Starting phenix.real_space_refine on Sat Mar 7 11:01:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6sl0_10233/03_2026/6sl0_10233.cif Found real_map, /net/cci-nas-00/data/ceres_data/6sl0_10233/03_2026/6sl0_10233.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6sl0_10233/03_2026/6sl0_10233.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6sl0_10233/03_2026/6sl0_10233.map" model { file = "/net/cci-nas-00/data/ceres_data/6sl0_10233/03_2026/6sl0_10233.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6sl0_10233/03_2026/6sl0_10233.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 190 5.16 5 C 26604 2.51 5 N 7286 2.21 5 O 7772 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 276 residue(s): 0.05s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 41860 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 20898 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2638, 20898 Classifications: {'peptide': 2638} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 111, 'TRANS': 2526} Chain breaks: 20 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Restraints were copied for chains: B Time building chain proxies: 39.45, per 1000 atoms: 0.94 Number of scatterers: 41860 At special positions: 0 Unit cell: (212.859, 111.195, 203.328, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 190 16.00 P 6 15.00 Mg 2 11.99 O 7772 8.00 N 7286 7.00 C 26604 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A1408 " - pdb=" SG CYS A1447 " distance=2.05 Simple disulfide: pdb=" SG CYS B1408 " - pdb=" SG CYS B1447 " distance=2.05 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.39 Conformation dependent library (CDL) restraints added in 1.7 seconds 10384 Ramachandran restraints generated. 5192 Oldfield, 0 Emsley, 5192 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10128 Finding SS restraints... Secondary structure from input PDB file: 290 helices and 8 sheets defined 73.6% alpha, 1.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.88 Creating SS restraints... Processing helix chain 'A' and resid 14 through 22 Processing helix chain 'A' and resid 26 through 40 WARNING: missing atoms! Processing helix chain 'A' and resid 56 through 73 Processing helix chain 'A' and resid 86 through 102 Proline residue: A 95 - end of helix Processing helix chain 'A' and resid 110 through 125 removed outlier: 3.879A pdb=" N LEU A 125 " --> pdb=" O ILE A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 150 removed outlier: 3.615A pdb=" N TYR A 140 " --> pdb=" O LEU A 136 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N ASN A 150 " --> pdb=" O GLU A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 157 removed outlier: 3.733A pdb=" N ALA A 154 " --> pdb=" O ASN A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 179 Processing helix chain 'A' and resid 218 through 233 Processing helix chain 'A' and resid 244 through 255 removed outlier: 4.432A pdb=" N HIS A 248 " --> pdb=" O ASP A 244 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLN A 255 " --> pdb=" O ILE A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 279 Processing helix chain 'A' and resid 283 through 295 Processing helix chain 'A' and resid 313 through 335 removed outlier: 5.515A pdb=" N LEU A 329 " --> pdb=" O TYR A 325 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N TYR A 330 " --> pdb=" O GLY A 326 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLN A 332 " --> pdb=" O ARG A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 360 removed outlier: 4.072A pdb=" N ARG A 360 " --> pdb=" O CYS A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 416 removed outlier: 3.991A pdb=" N TRP A 402 " --> pdb=" O GLY A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 454 Processing helix chain 'A' and resid 457 through 473 removed outlier: 4.196A pdb=" N ILE A 468 " --> pdb=" O ALA A 464 " (cutoff:3.500A) Proline residue: A 469 - end of helix Processing helix chain 'A' and resid 478 through 493 Processing helix chain 'A' and resid 497 through 512 Processing helix chain 'A' and resid 519 through 521 No H-bonds generated for 'chain 'A' and resid 519 through 521' Processing helix chain 'A' and resid 522 through 535 Processing helix chain 'A' and resid 542 through 557 removed outlier: 3.573A pdb=" N SER A 546 " --> pdb=" O ILE A 542 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 575 Processing helix chain 'A' and resid 584 through 602 Processing helix chain 'A' and resid 606 through 621 Processing helix chain 'A' and resid 625 through 632 Processing helix chain 'A' and resid 637 through 650 Processing helix chain 'A' and resid 665 through 674 Processing helix chain 'A' and resid 677 through 685 Processing helix chain 'A' and resid 716 through 741 Proline residue: A 730 - end of helix Processing helix chain 'A' and resid 754 through 771 removed outlier: 3.593A pdb=" N LEU A 771 " --> pdb=" O THR A 767 " (cutoff:3.500A) Processing helix chain 'A' and resid 783 through 803 removed outlier: 3.855A pdb=" N ASN A 803 " --> pdb=" O LYS A 799 " (cutoff:3.500A) Processing helix chain 'A' and resid 809 through 819 removed outlier: 3.531A pdb=" N MET A 813 " --> pdb=" O ASN A 809 " (cutoff:3.500A) Processing helix chain 'A' and resid 820 through 822 No H-bonds generated for 'chain 'A' and resid 820 through 822' Processing helix chain 'A' and resid 826 through 833 Processing helix chain 'A' and resid 837 through 858 removed outlier: 3.579A pdb=" N LEU A 841 " --> pdb=" O ARG A 837 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLU A 858 " --> pdb=" O ARG A 854 " (cutoff:3.500A) Processing helix chain 'A' and resid 895 through 898 Processing helix chain 'A' and resid 899 through 921 Processing helix chain 'A' and resid 928 through 936 Processing helix chain 'A' and resid 946 through 956 removed outlier: 3.763A pdb=" N SER A 956 " --> pdb=" O GLU A 952 " (cutoff:3.500A) Processing helix chain 'A' and resid 961 through 975 Processing helix chain 'A' and resid 976 through 978 No H-bonds generated for 'chain 'A' and resid 976 through 978' Processing helix chain 'A' and resid 984 through 998 removed outlier: 3.617A pdb=" N LEU A 988 " --> pdb=" O CYS A 984 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N PHE A 998 " --> pdb=" O ILE A 994 " (cutoff:3.500A) Processing helix chain 'A' and resid 998 through 1003 removed outlier: 4.745A pdb=" N TRP A1002 " --> pdb=" O PHE A 998 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N THR A1003 " --> pdb=" O ILE A 999 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 998 through 1003' Processing helix chain 'A' and resid 1009 through 1023 Processing helix chain 'A' and resid 1031 through 1046 Processing helix chain 'A' and resid 1051 through 1056 Processing helix chain 'A' and resid 1060 through 1071 Processing helix chain 'A' and resid 1073 through 1084 Processing helix chain 'A' and resid 1086 through 1090 removed outlier: 3.842A pdb=" N LEU A1090 " --> pdb=" O LEU A1087 " (cutoff:3.500A) Processing helix chain 'A' and resid 1092 through 1094 No H-bonds generated for 'chain 'A' and resid 1092 through 1094' Processing helix chain 'A' and resid 1095 through 1105 removed outlier: 3.673A pdb=" N ILE A1099 " --> pdb=" O THR A1095 " (cutoff:3.500A) Processing helix chain 'A' and resid 1113 through 1131 removed outlier: 4.008A pdb=" N LEU A1117 " --> pdb=" O VAL A1113 " (cutoff:3.500A) Processing helix chain 'A' and resid 1134 through 1145 removed outlier: 3.851A pdb=" N ILE A1145 " --> pdb=" O HIS A1141 " (cutoff:3.500A) Processing helix chain 'A' and resid 1161 through 1176 Processing helix chain 'A' and resid 1182 through 1199 removed outlier: 4.217A pdb=" N LEU A1188 " --> pdb=" O GLU A1184 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N PHE A1189 " --> pdb=" O LEU A1185 " (cutoff:3.500A) Proline residue: A1191 - end of helix Processing helix chain 'A' and resid 1200 through 1201 No H-bonds generated for 'chain 'A' and resid 1200 through 1201' Processing helix chain 'A' and resid 1202 through 1206 Processing helix chain 'A' and resid 1215 through 1221 removed outlier: 3.715A pdb=" N LEU A1219 " --> pdb=" O SER A1215 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ARG A1221 " --> pdb=" O LEU A1217 " (cutoff:3.500A) Processing helix chain 'A' and resid 1223 through 1235 Processing helix chain 'A' and resid 1236 through 1248 Processing helix chain 'A' and resid 1250 through 1258 Processing helix chain 'A' and resid 1258 through 1269 Processing helix chain 'A' and resid 1283 through 1288 Processing helix chain 'A' and resid 1294 through 1302 Processing helix chain 'A' and resid 1302 through 1314 removed outlier: 3.621A pdb=" N ILE A1313 " --> pdb=" O THR A1309 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N PHE A1314 " --> pdb=" O PHE A1310 " (cutoff:3.500A) Processing helix chain 'A' and resid 1318 through 1324 removed outlier: 3.797A pdb=" N LYS A1322 " --> pdb=" O ASP A1318 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N PHE A1324 " --> pdb=" O ILE A1320 " (cutoff:3.500A) Processing helix chain 'A' and resid 1332 through 1344 removed outlier: 3.978A pdb=" N GLY A1344 " --> pdb=" O ILE A1340 " (cutoff:3.500A) Processing helix chain 'A' and resid 1359 through 1361 No H-bonds generated for 'chain 'A' and resid 1359 through 1361' Processing helix chain 'A' and resid 1362 through 1372 Processing helix chain 'A' and resid 1383 through 1398 removed outlier: 3.794A pdb=" N ILE A1398 " --> pdb=" O LEU A1394 " (cutoff:3.500A) Processing helix chain 'A' and resid 1405 through 1422 removed outlier: 3.935A pdb=" N SER A1409 " --> pdb=" O LEU A1405 " (cutoff:3.500A) Processing helix chain 'A' and resid 1428 through 1443 removed outlier: 3.581A pdb=" N GLU A1432 " --> pdb=" O GLY A1428 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N SER A1437 " --> pdb=" O MET A1433 " (cutoff:3.500A) Processing helix chain 'A' and resid 1448 through 1462 removed outlier: 3.671A pdb=" N LEU A1452 " --> pdb=" O ALA A1448 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLY A1453 " --> pdb=" O ASP A1449 " (cutoff:3.500A) Processing helix chain 'A' and resid 1462 through 1467 Processing helix chain 'A' and resid 1469 through 1490 removed outlier: 3.624A pdb=" N GLY A1475 " --> pdb=" O SER A1471 " (cutoff:3.500A) Processing helix chain 'A' and resid 1497 through 1522 removed outlier: 3.923A pdb=" N LYS A1502 " --> pdb=" O GLU A1498 " (cutoff:3.500A) Processing helix chain 'A' and resid 1529 through 1544 removed outlier: 3.539A pdb=" N LYS A1533 " --> pdb=" O ASP A1529 " (cutoff:3.500A) Processing helix chain 'A' and resid 1556 through 1570 Processing helix chain 'A' and resid 1577 through 1589 Processing helix chain 'A' and resid 1605 through 1620 removed outlier: 5.078A pdb=" N ALA A1614 " --> pdb=" O ILE A1610 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N VAL A1615 " --> pdb=" O LYS A1611 " (cutoff:3.500A) Processing helix chain 'A' and resid 1626 through 1645 Processing helix chain 'A' and resid 1648 through 1652 Processing helix chain 'A' and resid 1656 through 1664 Processing helix chain 'A' and resid 1669 through 1684 removed outlier: 3.777A pdb=" N LEU A1681 " --> pdb=" O LEU A1677 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N THR A1682 " --> pdb=" O ILE A1678 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N ILE A1683 " --> pdb=" O LYS A1679 " (cutoff:3.500A) Processing helix chain 'A' and resid 1686 through 1707 Processing helix chain 'A' and resid 1709 through 1720 removed outlier: 3.574A pdb=" N GLU A1718 " --> pdb=" O SER A1714 " (cutoff:3.500A) Processing helix chain 'A' and resid 1721 through 1727 Processing helix chain 'A' and resid 1761 through 1772 Processing helix chain 'A' and resid 1777 through 1782 removed outlier: 3.599A pdb=" N VAL A1782 " --> pdb=" O VAL A1778 " (cutoff:3.500A) Processing helix chain 'A' and resid 1783 through 1788 Processing helix chain 'A' and resid 1792 through 1809 removed outlier: 3.779A pdb=" N ARG A1796 " --> pdb=" O GLY A1792 " (cutoff:3.500A) Proline residue: A1799 - end of helix Processing helix chain 'A' and resid 1814 through 1828 removed outlier: 3.711A pdb=" N ARG A1818 " --> pdb=" O GLN A1814 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N GLN A1825 " --> pdb=" O SER A1821 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N GLU A1826 " --> pdb=" O GLU A1822 " (cutoff:3.500A) Processing helix chain 'A' and resid 1835 through 1850 removed outlier: 3.759A pdb=" N LEU A1841 " --> pdb=" O GLU A1837 " (cutoff:3.500A) Processing helix chain 'A' and resid 1859 through 1866 removed outlier: 3.978A pdb=" N ALA A1864 " --> pdb=" O ALA A1861 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N TRP A1866 " --> pdb=" O ARG A1863 " (cutoff:3.500A) Processing helix chain 'A' and resid 1870 through 1881 Processing helix chain 'A' and resid 1883 through 1899 Processing helix chain 'A' and resid 1915 through 1924 removed outlier: 4.189A pdb=" N GLU A1919 " --> pdb=" O ASP A1915 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ASN A1923 " --> pdb=" O GLU A1919 " (cutoff:3.500A) Processing helix chain 'A' and resid 1928 through 1933 Processing helix chain 'A' and resid 1938 through 1949 Processing helix chain 'A' and resid 1952 through 1969 removed outlier: 3.799A pdb=" N PHE A1958 " --> pdb=" O LYS A1954 " (cutoff:3.500A) Processing helix chain 'A' and resid 1973 through 1989 removed outlier: 3.756A pdb=" N GLY A1989 " --> pdb=" O LEU A1985 " (cutoff:3.500A) Processing helix chain 'A' and resid 1990 through 2001 removed outlier: 3.610A pdb=" N SER A1994 " --> pdb=" O LEU A1990 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N SER A2000 " --> pdb=" O SER A1996 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLN A2001 " --> pdb=" O LEU A1997 " (cutoff:3.500A) Processing helix chain 'A' and resid 2008 through 2022 removed outlier: 3.955A pdb=" N PHE A2015 " --> pdb=" O LEU A2011 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N THR A2017 " --> pdb=" O ALA A2013 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ALA A2018 " --> pdb=" O THR A2014 " (cutoff:3.500A) Processing helix chain 'A' and resid 2034 through 2048 Processing helix chain 'A' and resid 2051 through 2072 removed outlier: 3.843A pdb=" N VAL A2055 " --> pdb=" O GLU A2051 " (cutoff:3.500A) Processing helix chain 'A' and resid 2076 through 2098 removed outlier: 3.628A pdb=" N ASN A2098 " --> pdb=" O ASP A2094 " (cutoff:3.500A) Processing helix chain 'A' and resid 2101 through 2120 Processing helix chain 'A' and resid 2123 through 2144 Processing helix chain 'A' and resid 2153 through 2175 Processing helix chain 'A' and resid 2177 through 2190 Processing helix chain 'A' and resid 2191 through 2197 removed outlier: 3.597A pdb=" N SER A2197 " --> pdb=" O PRO A2193 " (cutoff:3.500A) Processing helix chain 'A' and resid 2202 through 2217 Processing helix chain 'A' and resid 2219 through 2233 Processing helix chain 'A' and resid 2244 through 2259 Processing helix chain 'A' and resid 2263 through 2271 removed outlier: 3.918A pdb=" N GLN A2268 " --> pdb=" O PRO A2264 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LYS A2269 " --> pdb=" O ASP A2265 " (cutoff:3.500A) Processing helix chain 'A' and resid 2271 through 2279 Processing helix chain 'A' and resid 2285 through 2304 Processing helix chain 'A' and resid 2305 through 2330 Processing helix chain 'A' and resid 2349 through 2386 Processing helix chain 'A' and resid 2393 through 2405 removed outlier: 3.585A pdb=" N LYS A2405 " --> pdb=" O LEU A2401 " (cutoff:3.500A) Processing helix chain 'A' and resid 2408 through 2419 Processing helix chain 'A' and resid 2420 through 2422 No H-bonds generated for 'chain 'A' and resid 2420 through 2422' Processing helix chain 'A' and resid 2423 through 2427 Processing helix chain 'A' and resid 2430 through 2435 Processing helix chain 'A' and resid 2443 through 2460 removed outlier: 3.552A pdb=" N LYS A2447 " --> pdb=" O THR A2443 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ASP A2451 " --> pdb=" O LYS A2447 " (cutoff:3.500A) Processing helix chain 'A' and resid 2460 through 2473 removed outlier: 5.841A pdb=" N TYR A2466 " --> pdb=" O TYR A2462 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N HIS A2467 " --> pdb=" O HIS A2463 " (cutoff:3.500A) Processing helix chain 'A' and resid 2483 through 2498 Processing helix chain 'A' and resid 2506 through 2523 Processing helix chain 'A' and resid 2540 through 2553 Processing helix chain 'A' and resid 2615 through 2633 removed outlier: 4.210A pdb=" N ASP A2619 " --> pdb=" O ASP A2615 " (cutoff:3.500A) Processing helix chain 'A' and resid 2636 through 2642 removed outlier: 3.619A pdb=" N ARG A2642 " --> pdb=" O GLU A2638 " (cutoff:3.500A) Processing helix chain 'A' and resid 2670 through 2682 Proline residue: A2676 - end of helix removed outlier: 3.933A pdb=" N GLU A2679 " --> pdb=" O MET A2675 " (cutoff:3.500A) Processing helix chain 'A' and resid 2687 through 2698 removed outlier: 3.880A pdb=" N ALA A2698 " --> pdb=" O GLU A2694 " (cutoff:3.500A) Processing helix chain 'A' and resid 2702 through 2715 Processing helix chain 'A' and resid 2722 through 2729 removed outlier: 3.815A pdb=" N MET A2726 " --> pdb=" O ARG A2722 " (cutoff:3.500A) Processing helix chain 'A' and resid 2731 through 2756 removed outlier: 3.514A pdb=" N LEU A2756 " --> pdb=" O LEU A2752 " (cutoff:3.500A) Processing helix chain 'A' and resid 2785 through 2790 removed outlier: 3.675A pdb=" N VAL A2789 " --> pdb=" O MET A2786 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LEU A2790 " --> pdb=" O GLY A2787 " (cutoff:3.500A) Processing helix chain 'A' and resid 2801 through 2807 Processing helix chain 'A' and resid 2815 through 2829 Processing helix chain 'A' and resid 2831 through 2844 Processing helix chain 'A' and resid 2853 through 2861 removed outlier: 3.799A pdb=" N GLN A2861 " --> pdb=" O MET A2857 " (cutoff:3.500A) Processing helix chain 'A' and resid 2898 through 2910 removed outlier: 3.515A pdb=" N LEU A2910 " --> pdb=" O VAL A2906 " (cutoff:3.500A) Processing helix chain 'A' and resid 2915 through 2928 removed outlier: 3.542A pdb=" N THR A2928 " --> pdb=" O ILE A2924 " (cutoff:3.500A) Processing helix chain 'A' and resid 2929 through 2934 Processing helix chain 'B' and resid 15 through 22 Processing helix chain 'B' and resid 26 through 40 WARNING: missing atoms! Processing helix chain 'B' and resid 56 through 73 Processing helix chain 'B' and resid 86 through 102 Proline residue: B 95 - end of helix Processing helix chain 'B' and resid 110 through 125 removed outlier: 3.879A pdb=" N LEU B 125 " --> pdb=" O ILE B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 150 removed outlier: 3.615A pdb=" N TYR B 140 " --> pdb=" O LEU B 136 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N ASN B 150 " --> pdb=" O GLU B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 157 removed outlier: 3.733A pdb=" N ALA B 154 " --> pdb=" O ASN B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 179 Processing helix chain 'B' and resid 218 through 233 Processing helix chain 'B' and resid 244 through 255 removed outlier: 4.432A pdb=" N HIS B 248 " --> pdb=" O ASP B 244 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLN B 255 " --> pdb=" O ILE B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 262 through 279 Processing helix chain 'B' and resid 283 through 295 Processing helix chain 'B' and resid 313 through 335 removed outlier: 5.515A pdb=" N LEU B 329 " --> pdb=" O TYR B 325 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N TYR B 330 " --> pdb=" O GLY B 326 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLN B 332 " --> pdb=" O ARG B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 360 removed outlier: 4.072A pdb=" N ARG B 360 " --> pdb=" O CYS B 356 " (cutoff:3.500A) Processing helix chain 'B' and resid 398 through 416 removed outlier: 3.991A pdb=" N TRP B 402 " --> pdb=" O GLY B 398 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 454 Processing helix chain 'B' and resid 457 through 473 removed outlier: 4.196A pdb=" N ILE B 468 " --> pdb=" O ALA B 464 " (cutoff:3.500A) Proline residue: B 469 - end of helix Processing helix chain 'B' and resid 478 through 493 Processing helix chain 'B' and resid 497 through 512 Processing helix chain 'B' and resid 519 through 521 No H-bonds generated for 'chain 'B' and resid 519 through 521' Processing helix chain 'B' and resid 522 through 535 Processing helix chain 'B' and resid 542 through 557 removed outlier: 3.573A pdb=" N SER B 546 " --> pdb=" O ILE B 542 " (cutoff:3.500A) Processing helix chain 'B' and resid 565 through 575 Processing helix chain 'B' and resid 584 through 602 Processing helix chain 'B' and resid 606 through 621 Processing helix chain 'B' and resid 625 through 632 Processing helix chain 'B' and resid 637 through 650 Processing helix chain 'B' and resid 665 through 674 Processing helix chain 'B' and resid 677 through 685 Processing helix chain 'B' and resid 716 through 741 Proline residue: B 730 - end of helix Processing helix chain 'B' and resid 754 through 771 removed outlier: 3.593A pdb=" N LEU B 771 " --> pdb=" O THR B 767 " (cutoff:3.500A) Processing helix chain 'B' and resid 783 through 803 removed outlier: 3.855A pdb=" N ASN B 803 " --> pdb=" O LYS B 799 " (cutoff:3.500A) Processing helix chain 'B' and resid 809 through 819 removed outlier: 3.531A pdb=" N MET B 813 " --> pdb=" O ASN B 809 " (cutoff:3.500A) Processing helix chain 'B' and resid 820 through 822 No H-bonds generated for 'chain 'B' and resid 820 through 822' Processing helix chain 'B' and resid 826 through 833 Processing helix chain 'B' and resid 837 through 858 removed outlier: 3.579A pdb=" N LEU B 841 " --> pdb=" O ARG B 837 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLU B 858 " --> pdb=" O ARG B 854 " (cutoff:3.500A) Processing helix chain 'B' and resid 895 through 898 Processing helix chain 'B' and resid 899 through 921 Processing helix chain 'B' and resid 928 through 936 Processing helix chain 'B' and resid 946 through 956 removed outlier: 3.763A pdb=" N SER B 956 " --> pdb=" O GLU B 952 " (cutoff:3.500A) Processing helix chain 'B' and resid 961 through 975 Processing helix chain 'B' and resid 976 through 978 No H-bonds generated for 'chain 'B' and resid 976 through 978' Processing helix chain 'B' and resid 984 through 998 removed outlier: 3.617A pdb=" N LEU B 988 " --> pdb=" O CYS B 984 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N PHE B 998 " --> pdb=" O ILE B 994 " (cutoff:3.500A) Processing helix chain 'B' and resid 998 through 1003 removed outlier: 4.745A pdb=" N TRP B1002 " --> pdb=" O PHE B 998 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N THR B1003 " --> pdb=" O ILE B 999 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 998 through 1003' Processing helix chain 'B' and resid 1009 through 1023 Processing helix chain 'B' and resid 1031 through 1046 Processing helix chain 'B' and resid 1051 through 1056 Processing helix chain 'B' and resid 1060 through 1071 Processing helix chain 'B' and resid 1073 through 1084 Processing helix chain 'B' and resid 1086 through 1090 removed outlier: 3.842A pdb=" N LEU B1090 " --> pdb=" O LEU B1087 " (cutoff:3.500A) Processing helix chain 'B' and resid 1092 through 1094 No H-bonds generated for 'chain 'B' and resid 1092 through 1094' Processing helix chain 'B' and resid 1095 through 1105 removed outlier: 3.673A pdb=" N ILE B1099 " --> pdb=" O THR B1095 " (cutoff:3.500A) Processing helix chain 'B' and resid 1113 through 1131 removed outlier: 4.008A pdb=" N LEU B1117 " --> pdb=" O VAL B1113 " (cutoff:3.500A) Processing helix chain 'B' and resid 1134 through 1145 removed outlier: 3.851A pdb=" N ILE B1145 " --> pdb=" O HIS B1141 " (cutoff:3.500A) Processing helix chain 'B' and resid 1161 through 1176 Processing helix chain 'B' and resid 1182 through 1199 removed outlier: 4.217A pdb=" N LEU B1188 " --> pdb=" O GLU B1184 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N PHE B1189 " --> pdb=" O LEU B1185 " (cutoff:3.500A) Proline residue: B1191 - end of helix Processing helix chain 'B' and resid 1200 through 1201 No H-bonds generated for 'chain 'B' and resid 1200 through 1201' Processing helix chain 'B' and resid 1202 through 1206 Processing helix chain 'B' and resid 1215 through 1221 removed outlier: 3.715A pdb=" N LEU B1219 " --> pdb=" O SER B1215 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ARG B1221 " --> pdb=" O LEU B1217 " (cutoff:3.500A) Processing helix chain 'B' and resid 1223 through 1235 Processing helix chain 'B' and resid 1236 through 1248 Processing helix chain 'B' and resid 1250 through 1258 Processing helix chain 'B' and resid 1258 through 1269 Processing helix chain 'B' and resid 1283 through 1288 Processing helix chain 'B' and resid 1294 through 1302 Processing helix chain 'B' and resid 1302 through 1314 removed outlier: 3.621A pdb=" N ILE B1313 " --> pdb=" O THR B1309 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N PHE B1314 " --> pdb=" O PHE B1310 " (cutoff:3.500A) Processing helix chain 'B' and resid 1318 through 1324 removed outlier: 3.797A pdb=" N LYS B1322 " --> pdb=" O ASP B1318 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N PHE B1324 " --> pdb=" O ILE B1320 " (cutoff:3.500A) Processing helix chain 'B' and resid 1332 through 1344 removed outlier: 3.978A pdb=" N GLY B1344 " --> pdb=" O ILE B1340 " (cutoff:3.500A) Processing helix chain 'B' and resid 1359 through 1361 No H-bonds generated for 'chain 'B' and resid 1359 through 1361' Processing helix chain 'B' and resid 1362 through 1372 Processing helix chain 'B' and resid 1383 through 1398 removed outlier: 3.794A pdb=" N ILE B1398 " --> pdb=" O LEU B1394 " (cutoff:3.500A) Processing helix chain 'B' and resid 1405 through 1422 removed outlier: 3.935A pdb=" N SER B1409 " --> pdb=" O LEU B1405 " (cutoff:3.500A) Processing helix chain 'B' and resid 1428 through 1443 removed outlier: 3.581A pdb=" N GLU B1432 " --> pdb=" O GLY B1428 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N SER B1437 " --> pdb=" O MET B1433 " (cutoff:3.500A) Processing helix chain 'B' and resid 1448 through 1462 removed outlier: 3.671A pdb=" N LEU B1452 " --> pdb=" O ALA B1448 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLY B1453 " --> pdb=" O ASP B1449 " (cutoff:3.500A) Processing helix chain 'B' and resid 1462 through 1467 Processing helix chain 'B' and resid 1469 through 1490 removed outlier: 3.624A pdb=" N GLY B1475 " --> pdb=" O SER B1471 " (cutoff:3.500A) Processing helix chain 'B' and resid 1497 through 1522 removed outlier: 3.923A pdb=" N LYS B1502 " --> pdb=" O GLU B1498 " (cutoff:3.500A) Processing helix chain 'B' and resid 1529 through 1544 removed outlier: 3.539A pdb=" N LYS B1533 " --> pdb=" O ASP B1529 " (cutoff:3.500A) Processing helix chain 'B' and resid 1556 through 1570 Processing helix chain 'B' and resid 1577 through 1589 Processing helix chain 'B' and resid 1605 through 1620 removed outlier: 5.078A pdb=" N ALA B1614 " --> pdb=" O ILE B1610 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N VAL B1615 " --> pdb=" O LYS B1611 " (cutoff:3.500A) Processing helix chain 'B' and resid 1626 through 1645 Processing helix chain 'B' and resid 1648 through 1652 Processing helix chain 'B' and resid 1656 through 1664 Processing helix chain 'B' and resid 1669 through 1684 removed outlier: 3.777A pdb=" N LEU B1681 " --> pdb=" O LEU B1677 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N THR B1682 " --> pdb=" O ILE B1678 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N ILE B1683 " --> pdb=" O LYS B1679 " (cutoff:3.500A) Processing helix chain 'B' and resid 1686 through 1707 Processing helix chain 'B' and resid 1709 through 1720 removed outlier: 3.574A pdb=" N GLU B1718 " --> pdb=" O SER B1714 " (cutoff:3.500A) Processing helix chain 'B' and resid 1721 through 1727 Processing helix chain 'B' and resid 1761 through 1772 Processing helix chain 'B' and resid 1777 through 1782 removed outlier: 3.599A pdb=" N VAL B1782 " --> pdb=" O VAL B1778 " (cutoff:3.500A) Processing helix chain 'B' and resid 1783 through 1788 Processing helix chain 'B' and resid 1792 through 1809 removed outlier: 3.779A pdb=" N ARG B1796 " --> pdb=" O GLY B1792 " (cutoff:3.500A) Proline residue: B1799 - end of helix Processing helix chain 'B' and resid 1814 through 1828 removed outlier: 3.711A pdb=" N ARG B1818 " --> pdb=" O GLN B1814 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N GLN B1825 " --> pdb=" O SER B1821 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N GLU B1826 " --> pdb=" O GLU B1822 " (cutoff:3.500A) Processing helix chain 'B' and resid 1835 through 1850 removed outlier: 3.759A pdb=" N LEU B1841 " --> pdb=" O GLU B1837 " (cutoff:3.500A) Processing helix chain 'B' and resid 1859 through 1866 removed outlier: 3.978A pdb=" N ALA B1864 " --> pdb=" O ALA B1861 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N TRP B1866 " --> pdb=" O ARG B1863 " (cutoff:3.500A) Processing helix chain 'B' and resid 1870 through 1881 Processing helix chain 'B' and resid 1883 through 1899 Processing helix chain 'B' and resid 1915 through 1924 removed outlier: 4.189A pdb=" N GLU B1919 " --> pdb=" O ASP B1915 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ASN B1923 " --> pdb=" O GLU B1919 " (cutoff:3.500A) Processing helix chain 'B' and resid 1928 through 1933 Processing helix chain 'B' and resid 1938 through 1949 Processing helix chain 'B' and resid 1952 through 1969 removed outlier: 3.799A pdb=" N PHE B1958 " --> pdb=" O LYS B1954 " (cutoff:3.500A) Processing helix chain 'B' and resid 1973 through 1989 removed outlier: 3.756A pdb=" N GLY B1989 " --> pdb=" O LEU B1985 " (cutoff:3.500A) Processing helix chain 'B' and resid 1990 through 2001 removed outlier: 3.610A pdb=" N SER B1994 " --> pdb=" O LEU B1990 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N SER B2000 " --> pdb=" O SER B1996 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLN B2001 " --> pdb=" O LEU B1997 " (cutoff:3.500A) Processing helix chain 'B' and resid 2008 through 2022 removed outlier: 3.955A pdb=" N PHE B2015 " --> pdb=" O LEU B2011 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N THR B2017 " --> pdb=" O ALA B2013 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ALA B2018 " --> pdb=" O THR B2014 " (cutoff:3.500A) Processing helix chain 'B' and resid 2034 through 2048 Processing helix chain 'B' and resid 2051 through 2072 removed outlier: 3.843A pdb=" N VAL B2055 " --> pdb=" O GLU B2051 " (cutoff:3.500A) Processing helix chain 'B' and resid 2076 through 2098 removed outlier: 3.628A pdb=" N ASN B2098 " --> pdb=" O ASP B2094 " (cutoff:3.500A) Processing helix chain 'B' and resid 2101 through 2120 Processing helix chain 'B' and resid 2123 through 2144 Processing helix chain 'B' and resid 2153 through 2175 Processing helix chain 'B' and resid 2177 through 2190 Processing helix chain 'B' and resid 2191 through 2197 removed outlier: 3.597A pdb=" N SER B2197 " --> pdb=" O PRO B2193 " (cutoff:3.500A) Processing helix chain 'B' and resid 2202 through 2217 Processing helix chain 'B' and resid 2219 through 2233 Processing helix chain 'B' and resid 2244 through 2259 Processing helix chain 'B' and resid 2263 through 2271 removed outlier: 3.918A pdb=" N GLN B2268 " --> pdb=" O PRO B2264 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LYS B2269 " --> pdb=" O ASP B2265 " (cutoff:3.500A) Processing helix chain 'B' and resid 2271 through 2279 Processing helix chain 'B' and resid 2285 through 2304 Processing helix chain 'B' and resid 2305 through 2330 Processing helix chain 'B' and resid 2349 through 2386 Processing helix chain 'B' and resid 2393 through 2405 removed outlier: 3.585A pdb=" N LYS B2405 " --> pdb=" O LEU B2401 " (cutoff:3.500A) Processing helix chain 'B' and resid 2408 through 2419 Processing helix chain 'B' and resid 2420 through 2422 No H-bonds generated for 'chain 'B' and resid 2420 through 2422' Processing helix chain 'B' and resid 2423 through 2427 Processing helix chain 'B' and resid 2430 through 2435 Processing helix chain 'B' and resid 2443 through 2460 removed outlier: 3.552A pdb=" N LYS B2447 " --> pdb=" O THR B2443 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ASP B2451 " --> pdb=" O LYS B2447 " (cutoff:3.500A) Processing helix chain 'B' and resid 2460 through 2473 removed outlier: 5.841A pdb=" N TYR B2466 " --> pdb=" O TYR B2462 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N HIS B2467 " --> pdb=" O HIS B2463 " (cutoff:3.500A) Processing helix chain 'B' and resid 2483 through 2498 Processing helix chain 'B' and resid 2506 through 2523 Processing helix chain 'B' and resid 2540 through 2553 Processing helix chain 'B' and resid 2615 through 2633 removed outlier: 4.210A pdb=" N ASP B2619 " --> pdb=" O ASP B2615 " (cutoff:3.500A) Processing helix chain 'B' and resid 2636 through 2642 removed outlier: 3.619A pdb=" N ARG B2642 " --> pdb=" O GLU B2638 " (cutoff:3.500A) Processing helix chain 'B' and resid 2670 through 2682 Proline residue: B2676 - end of helix removed outlier: 3.933A pdb=" N GLU B2679 " --> pdb=" O MET B2675 " (cutoff:3.500A) Processing helix chain 'B' and resid 2687 through 2698 removed outlier: 3.880A pdb=" N ALA B2698 " --> pdb=" O GLU B2694 " (cutoff:3.500A) Processing helix chain 'B' and resid 2702 through 2715 Processing helix chain 'B' and resid 2722 through 2729 removed outlier: 3.815A pdb=" N MET B2726 " --> pdb=" O ARG B2722 " (cutoff:3.500A) Processing helix chain 'B' and resid 2731 through 2756 removed outlier: 3.514A pdb=" N LEU B2756 " --> pdb=" O LEU B2752 " (cutoff:3.500A) Processing helix chain 'B' and resid 2785 through 2790 removed outlier: 3.675A pdb=" N VAL B2789 " --> pdb=" O MET B2786 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LEU B2790 " --> pdb=" O GLY B2787 " (cutoff:3.500A) Processing helix chain 'B' and resid 2801 through 2807 Processing helix chain 'B' and resid 2815 through 2829 Processing helix chain 'B' and resid 2831 through 2844 Processing helix chain 'B' and resid 2853 through 2861 removed outlier: 3.799A pdb=" N GLN B2861 " --> pdb=" O MET B2857 " (cutoff:3.500A) Processing helix chain 'B' and resid 2898 through 2910 removed outlier: 3.515A pdb=" N LEU B2910 " --> pdb=" O VAL B2906 " (cutoff:3.500A) Processing helix chain 'B' and resid 2915 through 2928 removed outlier: 3.542A pdb=" N THR B2928 " --> pdb=" O ILE B2924 " (cutoff:3.500A) Processing helix chain 'B' and resid 2929 through 2934 Processing sheet with id=AA1, first strand: chain 'A' and resid 372 through 373 removed outlier: 3.551A pdb=" N PHE A 389 " --> pdb=" O THR A 386 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 2534 through 2536 removed outlier: 7.138A pdb=" N GLU A2582 " --> pdb=" O THR A2596 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N THR A2596 " --> pdb=" O GLU A2582 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 2534 through 2536 removed outlier: 7.138A pdb=" N GLU A2582 " --> pdb=" O THR A2596 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N THR A2596 " --> pdb=" O GLU A2582 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LYS A2593 " --> pdb=" O VAL A2609 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N SER A2658 " --> pdb=" O LEU A2654 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 2667 through 2669 Processing sheet with id=AA5, first strand: chain 'B' and resid 372 through 373 removed outlier: 3.551A pdb=" N PHE B 389 " --> pdb=" O THR B 386 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 2534 through 2536 removed outlier: 7.138A pdb=" N GLU B2582 " --> pdb=" O THR B2596 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N THR B2596 " --> pdb=" O GLU B2582 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 2534 through 2536 removed outlier: 7.138A pdb=" N GLU B2582 " --> pdb=" O THR B2596 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N THR B2596 " --> pdb=" O GLU B2582 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LYS B2593 " --> pdb=" O VAL B2609 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N SER B2658 " --> pdb=" O LEU B2654 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 2667 through 2669 2595 hydrogen bonds defined for protein. 7695 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: 10.59 Time building geometry restraints manager: 4.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.36: 14476 1.36 - 1.51: 13860 1.51 - 1.65: 14044 1.65 - 1.80: 260 1.80 - 1.95: 38 Bond restraints: 42678 Sorted by residual: bond pdb=" C ILE B1084 " pdb=" N PRO B1085 " ideal model delta sigma weight residual 1.337 1.364 -0.028 9.80e-03 1.04e+04 8.01e+00 bond pdb=" C ILE A1084 " pdb=" N PRO A1085 " ideal model delta sigma weight residual 1.337 1.364 -0.028 9.80e-03 1.04e+04 8.01e+00 bond pdb=" CG LEU A1917 " pdb=" CD2 LEU A1917 " ideal model delta sigma weight residual 1.521 1.431 0.090 3.30e-02 9.18e+02 7.37e+00 bond pdb=" CG LEU B1917 " pdb=" CD2 LEU B1917 " ideal model delta sigma weight residual 1.521 1.431 0.090 3.30e-02 9.18e+02 7.37e+00 bond pdb=" CB THR B2740 " pdb=" CG2 THR B2740 " ideal model delta sigma weight residual 1.521 1.438 0.083 3.30e-02 9.18e+02 6.34e+00 ... (remaining 42673 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.84: 57098 2.84 - 5.68: 668 5.68 - 8.52: 46 8.52 - 11.36: 4 11.36 - 14.21: 4 Bond angle restraints: 57820 Sorted by residual: angle pdb=" N SER B2007 " pdb=" CA SER B2007 " pdb=" CB SER B2007 " ideal model delta sigma weight residual 110.49 98.95 11.54 1.69e+00 3.50e-01 4.66e+01 angle pdb=" N SER A2007 " pdb=" CA SER A2007 " pdb=" CB SER A2007 " ideal model delta sigma weight residual 110.49 98.95 11.54 1.69e+00 3.50e-01 4.66e+01 angle pdb=" N GLY B 162 " pdb=" CA GLY B 162 " pdb=" C GLY B 162 " ideal model delta sigma weight residual 115.64 107.79 7.85 1.46e+00 4.69e-01 2.89e+01 angle pdb=" N GLY A 162 " pdb=" CA GLY A 162 " pdb=" C GLY A 162 " ideal model delta sigma weight residual 115.64 107.79 7.85 1.46e+00 4.69e-01 2.89e+01 angle pdb=" C GLY A2006 " pdb=" N SER A2007 " pdb=" CA SER A2007 " ideal model delta sigma weight residual 121.54 128.56 -7.02 1.91e+00 2.74e-01 1.35e+01 ... (remaining 57815 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 23372 17.93 - 35.86: 2024 35.86 - 53.79: 490 53.79 - 71.72: 108 71.72 - 89.65: 36 Dihedral angle restraints: 26030 sinusoidal: 10516 harmonic: 15514 Sorted by residual: dihedral pdb=" CA GLY B2006 " pdb=" C GLY B2006 " pdb=" N SER B2007 " pdb=" CA SER B2007 " ideal model delta harmonic sigma weight residual -180.00 -144.04 -35.96 0 5.00e+00 4.00e-02 5.17e+01 dihedral pdb=" CA GLY A2006 " pdb=" C GLY A2006 " pdb=" N SER A2007 " pdb=" CA SER A2007 " ideal model delta harmonic sigma weight residual -180.00 -144.04 -35.96 0 5.00e+00 4.00e-02 5.17e+01 dihedral pdb=" CA MET B 259 " pdb=" C MET B 259 " pdb=" N LYS B 260 " pdb=" CA LYS B 260 " ideal model delta harmonic sigma weight residual -180.00 -147.24 -32.76 0 5.00e+00 4.00e-02 4.29e+01 ... (remaining 26027 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 3794 0.039 - 0.078: 2160 0.078 - 0.117: 536 0.117 - 0.156: 130 0.156 - 0.195: 10 Chirality restraints: 6630 Sorted by residual: chirality pdb=" CA PRO A 666 " pdb=" N PRO A 666 " pdb=" C PRO A 666 " pdb=" CB PRO A 666 " both_signs ideal model delta sigma weight residual False 2.72 2.52 0.19 2.00e-01 2.50e+01 9.47e-01 chirality pdb=" CA PRO B 666 " pdb=" N PRO B 666 " pdb=" C PRO B 666 " pdb=" CB PRO B 666 " both_signs ideal model delta sigma weight residual False 2.72 2.52 0.19 2.00e-01 2.50e+01 9.47e-01 chirality pdb=" CB ILE B 233 " pdb=" CA ILE B 233 " pdb=" CG1 ILE B 233 " pdb=" CG2 ILE B 233 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.19 2.00e-01 2.50e+01 9.45e-01 ... (remaining 6627 not shown) Planarity restraints: 7372 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B1854 " -0.051 5.00e-02 4.00e+02 7.81e-02 9.76e+00 pdb=" N PRO B1855 " 0.135 5.00e-02 4.00e+02 pdb=" CA PRO B1855 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO B1855 " -0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A1854 " 0.051 5.00e-02 4.00e+02 7.81e-02 9.76e+00 pdb=" N PRO A1855 " -0.135 5.00e-02 4.00e+02 pdb=" CA PRO A1855 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO A1855 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS B 383 " 0.048 5.00e-02 4.00e+02 7.33e-02 8.59e+00 pdb=" N PRO B 384 " -0.127 5.00e-02 4.00e+02 pdb=" CA PRO B 384 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO B 384 " 0.040 5.00e-02 4.00e+02 ... (remaining 7369 not shown) Histogram of nonbonded interaction distances: 1.03 - 1.80: 4 1.80 - 2.58: 367 2.58 - 3.35: 53628 3.35 - 4.13: 94897 4.13 - 4.90: 186507 Nonbonded interactions: 335403 Sorted by model distance: nonbonded pdb=" CG1 ILE A 577 " pdb=" OE2 GLU B 726 " model vdw 1.031 3.440 nonbonded pdb=" OE2 GLU A 726 " pdb=" CG1 ILE B 577 " model vdw 1.031 3.440 nonbonded pdb=" OD2 ASP A2190 " pdb=" OG SER B1965 " model vdw 1.792 3.040 nonbonded pdb=" OG SER A1965 " pdb=" OD2 ASP B2190 " model vdw 1.792 3.040 nonbonded pdb=" OD1 ASP B2012 " pdb=" OG SER B2034 " model vdw 1.871 3.040 ... (remaining 335398 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: 0.07 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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 group one per residue 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: 3.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.630 Check model and map are aligned: 0.140 Set scattering table: 0.130 Process input model: 69.500 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7444 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 : 0.011 0.090 42680 Z= 0.443 Angle : 0.817 14.205 57824 Z= 0.443 Chirality : 0.048 0.195 6630 Planarity : 0.005 0.078 7372 Dihedral : 14.877 89.654 15896 Min Nonbonded Distance : 1.031 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.47 % Favored : 92.45 % Rotamer: Outliers : 5.39 % Allowed : 10.35 % Favored : 84.26 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.09 (0.10), residues: 5192 helix: -1.48 (0.07), residues: 3674 sheet: -0.93 (0.64), residues: 62 loop : -3.27 (0.13), residues: 1456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B2788 TYR 0.026 0.003 TYR A1295 PHE 0.020 0.003 PHE B1741 TRP 0.025 0.003 TRP A2735 HIS 0.007 0.001 HIS A1512 Details of bonding type rmsd covalent geometry : bond 0.01062 (42678) covalent geometry : angle 0.81618 (57820) SS BOND : bond 0.01729 ( 2) SS BOND : angle 4.47462 ( 4) hydrogen bonds : bond 0.14605 ( 2587) hydrogen bonds : angle 6.16986 ( 7695) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10384 Ramachandran restraints generated. 5192 Oldfield, 0 Emsley, 5192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10384 Ramachandran restraints generated. 5192 Oldfield, 0 Emsley, 5192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1393 residues out of total 4562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 246 poor density : 1147 time to evaluate : 1.587 Fit side-chains TARDY: cannot create tardy model for: "THR A 27 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "THR B 27 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 325 TYR cc_start: 0.7709 (OUTLIER) cc_final: 0.7177 (t80) REVERT: A 362 GLU cc_start: 0.5844 (OUTLIER) cc_final: 0.5390 (pm20) REVERT: A 607 GLN cc_start: 0.8834 (OUTLIER) cc_final: 0.8512 (mm-40) REVERT: A 762 VAL cc_start: 0.8559 (OUTLIER) cc_final: 0.8280 (p) REVERT: A 1002 TRP cc_start: 0.8154 (OUTLIER) cc_final: 0.7507 (p-90) REVERT: A 1162 SER cc_start: 0.7654 (OUTLIER) cc_final: 0.6922 (t) REVERT: A 1300 HIS cc_start: 0.6237 (OUTLIER) cc_final: 0.5653 (m-70) REVERT: A 1376 TYR cc_start: 0.5557 (OUTLIER) cc_final: 0.3887 (m-80) REVERT: A 1589 CYS cc_start: 0.7993 (m) cc_final: 0.7771 (m) REVERT: A 1925 ASP cc_start: 0.7783 (t0) cc_final: 0.7110 (t0) REVERT: A 2119 MET cc_start: 0.8947 (mtt) cc_final: 0.8603 (mtt) REVERT: A 2564 VAL cc_start: 0.9175 (t) cc_final: 0.8917 (m) REVERT: B 325 TYR cc_start: 0.7699 (OUTLIER) cc_final: 0.7176 (t80) REVERT: B 362 GLU cc_start: 0.5845 (OUTLIER) cc_final: 0.5389 (pm20) REVERT: B 502 SER cc_start: 0.8508 (OUTLIER) cc_final: 0.8307 (t) REVERT: B 607 GLN cc_start: 0.8836 (OUTLIER) cc_final: 0.8524 (mm-40) REVERT: B 762 VAL cc_start: 0.8563 (OUTLIER) cc_final: 0.8284 (p) REVERT: B 1002 TRP cc_start: 0.8160 (OUTLIER) cc_final: 0.7516 (p-90) REVERT: B 1162 SER cc_start: 0.7649 (OUTLIER) cc_final: 0.6916 (t) REVERT: B 1300 HIS cc_start: 0.6234 (OUTLIER) cc_final: 0.5649 (m-70) REVERT: B 1376 TYR cc_start: 0.5554 (OUTLIER) cc_final: 0.3888 (m-80) REVERT: B 1925 ASP cc_start: 0.7780 (t0) cc_final: 0.7102 (t0) REVERT: B 2119 MET cc_start: 0.8945 (mtt) cc_final: 0.8605 (mtt) REVERT: B 2564 VAL cc_start: 0.9183 (t) cc_final: 0.8922 (m) outliers start: 246 outliers final: 61 residues processed: 1321 average time/residue: 0.2760 time to fit residues: 574.8815 Evaluate side-chains 597 residues out of total 4562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 519 time to evaluate : 1.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 31 ASP Chi-restraints excluded: chain A residue 66 CYS Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 325 TYR Chi-restraints excluded: chain A residue 356 CYS Chi-restraints excluded: chain A residue 362 GLU Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain A residue 607 GLN Chi-restraints excluded: chain A residue 613 ILE Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 741 SER Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain A residue 907 THR Chi-restraints excluded: chain A residue 998 PHE Chi-restraints excluded: chain A residue 1002 TRP Chi-restraints excluded: chain A residue 1098 ASP Chi-restraints excluded: chain A residue 1162 SER Chi-restraints excluded: chain A residue 1215 SER Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1255 VAL Chi-restraints excluded: chain A residue 1300 HIS Chi-restraints excluded: chain A residue 1314 PHE Chi-restraints excluded: chain A residue 1324 PHE Chi-restraints excluded: chain A residue 1376 TYR Chi-restraints excluded: chain A residue 1381 ILE Chi-restraints excluded: chain A residue 1397 THR Chi-restraints excluded: chain A residue 1398 ILE Chi-restraints excluded: chain A residue 1410 VAL Chi-restraints excluded: chain A residue 1414 ILE Chi-restraints excluded: chain A residue 1585 LEU Chi-restraints excluded: chain A residue 1608 ASP Chi-restraints excluded: chain A residue 1854 LEU Chi-restraints excluded: chain A residue 2126 ASP Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 66 CYS Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 251 ILE Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain B residue 325 TYR Chi-restraints excluded: chain B residue 356 CYS Chi-restraints excluded: chain B residue 362 GLU Chi-restraints excluded: chain B residue 388 ILE Chi-restraints excluded: chain B residue 449 VAL Chi-restraints excluded: chain B residue 502 SER Chi-restraints excluded: chain B residue 522 LEU Chi-restraints excluded: chain B residue 607 GLN Chi-restraints excluded: chain B residue 641 LEU Chi-restraints excluded: chain B residue 741 SER Chi-restraints excluded: chain B residue 762 VAL Chi-restraints excluded: chain B residue 907 THR Chi-restraints excluded: chain B residue 998 PHE Chi-restraints excluded: chain B residue 1002 TRP Chi-restraints excluded: chain B residue 1098 ASP Chi-restraints excluded: chain B residue 1162 SER Chi-restraints excluded: chain B residue 1215 SER Chi-restraints excluded: chain B residue 1243 LEU Chi-restraints excluded: chain B residue 1255 VAL Chi-restraints excluded: chain B residue 1300 HIS Chi-restraints excluded: chain B residue 1314 PHE Chi-restraints excluded: chain B residue 1324 PHE Chi-restraints excluded: chain B residue 1376 TYR Chi-restraints excluded: chain B residue 1381 ILE Chi-restraints excluded: chain B residue 1397 THR Chi-restraints excluded: chain B residue 1398 ILE Chi-restraints excluded: chain B residue 1410 VAL Chi-restraints excluded: chain B residue 1414 ILE Chi-restraints excluded: chain B residue 1585 LEU Chi-restraints excluded: chain B residue 1608 ASP Chi-restraints excluded: chain B residue 1854 LEU Chi-restraints excluded: chain B residue 2126 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 526 random chunks: chunk 394 optimal weight: 1.9990 chunk 430 optimal weight: 0.6980 chunk 41 optimal weight: 1.9990 chunk 265 optimal weight: 5.9990 chunk 523 optimal weight: 1.9990 chunk 497 optimal weight: 0.9990 chunk 414 optimal weight: 4.9990 chunk 310 optimal weight: 0.6980 chunk 488 optimal weight: 3.9990 chunk 366 optimal weight: 0.8980 chunk 223 optimal weight: 0.6980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 235 HIS A 273 ASN A 368 GLN A 519 HIS A 612 HIS ** A 632 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 670 HIS A 674 GLN A 839 HIS A1000 ASN A1028 ASN A1062 GLN A1096 HIS A1161 HIS A1175 GLN A1399 HIS A1512 HIS A1573 ASN ** A1740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1844 ASN A2031 ASN A2069 HIS A2179 GLN A2239 GLN A2255 GLN A2294 GLN A2354 GLN A2356 GLN A2420 ASN A2446 GLN A2518 HIS A2624 GLN A2641 GLN A2754 HIS A2849 GLN A2862 ASN A2925 ASN B 235 HIS B 273 ASN B 368 GLN B 519 HIS B 612 HIS ** B 632 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 670 HIS B 674 GLN B1000 ASN B1028 ASN B1062 GLN B1096 HIS B1175 GLN B1399 HIS B1512 HIS B1573 ASN ** B1740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1844 ASN B2031 ASN B2069 HIS B2179 GLN B2239 GLN B2255 GLN B2294 GLN B2354 GLN B2356 GLN B2360 GLN B2361 GLN B2420 ASN B2446 GLN B2518 HIS B2624 GLN B2641 GLN B2754 HIS B2849 GLN B2925 ASN Total number of N/Q/H flips: 69 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.129744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.103477 restraints weight = 72992.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.102960 restraints weight = 60940.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.103783 restraints weight = 65068.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.104919 restraints weight = 45401.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.105116 restraints weight = 40215.526| |-----------------------------------------------------------------------------| r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.2963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 42680 Z= 0.151 Angle : 0.646 10.552 57824 Z= 0.330 Chirality : 0.041 0.272 6630 Planarity : 0.005 0.059 7372 Dihedral : 7.434 79.388 5883 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 4.03 % Allowed : 15.74 % Favored : 80.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.79 (0.11), residues: 5192 helix: 0.32 (0.08), residues: 3740 sheet: -0.71 (0.65), residues: 66 loop : -2.79 (0.15), residues: 1386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 336 TYR 0.018 0.002 TYR A1195 PHE 0.024 0.002 PHE B 64 TRP 0.016 0.001 TRP B1002 HIS 0.016 0.001 HIS B1399 Details of bonding type rmsd covalent geometry : bond 0.00329 (42678) covalent geometry : angle 0.64595 (57820) SS BOND : bond 0.01226 ( 2) SS BOND : angle 0.52289 ( 4) hydrogen bonds : bond 0.04934 ( 2587) hydrogen bonds : angle 4.30944 ( 7695) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10384 Ramachandran restraints generated. 5192 Oldfield, 0 Emsley, 5192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10384 Ramachandran restraints generated. 5192 Oldfield, 0 Emsley, 5192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 800 residues out of total 4562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 184 poor density : 616 time to evaluate : 1.569 Fit side-chains TARDY: cannot create tardy model for: "THR A 27 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 230 MET cc_start: 0.8307 (tpt) cc_final: 0.8045 (mtm) REVERT: A 251 ILE cc_start: 0.8772 (pt) cc_final: 0.8504 (mp) REVERT: A 325 TYR cc_start: 0.7954 (OUTLIER) cc_final: 0.7119 (t80) REVERT: A 362 GLU cc_start: 0.6382 (OUTLIER) cc_final: 0.6139 (pm20) REVERT: A 591 MET cc_start: 0.8283 (mmp) cc_final: 0.7958 (mmm) REVERT: A 771 LEU cc_start: 0.8605 (OUTLIER) cc_final: 0.7981 (pp) REVERT: A 841 LEU cc_start: 0.9218 (OUTLIER) cc_final: 0.9014 (tp) REVERT: A 1030 MET cc_start: 0.7534 (mmm) cc_final: 0.7289 (mtt) REVERT: A 1292 LYS cc_start: 0.7167 (OUTLIER) cc_final: 0.6624 (tppt) REVERT: A 1300 HIS cc_start: 0.7229 (OUTLIER) cc_final: 0.6740 (m170) REVERT: A 1376 TYR cc_start: 0.4929 (OUTLIER) cc_final: 0.3243 (m-80) REVERT: A 1589 CYS cc_start: 0.8367 (m) cc_final: 0.7879 (m) REVERT: A 1789 LYS cc_start: 0.8087 (mppt) cc_final: 0.7819 (tptp) REVERT: A 1854 LEU cc_start: 0.8260 (OUTLIER) cc_final: 0.7958 (tp) REVERT: A 1925 ASP cc_start: 0.7630 (t0) cc_final: 0.7317 (t0) REVERT: A 2681 TYR cc_start: 0.8844 (m-80) cc_final: 0.8467 (m-80) REVERT: A 2758 LEU cc_start: 0.9226 (tp) cc_final: 0.9004 (tp) REVERT: A 2806 ASP cc_start: 0.8437 (t0) cc_final: 0.8178 (m-30) REVERT: A 2925 ASN cc_start: 0.8491 (m-40) cc_final: 0.7980 (m110) REVERT: B 230 MET cc_start: 0.8310 (tpt) cc_final: 0.8046 (mtm) REVERT: B 251 ILE cc_start: 0.8701 (pt) cc_final: 0.8440 (mp) REVERT: B 325 TYR cc_start: 0.7953 (OUTLIER) cc_final: 0.7121 (t80) REVERT: B 362 GLU cc_start: 0.6382 (OUTLIER) cc_final: 0.6143 (pm20) REVERT: B 591 MET cc_start: 0.8259 (mmp) cc_final: 0.7906 (mmm) REVERT: B 771 LEU cc_start: 0.8605 (OUTLIER) cc_final: 0.7980 (pp) REVERT: B 841 LEU cc_start: 0.9220 (OUTLIER) cc_final: 0.9016 (tp) REVERT: B 1030 MET cc_start: 0.7537 (mmm) cc_final: 0.7293 (mtt) REVERT: B 1292 LYS cc_start: 0.7166 (OUTLIER) cc_final: 0.6620 (tppt) REVERT: B 1300 HIS cc_start: 0.7222 (OUTLIER) cc_final: 0.6736 (m170) REVERT: B 1376 TYR cc_start: 0.4932 (OUTLIER) cc_final: 0.3249 (m-80) REVERT: B 1589 CYS cc_start: 0.8316 (m) cc_final: 0.8022 (m) REVERT: B 1789 LYS cc_start: 0.8082 (mppt) cc_final: 0.7818 (tptp) REVERT: B 1854 LEU cc_start: 0.8260 (OUTLIER) cc_final: 0.7954 (tp) REVERT: B 1925 ASP cc_start: 0.7604 (t0) cc_final: 0.7295 (t0) REVERT: B 2681 TYR cc_start: 0.8847 (m-80) cc_final: 0.8466 (m-80) REVERT: B 2758 LEU cc_start: 0.9223 (tp) cc_final: 0.9002 (tp) REVERT: B 2806 ASP cc_start: 0.8439 (t0) cc_final: 0.8182 (m-30) REVERT: B 2925 ASN cc_start: 0.8488 (m-40) cc_final: 0.8013 (m110) outliers start: 184 outliers final: 102 residues processed: 762 average time/residue: 0.2410 time to fit residues: 305.4320 Evaluate side-chains 584 residues out of total 4562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 466 time to evaluate : 0.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 31 ASP Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 325 TYR Chi-restraints excluded: chain A residue 362 GLU Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 399 GLU Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain A residue 555 LYS Chi-restraints excluded: chain A residue 637 THR Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 893 ASP Chi-restraints excluded: chain A residue 897 SER Chi-restraints excluded: chain A residue 1002 TRP Chi-restraints excluded: chain A residue 1054 SER Chi-restraints excluded: chain A residue 1098 ASP Chi-restraints excluded: chain A residue 1217 LEU Chi-restraints excluded: chain A residue 1292 LYS Chi-restraints excluded: chain A residue 1300 HIS Chi-restraints excluded: chain A residue 1306 ILE Chi-restraints excluded: chain A residue 1314 PHE Chi-restraints excluded: chain A residue 1324 PHE Chi-restraints excluded: chain A residue 1376 TYR Chi-restraints excluded: chain A residue 1381 ILE Chi-restraints excluded: chain A residue 1397 THR Chi-restraints excluded: chain A residue 1398 ILE Chi-restraints excluded: chain A residue 1410 VAL Chi-restraints excluded: chain A residue 1414 ILE Chi-restraints excluded: chain A residue 1443 VAL Chi-restraints excluded: chain A residue 1541 GLU Chi-restraints excluded: chain A residue 1585 LEU Chi-restraints excluded: chain A residue 1644 SER Chi-restraints excluded: chain A residue 1709 ASP Chi-restraints excluded: chain A residue 1738 SER Chi-restraints excluded: chain A residue 1830 PHE Chi-restraints excluded: chain A residue 1854 LEU Chi-restraints excluded: chain A residue 2072 SER Chi-restraints excluded: chain A residue 2118 TRP Chi-restraints excluded: chain A residue 2126 ASP Chi-restraints excluded: chain A residue 2208 MET Chi-restraints excluded: chain A residue 2234 SER Chi-restraints excluded: chain A residue 2247 ASP Chi-restraints excluded: chain A residue 2257 SER Chi-restraints excluded: chain A residue 2429 LEU Chi-restraints excluded: chain A residue 2443 THR Chi-restraints excluded: chain A residue 2482 VAL Chi-restraints excluded: chain A residue 2493 ILE Chi-restraints excluded: chain A residue 2499 LYS Chi-restraints excluded: chain A residue 2505 SER Chi-restraints excluded: chain A residue 2608 LEU Chi-restraints excluded: chain A residue 2792 VAL Chi-restraints excluded: chain A residue 2805 VAL Chi-restraints excluded: chain A residue 2855 VAL Chi-restraints excluded: chain A residue 2929 SER Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain B residue 325 TYR Chi-restraints excluded: chain B residue 362 GLU Chi-restraints excluded: chain B residue 388 ILE Chi-restraints excluded: chain B residue 399 GLU Chi-restraints excluded: chain B residue 449 VAL Chi-restraints excluded: chain B residue 516 VAL Chi-restraints excluded: chain B residue 522 LEU Chi-restraints excluded: chain B residue 555 LYS Chi-restraints excluded: chain B residue 637 THR Chi-restraints excluded: chain B residue 641 LEU Chi-restraints excluded: chain B residue 758 LEU Chi-restraints excluded: chain B residue 771 LEU Chi-restraints excluded: chain B residue 841 LEU Chi-restraints excluded: chain B residue 893 ASP Chi-restraints excluded: chain B residue 897 SER Chi-restraints excluded: chain B residue 1002 TRP Chi-restraints excluded: chain B residue 1054 SER Chi-restraints excluded: chain B residue 1098 ASP Chi-restraints excluded: chain B residue 1217 LEU Chi-restraints excluded: chain B residue 1292 LYS Chi-restraints excluded: chain B residue 1300 HIS Chi-restraints excluded: chain B residue 1306 ILE Chi-restraints excluded: chain B residue 1314 PHE Chi-restraints excluded: chain B residue 1324 PHE Chi-restraints excluded: chain B residue 1376 TYR Chi-restraints excluded: chain B residue 1381 ILE Chi-restraints excluded: chain B residue 1397 THR Chi-restraints excluded: chain B residue 1398 ILE Chi-restraints excluded: chain B residue 1410 VAL Chi-restraints excluded: chain B residue 1414 ILE Chi-restraints excluded: chain B residue 1443 VAL Chi-restraints excluded: chain B residue 1541 GLU Chi-restraints excluded: chain B residue 1644 SER Chi-restraints excluded: chain B residue 1709 ASP Chi-restraints excluded: chain B residue 1738 SER Chi-restraints excluded: chain B residue 1830 PHE Chi-restraints excluded: chain B residue 1854 LEU Chi-restraints excluded: chain B residue 2072 SER Chi-restraints excluded: chain B residue 2118 TRP Chi-restraints excluded: chain B residue 2126 ASP Chi-restraints excluded: chain B residue 2208 MET Chi-restraints excluded: chain B residue 2234 SER Chi-restraints excluded: chain B residue 2247 ASP Chi-restraints excluded: chain B residue 2257 SER Chi-restraints excluded: chain B residue 2429 LEU Chi-restraints excluded: chain B residue 2443 THR Chi-restraints excluded: chain B residue 2482 VAL Chi-restraints excluded: chain B residue 2493 ILE Chi-restraints excluded: chain B residue 2499 LYS Chi-restraints excluded: chain B residue 2505 SER Chi-restraints excluded: chain B residue 2608 LEU Chi-restraints excluded: chain B residue 2792 VAL Chi-restraints excluded: chain B residue 2805 VAL Chi-restraints excluded: chain B residue 2855 VAL Chi-restraints excluded: chain B residue 2929 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 526 random chunks: chunk 148 optimal weight: 9.9990 chunk 138 optimal weight: 4.9990 chunk 251 optimal weight: 0.9980 chunk 345 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 244 optimal weight: 2.9990 chunk 322 optimal weight: 0.9980 chunk 63 optimal weight: 4.9990 chunk 298 optimal weight: 0.0030 chunk 62 optimal weight: 10.0000 chunk 385 optimal weight: 0.9980 overall best weight: 1.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 120 HIS A 368 GLN A 407 ASN A 466 GLN ** A 632 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 674 GLN A1106 HIS A2239 GLN A2501 ASN B 120 HIS B 407 ASN B 466 GLN ** B 632 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 674 GLN B 839 HIS B1106 HIS B2239 GLN B2501 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.127417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.100550 restraints weight = 73691.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.100529 restraints weight = 55765.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.101124 restraints weight = 66776.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.101739 restraints weight = 45649.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.102060 restraints weight = 40632.465| |-----------------------------------------------------------------------------| r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.3734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 42680 Z= 0.147 Angle : 0.600 8.720 57824 Z= 0.304 Chirality : 0.041 0.254 6630 Planarity : 0.004 0.051 7372 Dihedral : 6.612 83.332 5837 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 4.34 % Allowed : 16.88 % Favored : 78.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.12), residues: 5192 helix: 1.06 (0.08), residues: 3760 sheet: -0.30 (0.69), residues: 66 loop : -2.44 (0.16), residues: 1366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 65 TYR 0.019 0.001 TYR B2517 PHE 0.022 0.002 PHE A2546 TRP 0.016 0.001 TRP B1002 HIS 0.008 0.001 HIS A 120 Details of bonding type rmsd covalent geometry : bond 0.00340 (42678) covalent geometry : angle 0.59990 (57820) SS BOND : bond 0.01126 ( 2) SS BOND : angle 0.29112 ( 4) hydrogen bonds : bond 0.04322 ( 2587) hydrogen bonds : angle 3.97579 ( 7695) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10384 Ramachandran restraints generated. 5192 Oldfield, 0 Emsley, 5192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10384 Ramachandran restraints generated. 5192 Oldfield, 0 Emsley, 5192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 698 residues out of total 4562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 198 poor density : 500 time to evaluate : 1.448 Fit side-chains TARDY: cannot create tardy model for: "THR B 27 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 145 TYR cc_start: 0.7260 (t80) cc_final: 0.6893 (t80) REVERT: A 230 MET cc_start: 0.8397 (tpt) cc_final: 0.7861 (mtm) REVERT: A 267 MET cc_start: 0.8546 (mmm) cc_final: 0.7759 (mpp) REVERT: A 388 ILE cc_start: 0.8476 (OUTLIER) cc_final: 0.8119 (tp) REVERT: A 671 TRP cc_start: 0.7519 (t60) cc_final: 0.7318 (t-100) REVERT: A 755 MET cc_start: 0.7979 (tpp) cc_final: 0.7259 (tpt) REVERT: A 771 LEU cc_start: 0.8610 (OUTLIER) cc_final: 0.8327 (pp) REVERT: A 1102 ASP cc_start: 0.8129 (t0) cc_final: 0.7888 (t0) REVERT: A 1292 LYS cc_start: 0.6941 (OUTLIER) cc_final: 0.6549 (tppt) REVERT: A 1300 HIS cc_start: 0.7145 (OUTLIER) cc_final: 0.6774 (m170) REVERT: A 1376 TYR cc_start: 0.5042 (OUTLIER) cc_final: 0.2971 (m-80) REVERT: A 1589 CYS cc_start: 0.8393 (m) cc_final: 0.7818 (m) REVERT: A 1789 LYS cc_start: 0.8202 (mppt) cc_final: 0.7878 (tptp) REVERT: A 1854 LEU cc_start: 0.8305 (OUTLIER) cc_final: 0.7838 (tp) REVERT: A 1925 ASP cc_start: 0.7671 (t0) cc_final: 0.7398 (t0) REVERT: A 2546 PHE cc_start: 0.8022 (t80) cc_final: 0.7820 (t80) REVERT: A 2550 MET cc_start: 0.8047 (OUTLIER) cc_final: 0.7030 (mmm) REVERT: A 2608 LEU cc_start: 0.8877 (OUTLIER) cc_final: 0.8609 (mt) REVERT: A 2758 LEU cc_start: 0.9282 (tp) cc_final: 0.9030 (tp) REVERT: A 2925 ASN cc_start: 0.8415 (m-40) cc_final: 0.7938 (m110) REVERT: B 145 TYR cc_start: 0.7245 (t80) cc_final: 0.6881 (t80) REVERT: B 230 MET cc_start: 0.8415 (tpt) cc_final: 0.7892 (mtm) REVERT: B 267 MET cc_start: 0.8542 (mmm) cc_final: 0.7751 (mpp) REVERT: B 388 ILE cc_start: 0.8471 (OUTLIER) cc_final: 0.8119 (tp) REVERT: B 591 MET cc_start: 0.8286 (mmp) cc_final: 0.8057 (tpp) REVERT: B 755 MET cc_start: 0.7975 (tpp) cc_final: 0.7263 (tpt) REVERT: B 771 LEU cc_start: 0.8609 (OUTLIER) cc_final: 0.8325 (pp) REVERT: B 1102 ASP cc_start: 0.8130 (t0) cc_final: 0.7888 (t0) REVERT: B 1292 LYS cc_start: 0.6946 (OUTLIER) cc_final: 0.6554 (tppt) REVERT: B 1300 HIS cc_start: 0.7141 (OUTLIER) cc_final: 0.6776 (m170) REVERT: B 1376 TYR cc_start: 0.5039 (OUTLIER) cc_final: 0.2974 (m-80) REVERT: B 1589 CYS cc_start: 0.8366 (m) cc_final: 0.7996 (m) REVERT: B 1789 LYS cc_start: 0.8202 (mppt) cc_final: 0.7878 (tptp) REVERT: B 1854 LEU cc_start: 0.8304 (OUTLIER) cc_final: 0.7841 (tp) REVERT: B 1925 ASP cc_start: 0.7652 (t0) cc_final: 0.7388 (t0) REVERT: B 2546 PHE cc_start: 0.8031 (t80) cc_final: 0.7828 (t80) REVERT: B 2550 MET cc_start: 0.8050 (OUTLIER) cc_final: 0.7036 (mmm) REVERT: B 2608 LEU cc_start: 0.8878 (OUTLIER) cc_final: 0.8609 (mt) REVERT: B 2758 LEU cc_start: 0.9280 (tp) cc_final: 0.9021 (tp) REVERT: B 2925 ASN cc_start: 0.8408 (m-40) cc_final: 0.7924 (m110) outliers start: 198 outliers final: 114 residues processed: 637 average time/residue: 0.2291 time to fit residues: 247.2993 Evaluate side-chains 544 residues out of total 4562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 414 time to evaluate : 1.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ASP Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain A residue 587 SER Chi-restraints excluded: chain A residue 601 MET Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 648 CYS Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 893 ASP Chi-restraints excluded: chain A residue 897 SER Chi-restraints excluded: chain A residue 1002 TRP Chi-restraints excluded: chain A residue 1040 SER Chi-restraints excluded: chain A residue 1047 GLU Chi-restraints excluded: chain A residue 1098 ASP Chi-restraints excluded: chain A residue 1145 ILE Chi-restraints excluded: chain A residue 1164 LEU Chi-restraints excluded: chain A residue 1217 LEU Chi-restraints excluded: chain A residue 1292 LYS Chi-restraints excluded: chain A residue 1300 HIS Chi-restraints excluded: chain A residue 1314 PHE Chi-restraints excluded: chain A residue 1324 PHE Chi-restraints excluded: chain A residue 1376 TYR Chi-restraints excluded: chain A residue 1381 ILE Chi-restraints excluded: chain A residue 1397 THR Chi-restraints excluded: chain A residue 1398 ILE Chi-restraints excluded: chain A residue 1414 ILE Chi-restraints excluded: chain A residue 1469 THR Chi-restraints excluded: chain A residue 1523 ASP Chi-restraints excluded: chain A residue 1541 GLU Chi-restraints excluded: chain A residue 1644 SER Chi-restraints excluded: chain A residue 1709 ASP Chi-restraints excluded: chain A residue 1738 SER Chi-restraints excluded: chain A residue 1779 THR Chi-restraints excluded: chain A residue 1830 PHE Chi-restraints excluded: chain A residue 1854 LEU Chi-restraints excluded: chain A residue 1916 ILE Chi-restraints excluded: chain A residue 2118 TRP Chi-restraints excluded: chain A residue 2208 MET Chi-restraints excluded: chain A residue 2234 SER Chi-restraints excluded: chain A residue 2247 ASP Chi-restraints excluded: chain A residue 2257 SER Chi-restraints excluded: chain A residue 2263 SER Chi-restraints excluded: chain A residue 2429 LEU Chi-restraints excluded: chain A residue 2443 THR Chi-restraints excluded: chain A residue 2482 VAL Chi-restraints excluded: chain A residue 2499 LYS Chi-restraints excluded: chain A residue 2505 SER Chi-restraints excluded: chain A residue 2540 SER Chi-restraints excluded: chain A residue 2550 MET Chi-restraints excluded: chain A residue 2608 LEU Chi-restraints excluded: chain A residue 2704 GLU Chi-restraints excluded: chain A residue 2792 VAL Chi-restraints excluded: chain A residue 2805 VAL Chi-restraints excluded: chain A residue 2855 VAL Chi-restraints excluded: chain A residue 2929 SER Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 226 SER Chi-restraints excluded: chain B residue 239 ILE Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain B residue 388 ILE Chi-restraints excluded: chain B residue 449 VAL Chi-restraints excluded: chain B residue 516 VAL Chi-restraints excluded: chain B residue 522 LEU Chi-restraints excluded: chain B residue 587 SER Chi-restraints excluded: chain B residue 601 MET Chi-restraints excluded: chain B residue 631 LEU Chi-restraints excluded: chain B residue 641 LEU Chi-restraints excluded: chain B residue 648 CYS Chi-restraints excluded: chain B residue 771 LEU Chi-restraints excluded: chain B residue 893 ASP Chi-restraints excluded: chain B residue 897 SER Chi-restraints excluded: chain B residue 1002 TRP Chi-restraints excluded: chain B residue 1040 SER Chi-restraints excluded: chain B residue 1047 GLU Chi-restraints excluded: chain B residue 1098 ASP Chi-restraints excluded: chain B residue 1145 ILE Chi-restraints excluded: chain B residue 1164 LEU Chi-restraints excluded: chain B residue 1217 LEU Chi-restraints excluded: chain B residue 1292 LYS Chi-restraints excluded: chain B residue 1300 HIS Chi-restraints excluded: chain B residue 1314 PHE Chi-restraints excluded: chain B residue 1324 PHE Chi-restraints excluded: chain B residue 1376 TYR Chi-restraints excluded: chain B residue 1381 ILE Chi-restraints excluded: chain B residue 1397 THR Chi-restraints excluded: chain B residue 1398 ILE Chi-restraints excluded: chain B residue 1414 ILE Chi-restraints excluded: chain B residue 1469 THR Chi-restraints excluded: chain B residue 1523 ASP Chi-restraints excluded: chain B residue 1541 GLU Chi-restraints excluded: chain B residue 1585 LEU Chi-restraints excluded: chain B residue 1644 SER Chi-restraints excluded: chain B residue 1709 ASP Chi-restraints excluded: chain B residue 1738 SER Chi-restraints excluded: chain B residue 1779 THR Chi-restraints excluded: chain B residue 1830 PHE Chi-restraints excluded: chain B residue 1854 LEU Chi-restraints excluded: chain B residue 1916 ILE Chi-restraints excluded: chain B residue 2118 TRP Chi-restraints excluded: chain B residue 2208 MET Chi-restraints excluded: chain B residue 2234 SER Chi-restraints excluded: chain B residue 2247 ASP Chi-restraints excluded: chain B residue 2257 SER Chi-restraints excluded: chain B residue 2263 SER Chi-restraints excluded: chain B residue 2429 LEU Chi-restraints excluded: chain B residue 2443 THR Chi-restraints excluded: chain B residue 2482 VAL Chi-restraints excluded: chain B residue 2499 LYS Chi-restraints excluded: chain B residue 2505 SER Chi-restraints excluded: chain B residue 2540 SER Chi-restraints excluded: chain B residue 2550 MET Chi-restraints excluded: chain B residue 2608 LEU Chi-restraints excluded: chain B residue 2704 GLU Chi-restraints excluded: chain B residue 2792 VAL Chi-restraints excluded: chain B residue 2805 VAL Chi-restraints excluded: chain B residue 2855 VAL Chi-restraints excluded: chain B residue 2929 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 526 random chunks: chunk 503 optimal weight: 2.9990 chunk 313 optimal weight: 3.9990 chunk 119 optimal weight: 7.9990 chunk 193 optimal weight: 0.6980 chunk 317 optimal weight: 6.9990 chunk 505 optimal weight: 5.9990 chunk 124 optimal weight: 0.7980 chunk 314 optimal weight: 7.9990 chunk 242 optimal weight: 3.9990 chunk 201 optimal weight: 2.9990 chunk 446 optimal weight: 0.6980 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 407 ASN B 368 GLN B 407 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.123548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.097170 restraints weight = 74423.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.096128 restraints weight = 60403.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.097141 restraints weight = 69476.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.097561 restraints weight = 49078.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.098460 restraints weight = 44154.210| |-----------------------------------------------------------------------------| r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.4188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 42680 Z= 0.168 Angle : 0.590 9.003 57824 Z= 0.298 Chirality : 0.041 0.259 6630 Planarity : 0.004 0.045 7372 Dihedral : 6.191 84.383 5818 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 4.45 % Allowed : 17.69 % Favored : 77.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.12), residues: 5192 helix: 1.40 (0.09), residues: 3744 sheet: -0.32 (0.69), residues: 66 loop : -2.12 (0.16), residues: 1382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1130 TYR 0.018 0.001 TYR A1476 PHE 0.020 0.001 PHE A 272 TRP 0.016 0.001 TRP B1002 HIS 0.008 0.001 HIS A 120 Details of bonding type rmsd covalent geometry : bond 0.00396 (42678) covalent geometry : angle 0.59000 (57820) SS BOND : bond 0.00448 ( 2) SS BOND : angle 0.23658 ( 4) hydrogen bonds : bond 0.04369 ( 2587) hydrogen bonds : angle 3.91253 ( 7695) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10384 Ramachandran restraints generated. 5192 Oldfield, 0 Emsley, 5192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10384 Ramachandran restraints generated. 5192 Oldfield, 0 Emsley, 5192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 662 residues out of total 4562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 203 poor density : 459 time to evaluate : 1.089 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 145 TYR cc_start: 0.7425 (t80) cc_final: 0.7148 (t80) REVERT: A 230 MET cc_start: 0.8414 (tpt) cc_final: 0.7903 (mtm) REVERT: A 267 MET cc_start: 0.8475 (mmm) cc_final: 0.7768 (mpp) REVERT: A 388 ILE cc_start: 0.8563 (OUTLIER) cc_final: 0.8046 (tp) REVERT: A 671 TRP cc_start: 0.7699 (t60) cc_final: 0.7418 (t-100) REVERT: A 755 MET cc_start: 0.8015 (tpp) cc_final: 0.7270 (tpt) REVERT: A 771 LEU cc_start: 0.8727 (OUTLIER) cc_final: 0.8444 (pp) REVERT: A 1292 LYS cc_start: 0.6889 (OUTLIER) cc_final: 0.6550 (tppt) REVERT: A 1300 HIS cc_start: 0.7314 (OUTLIER) cc_final: 0.6926 (m-70) REVERT: A 1376 TYR cc_start: 0.4767 (OUTLIER) cc_final: 0.2787 (m-80) REVERT: A 1589 CYS cc_start: 0.8523 (m) cc_final: 0.7995 (m) REVERT: A 1757 LEU cc_start: 0.8318 (OUTLIER) cc_final: 0.8058 (tt) REVERT: A 1789 LYS cc_start: 0.8378 (mppt) cc_final: 0.8023 (tptp) REVERT: A 1925 ASP cc_start: 0.7640 (t0) cc_final: 0.7401 (t0) REVERT: A 2058 MET cc_start: 0.8690 (mmm) cc_final: 0.8449 (tpt) REVERT: A 2405 LYS cc_start: 0.8959 (OUTLIER) cc_final: 0.8643 (mmtm) REVERT: A 2431 MET cc_start: 0.8412 (tpp) cc_final: 0.8160 (mmt) REVERT: A 2608 LEU cc_start: 0.8948 (OUTLIER) cc_final: 0.8689 (mt) REVERT: A 2624 GLN cc_start: 0.7809 (tt0) cc_final: 0.7528 (tt0) REVERT: A 2758 LEU cc_start: 0.9261 (tp) cc_final: 0.9055 (tp) REVERT: A 2925 ASN cc_start: 0.8391 (m-40) cc_final: 0.7923 (m110) REVERT: B 145 TYR cc_start: 0.7416 (t80) cc_final: 0.7135 (t80) REVERT: B 230 MET cc_start: 0.8438 (tpt) cc_final: 0.7949 (mtm) REVERT: B 267 MET cc_start: 0.8476 (mmm) cc_final: 0.7764 (mpp) REVERT: B 388 ILE cc_start: 0.8562 (OUTLIER) cc_final: 0.8054 (tp) REVERT: B 674 GLN cc_start: 0.7784 (tm-30) cc_final: 0.7525 (tm-30) REVERT: B 755 MET cc_start: 0.8006 (tpp) cc_final: 0.7264 (tpt) REVERT: B 771 LEU cc_start: 0.8721 (OUTLIER) cc_final: 0.8434 (pp) REVERT: B 1292 LYS cc_start: 0.6890 (OUTLIER) cc_final: 0.6554 (tppt) REVERT: B 1300 HIS cc_start: 0.7303 (OUTLIER) cc_final: 0.6916 (m-70) REVERT: B 1376 TYR cc_start: 0.4778 (OUTLIER) cc_final: 0.2803 (m-80) REVERT: B 1589 CYS cc_start: 0.8428 (m) cc_final: 0.8050 (m) REVERT: B 1757 LEU cc_start: 0.8314 (OUTLIER) cc_final: 0.8053 (tt) REVERT: B 1789 LYS cc_start: 0.8370 (mppt) cc_final: 0.8017 (tptp) REVERT: B 1925 ASP cc_start: 0.7639 (t0) cc_final: 0.7407 (t0) REVERT: B 2058 MET cc_start: 0.8685 (mmm) cc_final: 0.8434 (tpt) REVERT: B 2362 GLU cc_start: 0.6984 (mt-10) cc_final: 0.6746 (mt-10) REVERT: B 2405 LYS cc_start: 0.8963 (OUTLIER) cc_final: 0.8642 (mmtm) REVERT: B 2431 MET cc_start: 0.8414 (tpp) cc_final: 0.8160 (mmt) REVERT: B 2608 LEU cc_start: 0.8949 (OUTLIER) cc_final: 0.8688 (mt) REVERT: B 2624 GLN cc_start: 0.7812 (tt0) cc_final: 0.7523 (tt0) REVERT: B 2758 LEU cc_start: 0.9264 (tp) cc_final: 0.9047 (tp) REVERT: B 2925 ASN cc_start: 0.8406 (m-40) cc_final: 0.7922 (m110) outliers start: 203 outliers final: 125 residues processed: 610 average time/residue: 0.2314 time to fit residues: 239.4783 Evaluate side-chains 567 residues out of total 4562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 426 time to evaluate : 1.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ASP Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 229 TYR Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 448 ARG Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain A residue 587 SER Chi-restraints excluded: chain A residue 637 THR Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 648 CYS Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 897 SER Chi-restraints excluded: chain A residue 1002 TRP Chi-restraints excluded: chain A residue 1040 SER Chi-restraints excluded: chain A residue 1047 GLU Chi-restraints excluded: chain A residue 1054 SER Chi-restraints excluded: chain A residue 1101 VAL Chi-restraints excluded: chain A residue 1217 LEU Chi-restraints excluded: chain A residue 1292 LYS Chi-restraints excluded: chain A residue 1300 HIS Chi-restraints excluded: chain A residue 1314 PHE Chi-restraints excluded: chain A residue 1324 PHE Chi-restraints excluded: chain A residue 1376 TYR Chi-restraints excluded: chain A residue 1381 ILE Chi-restraints excluded: chain A residue 1398 ILE Chi-restraints excluded: chain A residue 1408 CYS Chi-restraints excluded: chain A residue 1414 ILE Chi-restraints excluded: chain A residue 1523 ASP Chi-restraints excluded: chain A residue 1644 SER Chi-restraints excluded: chain A residue 1705 ILE Chi-restraints excluded: chain A residue 1709 ASP Chi-restraints excluded: chain A residue 1738 SER Chi-restraints excluded: chain A residue 1757 LEU Chi-restraints excluded: chain A residue 1779 THR Chi-restraints excluded: chain A residue 1783 LEU Chi-restraints excluded: chain A residue 1830 PHE Chi-restraints excluded: chain A residue 1845 THR Chi-restraints excluded: chain A residue 1854 LEU Chi-restraints excluded: chain A residue 1916 ILE Chi-restraints excluded: chain A residue 1934 SER Chi-restraints excluded: chain A residue 2072 SER Chi-restraints excluded: chain A residue 2096 ILE Chi-restraints excluded: chain A residue 2118 TRP Chi-restraints excluded: chain A residue 2208 MET Chi-restraints excluded: chain A residue 2234 SER Chi-restraints excluded: chain A residue 2247 ASP Chi-restraints excluded: chain A residue 2257 SER Chi-restraints excluded: chain A residue 2263 SER Chi-restraints excluded: chain A residue 2405 LYS Chi-restraints excluded: chain A residue 2443 THR Chi-restraints excluded: chain A residue 2450 ILE Chi-restraints excluded: chain A residue 2482 VAL Chi-restraints excluded: chain A residue 2499 LYS Chi-restraints excluded: chain A residue 2550 MET Chi-restraints excluded: chain A residue 2608 LEU Chi-restraints excluded: chain A residue 2704 GLU Chi-restraints excluded: chain A residue 2792 VAL Chi-restraints excluded: chain A residue 2805 VAL Chi-restraints excluded: chain A residue 2810 ILE Chi-restraints excluded: chain A residue 2841 SER Chi-restraints excluded: chain A residue 2855 VAL Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 226 SER Chi-restraints excluded: chain B residue 229 TYR Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain B residue 388 ILE Chi-restraints excluded: chain B residue 448 ARG Chi-restraints excluded: chain B residue 449 VAL Chi-restraints excluded: chain B residue 516 VAL Chi-restraints excluded: chain B residue 522 LEU Chi-restraints excluded: chain B residue 587 SER Chi-restraints excluded: chain B residue 637 THR Chi-restraints excluded: chain B residue 641 LEU Chi-restraints excluded: chain B residue 648 CYS Chi-restraints excluded: chain B residue 662 LEU Chi-restraints excluded: chain B residue 771 LEU Chi-restraints excluded: chain B residue 897 SER Chi-restraints excluded: chain B residue 1002 TRP Chi-restraints excluded: chain B residue 1040 SER Chi-restraints excluded: chain B residue 1047 GLU Chi-restraints excluded: chain B residue 1054 SER Chi-restraints excluded: chain B residue 1101 VAL Chi-restraints excluded: chain B residue 1139 ILE Chi-restraints excluded: chain B residue 1217 LEU Chi-restraints excluded: chain B residue 1292 LYS Chi-restraints excluded: chain B residue 1300 HIS Chi-restraints excluded: chain B residue 1314 PHE Chi-restraints excluded: chain B residue 1324 PHE Chi-restraints excluded: chain B residue 1376 TYR Chi-restraints excluded: chain B residue 1381 ILE Chi-restraints excluded: chain B residue 1398 ILE Chi-restraints excluded: chain B residue 1408 CYS Chi-restraints excluded: chain B residue 1414 ILE Chi-restraints excluded: chain B residue 1523 ASP Chi-restraints excluded: chain B residue 1644 SER Chi-restraints excluded: chain B residue 1705 ILE Chi-restraints excluded: chain B residue 1709 ASP Chi-restraints excluded: chain B residue 1738 SER Chi-restraints excluded: chain B residue 1757 LEU Chi-restraints excluded: chain B residue 1779 THR Chi-restraints excluded: chain B residue 1783 LEU Chi-restraints excluded: chain B residue 1830 PHE Chi-restraints excluded: chain B residue 1845 THR Chi-restraints excluded: chain B residue 1854 LEU Chi-restraints excluded: chain B residue 1916 ILE Chi-restraints excluded: chain B residue 1934 SER Chi-restraints excluded: chain B residue 2072 SER Chi-restraints excluded: chain B residue 2096 ILE Chi-restraints excluded: chain B residue 2118 TRP Chi-restraints excluded: chain B residue 2208 MET Chi-restraints excluded: chain B residue 2234 SER Chi-restraints excluded: chain B residue 2247 ASP Chi-restraints excluded: chain B residue 2257 SER Chi-restraints excluded: chain B residue 2263 SER Chi-restraints excluded: chain B residue 2405 LYS Chi-restraints excluded: chain B residue 2443 THR Chi-restraints excluded: chain B residue 2450 ILE Chi-restraints excluded: chain B residue 2482 VAL Chi-restraints excluded: chain B residue 2499 LYS Chi-restraints excluded: chain B residue 2550 MET Chi-restraints excluded: chain B residue 2608 LEU Chi-restraints excluded: chain B residue 2704 GLU Chi-restraints excluded: chain B residue 2792 VAL Chi-restraints excluded: chain B residue 2805 VAL Chi-restraints excluded: chain B residue 2810 ILE Chi-restraints excluded: chain B residue 2841 SER Chi-restraints excluded: chain B residue 2855 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 526 random chunks: chunk 32 optimal weight: 4.9990 chunk 186 optimal weight: 5.9990 chunk 388 optimal weight: 0.9990 chunk 304 optimal weight: 3.9990 chunk 185 optimal weight: 0.5980 chunk 117 optimal weight: 0.5980 chunk 96 optimal weight: 7.9990 chunk 1 optimal weight: 0.5980 chunk 451 optimal weight: 0.6980 chunk 102 optimal weight: 10.0000 chunk 452 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1161 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.125615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.099287 restraints weight = 74024.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.098386 restraints weight = 60697.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.099257 restraints weight = 63955.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.100035 restraints weight = 47639.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.100304 restraints weight = 43945.075| |-----------------------------------------------------------------------------| r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.4465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 42680 Z= 0.113 Angle : 0.539 9.356 57824 Z= 0.271 Chirality : 0.038 0.265 6630 Planarity : 0.004 0.042 7372 Dihedral : 5.820 82.779 5808 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 3.13 % Allowed : 19.86 % Favored : 77.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 1.20 (0.12), residues: 5192 helix: 1.77 (0.09), residues: 3722 sheet: -0.19 (0.71), residues: 66 loop : -1.91 (0.16), residues: 1404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1412 TYR 0.018 0.001 TYR A1017 PHE 0.023 0.001 PHE A 272 TRP 0.015 0.001 TRP B1002 HIS 0.014 0.001 HIS A 120 Details of bonding type rmsd covalent geometry : bond 0.00251 (42678) covalent geometry : angle 0.53862 (57820) SS BOND : bond 0.00390 ( 2) SS BOND : angle 0.16748 ( 4) hydrogen bonds : bond 0.03635 ( 2587) hydrogen bonds : angle 3.71776 ( 7695) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10384 Ramachandran restraints generated. 5192 Oldfield, 0 Emsley, 5192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10384 Ramachandran restraints generated. 5192 Oldfield, 0 Emsley, 5192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 633 residues out of total 4562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 490 time to evaluate : 1.816 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 145 TYR cc_start: 0.7386 (t80) cc_final: 0.7183 (t80) REVERT: A 230 MET cc_start: 0.8527 (tpt) cc_final: 0.7879 (mtm) REVERT: A 267 MET cc_start: 0.8432 (mmm) cc_final: 0.7831 (mpp) REVERT: A 272 PHE cc_start: 0.8656 (t80) cc_final: 0.8420 (t80) REVERT: A 328 ARG cc_start: 0.7840 (OUTLIER) cc_final: 0.7470 (ttp-170) REVERT: A 388 ILE cc_start: 0.8445 (OUTLIER) cc_final: 0.8028 (tp) REVERT: A 755 MET cc_start: 0.7996 (tpp) cc_final: 0.7256 (tpt) REVERT: A 771 LEU cc_start: 0.8579 (OUTLIER) cc_final: 0.8358 (pp) REVERT: A 1119 PHE cc_start: 0.9141 (t80) cc_final: 0.8890 (t80) REVERT: A 1292 LYS cc_start: 0.6901 (tppt) cc_final: 0.6521 (tppt) REVERT: A 1300 HIS cc_start: 0.7250 (OUTLIER) cc_final: 0.6860 (m-70) REVERT: A 1376 TYR cc_start: 0.4808 (OUTLIER) cc_final: 0.2846 (m-80) REVERT: A 1406 HIS cc_start: 0.7457 (OUTLIER) cc_final: 0.6522 (t70) REVERT: A 1589 CYS cc_start: 0.8449 (m) cc_final: 0.7863 (m) REVERT: A 1757 LEU cc_start: 0.8205 (OUTLIER) cc_final: 0.7978 (tt) REVERT: A 1789 LYS cc_start: 0.8370 (mppt) cc_final: 0.8043 (tptp) REVERT: A 1925 ASP cc_start: 0.7579 (t0) cc_final: 0.7343 (t0) REVERT: A 2058 MET cc_start: 0.8617 (mmm) cc_final: 0.8392 (tpt) REVERT: A 2276 LEU cc_start: 0.8918 (OUTLIER) cc_final: 0.8609 (mp) REVERT: A 2608 LEU cc_start: 0.8905 (OUTLIER) cc_final: 0.8675 (mt) REVERT: A 2624 GLN cc_start: 0.7805 (tt0) cc_final: 0.7508 (tt0) REVERT: A 2758 LEU cc_start: 0.9239 (tp) cc_final: 0.9029 (tp) REVERT: A 2925 ASN cc_start: 0.8368 (m-40) cc_final: 0.7875 (m-40) REVERT: B 145 TYR cc_start: 0.7387 (t80) cc_final: 0.7179 (t80) REVERT: B 230 MET cc_start: 0.8537 (tpt) cc_final: 0.7881 (mtm) REVERT: B 267 MET cc_start: 0.8435 (mmm) cc_final: 0.7830 (mpp) REVERT: B 272 PHE cc_start: 0.8661 (t80) cc_final: 0.8415 (t80) REVERT: B 328 ARG cc_start: 0.7803 (OUTLIER) cc_final: 0.7358 (ttm110) REVERT: B 388 ILE cc_start: 0.8444 (OUTLIER) cc_final: 0.8034 (tp) REVERT: B 544 ARG cc_start: 0.8661 (OUTLIER) cc_final: 0.8460 (ttt180) REVERT: B 674 GLN cc_start: 0.7814 (tm-30) cc_final: 0.7334 (tm-30) REVERT: B 755 MET cc_start: 0.7998 (tpp) cc_final: 0.7257 (tpt) REVERT: B 771 LEU cc_start: 0.8573 (OUTLIER) cc_final: 0.8357 (pp) REVERT: B 1119 PHE cc_start: 0.9141 (t80) cc_final: 0.8894 (t80) REVERT: B 1292 LYS cc_start: 0.6901 (tppt) cc_final: 0.6516 (tppt) REVERT: B 1300 HIS cc_start: 0.7239 (OUTLIER) cc_final: 0.6850 (m-70) REVERT: B 1376 TYR cc_start: 0.4813 (OUTLIER) cc_final: 0.2859 (m-80) REVERT: B 1406 HIS cc_start: 0.7459 (OUTLIER) cc_final: 0.6513 (t70) REVERT: B 1589 CYS cc_start: 0.8361 (m) cc_final: 0.7950 (m) REVERT: B 1757 LEU cc_start: 0.8200 (OUTLIER) cc_final: 0.7973 (tt) REVERT: B 1789 LYS cc_start: 0.8380 (mppt) cc_final: 0.8045 (tptp) REVERT: B 1925 ASP cc_start: 0.7577 (t0) cc_final: 0.7339 (t0) REVERT: B 2058 MET cc_start: 0.8604 (mmm) cc_final: 0.8375 (tpt) REVERT: B 2276 LEU cc_start: 0.8917 (OUTLIER) cc_final: 0.8612 (mp) REVERT: B 2608 LEU cc_start: 0.8905 (OUTLIER) cc_final: 0.8670 (mt) REVERT: B 2624 GLN cc_start: 0.7796 (tt0) cc_final: 0.7501 (tt0) REVERT: B 2758 LEU cc_start: 0.9230 (tp) cc_final: 0.9028 (tp) REVERT: B 2925 ASN cc_start: 0.8360 (m-40) cc_final: 0.7862 (m-40) outliers start: 143 outliers final: 86 residues processed: 603 average time/residue: 0.2338 time to fit residues: 236.8143 Evaluate side-chains 529 residues out of total 4562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 424 time to evaluate : 1.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ASP Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 328 ARG Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain A residue 587 SER Chi-restraints excluded: chain A residue 637 THR Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 893 ASP Chi-restraints excluded: chain A residue 1002 TRP Chi-restraints excluded: chain A residue 1009 ILE Chi-restraints excluded: chain A residue 1040 SER Chi-restraints excluded: chain A residue 1054 SER Chi-restraints excluded: chain A residue 1299 ILE Chi-restraints excluded: chain A residue 1300 HIS Chi-restraints excluded: chain A residue 1314 PHE Chi-restraints excluded: chain A residue 1324 PHE Chi-restraints excluded: chain A residue 1376 TYR Chi-restraints excluded: chain A residue 1381 ILE Chi-restraints excluded: chain A residue 1398 ILE Chi-restraints excluded: chain A residue 1406 HIS Chi-restraints excluded: chain A residue 1414 ILE Chi-restraints excluded: chain A residue 1523 ASP Chi-restraints excluded: chain A residue 1541 GLU Chi-restraints excluded: chain A residue 1644 SER Chi-restraints excluded: chain A residue 1738 SER Chi-restraints excluded: chain A residue 1757 LEU Chi-restraints excluded: chain A residue 1830 PHE Chi-restraints excluded: chain A residue 1854 LEU Chi-restraints excluded: chain A residue 2072 SER Chi-restraints excluded: chain A residue 2096 ILE Chi-restraints excluded: chain A residue 2118 TRP Chi-restraints excluded: chain A residue 2208 MET Chi-restraints excluded: chain A residue 2234 SER Chi-restraints excluded: chain A residue 2247 ASP Chi-restraints excluded: chain A residue 2257 SER Chi-restraints excluded: chain A residue 2276 LEU Chi-restraints excluded: chain A residue 2429 LEU Chi-restraints excluded: chain A residue 2443 THR Chi-restraints excluded: chain A residue 2499 LYS Chi-restraints excluded: chain A residue 2505 SER Chi-restraints excluded: chain A residue 2540 SER Chi-restraints excluded: chain A residue 2550 MET Chi-restraints excluded: chain A residue 2608 LEU Chi-restraints excluded: chain A residue 2704 GLU Chi-restraints excluded: chain A residue 2855 VAL Chi-restraints excluded: chain A residue 2917 MET Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 226 SER Chi-restraints excluded: chain B residue 328 ARG Chi-restraints excluded: chain B residue 388 ILE Chi-restraints excluded: chain B residue 449 VAL Chi-restraints excluded: chain B residue 522 LEU Chi-restraints excluded: chain B residue 544 ARG Chi-restraints excluded: chain B residue 587 SER Chi-restraints excluded: chain B residue 637 THR Chi-restraints excluded: chain B residue 641 LEU Chi-restraints excluded: chain B residue 771 LEU Chi-restraints excluded: chain B residue 893 ASP Chi-restraints excluded: chain B residue 1002 TRP Chi-restraints excluded: chain B residue 1009 ILE Chi-restraints excluded: chain B residue 1040 SER Chi-restraints excluded: chain B residue 1054 SER Chi-restraints excluded: chain B residue 1139 ILE Chi-restraints excluded: chain B residue 1217 LEU Chi-restraints excluded: chain B residue 1299 ILE Chi-restraints excluded: chain B residue 1300 HIS Chi-restraints excluded: chain B residue 1314 PHE Chi-restraints excluded: chain B residue 1324 PHE Chi-restraints excluded: chain B residue 1376 TYR Chi-restraints excluded: chain B residue 1381 ILE Chi-restraints excluded: chain B residue 1398 ILE Chi-restraints excluded: chain B residue 1406 HIS Chi-restraints excluded: chain B residue 1414 ILE Chi-restraints excluded: chain B residue 1523 ASP Chi-restraints excluded: chain B residue 1541 GLU Chi-restraints excluded: chain B residue 1644 SER Chi-restraints excluded: chain B residue 1738 SER Chi-restraints excluded: chain B residue 1757 LEU Chi-restraints excluded: chain B residue 1830 PHE Chi-restraints excluded: chain B residue 1854 LEU Chi-restraints excluded: chain B residue 2072 SER Chi-restraints excluded: chain B residue 2096 ILE Chi-restraints excluded: chain B residue 2118 TRP Chi-restraints excluded: chain B residue 2208 MET Chi-restraints excluded: chain B residue 2234 SER Chi-restraints excluded: chain B residue 2247 ASP Chi-restraints excluded: chain B residue 2257 SER Chi-restraints excluded: chain B residue 2276 LEU Chi-restraints excluded: chain B residue 2429 LEU Chi-restraints excluded: chain B residue 2443 THR Chi-restraints excluded: chain B residue 2499 LYS Chi-restraints excluded: chain B residue 2505 SER Chi-restraints excluded: chain B residue 2540 SER Chi-restraints excluded: chain B residue 2550 MET Chi-restraints excluded: chain B residue 2608 LEU Chi-restraints excluded: chain B residue 2704 GLU Chi-restraints excluded: chain B residue 2855 VAL Chi-restraints excluded: chain B residue 2917 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 526 random chunks: chunk 446 optimal weight: 0.4980 chunk 389 optimal weight: 10.0000 chunk 90 optimal weight: 6.9990 chunk 459 optimal weight: 2.9990 chunk 364 optimal weight: 10.0000 chunk 9 optimal weight: 8.9990 chunk 409 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 146 optimal weight: 2.9990 chunk 15 optimal weight: 7.9990 chunk 502 optimal weight: 2.9990 overall best weight: 2.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 407 ASN A2217 HIS A2690 GLN B 407 ASN B 933 ASN B2690 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.121908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.095870 restraints weight = 74878.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.095083 restraints weight = 62836.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.095985 restraints weight = 73209.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.096664 restraints weight = 48993.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.097414 restraints weight = 43721.078| |-----------------------------------------------------------------------------| r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.4685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 42680 Z= 0.198 Angle : 0.602 9.500 57824 Z= 0.303 Chirality : 0.041 0.284 6630 Planarity : 0.004 0.044 7372 Dihedral : 5.788 80.603 5808 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 4.01 % Allowed : 19.29 % Favored : 76.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 1.15 (0.12), residues: 5192 helix: 1.70 (0.09), residues: 3726 sheet: -0.43 (0.68), residues: 66 loop : -1.81 (0.16), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B2286 TYR 0.017 0.002 TYR B1629 PHE 0.031 0.002 PHE B2546 TRP 0.016 0.001 TRP B1002 HIS 0.012 0.001 HIS A 120 Details of bonding type rmsd covalent geometry : bond 0.00480 (42678) covalent geometry : angle 0.60235 (57820) SS BOND : bond 0.01776 ( 2) SS BOND : angle 0.76367 ( 4) hydrogen bonds : bond 0.04434 ( 2587) hydrogen bonds : angle 3.88640 ( 7695) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10384 Ramachandran restraints generated. 5192 Oldfield, 0 Emsley, 5192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10384 Ramachandran restraints generated. 5192 Oldfield, 0 Emsley, 5192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 620 residues out of total 4562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 183 poor density : 437 time to evaluate : 1.421 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 145 TYR cc_start: 0.7500 (t80) cc_final: 0.7266 (t80) REVERT: A 149 ASP cc_start: 0.7398 (t0) cc_final: 0.7158 (t0) REVERT: A 230 MET cc_start: 0.8582 (tpt) cc_final: 0.7919 (mtm) REVERT: A 260 LYS cc_start: 0.7670 (OUTLIER) cc_final: 0.7368 (mmtm) REVERT: A 267 MET cc_start: 0.8486 (mmm) cc_final: 0.7858 (mpp) REVERT: A 272 PHE cc_start: 0.8753 (t80) cc_final: 0.8502 (t80) REVERT: A 301 TRP cc_start: 0.8259 (m100) cc_final: 0.7828 (m100) REVERT: A 328 ARG cc_start: 0.7901 (OUTLIER) cc_final: 0.7515 (ttp-170) REVERT: A 388 ILE cc_start: 0.8557 (OUTLIER) cc_final: 0.8029 (tp) REVERT: A 755 MET cc_start: 0.8069 (tpp) cc_final: 0.7315 (tpt) REVERT: A 771 LEU cc_start: 0.8741 (OUTLIER) cc_final: 0.8477 (pp) REVERT: A 1002 TRP cc_start: 0.8767 (OUTLIER) cc_final: 0.7446 (p-90) REVERT: A 1119 PHE cc_start: 0.9199 (t80) cc_final: 0.8933 (t80) REVERT: A 1300 HIS cc_start: 0.7382 (OUTLIER) cc_final: 0.7001 (m-70) REVERT: A 1376 TYR cc_start: 0.4826 (OUTLIER) cc_final: 0.2776 (m-80) REVERT: A 1412 ARG cc_start: 0.7654 (mtt90) cc_final: 0.6990 (mmt180) REVERT: A 1589 CYS cc_start: 0.8496 (m) cc_final: 0.7983 (m) REVERT: A 1672 GLU cc_start: 0.7656 (OUTLIER) cc_final: 0.7404 (mt-10) REVERT: A 1757 LEU cc_start: 0.8332 (OUTLIER) cc_final: 0.8073 (tt) REVERT: A 1789 LYS cc_start: 0.8497 (mppt) cc_final: 0.8073 (tptp) REVERT: A 1925 ASP cc_start: 0.7634 (t0) cc_final: 0.7380 (t0) REVERT: A 2058 MET cc_start: 0.8621 (mmm) cc_final: 0.8345 (tpp) REVERT: A 2276 LEU cc_start: 0.8993 (OUTLIER) cc_final: 0.8739 (mp) REVERT: A 2608 LEU cc_start: 0.8948 (OUTLIER) cc_final: 0.8684 (mt) REVERT: A 2812 LYS cc_start: 0.8352 (mtmt) cc_final: 0.8083 (mttp) REVERT: A 2925 ASN cc_start: 0.8338 (m-40) cc_final: 0.7908 (m-40) REVERT: B 145 TYR cc_start: 0.7495 (t80) cc_final: 0.7259 (t80) REVERT: B 149 ASP cc_start: 0.7406 (t0) cc_final: 0.7168 (t0) REVERT: B 230 MET cc_start: 0.8592 (tpt) cc_final: 0.7927 (mtm) REVERT: B 260 LYS cc_start: 0.7640 (OUTLIER) cc_final: 0.7348 (mmtm) REVERT: B 267 MET cc_start: 0.8483 (mmm) cc_final: 0.7854 (mpp) REVERT: B 272 PHE cc_start: 0.8781 (t80) cc_final: 0.8515 (t80) REVERT: B 301 TRP cc_start: 0.8257 (m100) cc_final: 0.7834 (m100) REVERT: B 328 ARG cc_start: 0.7860 (OUTLIER) cc_final: 0.7451 (ttm110) REVERT: B 388 ILE cc_start: 0.8548 (OUTLIER) cc_final: 0.8018 (tp) REVERT: B 674 GLN cc_start: 0.8080 (tm-30) cc_final: 0.7530 (tm-30) REVERT: B 755 MET cc_start: 0.8073 (tpp) cc_final: 0.7318 (tpt) REVERT: B 771 LEU cc_start: 0.8743 (OUTLIER) cc_final: 0.8480 (pp) REVERT: B 1002 TRP cc_start: 0.8760 (OUTLIER) cc_final: 0.7442 (p-90) REVERT: B 1119 PHE cc_start: 0.9179 (t80) cc_final: 0.8919 (t80) REVERT: B 1300 HIS cc_start: 0.7386 (OUTLIER) cc_final: 0.7006 (m-70) REVERT: B 1376 TYR cc_start: 0.4836 (OUTLIER) cc_final: 0.2788 (m-80) REVERT: B 1412 ARG cc_start: 0.7635 (mtt90) cc_final: 0.6976 (mmt180) REVERT: B 1672 GLU cc_start: 0.7657 (OUTLIER) cc_final: 0.7406 (mt-10) REVERT: B 1757 LEU cc_start: 0.8331 (OUTLIER) cc_final: 0.8071 (tt) REVERT: B 1789 LYS cc_start: 0.8505 (mppt) cc_final: 0.8078 (tptp) REVERT: B 1925 ASP cc_start: 0.7626 (t0) cc_final: 0.7370 (t0) REVERT: B 2058 MET cc_start: 0.8619 (mmm) cc_final: 0.8342 (tpp) REVERT: B 2276 LEU cc_start: 0.8995 (OUTLIER) cc_final: 0.8741 (mp) REVERT: B 2608 LEU cc_start: 0.8946 (OUTLIER) cc_final: 0.8677 (mt) REVERT: B 2812 LYS cc_start: 0.8358 (mtmt) cc_final: 0.8092 (mttp) REVERT: B 2925 ASN cc_start: 0.8328 (m-40) cc_final: 0.7884 (m-40) outliers start: 183 outliers final: 129 residues processed: 578 average time/residue: 0.2256 time to fit residues: 219.8462 Evaluate side-chains 555 residues out of total 4562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 151 poor density : 404 time to evaluate : 1.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ASP Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 229 TYR Chi-restraints excluded: chain A residue 260 LYS Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 328 ARG Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 448 ARG Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain A residue 587 SER Chi-restraints excluded: chain A residue 637 THR Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 804 SER Chi-restraints excluded: chain A residue 897 SER Chi-restraints excluded: chain A residue 1002 TRP Chi-restraints excluded: chain A residue 1009 ILE Chi-restraints excluded: chain A residue 1040 SER Chi-restraints excluded: chain A residue 1054 SER Chi-restraints excluded: chain A residue 1217 LEU Chi-restraints excluded: chain A residue 1300 HIS Chi-restraints excluded: chain A residue 1305 ASP Chi-restraints excluded: chain A residue 1314 PHE Chi-restraints excluded: chain A residue 1324 PHE Chi-restraints excluded: chain A residue 1376 TYR Chi-restraints excluded: chain A residue 1381 ILE Chi-restraints excluded: chain A residue 1398 ILE Chi-restraints excluded: chain A residue 1408 CYS Chi-restraints excluded: chain A residue 1414 ILE Chi-restraints excluded: chain A residue 1523 ASP Chi-restraints excluded: chain A residue 1541 GLU Chi-restraints excluded: chain A residue 1594 ILE Chi-restraints excluded: chain A residue 1644 SER Chi-restraints excluded: chain A residue 1672 GLU Chi-restraints excluded: chain A residue 1705 ILE Chi-restraints excluded: chain A residue 1709 ASP Chi-restraints excluded: chain A residue 1728 SER Chi-restraints excluded: chain A residue 1738 SER Chi-restraints excluded: chain A residue 1757 LEU Chi-restraints excluded: chain A residue 1783 LEU Chi-restraints excluded: chain A residue 1830 PHE Chi-restraints excluded: chain A residue 1845 THR Chi-restraints excluded: chain A residue 1854 LEU Chi-restraints excluded: chain A residue 1916 ILE Chi-restraints excluded: chain A residue 1934 SER Chi-restraints excluded: chain A residue 2072 SER Chi-restraints excluded: chain A residue 2096 ILE Chi-restraints excluded: chain A residue 2118 TRP Chi-restraints excluded: chain A residue 2208 MET Chi-restraints excluded: chain A residue 2234 SER Chi-restraints excluded: chain A residue 2247 ASP Chi-restraints excluded: chain A residue 2257 SER Chi-restraints excluded: chain A residue 2263 SER Chi-restraints excluded: chain A residue 2276 LEU Chi-restraints excluded: chain A residue 2429 LEU Chi-restraints excluded: chain A residue 2443 THR Chi-restraints excluded: chain A residue 2482 VAL Chi-restraints excluded: chain A residue 2499 LYS Chi-restraints excluded: chain A residue 2505 SER Chi-restraints excluded: chain A residue 2540 SER Chi-restraints excluded: chain A residue 2550 MET Chi-restraints excluded: chain A residue 2608 LEU Chi-restraints excluded: chain A residue 2704 GLU Chi-restraints excluded: chain A residue 2792 VAL Chi-restraints excluded: chain A residue 2810 ILE Chi-restraints excluded: chain A residue 2841 SER Chi-restraints excluded: chain A residue 2855 VAL Chi-restraints excluded: chain A residue 2917 MET Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 226 SER Chi-restraints excluded: chain B residue 229 TYR Chi-restraints excluded: chain B residue 260 LYS Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 328 ARG Chi-restraints excluded: chain B residue 388 ILE Chi-restraints excluded: chain B residue 448 ARG Chi-restraints excluded: chain B residue 449 VAL Chi-restraints excluded: chain B residue 522 LEU Chi-restraints excluded: chain B residue 587 SER Chi-restraints excluded: chain B residue 637 THR Chi-restraints excluded: chain B residue 641 LEU Chi-restraints excluded: chain B residue 662 LEU Chi-restraints excluded: chain B residue 771 LEU Chi-restraints excluded: chain B residue 804 SER Chi-restraints excluded: chain B residue 897 SER Chi-restraints excluded: chain B residue 1002 TRP Chi-restraints excluded: chain B residue 1009 ILE Chi-restraints excluded: chain B residue 1040 SER Chi-restraints excluded: chain B residue 1054 SER Chi-restraints excluded: chain B residue 1139 ILE Chi-restraints excluded: chain B residue 1217 LEU Chi-restraints excluded: chain B residue 1300 HIS Chi-restraints excluded: chain B residue 1305 ASP Chi-restraints excluded: chain B residue 1314 PHE Chi-restraints excluded: chain B residue 1324 PHE Chi-restraints excluded: chain B residue 1376 TYR Chi-restraints excluded: chain B residue 1381 ILE Chi-restraints excluded: chain B residue 1398 ILE Chi-restraints excluded: chain B residue 1408 CYS Chi-restraints excluded: chain B residue 1414 ILE Chi-restraints excluded: chain B residue 1523 ASP Chi-restraints excluded: chain B residue 1541 GLU Chi-restraints excluded: chain B residue 1594 ILE Chi-restraints excluded: chain B residue 1644 SER Chi-restraints excluded: chain B residue 1672 GLU Chi-restraints excluded: chain B residue 1705 ILE Chi-restraints excluded: chain B residue 1709 ASP Chi-restraints excluded: chain B residue 1728 SER Chi-restraints excluded: chain B residue 1738 SER Chi-restraints excluded: chain B residue 1757 LEU Chi-restraints excluded: chain B residue 1783 LEU Chi-restraints excluded: chain B residue 1830 PHE Chi-restraints excluded: chain B residue 1845 THR Chi-restraints excluded: chain B residue 1854 LEU Chi-restraints excluded: chain B residue 1916 ILE Chi-restraints excluded: chain B residue 1934 SER Chi-restraints excluded: chain B residue 2072 SER Chi-restraints excluded: chain B residue 2096 ILE Chi-restraints excluded: chain B residue 2118 TRP Chi-restraints excluded: chain B residue 2208 MET Chi-restraints excluded: chain B residue 2234 SER Chi-restraints excluded: chain B residue 2247 ASP Chi-restraints excluded: chain B residue 2257 SER Chi-restraints excluded: chain B residue 2263 SER Chi-restraints excluded: chain B residue 2276 LEU Chi-restraints excluded: chain B residue 2429 LEU Chi-restraints excluded: chain B residue 2443 THR Chi-restraints excluded: chain B residue 2482 VAL Chi-restraints excluded: chain B residue 2499 LYS Chi-restraints excluded: chain B residue 2505 SER Chi-restraints excluded: chain B residue 2540 SER Chi-restraints excluded: chain B residue 2550 MET Chi-restraints excluded: chain B residue 2608 LEU Chi-restraints excluded: chain B residue 2704 GLU Chi-restraints excluded: chain B residue 2792 VAL Chi-restraints excluded: chain B residue 2810 ILE Chi-restraints excluded: chain B residue 2841 SER Chi-restraints excluded: chain B residue 2855 VAL Chi-restraints excluded: chain B residue 2917 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 526 random chunks: chunk 293 optimal weight: 0.8980 chunk 68 optimal weight: 0.5980 chunk 103 optimal weight: 6.9990 chunk 492 optimal weight: 4.9990 chunk 423 optimal weight: 0.9990 chunk 401 optimal weight: 0.9980 chunk 360 optimal weight: 0.8980 chunk 112 optimal weight: 0.9990 chunk 395 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 270 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B2552 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.123625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.097746 restraints weight = 74521.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.097074 restraints weight = 60545.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.097975 restraints weight = 70918.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.098331 restraints weight = 49173.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.098808 restraints weight = 44206.628| |-----------------------------------------------------------------------------| r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.4881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 42680 Z= 0.121 Angle : 0.555 10.480 57824 Z= 0.276 Chirality : 0.039 0.254 6630 Planarity : 0.004 0.044 7372 Dihedral : 5.602 79.367 5808 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 3.31 % Allowed : 20.39 % Favored : 76.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 1.39 (0.12), residues: 5192 helix: 1.87 (0.09), residues: 3738 sheet: -0.51 (0.66), residues: 66 loop : -1.72 (0.17), residues: 1388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B2286 TYR 0.017 0.001 TYR B1476 PHE 0.037 0.001 PHE B2546 TRP 0.015 0.001 TRP B1002 HIS 0.010 0.001 HIS B 120 Details of bonding type rmsd covalent geometry : bond 0.00280 (42678) covalent geometry : angle 0.55455 (57820) SS BOND : bond 0.00775 ( 2) SS BOND : angle 0.96456 ( 4) hydrogen bonds : bond 0.03701 ( 2587) hydrogen bonds : angle 3.72896 ( 7695) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10384 Ramachandran restraints generated. 5192 Oldfield, 0 Emsley, 5192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10384 Ramachandran restraints generated. 5192 Oldfield, 0 Emsley, 5192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 609 residues out of total 4562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 151 poor density : 458 time to evaluate : 1.702 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 149 ASP cc_start: 0.7340 (t0) cc_final: 0.7089 (t0) REVERT: A 230 MET cc_start: 0.8444 (tpt) cc_final: 0.7782 (mtm) REVERT: A 267 MET cc_start: 0.8454 (mmm) cc_final: 0.7890 (mpp) REVERT: A 272 PHE cc_start: 0.8744 (t80) cc_final: 0.8490 (t80) REVERT: A 301 TRP cc_start: 0.8146 (m100) cc_final: 0.7741 (m100) REVERT: A 328 ARG cc_start: 0.7875 (OUTLIER) cc_final: 0.7531 (ttp-170) REVERT: A 388 ILE cc_start: 0.8449 (OUTLIER) cc_final: 0.7978 (tp) REVERT: A 755 MET cc_start: 0.8055 (tpp) cc_final: 0.7339 (tpt) REVERT: A 771 LEU cc_start: 0.8625 (OUTLIER) cc_final: 0.8393 (pp) REVERT: A 1002 TRP cc_start: 0.8740 (OUTLIER) cc_final: 0.7719 (p-90) REVERT: A 1119 PHE cc_start: 0.9128 (t80) cc_final: 0.8871 (t80) REVERT: A 1300 HIS cc_start: 0.7313 (OUTLIER) cc_final: 0.6962 (m170) REVERT: A 1376 TYR cc_start: 0.4767 (OUTLIER) cc_final: 0.2754 (m-80) REVERT: A 1412 ARG cc_start: 0.7696 (mtt90) cc_final: 0.7257 (mmt90) REVERT: A 1719 SER cc_start: 0.8970 (m) cc_final: 0.8720 (p) REVERT: A 1757 LEU cc_start: 0.8335 (OUTLIER) cc_final: 0.8114 (tt) REVERT: A 1789 LYS cc_start: 0.8484 (mppt) cc_final: 0.8059 (tptp) REVERT: A 1925 ASP cc_start: 0.7551 (t0) cc_final: 0.7319 (t0) REVERT: A 2058 MET cc_start: 0.8560 (mmm) cc_final: 0.8305 (tpp) REVERT: A 2276 LEU cc_start: 0.8968 (OUTLIER) cc_final: 0.8709 (mp) REVERT: A 2546 PHE cc_start: 0.8075 (t80) cc_final: 0.7552 (t80) REVERT: A 2550 MET cc_start: 0.7858 (OUTLIER) cc_final: 0.6826 (mmm) REVERT: A 2608 LEU cc_start: 0.8903 (OUTLIER) cc_final: 0.8666 (mt) REVERT: A 2925 ASN cc_start: 0.8256 (m-40) cc_final: 0.7816 (m-40) REVERT: B 149 ASP cc_start: 0.7330 (t0) cc_final: 0.7093 (t0) REVERT: B 230 MET cc_start: 0.8452 (tpt) cc_final: 0.7786 (mtm) REVERT: B 267 MET cc_start: 0.8448 (mmm) cc_final: 0.7888 (mpp) REVERT: B 272 PHE cc_start: 0.8749 (t80) cc_final: 0.8506 (t80) REVERT: B 301 TRP cc_start: 0.8143 (m100) cc_final: 0.7737 (m100) REVERT: B 328 ARG cc_start: 0.7858 (OUTLIER) cc_final: 0.7437 (ttm110) REVERT: B 388 ILE cc_start: 0.8445 (OUTLIER) cc_final: 0.7978 (tp) REVERT: B 674 GLN cc_start: 0.8106 (tm-30) cc_final: 0.7224 (tm-30) REVERT: B 755 MET cc_start: 0.8059 (tpp) cc_final: 0.7342 (tpt) REVERT: B 771 LEU cc_start: 0.8621 (OUTLIER) cc_final: 0.8397 (pp) REVERT: B 1002 TRP cc_start: 0.8735 (OUTLIER) cc_final: 0.7726 (p-90) REVERT: B 1119 PHE cc_start: 0.9111 (t80) cc_final: 0.8859 (t80) REVERT: B 1300 HIS cc_start: 0.7308 (OUTLIER) cc_final: 0.6960 (m170) REVERT: B 1376 TYR cc_start: 0.4772 (OUTLIER) cc_final: 0.2766 (m-80) REVERT: B 1412 ARG cc_start: 0.7691 (mtt90) cc_final: 0.7262 (mmt90) REVERT: B 1719 SER cc_start: 0.8976 (m) cc_final: 0.8726 (p) REVERT: B 1757 LEU cc_start: 0.8329 (OUTLIER) cc_final: 0.8105 (tt) REVERT: B 1789 LYS cc_start: 0.8484 (mppt) cc_final: 0.8056 (tptp) REVERT: B 1925 ASP cc_start: 0.7538 (t0) cc_final: 0.7306 (t0) REVERT: B 2058 MET cc_start: 0.8564 (mmm) cc_final: 0.8306 (tpp) REVERT: B 2276 LEU cc_start: 0.8967 (OUTLIER) cc_final: 0.8704 (mp) REVERT: B 2303 LEU cc_start: 0.9005 (mt) cc_final: 0.8739 (tp) REVERT: B 2608 LEU cc_start: 0.8902 (OUTLIER) cc_final: 0.8661 (mt) REVERT: B 2925 ASN cc_start: 0.8255 (m-40) cc_final: 0.7803 (m-40) outliers start: 151 outliers final: 100 residues processed: 576 average time/residue: 0.2334 time to fit residues: 226.9866 Evaluate side-chains 537 residues out of total 4562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 418 time to evaluate : 1.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 328 ARG Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 448 ARG Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain A residue 587 SER Chi-restraints excluded: chain A residue 637 THR Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 794 VAL Chi-restraints excluded: chain A residue 852 TYR Chi-restraints excluded: chain A residue 897 SER Chi-restraints excluded: chain A residue 980 GLU Chi-restraints excluded: chain A residue 1002 TRP Chi-restraints excluded: chain A residue 1009 ILE Chi-restraints excluded: chain A residue 1040 SER Chi-restraints excluded: chain A residue 1054 SER Chi-restraints excluded: chain A residue 1217 LEU Chi-restraints excluded: chain A residue 1299 ILE Chi-restraints excluded: chain A residue 1300 HIS Chi-restraints excluded: chain A residue 1314 PHE Chi-restraints excluded: chain A residue 1324 PHE Chi-restraints excluded: chain A residue 1376 TYR Chi-restraints excluded: chain A residue 1381 ILE Chi-restraints excluded: chain A residue 1398 ILE Chi-restraints excluded: chain A residue 1408 CYS Chi-restraints excluded: chain A residue 1414 ILE Chi-restraints excluded: chain A residue 1523 ASP Chi-restraints excluded: chain A residue 1541 GLU Chi-restraints excluded: chain A residue 1644 SER Chi-restraints excluded: chain A residue 1738 SER Chi-restraints excluded: chain A residue 1757 LEU Chi-restraints excluded: chain A residue 1779 THR Chi-restraints excluded: chain A residue 1783 LEU Chi-restraints excluded: chain A residue 1830 PHE Chi-restraints excluded: chain A residue 1854 LEU Chi-restraints excluded: chain A residue 1916 ILE Chi-restraints excluded: chain A residue 2072 SER Chi-restraints excluded: chain A residue 2096 ILE Chi-restraints excluded: chain A residue 2118 TRP Chi-restraints excluded: chain A residue 2208 MET Chi-restraints excluded: chain A residue 2234 SER Chi-restraints excluded: chain A residue 2247 ASP Chi-restraints excluded: chain A residue 2257 SER Chi-restraints excluded: chain A residue 2263 SER Chi-restraints excluded: chain A residue 2276 LEU Chi-restraints excluded: chain A residue 2443 THR Chi-restraints excluded: chain A residue 2499 LYS Chi-restraints excluded: chain A residue 2505 SER Chi-restraints excluded: chain A residue 2540 SER Chi-restraints excluded: chain A residue 2550 MET Chi-restraints excluded: chain A residue 2608 LEU Chi-restraints excluded: chain A residue 2704 GLU Chi-restraints excluded: chain A residue 2841 SER Chi-restraints excluded: chain A residue 2855 VAL Chi-restraints excluded: chain A residue 2917 MET Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 328 ARG Chi-restraints excluded: chain B residue 388 ILE Chi-restraints excluded: chain B residue 448 ARG Chi-restraints excluded: chain B residue 522 LEU Chi-restraints excluded: chain B residue 587 SER Chi-restraints excluded: chain B residue 637 THR Chi-restraints excluded: chain B residue 641 LEU Chi-restraints excluded: chain B residue 771 LEU Chi-restraints excluded: chain B residue 794 VAL Chi-restraints excluded: chain B residue 852 TYR Chi-restraints excluded: chain B residue 897 SER Chi-restraints excluded: chain B residue 980 GLU Chi-restraints excluded: chain B residue 1002 TRP Chi-restraints excluded: chain B residue 1009 ILE Chi-restraints excluded: chain B residue 1040 SER Chi-restraints excluded: chain B residue 1054 SER Chi-restraints excluded: chain B residue 1139 ILE Chi-restraints excluded: chain B residue 1217 LEU Chi-restraints excluded: chain B residue 1299 ILE Chi-restraints excluded: chain B residue 1300 HIS Chi-restraints excluded: chain B residue 1314 PHE Chi-restraints excluded: chain B residue 1324 PHE Chi-restraints excluded: chain B residue 1376 TYR Chi-restraints excluded: chain B residue 1381 ILE Chi-restraints excluded: chain B residue 1398 ILE Chi-restraints excluded: chain B residue 1408 CYS Chi-restraints excluded: chain B residue 1414 ILE Chi-restraints excluded: chain B residue 1523 ASP Chi-restraints excluded: chain B residue 1541 GLU Chi-restraints excluded: chain B residue 1644 SER Chi-restraints excluded: chain B residue 1738 SER Chi-restraints excluded: chain B residue 1757 LEU Chi-restraints excluded: chain B residue 1779 THR Chi-restraints excluded: chain B residue 1783 LEU Chi-restraints excluded: chain B residue 1830 PHE Chi-restraints excluded: chain B residue 1854 LEU Chi-restraints excluded: chain B residue 1916 ILE Chi-restraints excluded: chain B residue 2072 SER Chi-restraints excluded: chain B residue 2096 ILE Chi-restraints excluded: chain B residue 2118 TRP Chi-restraints excluded: chain B residue 2208 MET Chi-restraints excluded: chain B residue 2234 SER Chi-restraints excluded: chain B residue 2247 ASP Chi-restraints excluded: chain B residue 2257 SER Chi-restraints excluded: chain B residue 2263 SER Chi-restraints excluded: chain B residue 2276 LEU Chi-restraints excluded: chain B residue 2443 THR Chi-restraints excluded: chain B residue 2499 LYS Chi-restraints excluded: chain B residue 2505 SER Chi-restraints excluded: chain B residue 2540 SER Chi-restraints excluded: chain B residue 2550 MET Chi-restraints excluded: chain B residue 2608 LEU Chi-restraints excluded: chain B residue 2704 GLU Chi-restraints excluded: chain B residue 2841 SER Chi-restraints excluded: chain B residue 2855 VAL Chi-restraints excluded: chain B residue 2917 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 526 random chunks: chunk 45 optimal weight: 0.6980 chunk 452 optimal weight: 1.9990 chunk 21 optimal weight: 6.9990 chunk 450 optimal weight: 3.9990 chunk 320 optimal weight: 0.7980 chunk 170 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 460 optimal weight: 2.9990 chunk 314 optimal weight: 2.9990 chunk 519 optimal weight: 0.6980 chunk 514 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 407 ASN A 809 ASN A 933 ASN B 809 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.125934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.100446 restraints weight = 73817.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.099876 restraints weight = 62040.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.100686 restraints weight = 71284.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.101362 restraints weight = 49222.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.101940 restraints weight = 44711.106| |-----------------------------------------------------------------------------| r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.5047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 42680 Z= 0.118 Angle : 0.551 11.654 57824 Z= 0.275 Chirality : 0.039 0.234 6630 Planarity : 0.004 0.043 7372 Dihedral : 5.398 79.387 5804 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 3.22 % Allowed : 20.60 % Favored : 76.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.58 (0.12), residues: 5192 helix: 2.02 (0.09), residues: 3722 sheet: -0.55 (0.64), residues: 66 loop : -1.64 (0.16), residues: 1404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A2286 TYR 0.014 0.001 TYR B1476 PHE 0.021 0.001 PHE B2546 TRP 0.013 0.001 TRP B1002 HIS 0.011 0.001 HIS B 120 Details of bonding type rmsd covalent geometry : bond 0.00273 (42678) covalent geometry : angle 0.55140 (57820) SS BOND : bond 0.00428 ( 2) SS BOND : angle 0.92325 ( 4) hydrogen bonds : bond 0.03558 ( 2587) hydrogen bonds : angle 3.64664 ( 7695) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10384 Ramachandran restraints generated. 5192 Oldfield, 0 Emsley, 5192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10384 Ramachandran restraints generated. 5192 Oldfield, 0 Emsley, 5192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 598 residues out of total 4562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 147 poor density : 451 time to evaluate : 1.546 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 149 ASP cc_start: 0.7402 (t0) cc_final: 0.7038 (m-30) REVERT: A 230 MET cc_start: 0.8586 (tpt) cc_final: 0.7979 (mtm) REVERT: A 260 LYS cc_start: 0.7677 (OUTLIER) cc_final: 0.7418 (mmtm) REVERT: A 267 MET cc_start: 0.8521 (mmm) cc_final: 0.7954 (mpp) REVERT: A 272 PHE cc_start: 0.8733 (t80) cc_final: 0.8470 (t80) REVERT: A 328 ARG cc_start: 0.7968 (OUTLIER) cc_final: 0.7620 (ttp-170) REVERT: A 484 GLU cc_start: 0.6619 (tp30) cc_final: 0.6222 (tt0) REVERT: A 674 GLN cc_start: 0.7920 (tm-30) cc_final: 0.7127 (tm-30) REVERT: A 755 MET cc_start: 0.8031 (tpp) cc_final: 0.7401 (tpt) REVERT: A 1002 TRP cc_start: 0.8695 (OUTLIER) cc_final: 0.7767 (p-90) REVERT: A 1119 PHE cc_start: 0.9082 (t80) cc_final: 0.8835 (t80) REVERT: A 1300 HIS cc_start: 0.7246 (OUTLIER) cc_final: 0.6929 (m90) REVERT: A 1376 TYR cc_start: 0.4795 (OUTLIER) cc_final: 0.2858 (m-80) REVERT: A 1412 ARG cc_start: 0.7607 (mtt90) cc_final: 0.7207 (mmt90) REVERT: A 1719 SER cc_start: 0.8911 (m) cc_final: 0.8660 (p) REVERT: A 1757 LEU cc_start: 0.8272 (OUTLIER) cc_final: 0.8050 (tt) REVERT: A 1789 LYS cc_start: 0.8436 (mppt) cc_final: 0.8042 (tptp) REVERT: A 1925 ASP cc_start: 0.7495 (t0) cc_final: 0.7270 (t0) REVERT: A 2058 MET cc_start: 0.8481 (mmm) cc_final: 0.8260 (tpp) REVERT: A 2276 LEU cc_start: 0.8932 (OUTLIER) cc_final: 0.8654 (mp) REVERT: A 2303 LEU cc_start: 0.8990 (mt) cc_final: 0.8728 (tp) REVERT: A 2550 MET cc_start: 0.7856 (OUTLIER) cc_final: 0.6796 (mmm) REVERT: A 2608 LEU cc_start: 0.8895 (OUTLIER) cc_final: 0.8671 (mt) REVERT: A 2925 ASN cc_start: 0.8211 (m-40) cc_final: 0.7831 (m-40) REVERT: B 149 ASP cc_start: 0.7400 (t0) cc_final: 0.7063 (m-30) REVERT: B 230 MET cc_start: 0.8590 (tpt) cc_final: 0.7977 (mtm) REVERT: B 260 LYS cc_start: 0.7676 (OUTLIER) cc_final: 0.7426 (mmtm) REVERT: B 267 MET cc_start: 0.8518 (mmm) cc_final: 0.7913 (mpp) REVERT: B 272 PHE cc_start: 0.8731 (t80) cc_final: 0.8476 (t80) REVERT: B 328 ARG cc_start: 0.7830 (OUTLIER) cc_final: 0.7457 (ttm110) REVERT: B 448 ARG cc_start: 0.8257 (OUTLIER) cc_final: 0.7954 (mtp85) REVERT: B 484 GLU cc_start: 0.6598 (tp30) cc_final: 0.6387 (tm-30) REVERT: B 555 LYS cc_start: 0.8585 (OUTLIER) cc_final: 0.8269 (ptmt) REVERT: B 632 HIS cc_start: 0.8237 (OUTLIER) cc_final: 0.7664 (p90) REVERT: B 674 GLN cc_start: 0.8183 (tm-30) cc_final: 0.7732 (tm-30) REVERT: B 755 MET cc_start: 0.8026 (tpp) cc_final: 0.7395 (tpt) REVERT: B 1002 TRP cc_start: 0.8694 (OUTLIER) cc_final: 0.7769 (p-90) REVERT: B 1119 PHE cc_start: 0.9106 (t80) cc_final: 0.8860 (t80) REVERT: B 1300 HIS cc_start: 0.7230 (OUTLIER) cc_final: 0.6913 (m90) REVERT: B 1376 TYR cc_start: 0.4798 (OUTLIER) cc_final: 0.2863 (m-80) REVERT: B 1412 ARG cc_start: 0.7608 (mtt90) cc_final: 0.7206 (mmt90) REVERT: B 1719 SER cc_start: 0.8917 (m) cc_final: 0.8663 (p) REVERT: B 1757 LEU cc_start: 0.8281 (OUTLIER) cc_final: 0.8058 (tt) REVERT: B 1789 LYS cc_start: 0.8436 (mppt) cc_final: 0.8044 (tptp) REVERT: B 1925 ASP cc_start: 0.7484 (t0) cc_final: 0.7265 (t0) REVERT: B 2058 MET cc_start: 0.8490 (mmm) cc_final: 0.8271 (tpp) REVERT: B 2276 LEU cc_start: 0.8924 (OUTLIER) cc_final: 0.8657 (mp) REVERT: B 2303 LEU cc_start: 0.8990 (mt) cc_final: 0.8780 (tp) REVERT: B 2550 MET cc_start: 0.7840 (OUTLIER) cc_final: 0.6816 (mmm) REVERT: B 2608 LEU cc_start: 0.8898 (OUTLIER) cc_final: 0.8672 (mt) REVERT: B 2925 ASN cc_start: 0.8239 (m-40) cc_final: 0.7851 (m-40) outliers start: 147 outliers final: 95 residues processed: 566 average time/residue: 0.2366 time to fit residues: 225.6589 Evaluate side-chains 538 residues out of total 4562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 422 time to evaluate : 1.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 260 LYS Chi-restraints excluded: chain A residue 328 ARG Chi-restraints excluded: chain A residue 448 ARG Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain A residue 637 THR Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 852 TYR Chi-restraints excluded: chain A residue 897 SER Chi-restraints excluded: chain A residue 980 GLU Chi-restraints excluded: chain A residue 1002 TRP Chi-restraints excluded: chain A residue 1040 SER Chi-restraints excluded: chain A residue 1054 SER Chi-restraints excluded: chain A residue 1217 LEU Chi-restraints excluded: chain A residue 1300 HIS Chi-restraints excluded: chain A residue 1314 PHE Chi-restraints excluded: chain A residue 1324 PHE Chi-restraints excluded: chain A residue 1376 TYR Chi-restraints excluded: chain A residue 1398 ILE Chi-restraints excluded: chain A residue 1408 CYS Chi-restraints excluded: chain A residue 1414 ILE Chi-restraints excluded: chain A residue 1506 SER Chi-restraints excluded: chain A residue 1523 ASP Chi-restraints excluded: chain A residue 1541 GLU Chi-restraints excluded: chain A residue 1640 SER Chi-restraints excluded: chain A residue 1644 SER Chi-restraints excluded: chain A residue 1738 SER Chi-restraints excluded: chain A residue 1757 LEU Chi-restraints excluded: chain A residue 1779 THR Chi-restraints excluded: chain A residue 1830 PHE Chi-restraints excluded: chain A residue 1854 LEU Chi-restraints excluded: chain A residue 1934 SER Chi-restraints excluded: chain A residue 2072 SER Chi-restraints excluded: chain A residue 2096 ILE Chi-restraints excluded: chain A residue 2118 TRP Chi-restraints excluded: chain A residue 2208 MET Chi-restraints excluded: chain A residue 2234 SER Chi-restraints excluded: chain A residue 2247 ASP Chi-restraints excluded: chain A residue 2263 SER Chi-restraints excluded: chain A residue 2276 LEU Chi-restraints excluded: chain A residue 2443 THR Chi-restraints excluded: chain A residue 2499 LYS Chi-restraints excluded: chain A residue 2540 SER Chi-restraints excluded: chain A residue 2550 MET Chi-restraints excluded: chain A residue 2608 LEU Chi-restraints excluded: chain A residue 2632 LEU Chi-restraints excluded: chain A residue 2704 GLU Chi-restraints excluded: chain A residue 2810 ILE Chi-restraints excluded: chain A residue 2841 SER Chi-restraints excluded: chain A residue 2855 VAL Chi-restraints excluded: chain A residue 2917 MET Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 260 LYS Chi-restraints excluded: chain B residue 328 ARG Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain B residue 448 ARG Chi-restraints excluded: chain B residue 522 LEU Chi-restraints excluded: chain B residue 538 SER Chi-restraints excluded: chain B residue 555 LYS Chi-restraints excluded: chain B residue 582 ILE Chi-restraints excluded: chain B residue 587 SER Chi-restraints excluded: chain B residue 632 HIS Chi-restraints excluded: chain B residue 637 THR Chi-restraints excluded: chain B residue 641 LEU Chi-restraints excluded: chain B residue 852 TYR Chi-restraints excluded: chain B residue 897 SER Chi-restraints excluded: chain B residue 980 GLU Chi-restraints excluded: chain B residue 1002 TRP Chi-restraints excluded: chain B residue 1040 SER Chi-restraints excluded: chain B residue 1054 SER Chi-restraints excluded: chain B residue 1139 ILE Chi-restraints excluded: chain B residue 1217 LEU Chi-restraints excluded: chain B residue 1300 HIS Chi-restraints excluded: chain B residue 1314 PHE Chi-restraints excluded: chain B residue 1324 PHE Chi-restraints excluded: chain B residue 1376 TYR Chi-restraints excluded: chain B residue 1398 ILE Chi-restraints excluded: chain B residue 1408 CYS Chi-restraints excluded: chain B residue 1414 ILE Chi-restraints excluded: chain B residue 1506 SER Chi-restraints excluded: chain B residue 1523 ASP Chi-restraints excluded: chain B residue 1541 GLU Chi-restraints excluded: chain B residue 1594 ILE Chi-restraints excluded: chain B residue 1644 SER Chi-restraints excluded: chain B residue 1738 SER Chi-restraints excluded: chain B residue 1757 LEU Chi-restraints excluded: chain B residue 1779 THR Chi-restraints excluded: chain B residue 1830 PHE Chi-restraints excluded: chain B residue 1854 LEU Chi-restraints excluded: chain B residue 1916 ILE Chi-restraints excluded: chain B residue 1934 SER Chi-restraints excluded: chain B residue 2072 SER Chi-restraints excluded: chain B residue 2096 ILE Chi-restraints excluded: chain B residue 2118 TRP Chi-restraints excluded: chain B residue 2208 MET Chi-restraints excluded: chain B residue 2234 SER Chi-restraints excluded: chain B residue 2247 ASP Chi-restraints excluded: chain B residue 2263 SER Chi-restraints excluded: chain B residue 2276 LEU Chi-restraints excluded: chain B residue 2443 THR Chi-restraints excluded: chain B residue 2499 LYS Chi-restraints excluded: chain B residue 2540 SER Chi-restraints excluded: chain B residue 2550 MET Chi-restraints excluded: chain B residue 2608 LEU Chi-restraints excluded: chain B residue 2632 LEU Chi-restraints excluded: chain B residue 2704 GLU Chi-restraints excluded: chain B residue 2810 ILE Chi-restraints excluded: chain B residue 2841 SER Chi-restraints excluded: chain B residue 2855 VAL Chi-restraints excluded: chain B residue 2917 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 526 random chunks: chunk 521 optimal weight: 2.9990 chunk 274 optimal weight: 9.9990 chunk 22 optimal weight: 0.9990 chunk 420 optimal weight: 0.6980 chunk 199 optimal weight: 7.9990 chunk 263 optimal weight: 10.0000 chunk 402 optimal weight: 7.9990 chunk 406 optimal weight: 0.0370 chunk 184 optimal weight: 0.8980 chunk 313 optimal weight: 7.9990 chunk 230 optimal weight: 0.7980 overall best weight: 0.6860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.126220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.100708 restraints weight = 73999.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.100506 restraints weight = 60207.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.101161 restraints weight = 63610.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.102135 restraints weight = 45742.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.102286 restraints weight = 41129.064| |-----------------------------------------------------------------------------| r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.5169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 42680 Z= 0.115 Angle : 0.554 11.699 57824 Z= 0.275 Chirality : 0.038 0.179 6630 Planarity : 0.004 0.046 7372 Dihedral : 5.190 78.716 5794 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 2.74 % Allowed : 20.91 % Favored : 76.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.74 (0.12), residues: 5192 helix: 2.14 (0.09), residues: 3716 sheet: -0.54 (0.63), residues: 66 loop : -1.58 (0.17), residues: 1410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A2286 TYR 0.016 0.001 TYR A1017 PHE 0.015 0.001 PHE B2546 TRP 0.013 0.001 TRP B1002 HIS 0.010 0.001 HIS A 120 Details of bonding type rmsd covalent geometry : bond 0.00268 (42678) covalent geometry : angle 0.55398 (57820) SS BOND : bond 0.00384 ( 2) SS BOND : angle 0.86181 ( 4) hydrogen bonds : bond 0.03415 ( 2587) hydrogen bonds : angle 3.58507 ( 7695) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10384 Ramachandran restraints generated. 5192 Oldfield, 0 Emsley, 5192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10384 Ramachandran restraints generated. 5192 Oldfield, 0 Emsley, 5192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 575 residues out of total 4562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 450 time to evaluate : 1.572 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 145 TYR cc_start: 0.7199 (t80) cc_final: 0.6986 (t80) REVERT: A 149 ASP cc_start: 0.7384 (t0) cc_final: 0.7018 (m-30) REVERT: A 163 GLU cc_start: 0.5859 (pm20) cc_final: 0.5603 (pm20) REVERT: A 230 MET cc_start: 0.8562 (tpt) cc_final: 0.7976 (mtm) REVERT: A 267 MET cc_start: 0.8495 (mmm) cc_final: 0.7936 (mpp) REVERT: A 272 PHE cc_start: 0.8740 (t80) cc_final: 0.8485 (t80) REVERT: A 328 ARG cc_start: 0.8009 (OUTLIER) cc_final: 0.7721 (ttp-170) REVERT: A 448 ARG cc_start: 0.8258 (OUTLIER) cc_final: 0.7961 (mtp85) REVERT: A 555 LYS cc_start: 0.8588 (OUTLIER) cc_final: 0.8305 (ptmt) REVERT: A 632 HIS cc_start: 0.8236 (OUTLIER) cc_final: 0.7666 (p90) REVERT: A 674 GLN cc_start: 0.7951 (tm-30) cc_final: 0.7581 (tm-30) REVERT: A 755 MET cc_start: 0.8035 (tpp) cc_final: 0.7423 (tpt) REVERT: A 1002 TRP cc_start: 0.8665 (OUTLIER) cc_final: 0.7792 (p-90) REVERT: A 1119 PHE cc_start: 0.9063 (t80) cc_final: 0.8820 (t80) REVERT: A 1376 TYR cc_start: 0.4693 (OUTLIER) cc_final: 0.3081 (m-80) REVERT: A 1412 ARG cc_start: 0.7602 (mtt90) cc_final: 0.7192 (mmt90) REVERT: A 1719 SER cc_start: 0.8944 (m) cc_final: 0.8625 (p) REVERT: A 1757 LEU cc_start: 0.8267 (OUTLIER) cc_final: 0.8056 (tt) REVERT: A 1789 LYS cc_start: 0.8440 (mppt) cc_final: 0.8030 (tptp) REVERT: A 1925 ASP cc_start: 0.7462 (t0) cc_final: 0.7260 (t0) REVERT: A 2276 LEU cc_start: 0.8907 (OUTLIER) cc_final: 0.8644 (mp) REVERT: A 2303 LEU cc_start: 0.8931 (mt) cc_final: 0.8723 (tp) REVERT: A 2546 PHE cc_start: 0.8083 (t80) cc_final: 0.7607 (t80) REVERT: A 2550 MET cc_start: 0.7772 (OUTLIER) cc_final: 0.6779 (mmm) REVERT: A 2608 LEU cc_start: 0.8870 (OUTLIER) cc_final: 0.8645 (mt) REVERT: A 2925 ASN cc_start: 0.8239 (m-40) cc_final: 0.7894 (m-40) REVERT: B 145 TYR cc_start: 0.7174 (t80) cc_final: 0.6959 (t80) REVERT: B 149 ASP cc_start: 0.7385 (t0) cc_final: 0.7042 (m-30) REVERT: B 163 GLU cc_start: 0.5855 (pm20) cc_final: 0.5603 (pm20) REVERT: B 230 MET cc_start: 0.8565 (tpt) cc_final: 0.7981 (mtm) REVERT: B 267 MET cc_start: 0.8489 (mmm) cc_final: 0.7928 (mpp) REVERT: B 272 PHE cc_start: 0.8724 (t80) cc_final: 0.8466 (t80) REVERT: B 328 ARG cc_start: 0.7803 (OUTLIER) cc_final: 0.7440 (ttm110) REVERT: B 555 LYS cc_start: 0.8583 (OUTLIER) cc_final: 0.8287 (ptmt) REVERT: B 674 GLN cc_start: 0.8220 (tm-30) cc_final: 0.7782 (tm-30) REVERT: B 755 MET cc_start: 0.8016 (tpp) cc_final: 0.7408 (tpt) REVERT: B 1002 TRP cc_start: 0.8666 (OUTLIER) cc_final: 0.7796 (p-90) REVERT: B 1119 PHE cc_start: 0.9087 (t80) cc_final: 0.8854 (t80) REVERT: B 1376 TYR cc_start: 0.4694 (OUTLIER) cc_final: 0.3096 (m-80) REVERT: B 1412 ARG cc_start: 0.7604 (mtt90) cc_final: 0.7194 (mmt90) REVERT: B 1719 SER cc_start: 0.8943 (m) cc_final: 0.8626 (p) REVERT: B 1757 LEU cc_start: 0.8274 (OUTLIER) cc_final: 0.8059 (tt) REVERT: B 1789 LYS cc_start: 0.8440 (mppt) cc_final: 0.8036 (tptp) REVERT: B 1925 ASP cc_start: 0.7464 (t0) cc_final: 0.7261 (t0) REVERT: B 2276 LEU cc_start: 0.8902 (OUTLIER) cc_final: 0.8645 (mp) REVERT: B 2546 PHE cc_start: 0.8055 (t80) cc_final: 0.7441 (t80) REVERT: B 2550 MET cc_start: 0.7816 (OUTLIER) cc_final: 0.6841 (mmm) REVERT: B 2608 LEU cc_start: 0.8875 (OUTLIER) cc_final: 0.8650 (mt) REVERT: B 2925 ASN cc_start: 0.8262 (m-40) cc_final: 0.7909 (m-40) outliers start: 125 outliers final: 96 residues processed: 550 average time/residue: 0.2462 time to fit residues: 228.6495 Evaluate side-chains 530 residues out of total 4562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 416 time to evaluate : 1.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 328 ARG Chi-restraints excluded: chain A residue 448 ARG Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain A residue 555 LYS Chi-restraints excluded: chain A residue 582 ILE Chi-restraints excluded: chain A residue 587 SER Chi-restraints excluded: chain A residue 632 HIS Chi-restraints excluded: chain A residue 637 THR Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 852 TYR Chi-restraints excluded: chain A residue 897 SER Chi-restraints excluded: chain A residue 980 GLU Chi-restraints excluded: chain A residue 1002 TRP Chi-restraints excluded: chain A residue 1040 SER Chi-restraints excluded: chain A residue 1054 SER Chi-restraints excluded: chain A residue 1217 LEU Chi-restraints excluded: chain A residue 1225 THR Chi-restraints excluded: chain A residue 1314 PHE Chi-restraints excluded: chain A residue 1324 PHE Chi-restraints excluded: chain A residue 1376 TYR Chi-restraints excluded: chain A residue 1397 THR Chi-restraints excluded: chain A residue 1398 ILE Chi-restraints excluded: chain A residue 1408 CYS Chi-restraints excluded: chain A residue 1414 ILE Chi-restraints excluded: chain A residue 1506 SER Chi-restraints excluded: chain A residue 1523 ASP Chi-restraints excluded: chain A residue 1541 GLU Chi-restraints excluded: chain A residue 1644 SER Chi-restraints excluded: chain A residue 1709 ASP Chi-restraints excluded: chain A residue 1728 SER Chi-restraints excluded: chain A residue 1738 SER Chi-restraints excluded: chain A residue 1757 LEU Chi-restraints excluded: chain A residue 1779 THR Chi-restraints excluded: chain A residue 1830 PHE Chi-restraints excluded: chain A residue 1916 ILE Chi-restraints excluded: chain A residue 2007 SER Chi-restraints excluded: chain A residue 2072 SER Chi-restraints excluded: chain A residue 2096 ILE Chi-restraints excluded: chain A residue 2118 TRP Chi-restraints excluded: chain A residue 2208 MET Chi-restraints excluded: chain A residue 2234 SER Chi-restraints excluded: chain A residue 2247 ASP Chi-restraints excluded: chain A residue 2263 SER Chi-restraints excluded: chain A residue 2276 LEU Chi-restraints excluded: chain A residue 2443 THR Chi-restraints excluded: chain A residue 2499 LYS Chi-restraints excluded: chain A residue 2540 SER Chi-restraints excluded: chain A residue 2550 MET Chi-restraints excluded: chain A residue 2608 LEU Chi-restraints excluded: chain A residue 2704 GLU Chi-restraints excluded: chain A residue 2841 SER Chi-restraints excluded: chain A residue 2855 VAL Chi-restraints excluded: chain A residue 2917 MET Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 328 ARG Chi-restraints excluded: chain B residue 522 LEU Chi-restraints excluded: chain B residue 538 SER Chi-restraints excluded: chain B residue 555 LYS Chi-restraints excluded: chain B residue 582 ILE Chi-restraints excluded: chain B residue 637 THR Chi-restraints excluded: chain B residue 641 LEU Chi-restraints excluded: chain B residue 852 TYR Chi-restraints excluded: chain B residue 980 GLU Chi-restraints excluded: chain B residue 1002 TRP Chi-restraints excluded: chain B residue 1040 SER Chi-restraints excluded: chain B residue 1054 SER Chi-restraints excluded: chain B residue 1139 ILE Chi-restraints excluded: chain B residue 1217 LEU Chi-restraints excluded: chain B residue 1225 THR Chi-restraints excluded: chain B residue 1314 PHE Chi-restraints excluded: chain B residue 1324 PHE Chi-restraints excluded: chain B residue 1376 TYR Chi-restraints excluded: chain B residue 1397 THR Chi-restraints excluded: chain B residue 1398 ILE Chi-restraints excluded: chain B residue 1408 CYS Chi-restraints excluded: chain B residue 1414 ILE Chi-restraints excluded: chain B residue 1506 SER Chi-restraints excluded: chain B residue 1523 ASP Chi-restraints excluded: chain B residue 1541 GLU Chi-restraints excluded: chain B residue 1640 SER Chi-restraints excluded: chain B residue 1644 SER Chi-restraints excluded: chain B residue 1709 ASP Chi-restraints excluded: chain B residue 1728 SER Chi-restraints excluded: chain B residue 1738 SER Chi-restraints excluded: chain B residue 1757 LEU Chi-restraints excluded: chain B residue 1779 THR Chi-restraints excluded: chain B residue 1830 PHE Chi-restraints excluded: chain B residue 1854 LEU Chi-restraints excluded: chain B residue 2007 SER Chi-restraints excluded: chain B residue 2072 SER Chi-restraints excluded: chain B residue 2096 ILE Chi-restraints excluded: chain B residue 2118 TRP Chi-restraints excluded: chain B residue 2208 MET Chi-restraints excluded: chain B residue 2234 SER Chi-restraints excluded: chain B residue 2247 ASP Chi-restraints excluded: chain B residue 2263 SER Chi-restraints excluded: chain B residue 2276 LEU Chi-restraints excluded: chain B residue 2443 THR Chi-restraints excluded: chain B residue 2499 LYS Chi-restraints excluded: chain B residue 2540 SER Chi-restraints excluded: chain B residue 2550 MET Chi-restraints excluded: chain B residue 2608 LEU Chi-restraints excluded: chain B residue 2704 GLU Chi-restraints excluded: chain B residue 2841 SER Chi-restraints excluded: chain B residue 2855 VAL Chi-restraints excluded: chain B residue 2917 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 526 random chunks: chunk 409 optimal weight: 6.9990 chunk 265 optimal weight: 4.9990 chunk 341 optimal weight: 1.9990 chunk 39 optimal weight: 8.9990 chunk 487 optimal weight: 4.9990 chunk 103 optimal weight: 3.9990 chunk 157 optimal weight: 0.0370 chunk 79 optimal weight: 0.9980 chunk 168 optimal weight: 0.3980 chunk 327 optimal weight: 2.9990 chunk 261 optimal weight: 0.7980 overall best weight: 0.8460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 407 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.125852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.100332 restraints weight = 73758.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.100194 restraints weight = 59586.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.101004 restraints weight = 67749.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.101353 restraints weight = 47152.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.101789 restraints weight = 43169.984| |-----------------------------------------------------------------------------| r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.5247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 42680 Z= 0.121 Angle : 0.565 11.761 57824 Z= 0.280 Chirality : 0.039 0.186 6630 Planarity : 0.004 0.046 7372 Dihedral : 5.091 78.181 5788 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 2.56 % Allowed : 21.28 % Favored : 76.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.76 (0.12), residues: 5192 helix: 2.16 (0.09), residues: 3718 sheet: -0.58 (0.61), residues: 66 loop : -1.57 (0.17), residues: 1408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B2286 TYR 0.016 0.001 TYR A1017 PHE 0.013 0.001 PHE B1211 TRP 0.013 0.001 TRP B1002 HIS 0.011 0.001 HIS B 120 Details of bonding type rmsd covalent geometry : bond 0.00285 (42678) covalent geometry : angle 0.56536 (57820) SS BOND : bond 0.00372 ( 2) SS BOND : angle 0.93252 ( 4) hydrogen bonds : bond 0.03481 ( 2587) hydrogen bonds : angle 3.59940 ( 7695) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10384 Ramachandran restraints generated. 5192 Oldfield, 0 Emsley, 5192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10384 Ramachandran restraints generated. 5192 Oldfield, 0 Emsley, 5192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 543 residues out of total 4562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 426 time to evaluate : 1.994 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 149 ASP cc_start: 0.7389 (t0) cc_final: 0.6959 (m-30) REVERT: A 230 MET cc_start: 0.8585 (tpt) cc_final: 0.8021 (mtm) REVERT: A 267 MET cc_start: 0.8504 (mmm) cc_final: 0.7949 (mpp) REVERT: A 272 PHE cc_start: 0.8729 (t80) cc_final: 0.8485 (t80) REVERT: A 301 TRP cc_start: 0.8174 (m100) cc_final: 0.7486 (m100) REVERT: A 632 HIS cc_start: 0.8184 (OUTLIER) cc_final: 0.7616 (p90) REVERT: A 674 GLN cc_start: 0.8010 (tm-30) cc_final: 0.7583 (tm-30) REVERT: A 755 MET cc_start: 0.8016 (tpp) cc_final: 0.7419 (tpt) REVERT: A 1002 TRP cc_start: 0.8653 (OUTLIER) cc_final: 0.7878 (p-90) REVERT: A 1119 PHE cc_start: 0.9046 (t80) cc_final: 0.8812 (t80) REVERT: A 1376 TYR cc_start: 0.4778 (OUTLIER) cc_final: 0.3128 (m-80) REVERT: A 1412 ARG cc_start: 0.7690 (mtt90) cc_final: 0.7268 (mmt90) REVERT: A 1719 SER cc_start: 0.8874 (m) cc_final: 0.8655 (p) REVERT: A 1757 LEU cc_start: 0.8300 (OUTLIER) cc_final: 0.8085 (tt) REVERT: A 1789 LYS cc_start: 0.8432 (mppt) cc_final: 0.8017 (tptp) REVERT: A 1925 ASP cc_start: 0.7466 (t0) cc_final: 0.7262 (t0) REVERT: A 2276 LEU cc_start: 0.8916 (OUTLIER) cc_final: 0.8647 (mp) REVERT: A 2303 LEU cc_start: 0.8934 (mt) cc_final: 0.8720 (tp) REVERT: A 2546 PHE cc_start: 0.8095 (t80) cc_final: 0.7628 (t80) REVERT: A 2550 MET cc_start: 0.7773 (OUTLIER) cc_final: 0.6777 (mmm) REVERT: A 2608 LEU cc_start: 0.8878 (OUTLIER) cc_final: 0.8658 (mt) REVERT: A 2925 ASN cc_start: 0.8253 (m-40) cc_final: 0.7892 (m110) REVERT: B 149 ASP cc_start: 0.7390 (t0) cc_final: 0.6980 (m-30) REVERT: B 230 MET cc_start: 0.8581 (tpt) cc_final: 0.8026 (mtm) REVERT: B 267 MET cc_start: 0.8493 (mmm) cc_final: 0.7931 (mpp) REVERT: B 272 PHE cc_start: 0.8718 (t80) cc_final: 0.8473 (t80) REVERT: B 301 TRP cc_start: 0.8167 (m100) cc_final: 0.7486 (m100) REVERT: B 555 LYS cc_start: 0.8595 (OUTLIER) cc_final: 0.8295 (ptmt) REVERT: B 674 GLN cc_start: 0.8279 (tm-30) cc_final: 0.7596 (tm-30) REVERT: B 755 MET cc_start: 0.7999 (tpp) cc_final: 0.7436 (tpt) REVERT: B 761 MET cc_start: 0.7072 (tpt) cc_final: 0.6772 (tpt) REVERT: B 1002 TRP cc_start: 0.8653 (OUTLIER) cc_final: 0.7884 (p-90) REVERT: B 1119 PHE cc_start: 0.9075 (t80) cc_final: 0.8844 (t80) REVERT: B 1376 TYR cc_start: 0.4800 (OUTLIER) cc_final: 0.3143 (m-80) REVERT: B 1412 ARG cc_start: 0.7675 (mtt90) cc_final: 0.7258 (mmt90) REVERT: B 1719 SER cc_start: 0.8874 (m) cc_final: 0.8657 (p) REVERT: B 1757 LEU cc_start: 0.8310 (OUTLIER) cc_final: 0.8089 (tt) REVERT: B 1789 LYS cc_start: 0.8434 (mppt) cc_final: 0.8017 (tptp) REVERT: B 2276 LEU cc_start: 0.8915 (OUTLIER) cc_final: 0.8645 (mp) REVERT: B 2546 PHE cc_start: 0.8093 (t80) cc_final: 0.7562 (t80) REVERT: B 2550 MET cc_start: 0.7804 (OUTLIER) cc_final: 0.6811 (mmm) REVERT: B 2608 LEU cc_start: 0.8886 (OUTLIER) cc_final: 0.8662 (mt) REVERT: B 2925 ASN cc_start: 0.8253 (m-40) cc_final: 0.7882 (m110) outliers start: 117 outliers final: 98 residues processed: 522 average time/residue: 0.2352 time to fit residues: 208.9214 Evaluate side-chains 521 residues out of total 4562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 409 time to evaluate : 1.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain A residue 582 ILE Chi-restraints excluded: chain A residue 587 SER Chi-restraints excluded: chain A residue 632 HIS Chi-restraints excluded: chain A residue 637 THR Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 852 TYR Chi-restraints excluded: chain A residue 897 SER Chi-restraints excluded: chain A residue 980 GLU Chi-restraints excluded: chain A residue 1002 TRP Chi-restraints excluded: chain A residue 1040 SER Chi-restraints excluded: chain A residue 1054 SER Chi-restraints excluded: chain A residue 1217 LEU Chi-restraints excluded: chain A residue 1225 THR Chi-restraints excluded: chain A residue 1314 PHE Chi-restraints excluded: chain A residue 1324 PHE Chi-restraints excluded: chain A residue 1376 TYR Chi-restraints excluded: chain A residue 1397 THR Chi-restraints excluded: chain A residue 1398 ILE Chi-restraints excluded: chain A residue 1408 CYS Chi-restraints excluded: chain A residue 1506 SER Chi-restraints excluded: chain A residue 1523 ASP Chi-restraints excluded: chain A residue 1541 GLU Chi-restraints excluded: chain A residue 1594 ILE Chi-restraints excluded: chain A residue 1640 SER Chi-restraints excluded: chain A residue 1644 SER Chi-restraints excluded: chain A residue 1709 ASP Chi-restraints excluded: chain A residue 1728 SER Chi-restraints excluded: chain A residue 1738 SER Chi-restraints excluded: chain A residue 1757 LEU Chi-restraints excluded: chain A residue 1779 THR Chi-restraints excluded: chain A residue 1830 PHE Chi-restraints excluded: chain A residue 1916 ILE Chi-restraints excluded: chain A residue 2007 SER Chi-restraints excluded: chain A residue 2072 SER Chi-restraints excluded: chain A residue 2096 ILE Chi-restraints excluded: chain A residue 2118 TRP Chi-restraints excluded: chain A residue 2208 MET Chi-restraints excluded: chain A residue 2234 SER Chi-restraints excluded: chain A residue 2247 ASP Chi-restraints excluded: chain A residue 2257 SER Chi-restraints excluded: chain A residue 2263 SER Chi-restraints excluded: chain A residue 2276 LEU Chi-restraints excluded: chain A residue 2443 THR Chi-restraints excluded: chain A residue 2499 LYS Chi-restraints excluded: chain A residue 2540 SER Chi-restraints excluded: chain A residue 2550 MET Chi-restraints excluded: chain A residue 2608 LEU Chi-restraints excluded: chain A residue 2704 GLU Chi-restraints excluded: chain A residue 2841 SER Chi-restraints excluded: chain A residue 2855 VAL Chi-restraints excluded: chain A residue 2917 MET Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 522 LEU Chi-restraints excluded: chain B residue 538 SER Chi-restraints excluded: chain B residue 555 LYS Chi-restraints excluded: chain B residue 582 ILE Chi-restraints excluded: chain B residue 637 THR Chi-restraints excluded: chain B residue 641 LEU Chi-restraints excluded: chain B residue 852 TYR Chi-restraints excluded: chain B residue 897 SER Chi-restraints excluded: chain B residue 980 GLU Chi-restraints excluded: chain B residue 1002 TRP Chi-restraints excluded: chain B residue 1040 SER Chi-restraints excluded: chain B residue 1054 SER Chi-restraints excluded: chain B residue 1139 ILE Chi-restraints excluded: chain B residue 1217 LEU Chi-restraints excluded: chain B residue 1225 THR Chi-restraints excluded: chain B residue 1314 PHE Chi-restraints excluded: chain B residue 1324 PHE Chi-restraints excluded: chain B residue 1376 TYR Chi-restraints excluded: chain B residue 1397 THR Chi-restraints excluded: chain B residue 1398 ILE Chi-restraints excluded: chain B residue 1408 CYS Chi-restraints excluded: chain B residue 1506 SER Chi-restraints excluded: chain B residue 1523 ASP Chi-restraints excluded: chain B residue 1541 GLU Chi-restraints excluded: chain B residue 1640 SER Chi-restraints excluded: chain B residue 1644 SER Chi-restraints excluded: chain B residue 1709 ASP Chi-restraints excluded: chain B residue 1728 SER Chi-restraints excluded: chain B residue 1738 SER Chi-restraints excluded: chain B residue 1757 LEU Chi-restraints excluded: chain B residue 1779 THR Chi-restraints excluded: chain B residue 1830 PHE Chi-restraints excluded: chain B residue 2007 SER Chi-restraints excluded: chain B residue 2072 SER Chi-restraints excluded: chain B residue 2096 ILE Chi-restraints excluded: chain B residue 2118 TRP Chi-restraints excluded: chain B residue 2208 MET Chi-restraints excluded: chain B residue 2234 SER Chi-restraints excluded: chain B residue 2247 ASP Chi-restraints excluded: chain B residue 2263 SER Chi-restraints excluded: chain B residue 2276 LEU Chi-restraints excluded: chain B residue 2443 THR Chi-restraints excluded: chain B residue 2499 LYS Chi-restraints excluded: chain B residue 2540 SER Chi-restraints excluded: chain B residue 2550 MET Chi-restraints excluded: chain B residue 2608 LEU Chi-restraints excluded: chain B residue 2704 GLU Chi-restraints excluded: chain B residue 2841 SER Chi-restraints excluded: chain B residue 2855 VAL Chi-restraints excluded: chain B residue 2917 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 526 random chunks: chunk 113 optimal weight: 7.9990 chunk 297 optimal weight: 3.9990 chunk 94 optimal weight: 3.9990 chunk 201 optimal weight: 0.2980 chunk 264 optimal weight: 4.9990 chunk 328 optimal weight: 0.0470 chunk 314 optimal weight: 0.1980 chunk 399 optimal weight: 0.0470 chunk 33 optimal weight: 3.9990 chunk 287 optimal weight: 9.9990 chunk 452 optimal weight: 3.9990 overall best weight: 0.9178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1256 GLN A2544 GLN B1256 GLN B2544 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.125353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.099874 restraints weight = 74457.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.100046 restraints weight = 60451.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.100992 restraints weight = 57827.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.101254 restraints weight = 43412.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.101518 restraints weight = 41298.045| |-----------------------------------------------------------------------------| r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.5322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 42680 Z= 0.123 Angle : 0.560 11.720 57824 Z= 0.279 Chirality : 0.039 0.186 6630 Planarity : 0.004 0.044 7372 Dihedral : 5.015 77.404 5782 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 2.83 % Allowed : 21.11 % Favored : 76.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.83 (0.12), residues: 5192 helix: 2.20 (0.09), residues: 3712 sheet: -0.60 (0.61), residues: 66 loop : -1.47 (0.17), residues: 1414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A2286 TYR 0.015 0.001 TYR A1017 PHE 0.013 0.001 PHE B1211 TRP 0.013 0.001 TRP B1002 HIS 0.012 0.001 HIS A 824 Details of bonding type rmsd covalent geometry : bond 0.00292 (42678) covalent geometry : angle 0.56041 (57820) SS BOND : bond 0.00404 ( 2) SS BOND : angle 0.86245 ( 4) hydrogen bonds : bond 0.03495 ( 2587) hydrogen bonds : angle 3.59391 ( 7695) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6654.43 seconds wall clock time: 116 minutes 8.31 seconds (6968.31 seconds total)