out of total 4292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 350 time to evaluate : 1.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 63 ASN Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain A residue 441 LYS Chi-restraints excluded: chain A residue 442 LYS Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 446 LYS Chi-restraints excluded: chain A residue 581 TYR Chi-restraints excluded: chain A residue 585 GLU Chi-restraints excluded: chain A residue 1004 SER Chi-restraints excluded: chain A residue 1021 ASP Chi-restraints excluded: chain A residue 1175 PHE Chi-restraints excluded: chain A residue 1206 GLN Chi-restraints excluded: chain A residue 1215 SER Chi-restraints excluded: chain A residue 1386 ASP Chi-restraints excluded: chain A residue 1440 GLU Chi-restraints excluded: chain A residue 1486 SER Chi-restraints excluded: chain A residue 1532 SER Chi-restraints excluded: chain A residue 1734 SER Chi-restraints excluded: chain A residue 2240 ILE Chi-restraints excluded: chain A residue 3312 HIS Chi-restraints excluded: chain A residue 3421 SER Chi-restraints excluded: chain A residue 3436 LEU Chi-restraints excluded: chain A residue 3570 GLU Chi-restraints excluded: chain A residue 3641 SER Chi-restraints excluded: chain A residue 3779 SER Chi-restraints excluded: chain A residue 3905 SER Chi-restraints excluded: chain A residue 4005 LYS Chi-restraints excluded: chain A residue 4036 LEU Chi-restraints excluded: chain A residue 4254 LYS Chi-restraints excluded: chain A residue 4733 SER Chi-restraints excluded: chain A residue 4817 SER Chi-restraints excluded: chain A residue 4846 ASN Chi-restraints excluded: chain A residue 4907 SER Chi-restraints excluded: chain A residue 5174 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 475 random chunks: chunk 432 optimal weight: 0.5980 chunk 197 optimal weight: 1.9990 chunk 388 optimal weight: 0.6980 chunk 455 optimal weight: 4.9990 chunk 215 optimal weight: 0.2980 chunk 20 optimal weight: 0.0970 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 0.7980 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 0.4980 chunk 470 optimal weight: 0.0770 overall best weight: 0.3136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 119 GLN B 220 ASN B 249 HIS A 398 HIS ** A 443 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 714 GLN A 951 HIS A1182 HIS A1290 HIS A1380 ASN A1526 HIS ** A1564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1602 ASN A1693 GLN A1837 HIS A1945 GLN A2599 GLN A2861 HIS A2929 GLN A3057 GLN A3065 GLN A3104 ASN A3184 GLN A3200 ASN A3222 HIS A3285 GLN A3433 HIS A3599 HIS A3611 GLN A3615 GLN A3696 GLN ** A3903 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3951 HIS ** A4014 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A4262 GLN A4293 GLN A4529 HIS A4557 HIS A4654 HIS A4675 ASN A4770 HIS A4936 ASN A4986 ASN A5085 HIS A5089 GLN Total number of N/Q/H flips: 41 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.098544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.081909 restraints weight = 86945.097| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 2.19 r_work: 0.3114 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2961 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.2452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 39257 Z= 0.130 Angle : 0.596 13.308 53127 Z= 0.307 Chirality : 0.041 0.254 6004 Planarity : 0.005 0.069 6780 Dihedral : 6.012 87.276 5245 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.90 % Favored : 96.08 % Rotamer: Outliers : 2.26 % Allowed : 13.14 % Favored : 84.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.95 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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 (0.12), residues: 4714 helix: 1.67 (0.10), residues: 2675 sheet: 0.38 (0.28), residues: 338 loop : -0.87 (0.16), residues: 1701 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A1823 TYR 0.018 0.001 TYR A 773 PHE 0.025 0.002 PHE B 120 TRP 0.019 0.001 TRP A 953 HIS 0.008 0.001 HIS A5062 Details of bonding type rmsd covalent geometry : bond 0.00280 (39249) covalent geometry : angle 0.59555 (53127) hydrogen bonds : bond 0.04416 ( 2109) hydrogen bonds : angle 4.30021 ( 6090) metal coordination : bond 0.01736 ( 7) Misc. bond : bond 0.00048 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9428 Ramachandran restraints generated. 4714 Oldfield, 0 Emsley, 4714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9428 Ramachandran restraints generated. 4714 Oldfield, 0 Emsley, 4714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 465 residues out of total 4292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 368 time to evaluate : 1.466 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 42 LEU cc_start: 0.9042 (OUTLIER) cc_final: 0.8561 (mt) REVERT: B 58 ARG cc_start: 0.6397 (mtt180) cc_final: 0.6122 (mtt-85) REVERT: B 108 ASP cc_start: 0.4298 (OUTLIER) cc_final: 0.3972 (p0) REVERT: B 193 LEU cc_start: 0.7720 (tp) cc_final: 0.7332 (tp) REVERT: B 202 PHE cc_start: 0.7187 (m-80) cc_final: 0.6884 (m-10) REVERT: B 272 MET cc_start: 0.0593 (mtm) cc_final: -0.2359 (ptt) REVERT: A 406 GLU cc_start: 0.7424 (OUTLIER) cc_final: 0.6910 (pm20) REVERT: A 430 ARG cc_start: 0.7421 (mtt90) cc_final: 0.6953 (mtt-85) REVERT: A 533 MET cc_start: 0.7091 (tmm) cc_final: 0.6869 (tmm) REVERT: A 567 MET cc_start: 0.6756 (mmm) cc_final: 0.5995 (mmm) REVERT: A 575 LEU cc_start: 0.8366 (tt) cc_final: 0.7704 (mt) REVERT: A 713 ARG cc_start: 0.7632 (mtt-85) cc_final: 0.7419 (mtt-85) REVERT: A 922 MET cc_start: 0.8649 (ttt) cc_final: 0.8427 (ttt) REVERT: A 1146 GLU cc_start: 0.6657 (mt-10) cc_final: 0.6206 (mt-10) REVERT: A 1755 TYR cc_start: 0.8021 (t80) cc_final: 0.7738 (t80) REVERT: A 1889 HIS cc_start: 0.8241 (m90) cc_final: 0.7663 (m90) REVERT: A 2607 LEU cc_start: 0.9012 (OUTLIER) cc_final: 0.8779 (tp) REVERT: A 2626 MET cc_start: 0.9012 (mmm) cc_final: 0.8775 (mmm) REVERT: A 3328 HIS cc_start: 0.7816 (t70) cc_final: 0.7573 (t-170) REVERT: A 3676 ASN cc_start: 0.7730 (t0) cc_final: 0.7301 (p0) REVERT: A 3809 VAL cc_start: 0.8419 (t) cc_final: 0.7973 (p) REVERT: A 4034 TYR cc_start: 0.7989 (OUTLIER) cc_final: 0.7077 (t80) REVERT: A 4142 SER cc_start: 0.8807 (OUTLIER) cc_final: 0.8508 (m) REVERT: A 4191 ARG cc_start: 0.7497 (tpt170) cc_final: 0.7254 (tpt90) REVERT: A 4225 TYR cc_start: 0.8380 (t80) cc_final: 0.8012 (t80) REVERT: A 4765 VAL cc_start: 0.9178 (OUTLIER) cc_final: 0.8716 (m) REVERT: A 4986 ASN cc_start: 0.5628 (t0) cc_final: 0.5141 (p0) REVERT: A 4989 HIS cc_start: 0.5988 (t-90) cc_final: 0.5541 (t-90) outliers start: 97 outliers final: 40 residues processed: 442 average time/residue: 0.2530 time to fit residues: 177.5921 Evaluate side-chains 364 residues out of total 4292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 317 time to evaluate : 1.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 47 GLU Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain B residue 108 ASP Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain A residue 386 ILE Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain A residue 418 CYS Chi-restraints excluded: chain A residue 496 TYR Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 569 TYR Chi-restraints excluded: chain A residue 1175 PHE Chi-restraints excluded: chain A residue 1235 LEU Chi-restraints excluded: chain A residue 1438 ILE Chi-restraints excluded: chain A residue 1525 SER Chi-restraints excluded: chain A residue 1532 SER Chi-restraints excluded: chain A residue 2016 LYS Chi-restraints excluded: chain A residue 2233 LEU Chi-restraints excluded: chain A residue 2298 TRP Chi-restraints excluded: chain A residue 2607 LEU Chi-restraints excluded: chain A residue 2689 ILE Chi-restraints excluded: chain A residue 2736 VAL Chi-restraints excluded: chain A residue 2852 SER Chi-restraints excluded: chain A residue 2854 LYS Chi-restraints excluded: chain A residue 2861 HIS Chi-restraints excluded: chain A residue 2991 ASP Chi-restraints excluded: chain A residue 3012 VAL Chi-restraints excluded: chain A residue 3042 LEU Chi-restraints excluded: chain A residue 3113 TYR Chi-restraints excluded: chain A residue 3130 ASP Chi-restraints excluded: chain A residue 3312 HIS Chi-restraints excluded: chain A residue 3330 CYS Chi-restraints excluded: chain A residue 3570 GLU Chi-restraints excluded: chain A residue 3754 GLN Chi-restraints excluded: chain A residue 3937 THR Chi-restraints excluded: chain A residue 4005 LYS Chi-restraints excluded: chain A residue 4034 TYR Chi-restraints excluded: chain A residue 4053 GLU Chi-restraints excluded: chain A residue 4142 SER Chi-restraints excluded: chain A residue 4292 VAL Chi-restraints excluded: chain A residue 4354 LYS Chi-restraints excluded: chain A residue 4670 THR Chi-restraints excluded: chain A residue 4765 VAL Chi-restraints excluded: chain A residue 5061 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 475 random chunks: chunk 282 optimal weight: 0.9980 chunk 93 optimal weight: 0.6980 chunk 425 optimal weight: 0.7980 chunk 280 optimal weight: 0.5980 chunk 337 optimal weight: 0.9980 chunk 90 optimal weight: 1.9990 chunk 359 optimal weight: 0.9990 chunk 339 optimal weight: 0.9990 chunk 140 optimal weight: 3.9990 chunk 212 optimal weight: 5.9990 chunk 382 optimal weight: 3.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 ASN B 249 HIS A 390 HIS ** A 443 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 477 ASN A 564 GLN A 769 HIS A1350 HIS A2200 HIS A3104 ASN A3788 GLN A3903 GLN ** A4014 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A4561 ASN A4675 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.094801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.077546 restraints weight = 87397.976| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 2.14 r_work: 0.3013 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2862 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.2997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 39257 Z= 0.156 Angle : 0.565 12.474 53127 Z= 0.290 Chirality : 0.041 0.272 6004 Planarity : 0.005 0.066 6780 Dihedral : 5.241 89.437 5187 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.99 % Favored : 95.97 % Rotamer: Outliers : 2.31 % Allowed : 13.61 % Favored : 84.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.95 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 1.38 (0.12), residues: 4714 helix: 1.96 (0.10), residues: 2683 sheet: 0.36 (0.28), residues: 343 loop : -0.66 (0.16), residues: 1688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 713 TYR 0.019 0.002 TYR A3718 PHE 0.027 0.002 PHE B 120 TRP 0.027 0.002 TRP A 591 HIS 0.029 0.001 HIS A2861 Details of bonding type rmsd covalent geometry : bond 0.00364 (39249) covalent geometry : angle 0.56537 (53127) hydrogen bonds : bond 0.04457 ( 2109) hydrogen bonds : angle 4.10094 ( 6090) metal coordination : bond 0.00479 ( 7) Misc. bond : bond 0.00169 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9428 Ramachandran restraints generated. 4714 Oldfield, 0 Emsley, 4714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9428 Ramachandran restraints generated. 4714 Oldfield, 0 Emsley, 4714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 4292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 338 time to evaluate : 1.443 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 42 LEU cc_start: 0.9084 (tm) cc_final: 0.8642 (mt) REVERT: B 108 ASP cc_start: 0.4685 (OUTLIER) cc_final: 0.4275 (p0) REVERT: B 158 VAL cc_start: 0.9083 (OUTLIER) cc_final: 0.8873 (t) REVERT: B 162 ARG cc_start: 0.7669 (mmm160) cc_final: 0.7172 (mmm-85) REVERT: B 178 VAL cc_start: 0.8936 (OUTLIER) cc_final: 0.8699 (p) REVERT: B 251 MET cc_start: 0.7147 (mmm) cc_final: 0.6723 (mtt) REVERT: B 272 MET cc_start: 0.1042 (mtm) cc_final: -0.2148 (ptt) REVERT: A 406 GLU cc_start: 0.7508 (OUTLIER) cc_final: 0.6926 (pm20) REVERT: A 430 ARG cc_start: 0.7345 (mtt90) cc_final: 0.7067 (mtt-85) REVERT: A 441 LYS cc_start: 0.5040 (OUTLIER) cc_final: 0.3716 (mtpt) REVERT: A 567 MET cc_start: 0.6956 (mmm) cc_final: 0.6555 (mmm) REVERT: A 575 LEU cc_start: 0.8460 (tt) cc_final: 0.8076 (mt) REVERT: A 702 MET cc_start: 0.8224 (mtt) cc_final: 0.7722 (mtt) REVERT: A 713 ARG cc_start: 0.7796 (mtt-85) cc_final: 0.7566 (mtt-85) REVERT: A 922 MET cc_start: 0.8711 (ttt) cc_final: 0.8427 (ttt) REVERT: A 1062 ARG cc_start: 0.8090 (ptp-110) cc_final: 0.7746 (ptp90) REVERT: A 1146 GLU cc_start: 0.6814 (mt-10) cc_final: 0.6406 (mt-10) REVERT: A 1372 PHE cc_start: 0.5602 (m-80) cc_final: 0.5233 (m-80) REVERT: A 1381 PHE cc_start: 0.8059 (t80) cc_final: 0.7835 (t80) REVERT: A 1758 ARG cc_start: 0.7677 (mtm-85) cc_final: 0.7396 (mtm-85) REVERT: A 1769 LEU cc_start: 0.8522 (mm) cc_final: 0.8314 (mp) REVERT: A 1889 HIS cc_start: 0.8318 (m90) cc_final: 0.7682 (m90) REVERT: A 2141 MET cc_start: 0.8282 (mtp) cc_final: 0.8007 (mtp) REVERT: A 2607 LEU cc_start: 0.8967 (OUTLIER) cc_final: 0.8717 (tp) REVERT: A 2626 MET cc_start: 0.9096 (mmm) cc_final: 0.8865 (mmm) REVERT: A 3209 ARG cc_start: 0.4095 (mpt180) cc_final: 0.3539 (mmm160) REVERT: A 3328 HIS cc_start: 0.7978 (t70) cc_final: 0.7728 (t-170) REVERT: A 3406 ARG cc_start: 0.6697 (ttp80) cc_final: 0.6365 (ttp-170) REVERT: A 3592 LYS cc_start: 0.8545 (tppt) cc_final: 0.8251 (tptt) REVERT: A 3676 ASN cc_start: 0.7867 (t0) cc_final: 0.7316 (p0) REVERT: A 3777 ARG cc_start: 0.8382 (ttm170) cc_final: 0.8154 (tpp80) REVERT: A 3809 VAL cc_start: 0.8517 (t) cc_final: 0.8080 (p) REVERT: A 4765 VAL cc_start: 0.9269 (OUTLIER) cc_final: 0.8821 (m) REVERT: A 4986 ASN cc_start: 0.5598 (t0) cc_final: 0.5090 (p0) REVERT: A 4989 HIS cc_start: 0.5984 (t-90) cc_final: 0.5631 (t-90) REVERT: A 4992 MET cc_start: 0.7898 (mmm) cc_final: 0.7601 (mmp) outliers start: 99 outliers final: 64 residues processed: 409 average time/residue: 0.2651 time to fit residues: 173.4512 Evaluate side-chains 387 residues out of total 4292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 316 time to evaluate : 1.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 GLU Chi-restraints excluded: chain B residue 63 ASN Chi-restraints excluded: chain B residue 108 ASP Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 185 SER Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain A residue 386 ILE Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain A residue 418 CYS Chi-restraints excluded: chain A residue 441 LYS Chi-restraints excluded: chain A residue 496 TYR Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 569 TYR Chi-restraints excluded: chain A residue 735 LEU Chi-restraints excluded: chain A residue 752 SER Chi-restraints excluded: chain A residue 1175 PHE Chi-restraints excluded: chain A residue 1220 MET Chi-restraints excluded: chain A residue 1235 LEU Chi-restraints excluded: chain A residue 1236 PHE Chi-restraints excluded: chain A residue 1289 LEU Chi-restraints excluded: chain A residue 1350 HIS Chi-restraints excluded: chain A residue 1353 VAL Chi-restraints excluded: chain A residue 1393 LEU Chi-restraints excluded: chain A residue 1396 ILE Chi-restraints excluded: chain A residue 1438 ILE Chi-restraints excluded: chain A residue 1532 SER Chi-restraints excluded: chain A residue 1557 ILE Chi-restraints excluded: chain A residue 1577 SER Chi-restraints excluded: chain A residue 1746 VAL Chi-restraints excluded: chain A residue 1748 CYS Chi-restraints excluded: chain A residue 1887 LEU Chi-restraints excluded: chain A residue 1980 PHE Chi-restraints excluded: chain A residue 2016 LYS Chi-restraints excluded: chain A residue 2233 LEU Chi-restraints excluded: chain A residue 2298 TRP Chi-restraints excluded: chain A residue 2607 LEU Chi-restraints excluded: chain A residue 2689 ILE Chi-restraints excluded: chain A residue 2736 VAL Chi-restraints excluded: chain A residue 2852 SER Chi-restraints excluded: chain A residue 2854 LYS Chi-restraints excluded: chain A residue 3012 VAL Chi-restraints excluded: chain A residue 3042 LEU Chi-restraints excluded: chain A residue 3113 TYR Chi-restraints excluded: chain A residue 3129 VAL Chi-restraints excluded: chain A residue 3130 ASP Chi-restraints excluded: chain A residue 3312 HIS Chi-restraints excluded: chain A residue 3330 CYS Chi-restraints excluded: chain A residue 3570 GLU Chi-restraints excluded: chain A residue 3638 SER Chi-restraints excluded: chain A residue 3776 MET Chi-restraints excluded: chain A residue 3854 CYS Chi-restraints excluded: chain A residue 3937 THR Chi-restraints excluded: chain A residue 3965 VAL Chi-restraints excluded: chain A residue 4005 LYS Chi-restraints excluded: chain A residue 4163 ILE Chi-restraints excluded: chain A residue 4292 VAL Chi-restraints excluded: chain A residue 4311 VAL Chi-restraints excluded: chain A residue 4354 LYS Chi-restraints excluded: chain A residue 4362 THR Chi-restraints excluded: chain A residue 4381 ILE Chi-restraints excluded: chain A residue 4390 LEU Chi-restraints excluded: chain A residue 4670 THR Chi-restraints excluded: chain A residue 4707 LYS Chi-restraints excluded: chain A residue 4735 VAL Chi-restraints excluded: chain A residue 4765 VAL Chi-restraints excluded: chain A residue 4972 SER Chi-restraints excluded: chain A residue 4980 VAL Chi-restraints excluded: chain A residue 5061 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 475 random chunks: chunk 460 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 425 optimal weight: 1.9990 chunk 272 optimal weight: 0.7980 chunk 370 optimal weight: 0.1980 chunk 468 optimal weight: 2.9990 chunk 161 optimal weight: 0.9980 chunk 244 optimal weight: 3.9990 chunk 431 optimal weight: 0.6980 chunk 352 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 ASN A 428 HIS ** A 443 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2014 ASN A2321 HIS A3082 GLN A3104 ASN A3698 HIS A4675 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.093953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.075949 restraints weight = 87489.800| |-----------------------------------------------------------------------------| r_work (start): 0.3135 rms_B_bonded: 2.25 r_work: 0.2970 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.3359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 39257 Z= 0.141 Angle : 0.540 14.416 53127 Z= 0.275 Chirality : 0.040 0.230 6004 Planarity : 0.004 0.059 6780 Dihedral : 5.159 86.050 5185 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.09 % Favored : 95.86 % Rotamer: Outliers : 2.21 % Allowed : 14.28 % Favored : 83.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.95 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 1.54 (0.12), residues: 4714 helix: 2.06 (0.10), residues: 2690 sheet: 0.43 (0.28), residues: 340 loop : -0.54 (0.16), residues: 1684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A3323 TYR 0.020 0.001 TYR A 496 PHE 0.020 0.001 PHE A 408 TRP 0.021 0.001 TRP A 591 HIS 0.022 0.001 HIS A1350 Details of bonding type rmsd covalent geometry : bond 0.00330 (39249) covalent geometry : angle 0.53958 (53127) hydrogen bonds : bond 0.04127 ( 2109) hydrogen bonds : angle 3.99983 ( 6090) metal coordination : bond 0.00286 ( 7) Misc. bond : bond 0.00132 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9428 Ramachandran restraints generated. 4714 Oldfield, 0 Emsley, 4714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9428 Ramachandran restraints generated. 4714 Oldfield, 0 Emsley, 4714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 4292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 326 time to evaluate : 1.575 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 42 LEU cc_start: 0.9045 (tm) cc_final: 0.8630 (mt) REVERT: B 108 ASP cc_start: 0.4873 (OUTLIER) cc_final: 0.4455 (p0) REVERT: B 213 MET cc_start: 0.6821 (mmm) cc_final: 0.6033 (mmt) REVERT: B 219 MET cc_start: 0.8189 (mpp) cc_final: 0.7935 (mmm) REVERT: B 251 MET cc_start: 0.7273 (mmm) cc_final: 0.6889 (mtt) REVERT: A 406 GLU cc_start: 0.7303 (OUTLIER) cc_final: 0.6781 (pm20) REVERT: A 430 ARG cc_start: 0.7296 (mtt90) cc_final: 0.7086 (mtt-85) REVERT: A 441 LYS cc_start: 0.4898 (OUTLIER) cc_final: 0.3616 (mtpt) REVERT: A 533 MET cc_start: 0.6756 (tmm) cc_final: 0.6028 (ttp) REVERT: A 559 PHE cc_start: 0.5792 (t80) cc_final: 0.5254 (t80) REVERT: A 567 MET cc_start: 0.6564 (mmm) cc_final: 0.5674 (mmm) REVERT: A 575 LEU cc_start: 0.8349 (tt) cc_final: 0.7716 (mt) REVERT: A 702 MET cc_start: 0.8053 (mtt) cc_final: 0.7706 (mtt) REVERT: A 873 GLU cc_start: 0.8278 (OUTLIER) cc_final: 0.8056 (mt-10) REVERT: A 922 MET cc_start: 0.8630 (ttt) cc_final: 0.8348 (ttt) REVERT: A 1062 ARG cc_start: 0.7904 (ptp-110) cc_final: 0.7667 (ptm160) REVERT: A 1146 GLU cc_start: 0.6590 (mt-10) cc_final: 0.6118 (mt-10) REVERT: A 1381 PHE cc_start: 0.7998 (t80) cc_final: 0.7775 (t80) REVERT: A 1769 LEU cc_start: 0.8584 (mm) cc_final: 0.8378 (mt) REVERT: A 2141 MET cc_start: 0.8254 (mtp) cc_final: 0.7980 (mtp) REVERT: A 2318 ILE cc_start: 0.8794 (OUTLIER) cc_final: 0.8584 (mp) REVERT: A 2607 LEU cc_start: 0.8975 (OUTLIER) cc_final: 0.8751 (tp) REVERT: A 2626 MET cc_start: 0.9103 (mmm) cc_final: 0.8861 (mmm) REVERT: A 3328 HIS cc_start: 0.7905 (t70) cc_final: 0.7628 (t-170) REVERT: A 3330 CYS cc_start: 0.8670 (OUTLIER) cc_final: 0.8214 (t) REVERT: A 3340 ARG cc_start: 0.7357 (OUTLIER) cc_final: 0.7023 (ttm-80) REVERT: A 3592 LYS cc_start: 0.8500 (tppt) cc_final: 0.8230 (tptt) REVERT: A 4034 TYR cc_start: 0.8154 (OUTLIER) cc_final: 0.7467 (t80) REVERT: A 4765 VAL cc_start: 0.9212 (OUTLIER) cc_final: 0.8744 (m) REVERT: A 4986 ASN cc_start: 0.5627 (t0) cc_final: 0.5155 (p0) REVERT: A 4989 HIS cc_start: 0.5792 (t-90) cc_final: 0.5489 (t-90) REVERT: A 4992 MET cc_start: 0.7823 (mmm) cc_final: 0.7452 (mmp) outliers start: 95 outliers final: 60 residues processed: 396 average time/residue: 0.2789 time to fit residues: 175.5288 Evaluate side-chains 377 residues out of total 4292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 307 time to evaluate : 1.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 GLU Chi-restraints excluded: chain B residue 63 ASN Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain B residue 108 ASP Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 220 ASN Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain A residue 418 CYS Chi-restraints excluded: chain A residue 428 HIS Chi-restraints excluded: chain A residue 441 LYS Chi-restraints excluded: chain A residue 496 TYR Chi-restraints excluded: chain A residue 735 LEU Chi-restraints excluded: chain A residue 752 SER Chi-restraints excluded: chain A residue 873 GLU Chi-restraints excluded: chain A residue 1175 PHE Chi-restraints excluded: chain A residue 1220 MET Chi-restraints excluded: chain A residue 1235 LEU Chi-restraints excluded: chain A residue 1236 PHE Chi-restraints excluded: chain A residue 1353 VAL Chi-restraints excluded: chain A residue 1396 ILE Chi-restraints excluded: chain A residue 1438 ILE Chi-restraints excluded: chain A residue 1457 ILE Chi-restraints excluded: chain A residue 1532 SER Chi-restraints excluded: chain A residue 1577 SER Chi-restraints excluded: chain A residue 1748 CYS Chi-restraints excluded: chain A residue 1887 LEU Chi-restraints excluded: chain A residue 1951 THR Chi-restraints excluded: chain A residue 1980 PHE Chi-restraints excluded: chain A residue 2016 LYS Chi-restraints excluded: chain A residue 2233 LEU Chi-restraints excluded: chain A residue 2298 TRP Chi-restraints excluded: chain A residue 2318 ILE Chi-restraints excluded: chain A residue 2607 LEU Chi-restraints excluded: chain A residue 2689 ILE Chi-restraints excluded: chain A residue 2736 VAL Chi-restraints excluded: chain A residue 2852 SER Chi-restraints excluded: chain A residue 2854 LYS Chi-restraints excluded: chain A residue 3012 VAL Chi-restraints excluded: chain A residue 3042 LEU Chi-restraints excluded: chain A residue 3080 TYR Chi-restraints excluded: chain A residue 3113 TYR Chi-restraints excluded: chain A residue 3129 VAL Chi-restraints excluded: chain A residue 3130 ASP Chi-restraints excluded: chain A residue 3312 HIS Chi-restraints excluded: chain A residue 3330 CYS Chi-restraints excluded: chain A residue 3340 ARG Chi-restraints excluded: chain A residue 3540 VAL Chi-restraints excluded: chain A residue 3570 GLU Chi-restraints excluded: chain A residue 3638 SER Chi-restraints excluded: chain A residue 3776 MET Chi-restraints excluded: chain A residue 3854 CYS Chi-restraints excluded: chain A residue 3937 THR Chi-restraints excluded: chain A residue 3965 VAL Chi-restraints excluded: chain A residue 4005 LYS Chi-restraints excluded: chain A residue 4034 TYR Chi-restraints excluded: chain A residue 4053 GLU Chi-restraints excluded: chain A residue 4292 VAL Chi-restraints excluded: chain A residue 4381 ILE Chi-restraints excluded: chain A residue 4390 LEU Chi-restraints excluded: chain A residue 4601 LEU Chi-restraints excluded: chain A residue 4670 THR Chi-restraints excluded: chain A residue 4707 LYS Chi-restraints excluded: chain A residue 4735 VAL Chi-restraints excluded: chain A residue 4765 VAL Chi-restraints excluded: chain A residue 4972 SER Chi-restraints excluded: chain A residue 4973 LEU Chi-restraints excluded: chain A residue 4980 VAL Chi-restraints excluded: chain A residue 5061 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 475 random chunks: chunk 257 optimal weight: 0.0670 chunk 367 optimal weight: 0.2980 chunk 399 optimal weight: 2.9990 chunk 44 optimal weight: 0.7980 chunk 71 optimal weight: 0.5980 chunk 236 optimal weight: 4.9990 chunk 336 optimal weight: 0.5980 chunk 152 optimal weight: 2.9990 chunk 293 optimal weight: 0.8980 chunk 19 optimal weight: 6.9990 chunk 327 optimal weight: 0.9980 overall best weight: 0.4718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 164 HIS A 428 HIS A2014 ASN A3104 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.094360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.077037 restraints weight = 87420.998| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 2.13 r_work: 0.3003 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2850 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.3581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 39257 Z= 0.116 Angle : 0.519 13.709 53127 Z= 0.264 Chirality : 0.039 0.261 6004 Planarity : 0.004 0.053 6780 Dihedral : 5.044 85.281 5185 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 2.26 % Allowed : 14.35 % Favored : 83.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.95 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 1.71 (0.12), residues: 4714 helix: 2.19 (0.10), residues: 2688 sheet: 0.39 (0.28), residues: 342 loop : -0.44 (0.16), residues: 1684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.000 ARG B 182 TYR 0.015 0.001 TYR A1700 PHE 0.021 0.001 PHE A 464 TRP 0.033 0.001 TRP A 576 HIS 0.019 0.001 HIS A 428 Details of bonding type rmsd covalent geometry : bond 0.00262 (39249) covalent geometry : angle 0.51921 (53127) hydrogen bonds : bond 0.03830 ( 2109) hydrogen bonds : angle 3.88985 ( 6090) metal coordination : bond 0.00300 ( 7) Misc. bond : bond 0.00088 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9428 Ramachandran restraints generated. 4714 Oldfield, 0 Emsley, 4714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9428 Ramachandran restraints generated. 4714 Oldfield, 0 Emsley, 4714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 4292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 324 time to evaluate : 1.690 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 42 LEU cc_start: 0.9045 (tm) cc_final: 0.8630 (mt) REVERT: B 108 ASP cc_start: 0.5054 (OUTLIER) cc_final: 0.4566 (p0) REVERT: B 112 MET cc_start: 0.6953 (mmm) cc_final: 0.6272 (ttp) REVERT: B 203 ILE cc_start: 0.8379 (mm) cc_final: 0.8042 (tp) REVERT: B 213 MET cc_start: 0.6853 (mmm) cc_final: 0.6186 (mmm) REVERT: B 219 MET cc_start: 0.8228 (mpp) cc_final: 0.7847 (mmm) REVERT: B 251 MET cc_start: 0.7263 (mmm) cc_final: 0.6918 (mtt) REVERT: A 428 HIS cc_start: 0.6567 (OUTLIER) cc_final: 0.6305 (t70) REVERT: A 429 ASP cc_start: 0.6973 (OUTLIER) cc_final: 0.6616 (p0) REVERT: A 430 ARG cc_start: 0.7387 (mtt90) cc_final: 0.7103 (mtt-85) REVERT: A 567 MET cc_start: 0.6891 (mmm) cc_final: 0.6314 (mmm) REVERT: A 575 LEU cc_start: 0.8283 (OUTLIER) cc_final: 0.7777 (mt) REVERT: A 702 MET cc_start: 0.8186 (mtt) cc_final: 0.7905 (mtt) REVERT: A 873 GLU cc_start: 0.8550 (OUTLIER) cc_final: 0.8336 (mt-10) REVERT: A 922 MET cc_start: 0.8748 (ttt) cc_final: 0.8466 (ttt) REVERT: A 1062 ARG cc_start: 0.8123 (ptp-110) cc_final: 0.7845 (ptm160) REVERT: A 1146 GLU cc_start: 0.6966 (mt-10) cc_final: 0.6547 (mt-10) REVERT: A 1372 PHE cc_start: 0.5509 (m-80) cc_final: 0.5150 (m-10) REVERT: A 1381 PHE cc_start: 0.8052 (t80) cc_final: 0.7725 (t80) REVERT: A 1385 PHE cc_start: 0.7693 (t80) cc_final: 0.6989 (t80) REVERT: A 2607 LEU cc_start: 0.8991 (OUTLIER) cc_final: 0.8772 (tp) REVERT: A 2626 MET cc_start: 0.9157 (mmm) cc_final: 0.8859 (mmm) REVERT: A 2855 MET cc_start: 0.8624 (mmt) cc_final: 0.8351 (mmt) REVERT: A 3328 HIS cc_start: 0.7930 (t70) cc_final: 0.7689 (t-170) REVERT: A 3330 CYS cc_start: 0.8776 (OUTLIER) cc_final: 0.8286 (t) REVERT: A 3340 ARG cc_start: 0.7532 (OUTLIER) cc_final: 0.7109 (ttm-80) REVERT: A 3592 LYS cc_start: 0.8566 (tppt) cc_final: 0.8302 (tptt) REVERT: A 4060 ARG cc_start: 0.8298 (mtt180) cc_final: 0.8017 (mtp180) REVERT: A 4765 VAL cc_start: 0.9276 (OUTLIER) cc_final: 0.8857 (m) REVERT: A 4986 ASN cc_start: 0.5826 (t0) cc_final: 0.5338 (p0) REVERT: A 4989 HIS cc_start: 0.6000 (t-90) cc_final: 0.5673 (t-90) REVERT: A 4992 MET cc_start: 0.7994 (mmm) cc_final: 0.7695 (mmp) outliers start: 97 outliers final: 64 residues processed: 394 average time/residue: 0.2705 time to fit residues: 169.5842 Evaluate side-chains 380 residues out of total 4292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 307 time to evaluate : 1.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 GLU Chi-restraints excluded: chain B residue 63 ASN Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain B residue 108 ASP Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain A residue 418 CYS Chi-restraints excluded: chain A residue 428 HIS Chi-restraints excluded: chain A residue 429 ASP Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 479 CYS Chi-restraints excluded: chain A residue 496 TYR Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 569 TYR Chi-restraints excluded: chain A residue 575 LEU Chi-restraints excluded: chain A residue 752 SER Chi-restraints excluded: chain A residue 753 ILE Chi-restraints excluded: chain A residue 873 GLU Chi-restraints excluded: chain A residue 1175 PHE Chi-restraints excluded: chain A residue 1209 THR Chi-restraints excluded: chain A residue 1220 MET Chi-restraints excluded: chain A residue 1235 LEU Chi-restraints excluded: chain A residue 1236 PHE Chi-restraints excluded: chain A residue 1353 VAL Chi-restraints excluded: chain A residue 1396 ILE Chi-restraints excluded: chain A residue 1438 ILE Chi-restraints excluded: chain A residue 1532 SER Chi-restraints excluded: chain A residue 1577 SER Chi-restraints excluded: chain A residue 1746 VAL Chi-restraints excluded: chain A residue 1748 CYS Chi-restraints excluded: chain A residue 1887 LEU Chi-restraints excluded: chain A residue 1951 THR Chi-restraints excluded: chain A residue 1980 PHE Chi-restraints excluded: chain A residue 2016 LYS Chi-restraints excluded: chain A residue 2233 LEU Chi-restraints excluded: chain A residue 2298 TRP Chi-restraints excluded: chain A residue 2607 LEU Chi-restraints excluded: chain A residue 2736 VAL Chi-restraints excluded: chain A residue 2852 SER Chi-restraints excluded: chain A residue 2854 LYS Chi-restraints excluded: chain A residue 2901 SER Chi-restraints excluded: chain A residue 3012 VAL Chi-restraints excluded: chain A residue 3042 LEU Chi-restraints excluded: chain A residue 3080 TYR Chi-restraints excluded: chain A residue 3113 TYR Chi-restraints excluded: chain A residue 3129 VAL Chi-restraints excluded: chain A residue 3130 ASP Chi-restraints excluded: chain A residue 3312 HIS Chi-restraints excluded: chain A residue 3330 CYS Chi-restraints excluded: chain A residue 3340 ARG Chi-restraints excluded: chain A residue 3436 LEU Chi-restraints excluded: chain A residue 3449 THR Chi-restraints excluded: chain A residue 3540 VAL Chi-restraints excluded: chain A residue 3570 GLU Chi-restraints excluded: chain A residue 3638 SER Chi-restraints excluded: chain A residue 3776 MET Chi-restraints excluded: chain A residue 3854 CYS Chi-restraints excluded: chain A residue 3907 SER Chi-restraints excluded: chain A residue 3965 VAL Chi-restraints excluded: chain A residue 4005 LYS Chi-restraints excluded: chain A residue 4163 ILE Chi-restraints excluded: chain A residue 4292 VAL Chi-restraints excluded: chain A residue 4362 THR Chi-restraints excluded: chain A residue 4381 ILE Chi-restraints excluded: chain A residue 4390 LEU Chi-restraints excluded: chain A residue 4670 THR Chi-restraints excluded: chain A residue 4735 VAL Chi-restraints excluded: chain A residue 4765 VAL Chi-restraints excluded: chain A residue 4973 LEU Chi-restraints excluded: chain A residue 4980 VAL Chi-restraints excluded: chain A residue 5061 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 475 random chunks: chunk 290 optimal weight: 0.8980 chunk 311 optimal weight: 0.1980 chunk 466 optimal weight: 0.0050 chunk 450 optimal weight: 0.9980 chunk 373 optimal weight: 0.6980 chunk 45 optimal weight: 2.9990 chunk 432 optimal weight: 0.6980 chunk 463 optimal weight: 1.9990 chunk 423 optimal weight: 0.4980 chunk 469 optimal weight: 0.9980 chunk 353 optimal weight: 0.8980 overall best weight: 0.4194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 ASN A 428 HIS A 574 GLN A3104 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.094666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.076365 restraints weight = 87825.319| |-----------------------------------------------------------------------------| r_work (start): 0.3144 rms_B_bonded: 2.29 r_work: 0.2972 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.3772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 39257 Z= 0.111 Angle : 0.509 14.880 53127 Z= 0.258 Chirality : 0.039 0.252 6004 Planarity : 0.004 0.052 6780 Dihedral : 4.938 83.440 5185 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 2.26 % Allowed : 14.63 % Favored : 83.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.95 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 1.83 (0.13), residues: 4714 helix: 2.29 (0.10), residues: 2688 sheet: 0.36 (0.28), residues: 342 loop : -0.37 (0.16), residues: 1684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A3323 TYR 0.018 0.001 TYR A 496 PHE 0.028 0.001 PHE A 559 TRP 0.049 0.001 TRP A 576 HIS 0.032 0.001 HIS A 428 Details of bonding type rmsd covalent geometry : bond 0.00250 (39249) covalent geometry : angle 0.50935 (53127) hydrogen bonds : bond 0.03671 ( 2109) hydrogen bonds : angle 3.80767 ( 6090) metal coordination : bond 0.00166 ( 7) Misc. bond : bond 0.00079 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9428 Ramachandran restraints generated. 4714 Oldfield, 0 Emsley, 4714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9428 Ramachandran restraints generated. 4714 Oldfield, 0 Emsley, 4714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 4292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 321 time to evaluate : 1.556 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 42 LEU cc_start: 0.8909 (tm) cc_final: 0.8559 (mt) REVERT: B 100 LYS cc_start: 0.8248 (mttt) cc_final: 0.7978 (mmmt) REVERT: B 112 MET cc_start: 0.6718 (mmm) cc_final: 0.6294 (ttp) REVERT: B 120 PHE cc_start: 0.6698 (t80) cc_final: 0.5941 (t80) REVERT: B 203 ILE cc_start: 0.8336 (mm) cc_final: 0.8036 (tp) REVERT: B 213 MET cc_start: 0.6574 (mmm) cc_final: 0.6019 (mmm) REVERT: B 219 MET cc_start: 0.8176 (mpp) cc_final: 0.7797 (mmm) REVERT: B 251 MET cc_start: 0.7232 (mmm) cc_final: 0.6932 (mtt) REVERT: A 429 ASP cc_start: 0.6958 (OUTLIER) cc_final: 0.6443 (t70) REVERT: A 441 LYS cc_start: 0.4997 (OUTLIER) cc_final: 0.3756 (mtpt) REVERT: A 533 MET cc_start: 0.6569 (tmm) cc_final: 0.5709 (ttp) REVERT: A 559 PHE cc_start: 0.5718 (t80) cc_final: 0.5264 (t80) REVERT: A 567 MET cc_start: 0.6933 (mmm) cc_final: 0.6328 (mmm) REVERT: A 575 LEU cc_start: 0.8204 (OUTLIER) cc_final: 0.7658 (mt) REVERT: A 873 GLU cc_start: 0.8324 (OUTLIER) cc_final: 0.8106 (mt-10) REVERT: A 922 MET cc_start: 0.8654 (ttt) cc_final: 0.8371 (ttt) REVERT: A 1146 GLU cc_start: 0.6663 (mt-10) cc_final: 0.6221 (mt-10) REVERT: A 1372 PHE cc_start: 0.5387 (m-80) cc_final: 0.5087 (m-10) REVERT: A 1381 PHE cc_start: 0.7893 (t80) cc_final: 0.7575 (t80) REVERT: A 1385 PHE cc_start: 0.7565 (t80) cc_final: 0.6792 (t80) REVERT: A 1509 LEU cc_start: 0.8638 (OUTLIER) cc_final: 0.8137 (tm) REVERT: A 2220 ARG cc_start: 0.8145 (OUTLIER) cc_final: 0.7624 (ttp-170) REVERT: A 2607 LEU cc_start: 0.8964 (OUTLIER) cc_final: 0.8756 (tp) REVERT: A 2626 MET cc_start: 0.9214 (mmm) cc_final: 0.8888 (mmm) REVERT: A 2855 MET cc_start: 0.8374 (mmt) cc_final: 0.8142 (mmt) REVERT: A 3209 ARG cc_start: 0.3815 (mpt180) cc_final: 0.2988 (mmm160) REVERT: A 3328 HIS cc_start: 0.7786 (t70) cc_final: 0.7541 (t-170) REVERT: A 3330 CYS cc_start: 0.8558 (OUTLIER) cc_final: 0.8085 (t) REVERT: A 3340 ARG cc_start: 0.7479 (OUTLIER) cc_final: 0.7092 (ttm-80) REVERT: A 3592 LYS cc_start: 0.8515 (tppt) cc_final: 0.8288 (tptt) REVERT: A 3681 MET cc_start: 0.5423 (OUTLIER) cc_final: 0.5112 (pmm) REVERT: A 4034 TYR cc_start: 0.8190 (OUTLIER) cc_final: 0.7499 (t80) REVERT: A 4765 VAL cc_start: 0.9231 (OUTLIER) cc_final: 0.8785 (m) REVERT: A 4986 ASN cc_start: 0.5674 (t0) cc_final: 0.5247 (p0) REVERT: A 4992 MET cc_start: 0.7842 (mmm) cc_final: 0.7565 (mmp) outliers start: 97 outliers final: 68 residues processed: 390 average time/residue: 0.2722 time to fit residues: 168.1833 Evaluate side-chains 380 residues out of total 4292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 300 time to evaluate : 1.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 GLU Chi-restraints excluded: chain B residue 63 ASN Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 247 SER Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 418 CYS Chi-restraints excluded: chain A residue 429 ASP Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 441 LYS Chi-restraints excluded: chain A residue 454 ILE Chi-restraints excluded: chain A residue 479 CYS Chi-restraints excluded: chain A residue 496 TYR Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 544 TRP Chi-restraints excluded: chain A residue 569 TYR Chi-restraints excluded: chain A residue 575 LEU Chi-restraints excluded: chain A residue 752 SER Chi-restraints excluded: chain A residue 753 ILE Chi-restraints excluded: chain A residue 873 GLU Chi-restraints excluded: chain A residue 1220 MET Chi-restraints excluded: chain A residue 1235 LEU Chi-restraints excluded: chain A residue 1236 PHE Chi-restraints excluded: chain A residue 1353 VAL Chi-restraints excluded: chain A residue 1396 ILE Chi-restraints excluded: chain A residue 1438 ILE Chi-restraints excluded: chain A residue 1457 ILE Chi-restraints excluded: chain A residue 1509 LEU Chi-restraints excluded: chain A residue 1532 SER Chi-restraints excluded: chain A residue 1557 ILE Chi-restraints excluded: chain A residue 1577 SER Chi-restraints excluded: chain A residue 1644 SER Chi-restraints excluded: chain A residue 1746 VAL Chi-restraints excluded: chain A residue 1748 CYS Chi-restraints excluded: chain A residue 1887 LEU Chi-restraints excluded: chain A residue 1951 THR Chi-restraints excluded: chain A residue 1980 PHE Chi-restraints excluded: chain A residue 2016 LYS Chi-restraints excluded: chain A residue 2220 ARG Chi-restraints excluded: chain A residue 2298 TRP Chi-restraints excluded: chain A residue 2607 LEU Chi-restraints excluded: chain A residue 2689 ILE Chi-restraints excluded: chain A residue 2736 VAL Chi-restraints excluded: chain A residue 2755 MET Chi-restraints excluded: chain A residue 2852 SER Chi-restraints excluded: chain A residue 2854 LYS Chi-restraints excluded: chain A residue 2901 SER Chi-restraints excluded: chain A residue 3012 VAL Chi-restraints excluded: chain A residue 3042 LEU Chi-restraints excluded: chain A residue 3080 TYR Chi-restraints excluded: chain A residue 3113 TYR Chi-restraints excluded: chain A residue 3129 VAL Chi-restraints excluded: chain A residue 3130 ASP Chi-restraints excluded: chain A residue 3312 HIS Chi-restraints excluded: chain A residue 3330 CYS Chi-restraints excluded: chain A residue 3340 ARG Chi-restraints excluded: chain A residue 3436 LEU Chi-restraints excluded: chain A residue 3449 THR Chi-restraints excluded: chain A residue 3540 VAL Chi-restraints excluded: chain A residue 3570 GLU Chi-restraints excluded: chain A residue 3681 MET Chi-restraints excluded: chain A residue 3776 MET Chi-restraints excluded: chain A residue 3854 CYS Chi-restraints excluded: chain A residue 3907 SER Chi-restraints excluded: chain A residue 3965 VAL Chi-restraints excluded: chain A residue 4005 LYS Chi-restraints excluded: chain A residue 4034 TYR Chi-restraints excluded: chain A residue 4292 VAL Chi-restraints excluded: chain A residue 4362 THR Chi-restraints excluded: chain A residue 4381 ILE Chi-restraints excluded: chain A residue 4390 LEU Chi-restraints excluded: chain A residue 4601 LEU Chi-restraints excluded: chain A residue 4670 THR Chi-restraints excluded: chain A residue 4735 VAL Chi-restraints excluded: chain A residue 4765 VAL Chi-restraints excluded: chain A residue 4972 SER Chi-restraints excluded: chain A residue 4973 LEU Chi-restraints excluded: chain A residue 4980 VAL Chi-restraints excluded: chain A residue 5061 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 475 random chunks: chunk 111 optimal weight: 3.9990 chunk 315 optimal weight: 6.9990 chunk 245 optimal weight: 0.0980 chunk 183 optimal weight: 0.9980 chunk 212 optimal weight: 4.9990 chunk 12 optimal weight: 0.7980 chunk 154 optimal weight: 0.6980 chunk 474 optimal weight: 0.5980 chunk 208 optimal weight: 6.9990 chunk 254 optimal weight: 0.9980 chunk 303 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 164 HIS B 205 GLN B 220 ASN A 548 ASN A3104 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.093652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.076082 restraints weight = 87810.366| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 2.15 r_work: 0.2980 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2831 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.3918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 39257 Z= 0.126 Angle : 0.516 13.247 53127 Z= 0.261 Chirality : 0.039 0.275 6004 Planarity : 0.004 0.056 6780 Dihedral : 4.908 80.232 5183 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 2.33 % Allowed : 15.14 % Favored : 82.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.95 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 1.85 (0.13), residues: 4714 helix: 2.29 (0.10), residues: 2688 sheet: 0.33 (0.28), residues: 342 loop : -0.32 (0.16), residues: 1684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A3323 TYR 0.015 0.001 TYR A 496 PHE 0.021 0.001 PHE A 464 TRP 0.037 0.001 TRP A 576 HIS 0.010 0.001 HIS A5062 Details of bonding type rmsd covalent geometry : bond 0.00296 (39249) covalent geometry : angle 0.51551 (53127) hydrogen bonds : bond 0.03793 ( 2109) hydrogen bonds : angle 3.81429 ( 6090) metal coordination : bond 0.00330 ( 7) Misc. bond : bond 0.00122 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9428 Ramachandran restraints generated. 4714 Oldfield, 0 Emsley, 4714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9428 Ramachandran restraints generated. 4714 Oldfield, 0 Emsley, 4714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 4292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 307 time to evaluate : 1.466 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 42 LEU cc_start: 0.8958 (tm) cc_final: 0.8583 (mt) REVERT: B 112 MET cc_start: 0.7020 (mmm) cc_final: 0.6452 (ttp) REVERT: B 203 ILE cc_start: 0.8333 (mm) cc_final: 0.8004 (tp) REVERT: B 213 MET cc_start: 0.6851 (mmm) cc_final: 0.6214 (mmm) REVERT: B 219 MET cc_start: 0.8199 (mpp) cc_final: 0.7883 (mmm) REVERT: B 251 MET cc_start: 0.7343 (mmm) cc_final: 0.7095 (mtt) REVERT: A 533 MET cc_start: 0.7026 (tmm) cc_final: 0.6152 (ttp) REVERT: A 559 PHE cc_start: 0.6067 (t80) cc_final: 0.5310 (t80) REVERT: A 567 MET cc_start: 0.7086 (mmm) cc_final: 0.6475 (mmm) REVERT: A 575 LEU cc_start: 0.8221 (OUTLIER) cc_final: 0.7598 (mt) REVERT: A 873 GLU cc_start: 0.8571 (OUTLIER) cc_final: 0.8342 (mt-10) REVERT: A 922 MET cc_start: 0.8756 (ttt) cc_final: 0.8458 (ttt) REVERT: A 1146 GLU cc_start: 0.6958 (mt-10) cc_final: 0.6548 (mt-10) REVERT: A 1372 PHE cc_start: 0.5454 (m-80) cc_final: 0.5161 (m-10) REVERT: A 1381 PHE cc_start: 0.7959 (t80) cc_final: 0.7736 (t80) REVERT: A 1385 PHE cc_start: 0.7783 (t80) cc_final: 0.7050 (t80) REVERT: A 1509 LEU cc_start: 0.8788 (OUTLIER) cc_final: 0.8295 (tm) REVERT: A 2220 ARG cc_start: 0.8309 (OUTLIER) cc_final: 0.7815 (ttp-170) REVERT: A 2592 LEU cc_start: 0.9187 (mt) cc_final: 0.8880 (tp) REVERT: A 2607 LEU cc_start: 0.8982 (OUTLIER) cc_final: 0.8762 (tp) REVERT: A 2626 MET cc_start: 0.9258 (mmm) cc_final: 0.8946 (mmm) REVERT: A 2855 MET cc_start: 0.8573 (mmt) cc_final: 0.8290 (mmt) REVERT: A 3209 ARG cc_start: 0.4014 (mpt180) cc_final: 0.2925 (mmm160) REVERT: A 3328 HIS cc_start: 0.7999 (t70) cc_final: 0.7762 (t-170) REVERT: A 3330 CYS cc_start: 0.8737 (OUTLIER) cc_final: 0.8233 (t) REVERT: A 3340 ARG cc_start: 0.7535 (OUTLIER) cc_final: 0.7197 (ttm-80) REVERT: A 3592 LYS cc_start: 0.8550 (tppt) cc_final: 0.8293 (tptt) REVERT: A 3681 MET cc_start: 0.5471 (OUTLIER) cc_final: 0.5213 (pmm) REVERT: A 4034 TYR cc_start: 0.8321 (OUTLIER) cc_final: 0.7672 (t80) REVERT: A 4060 ARG cc_start: 0.8078 (mtp180) cc_final: 0.7793 (mtm-85) REVERT: A 4765 VAL cc_start: 0.9290 (OUTLIER) cc_final: 0.8861 (m) REVERT: A 4986 ASN cc_start: 0.5749 (t0) cc_final: 0.5308 (p0) REVERT: A 4992 MET cc_start: 0.7922 (mmm) cc_final: 0.7628 (mmp) outliers start: 100 outliers final: 71 residues processed: 380 average time/residue: 0.2574 time to fit residues: 154.4479 Evaluate side-chains 383 residues out of total 4292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 302 time to evaluate : 1.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 63 ASN Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 220 ASN Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 247 SER Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain A residue 418 CYS Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 454 ILE Chi-restraints excluded: chain A residue 479 CYS Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 544 TRP Chi-restraints excluded: chain A residue 569 TYR Chi-restraints excluded: chain A residue 575 LEU Chi-restraints excluded: chain A residue 752 SER Chi-restraints excluded: chain A residue 753 ILE Chi-restraints excluded: chain A residue 873 GLU Chi-restraints excluded: chain A residue 1220 MET Chi-restraints excluded: chain A residue 1235 LEU Chi-restraints excluded: chain A residue 1236 PHE Chi-restraints excluded: chain A residue 1353 VAL Chi-restraints excluded: chain A residue 1396 ILE Chi-restraints excluded: chain A residue 1438 ILE Chi-restraints excluded: chain A residue 1457 ILE Chi-restraints excluded: chain A residue 1509 LEU Chi-restraints excluded: chain A residue 1532 SER Chi-restraints excluded: chain A residue 1557 ILE Chi-restraints excluded: chain A residue 1577 SER Chi-restraints excluded: chain A residue 1644 SER Chi-restraints excluded: chain A residue 1746 VAL Chi-restraints excluded: chain A residue 1748 CYS Chi-restraints excluded: chain A residue 1887 LEU Chi-restraints excluded: chain A residue 1951 THR Chi-restraints excluded: chain A residue 1980 PHE Chi-restraints excluded: chain A residue 2016 LYS Chi-restraints excluded: chain A residue 2220 ARG Chi-restraints excluded: chain A residue 2233 LEU Chi-restraints excluded: chain A residue 2292 PHE Chi-restraints excluded: chain A residue 2298 TRP Chi-restraints excluded: chain A residue 2607 LEU Chi-restraints excluded: chain A residue 2689 ILE Chi-restraints excluded: chain A residue 2736 VAL Chi-restraints excluded: chain A residue 2755 MET Chi-restraints excluded: chain A residue 2852 SER Chi-restraints excluded: chain A residue 2901 SER Chi-restraints excluded: chain A residue 3012 VAL Chi-restraints excluded: chain A residue 3042 LEU Chi-restraints excluded: chain A residue 3080 TYR Chi-restraints excluded: chain A residue 3113 TYR Chi-restraints excluded: chain A residue 3129 VAL Chi-restraints excluded: chain A residue 3130 ASP Chi-restraints excluded: chain A residue 3312 HIS Chi-restraints excluded: chain A residue 3330 CYS Chi-restraints excluded: chain A residue 3340 ARG Chi-restraints excluded: chain A residue 3436 LEU Chi-restraints excluded: chain A residue 3449 THR Chi-restraints excluded: chain A residue 3461 VAL Chi-restraints excluded: chain A residue 3540 VAL Chi-restraints excluded: chain A residue 3638 SER Chi-restraints excluded: chain A residue 3681 MET Chi-restraints excluded: chain A residue 3776 MET Chi-restraints excluded: chain A residue 3854 CYS Chi-restraints excluded: chain A residue 3907 SER Chi-restraints excluded: chain A residue 3965 VAL Chi-restraints excluded: chain A residue 4005 LYS Chi-restraints excluded: chain A residue 4034 TYR Chi-restraints excluded: chain A residue 4292 VAL Chi-restraints excluded: chain A residue 4311 VAL Chi-restraints excluded: chain A residue 4362 THR Chi-restraints excluded: chain A residue 4381 ILE Chi-restraints excluded: chain A residue 4390 LEU Chi-restraints excluded: chain A residue 4601 LEU Chi-restraints excluded: chain A residue 4670 THR Chi-restraints excluded: chain A residue 4735 VAL Chi-restraints excluded: chain A residue 4765 VAL Chi-restraints excluded: chain A residue 4972 SER Chi-restraints excluded: chain A residue 4973 LEU Chi-restraints excluded: chain A residue 4980 VAL Chi-restraints excluded: chain A residue 5061 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 475 random chunks: chunk 411 optimal weight: 0.0770 chunk 122 optimal weight: 2.9990 chunk 314 optimal weight: 0.2980 chunk 105 optimal weight: 3.9990 chunk 224 optimal weight: 3.9990 chunk 208 optimal weight: 5.9990 chunk 232 optimal weight: 3.9990 chunk 41 optimal weight: 0.8980 chunk 5 optimal weight: 0.9990 chunk 473 optimal weight: 2.9990 chunk 166 optimal weight: 3.9990 overall best weight: 1.0542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 ASN A3104 ASN A3285 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.092280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.074743 restraints weight = 87374.128| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 2.12 r_work: 0.2948 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2796 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.4057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 39257 Z= 0.173 Angle : 0.557 12.224 53127 Z= 0.283 Chirality : 0.041 0.283 6004 Planarity : 0.004 0.058 6780 Dihedral : 5.004 79.656 5180 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.22 % Favored : 95.76 % Rotamer: Outliers : 2.38 % Allowed : 15.26 % Favored : 82.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.95 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 1.74 (0.13), residues: 4714 helix: 2.20 (0.10), residues: 2680 sheet: 0.25 (0.28), residues: 340 loop : -0.34 (0.16), residues: 1694 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A3323 TYR 0.025 0.002 TYR A 496 PHE 0.015 0.001 PHE A3198 TRP 0.027 0.002 TRP A 576 HIS 0.011 0.001 HIS A5062 Details of bonding type rmsd covalent geometry : bond 0.00415 (39249) covalent geometry : angle 0.55669 (53127) hydrogen bonds : bond 0.04233 ( 2109) hydrogen bonds : angle 3.92251 ( 6090) metal coordination : bond 0.00259 ( 7) Misc. bond : bond 0.00204 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9428 Ramachandran restraints generated. 4714 Oldfield, 0 Emsley, 4714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9428 Ramachandran restraints generated. 4714 Oldfield, 0 Emsley, 4714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 4292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 316 time to evaluate : 1.820 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 42 LEU cc_start: 0.8927 (tm) cc_final: 0.8573 (mt) REVERT: B 96 LEU cc_start: 0.8733 (OUTLIER) cc_final: 0.8451 (tp) REVERT: B 112 MET cc_start: 0.7071 (mmm) cc_final: 0.6651 (ttp) REVERT: B 174 LYS cc_start: 0.8503 (mtmt) cc_final: 0.8236 (ttmm) REVERT: B 219 MET cc_start: 0.8338 (mpp) cc_final: 0.8127 (mmm) REVERT: B 251 MET cc_start: 0.7314 (mmm) cc_final: 0.7093 (mtt) REVERT: A 386 ILE cc_start: 0.8524 (OUTLIER) cc_final: 0.8248 (tt) REVERT: A 441 LYS cc_start: 0.5452 (OUTLIER) cc_final: 0.4245 (mtpt) REVERT: A 524 LYS cc_start: 0.7945 (mtmt) cc_final: 0.7627 (ptpt) REVERT: A 922 MET cc_start: 0.8749 (ttt) cc_final: 0.8493 (ttt) REVERT: A 1372 PHE cc_start: 0.5552 (m-80) cc_final: 0.5243 (m-10) REVERT: A 1381 PHE cc_start: 0.7960 (t80) cc_final: 0.7695 (t80) REVERT: A 1385 PHE cc_start: 0.7816 (t80) cc_final: 0.7245 (t80) REVERT: A 1509 LEU cc_start: 0.8869 (OUTLIER) cc_final: 0.8460 (tm) REVERT: A 2220 ARG cc_start: 0.8444 (OUTLIER) cc_final: 0.7938 (ttp-170) REVERT: A 2592 LEU cc_start: 0.9219 (mt) cc_final: 0.8950 (tp) REVERT: A 2626 MET cc_start: 0.9329 (mmm) cc_final: 0.9063 (mmm) REVERT: A 2855 MET cc_start: 0.8599 (mmt) cc_final: 0.8307 (mmt) REVERT: A 3328 HIS cc_start: 0.8076 (t70) cc_final: 0.7825 (t-170) REVERT: A 3330 CYS cc_start: 0.8806 (OUTLIER) cc_final: 0.8314 (t) REVERT: A 3340 ARG cc_start: 0.7544 (OUTLIER) cc_final: 0.7203 (ttm-80) REVERT: A 3592 LYS cc_start: 0.8585 (tppt) cc_final: 0.8329 (tptt) REVERT: A 4034 TYR cc_start: 0.8543 (OUTLIER) cc_final: 0.7947 (t80) REVERT: A 4060 ARG cc_start: 0.8147 (mtp180) cc_final: 0.7872 (mtm-85) REVERT: A 4765 VAL cc_start: 0.9256 (OUTLIER) cc_final: 0.8880 (m) REVERT: A 4986 ASN cc_start: 0.5797 (t0) cc_final: 0.5380 (p0) REVERT: A 4992 MET cc_start: 0.8025 (mmm) cc_final: 0.7767 (mmp) outliers start: 102 outliers final: 77 residues processed: 390 average time/residue: 0.2730 time to fit residues: 168.6262 Evaluate side-chains 396 residues out of total 4292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 310 time to evaluate : 1.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 63 ASN Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 220 ASN Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 247 SER Chi-restraints excluded: chain A residue 386 ILE Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain A residue 418 CYS Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain A residue 441 LYS Chi-restraints excluded: chain A residue 454 ILE Chi-restraints excluded: chain A residue 479 CYS Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 544 TRP Chi-restraints excluded: chain A residue 569 TYR Chi-restraints excluded: chain A residue 752 SER Chi-restraints excluded: chain A residue 753 ILE Chi-restraints excluded: chain A residue 1005 SER Chi-restraints excluded: chain A residue 1175 PHE Chi-restraints excluded: chain A residue 1220 MET Chi-restraints excluded: chain A residue 1235 LEU Chi-restraints excluded: chain A residue 1236 PHE Chi-restraints excluded: chain A residue 1289 LEU Chi-restraints excluded: chain A residue 1353 VAL Chi-restraints excluded: chain A residue 1393 LEU Chi-restraints excluded: chain A residue 1396 ILE Chi-restraints excluded: chain A residue 1438 ILE Chi-restraints excluded: chain A residue 1457 ILE Chi-restraints excluded: chain A residue 1509 LEU Chi-restraints excluded: chain A residue 1577 SER Chi-restraints excluded: chain A residue 1644 SER Chi-restraints excluded: chain A residue 1696 MET Chi-restraints excluded: chain A residue 1746 VAL Chi-restraints excluded: chain A residue 1748 CYS Chi-restraints excluded: chain A residue 1980 PHE Chi-restraints excluded: chain A residue 2016 LYS Chi-restraints excluded: chain A residue 2220 ARG Chi-restraints excluded: chain A residue 2292 PHE Chi-restraints excluded: chain A residue 2298 TRP Chi-restraints excluded: chain A residue 2689 ILE Chi-restraints excluded: chain A residue 2736 VAL Chi-restraints excluded: chain A residue 2755 MET Chi-restraints excluded: chain A residue 2852 SER Chi-restraints excluded: chain A residue 2901 SER Chi-restraints excluded: chain A residue 3012 VAL Chi-restraints excluded: chain A residue 3042 LEU Chi-restraints excluded: chain A residue 3080 TYR Chi-restraints excluded: chain A residue 3113 TYR Chi-restraints excluded: chain A residue 3129 VAL Chi-restraints excluded: chain A residue 3130 ASP Chi-restraints excluded: chain A residue 3312 HIS Chi-restraints excluded: chain A residue 3330 CYS Chi-restraints excluded: chain A residue 3340 ARG Chi-restraints excluded: chain A residue 3436 LEU Chi-restraints excluded: chain A residue 3449 THR Chi-restraints excluded: chain A residue 3461 VAL Chi-restraints excluded: chain A residue 3540 VAL Chi-restraints excluded: chain A residue 3638 SER Chi-restraints excluded: chain A residue 3776 MET Chi-restraints excluded: chain A residue 3854 CYS Chi-restraints excluded: chain A residue 3907 SER Chi-restraints excluded: chain A residue 3941 VAL Chi-restraints excluded: chain A residue 3965 VAL Chi-restraints excluded: chain A residue 4001 LEU Chi-restraints excluded: chain A residue 4005 LYS Chi-restraints excluded: chain A residue 4034 TYR Chi-restraints excluded: chain A residue 4292 VAL Chi-restraints excluded: chain A residue 4311 VAL Chi-restraints excluded: chain A residue 4362 THR Chi-restraints excluded: chain A residue 4381 ILE Chi-restraints excluded: chain A residue 4390 LEU Chi-restraints excluded: chain A residue 4601 LEU Chi-restraints excluded: chain A residue 4670 THR Chi-restraints excluded: chain A residue 4735 VAL Chi-restraints excluded: chain A residue 4765 VAL Chi-restraints excluded: chain A residue 4972 SER Chi-restraints excluded: chain A residue 4973 LEU Chi-restraints excluded: chain A residue 4980 VAL Chi-restraints excluded: chain A residue 4989 HIS Chi-restraints excluded: chain A residue 5044 MET Chi-restraints excluded: chain A residue 5061 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 475 random chunks: chunk 282 optimal weight: 1.9990 chunk 454 optimal weight: 0.7980 chunk 44 optimal weight: 0.6980 chunk 340 optimal weight: 0.5980 chunk 364 optimal weight: 0.5980 chunk 184 optimal weight: 0.9980 chunk 322 optimal weight: 1.9990 chunk 281 optimal weight: 0.7980 chunk 159 optimal weight: 0.5980 chunk 243 optimal weight: 0.0670 chunk 21 optimal weight: 8.9990 overall best weight: 0.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 ASN A1045 ASN A2225 GLN A3104 ASN A4675 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.093498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.076058 restraints weight = 87826.697| |-----------------------------------------------------------------------------| r_work (start): 0.3142 rms_B_bonded: 2.12 r_work: 0.2980 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2828 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.4159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 39257 Z= 0.120 Angle : 0.527 13.654 53127 Z= 0.267 Chirality : 0.039 0.301 6004 Planarity : 0.004 0.091 6780 Dihedral : 4.878 80.766 5179 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 2.00 % Allowed : 15.89 % Favored : 82.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.95 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 1.85 (0.13), residues: 4714 helix: 2.30 (0.10), residues: 2683 sheet: 0.21 (0.28), residues: 340 loop : -0.29 (0.16), residues: 1691 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A3323 TYR 0.019 0.001 TYR A 496 PHE 0.024 0.001 PHE A 464 TRP 0.026 0.001 TRP A 576 HIS 0.011 0.001 HIS A5062 Details of bonding type rmsd covalent geometry : bond 0.00275 (39249) covalent geometry : angle 0.52681 (53127) hydrogen bonds : bond 0.03795 ( 2109) hydrogen bonds : angle 3.82674 ( 6090) metal coordination : bond 0.00170 ( 7) Misc. bond : bond 0.00108 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9428 Ramachandran restraints generated. 4714 Oldfield, 0 Emsley, 4714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9428 Ramachandran restraints generated. 4714 Oldfield, 0 Emsley, 4714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 4292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 311 time to evaluate : 1.565 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 42 LEU cc_start: 0.8938 (tm) cc_final: 0.8588 (mt) REVERT: B 96 LEU cc_start: 0.8682 (OUTLIER) cc_final: 0.8412 (tp) REVERT: B 100 LYS cc_start: 0.7467 (tppt) cc_final: 0.6630 (tppt) REVERT: B 112 MET cc_start: 0.7047 (mmm) cc_final: 0.6559 (ttp) REVERT: B 174 LYS cc_start: 0.8504 (mtmt) cc_final: 0.8231 (ttmm) REVERT: A 441 LYS cc_start: 0.5657 (OUTLIER) cc_final: 0.4377 (mtpt) REVERT: A 524 LYS cc_start: 0.7911 (mtmt) cc_final: 0.7592 (ptpt) REVERT: A 567 MET cc_start: 0.7196 (mmm) cc_final: 0.6759 (mmm) REVERT: A 575 LEU cc_start: 0.8234 (tt) cc_final: 0.7885 (mm) REVERT: A 1381 PHE cc_start: 0.7898 (t80) cc_final: 0.7650 (t80) REVERT: A 1385 PHE cc_start: 0.7793 (t80) cc_final: 0.7296 (t80) REVERT: A 1509 LEU cc_start: 0.8810 (OUTLIER) cc_final: 0.8355 (tm) REVERT: A 2220 ARG cc_start: 0.8376 (OUTLIER) cc_final: 0.7892 (ttp-170) REVERT: A 2592 LEU cc_start: 0.9272 (mt) cc_final: 0.8955 (tp) REVERT: A 2626 MET cc_start: 0.9302 (mmm) cc_final: 0.9007 (mmm) REVERT: A 3323 ARG cc_start: 0.8537 (mtm110) cc_final: 0.8164 (ptp90) REVERT: A 3328 HIS cc_start: 0.8087 (t70) cc_final: 0.7817 (t-170) REVERT: A 3330 CYS cc_start: 0.8735 (OUTLIER) cc_final: 0.8272 (t) REVERT: A 3340 ARG cc_start: 0.7500 (OUTLIER) cc_final: 0.7175 (ttm-80) REVERT: A 3592 LYS cc_start: 0.8572 (tppt) cc_final: 0.8369 (tptt) REVERT: A 4034 TYR cc_start: 0.8424 (OUTLIER) cc_final: 0.7850 (t80) REVERT: A 4060 ARG cc_start: 0.8101 (mtp180) cc_final: 0.7830 (mtm-85) REVERT: A 4765 VAL cc_start: 0.9257 (OUTLIER) cc_final: 0.8830 (m) REVERT: A 4986 ASN cc_start: 0.5776 (t0) cc_final: 0.5376 (p0) REVERT: A 4992 MET cc_start: 0.7961 (mmm) cc_final: 0.7699 (mmp) outliers start: 86 outliers final: 67 residues processed: 372 average time/residue: 0.2679 time to fit residues: 158.8130 Evaluate side-chains 377 residues out of total 4292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 302 time to evaluate : 1.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 220 ASN Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 247 SER Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain A residue 418 CYS Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain A residue 441 LYS Chi-restraints excluded: chain A residue 454 ILE Chi-restraints excluded: chain A residue 479 CYS Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 544 TRP Chi-restraints excluded: chain A residue 752 SER Chi-restraints excluded: chain A residue 753 ILE Chi-restraints excluded: chain A residue 1220 MET Chi-restraints excluded: chain A residue 1235 LEU Chi-restraints excluded: chain A residue 1236 PHE Chi-restraints excluded: chain A residue 1353 VAL Chi-restraints excluded: chain A residue 1396 ILE Chi-restraints excluded: chain A residue 1438 ILE Chi-restraints excluded: chain A residue 1509 LEU Chi-restraints excluded: chain A residue 1577 SER Chi-restraints excluded: chain A residue 1644 SER Chi-restraints excluded: chain A residue 1746 VAL Chi-restraints excluded: chain A residue 1748 CYS Chi-restraints excluded: chain A residue 1980 PHE Chi-restraints excluded: chain A residue 2016 LYS Chi-restraints excluded: chain A residue 2220 ARG Chi-restraints excluded: chain A residue 2233 LEU Chi-restraints excluded: chain A residue 2292 PHE Chi-restraints excluded: chain A residue 2298 TRP Chi-restraints excluded: chain A residue 2689 ILE Chi-restraints excluded: chain A residue 2736 VAL Chi-restraints excluded: chain A residue 2755 MET Chi-restraints excluded: chain A residue 2852 SER Chi-restraints excluded: chain A residue 2901 SER Chi-restraints excluded: chain A residue 3012 VAL Chi-restraints excluded: chain A residue 3042 LEU Chi-restraints excluded: chain A residue 3080 TYR Chi-restraints excluded: chain A residue 3113 TYR Chi-restraints excluded: chain A residue 3129 VAL Chi-restraints excluded: chain A residue 3130 ASP Chi-restraints excluded: chain A residue 3312 HIS Chi-restraints excluded: chain A residue 3330 CYS Chi-restraints excluded: chain A residue 3340 ARG Chi-restraints excluded: chain A residue 3436 LEU Chi-restraints excluded: chain A residue 3449 THR Chi-restraints excluded: chain A residue 3461 VAL Chi-restraints excluded: chain A residue 3540 VAL Chi-restraints excluded: chain A residue 3638 SER Chi-restraints excluded: chain A residue 3776 MET Chi-restraints excluded: chain A residue 3854 CYS Chi-restraints excluded: chain A residue 3869 MET Chi-restraints excluded: chain A residue 3907 SER Chi-restraints excluded: chain A residue 3965 VAL Chi-restraints excluded: chain A residue 4005 LYS Chi-restraints excluded: chain A residue 4034 TYR Chi-restraints excluded: chain A residue 4292 VAL Chi-restraints excluded: chain A residue 4311 VAL Chi-restraints excluded: chain A residue 4362 THR Chi-restraints excluded: chain A residue 4381 ILE Chi-restraints excluded: chain A residue 4390 LEU Chi-restraints excluded: chain A residue 4601 LEU Chi-restraints excluded: chain A residue 4670 THR Chi-restraints excluded: chain A residue 4735 VAL Chi-restraints excluded: chain A residue 4765 VAL Chi-restraints excluded: chain A residue 4972 SER Chi-restraints excluded: chain A residue 4980 VAL Chi-restraints excluded: chain A residue 4989 HIS Chi-restraints excluded: chain A residue 5061 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 475 random chunks: chunk 317 optimal weight: 3.9990 chunk 129 optimal weight: 3.9990 chunk 412 optimal weight: 0.9990 chunk 443 optimal weight: 2.9990 chunk 205 optimal weight: 5.9990 chunk 203 optimal weight: 1.9990 chunk 100 optimal weight: 0.2980 chunk 467 optimal weight: 0.7980 chunk 420 optimal weight: 0.6980 chunk 314 optimal weight: 1.9990 chunk 106 optimal weight: 0.8980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 ASN A1045 ASN A3104 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.092887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.075353 restraints weight = 87845.865| |-----------------------------------------------------------------------------| r_work (start): 0.3127 rms_B_bonded: 2.13 r_work: 0.2964 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2809 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.4237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 39257 Z= 0.140 Angle : 0.553 17.691 53127 Z= 0.277 Chirality : 0.040 0.313 6004 Planarity : 0.004 0.065 6780 Dihedral : 4.875 80.755 5179 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 1.89 % Allowed : 15.91 % Favored : 82.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.95 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 1.82 (0.13), residues: 4714 helix: 2.27 (0.10), residues: 2684 sheet: 0.18 (0.28), residues: 340 loop : -0.30 (0.16), residues: 1690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A3323 TYR 0.023 0.001 TYR A 496 PHE 0.038 0.001 PHE B 202 TRP 0.028 0.001 TRP A 576 HIS 0.011 0.001 HIS A5062 Details of bonding type rmsd covalent geometry : bond 0.00330 (39249) covalent geometry : angle 0.55270 (53127) hydrogen bonds : bond 0.03964 ( 2109) hydrogen bonds : angle 3.85733 ( 6090) metal coordination : bond 0.00195 ( 7) Misc. bond : bond 0.00155 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9428 Ramachandran restraints generated. 4714 Oldfield, 0 Emsley, 4714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9428 Ramachandran restraints generated. 4714 Oldfield, 0 Emsley, 4714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 4292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 306 time to evaluate : 1.638 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 42 LEU cc_start: 0.8948 (tm) cc_final: 0.8596 (mt) REVERT: B 96 LEU cc_start: 0.8629 (OUTLIER) cc_final: 0.8358 (tp) REVERT: B 112 MET cc_start: 0.7124 (mmm) cc_final: 0.6686 (ttp) REVERT: B 174 LYS cc_start: 0.8509 (mtmt) cc_final: 0.8307 (mtmm) REVERT: B 203 ILE cc_start: 0.8362 (mm) cc_final: 0.7977 (tp) REVERT: B 251 MET cc_start: 0.7354 (mtt) cc_final: 0.6820 (mmm) REVERT: A 386 ILE cc_start: 0.8536 (OUTLIER) cc_final: 0.8287 (tt) REVERT: A 567 MET cc_start: 0.7245 (mmm) cc_final: 0.6812 (mmm) REVERT: A 575 LEU cc_start: 0.8247 (tt) cc_final: 0.7815 (mm) REVERT: A 1381 PHE cc_start: 0.7918 (t80) cc_final: 0.7665 (t80) REVERT: A 1385 PHE cc_start: 0.7785 (t80) cc_final: 0.7280 (t80) REVERT: A 1509 LEU cc_start: 0.8874 (OUTLIER) cc_final: 0.8424 (tm) REVERT: A 1758 ARG cc_start: 0.7624 (mtm-85) cc_final: 0.7305 (mtm-85) REVERT: A 2220 ARG cc_start: 0.8448 (OUTLIER) cc_final: 0.7965 (ttp-170) REVERT: A 2592 LEU cc_start: 0.9270 (mt) cc_final: 0.8962 (tp) REVERT: A 2626 MET cc_start: 0.9303 (mmm) cc_final: 0.9018 (mmm) REVERT: A 2962 MET cc_start: 0.8938 (mtt) cc_final: 0.8701 (mtp) REVERT: A 3323 ARG cc_start: 0.8528 (mtm110) cc_final: 0.8167 (ptp90) REVERT: A 3328 HIS cc_start: 0.8131 (t70) cc_final: 0.7856 (t-170) REVERT: A 3330 CYS cc_start: 0.8765 (OUTLIER) cc_final: 0.8333 (t) REVERT: A 3340 ARG cc_start: 0.7495 (OUTLIER) cc_final: 0.7163 (ttm-80) REVERT: A 3592 LYS cc_start: 0.8557 (tppt) cc_final: 0.8337 (tptt) REVERT: A 3681 MET cc_start: 0.5500 (OUTLIER) cc_final: 0.5294 (pmm) REVERT: A 4034 TYR cc_start: 0.8459 (OUTLIER) cc_final: 0.7863 (t80) REVERT: A 4060 ARG cc_start: 0.8119 (mtp180) cc_final: 0.7837 (mtm-85) REVERT: A 4309 ASP cc_start: 0.7348 (m-30) cc_final: 0.7105 (m-30) REVERT: A 4765 VAL cc_start: 0.9257 (OUTLIER) cc_final: 0.8837 (m) REVERT: A 4986 ASN cc_start: 0.5738 (t0) cc_final: 0.5341 (p0) REVERT: A 4992 MET cc_start: 0.8059 (mmm) cc_final: 0.7835 (mmp) REVERT: A 4993 ASP cc_start: 0.8544 (m-30) cc_final: 0.8271 (m-30) outliers start: 81 outliers final: 68 residues processed: 363 average time/residue: 0.2811 time to fit residues: 162.2159 Evaluate side-chains 377 residues out of total 4292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 300 time to evaluate : 1.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 211 PHE Chi-restraints excluded: chain B residue 220 ASN Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 247 SER Chi-restraints excluded: chain A residue 386 ILE Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain A residue 418 CYS Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain A residue 454 ILE Chi-restraints excluded: chain A residue 479 CYS Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 544 TRP Chi-restraints excluded: chain A residue 752 SER Chi-restraints excluded: chain A residue 753 ILE Chi-restraints excluded: chain A residue 1220 MET Chi-restraints excluded: chain A residue 1235 LEU Chi-restraints excluded: chain A residue 1236 PHE Chi-restraints excluded: chain A residue 1353 VAL Chi-restraints excluded: chain A residue 1396 ILE Chi-restraints excluded: chain A residue 1438 ILE Chi-restraints excluded: chain A residue 1509 LEU Chi-restraints excluded: chain A residue 1577 SER Chi-restraints excluded: chain A residue 1644 SER Chi-restraints excluded: chain A residue 1746 VAL Chi-restraints excluded: chain A residue 1748 CYS Chi-restraints excluded: chain A residue 1887 LEU Chi-restraints excluded: chain A residue 1980 PHE Chi-restraints excluded: chain A residue 2016 LYS Chi-restraints excluded: chain A residue 2220 ARG Chi-restraints excluded: chain A residue 2233 LEU Chi-restraints excluded: chain A residue 2292 PHE Chi-restraints excluded: chain A residue 2298 TRP Chi-restraints excluded: chain A residue 2689 ILE Chi-restraints excluded: chain A residue 2736 VAL Chi-restraints excluded: chain A residue 2755 MET Chi-restraints excluded: chain A residue 2852 SER Chi-restraints excluded: chain A residue 2901 SER Chi-restraints excluded: chain A residue 3012 VAL Chi-restraints excluded: chain A residue 3042 LEU Chi-restraints excluded: chain A residue 3080 TYR Chi-restraints excluded: chain A residue 3113 TYR Chi-restraints excluded: chain A residue 3129 VAL Chi-restraints excluded: chain A residue 3130 ASP Chi-restraints excluded: chain A residue 3312 HIS Chi-restraints excluded: chain A residue 3330 CYS Chi-restraints excluded: chain A residue 3340 ARG Chi-restraints excluded: chain A residue 3436 LEU Chi-restraints excluded: chain A residue 3449 THR Chi-restraints excluded: chain A residue 3461 VAL Chi-restraints excluded: chain A residue 3540 VAL Chi-restraints excluded: chain A residue 3638 SER Chi-restraints excluded: chain A residue 3681 MET Chi-restraints excluded: chain A residue 3776 MET Chi-restraints excluded: chain A residue 3854 CYS Chi-restraints excluded: chain A residue 3907 SER Chi-restraints excluded: chain A residue 3965 VAL Chi-restraints excluded: chain A residue 4005 LYS Chi-restraints excluded: chain A residue 4034 TYR Chi-restraints excluded: chain A residue 4292 VAL Chi-restraints excluded: chain A residue 4311 VAL Chi-restraints excluded: chain A residue 4362 THR Chi-restraints excluded: chain A residue 4381 ILE Chi-restraints excluded: chain A residue 4390 LEU Chi-restraints excluded: chain A residue 4601 LEU Chi-restraints excluded: chain A residue 4670 THR Chi-restraints excluded: chain A residue 4735 VAL Chi-restraints excluded: chain A residue 4765 VAL Chi-restraints excluded: chain A residue 4979 LEU Chi-restraints excluded: chain A residue 4980 VAL Chi-restraints excluded: chain A residue 4989 HIS Chi-restraints excluded: chain A residue 5061 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 475 random chunks: chunk 29 optimal weight: 0.5980 chunk 306 optimal weight: 0.7980 chunk 433 optimal weight: 0.3980 chunk 270 optimal weight: 0.3980 chunk 361 optimal weight: 3.9990 chunk 196 optimal weight: 0.0000 chunk 131 optimal weight: 0.6980 chunk 28 optimal weight: 0.9990 chunk 296 optimal weight: 0.7980 chunk 163 optimal weight: 5.9990 chunk 202 optimal weight: 0.0870 overall best weight: 0.2962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 122 GLN B 220 ASN A 384 HIS A1045 ASN ** A1564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3104 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.094400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.076971 restraints weight = 88088.442| |-----------------------------------------------------------------------------| r_work (start): 0.3163 rms_B_bonded: 2.13 r_work: 0.3000 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2853 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.4324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 39257 Z= 0.105 Angle : 0.531 16.637 53127 Z= 0.265 Chirality : 0.039 0.312 6004 Planarity : 0.004 0.066 6780 Dihedral : 4.769 81.971 5179 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 1.84 % Allowed : 16.12 % Favored : 82.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.95 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 1.99 (0.13), residues: 4714 helix: 2.39 (0.10), residues: 2685 sheet: 0.26 (0.28), residues: 338 loop : -0.20 (0.16), residues: 1691 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A3323 TYR 0.022 0.001 TYR A 496 PHE 0.025 0.001 PHE A 464 TRP 0.023 0.001 TRP A 576 HIS 0.017 0.001 HIS A5062 Details of bonding type rmsd covalent geometry : bond 0.00233 (39249) covalent geometry : angle 0.53098 (53127) hydrogen bonds : bond 0.03530 ( 2109) hydrogen bonds : angle 3.75276 ( 6090) metal coordination : bond 0.00133 ( 7) Misc. bond : bond 0.00082 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10098.97 seconds wall clock time: 174 minutes 2.16 seconds (10442.16 seconds total)