Starting phenix.real_space_refine on Thu Mar 5 10:00:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6skz_10232/03_2026/6skz_10232.cif Found real_map, /net/cci-nas-00/data/ceres_data/6skz_10232/03_2026/6skz_10232.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6skz_10232/03_2026/6skz_10232.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6skz_10232/03_2026/6skz_10232.map" model { file = "/net/cci-nas-00/data/ceres_data/6skz_10232/03_2026/6skz_10232.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6skz_10232/03_2026/6skz_10232.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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 3 5.49 5 Mg 1 5.21 5 S 95 5.16 5 C 13302 2.51 5 N 3643 2.21 5 O 3886 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 138 residue(s): 0.03s 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: 20930 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} Time building chain proxies: 4.91, per 1000 atoms: 0.23 Number of scatterers: 20930 At special positions: 0 Unit cell: (108.018, 138.729, 205.446, 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 95 16.00 P 3 15.00 Mg 1 11.99 O 3886 8.00 N 3643 7.00 C 13302 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A1408 " - pdb=" SG CYS A1447 " 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: 1.41 Conformation dependent library (CDL) restraints added in 984.3 milliseconds 5192 Ramachandran restraints generated. 2596 Oldfield, 0 Emsley, 2596 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5064 Finding SS restraints... Secondary structure from input PDB file: 145 helices and 4 sheets defined 73.6% alpha, 1.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.09 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: 5.306A 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: 3.592A pdb=" N LEU A 771 " --> pdb=" O THR A 767 " (cutoff:3.500A) Processing helix chain 'A' and resid 783 through 803 removed outlier: 3.854A 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: 3.764A 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: 3.618A pdb=" N LEU A 988 " --> pdb=" O CYS A 984 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N PHE A 998 " --> pdb=" O ILE A 994 " (cutoff:3.500A) Processing helix chain 'A' and resid 998 through 1003 removed outlier: 4.744A pdb=" N TRP A1002 " --> pdb=" O PHE A 998 " (cutoff:3.500A) removed outlier: 3.835A 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: 3.672A 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: 4.218A 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: 3.719A 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: 3.622A pdb=" N ILE A1313 " --> pdb=" O THR A1309 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHE A1314 " --> pdb=" O PHE A1310 " (cutoff:3.500A) Processing helix chain 'A' and resid 1318 through 1324 removed outlier: 3.796A 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: 3.793A 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: 3.648A 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: 3.600A 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: 3.780A 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: 3.712A 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: 4.421A 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: 3.611A pdb=" N SER A1994 " --> pdb=" O LEU A1990 " (cutoff:3.500A) removed outlier: 3.623A 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: 3.954A pdb=" N PHE A2015 " --> pdb=" O LEU A2011 " (cutoff:3.500A) removed outlier: 3.773A 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: 3.844A pdb=" N VAL A2055 " --> pdb=" O GLU A2051 " (cutoff:3.500A) Processing helix chain 'A' and resid 2076 through 2098 removed outlier: 3.629A 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: 3.919A pdb=" N GLN A2268 " --> pdb=" O PRO A2264 " (cutoff:3.500A) removed outlier: 3.684A 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: 3.586A 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: 3.551A 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: 3.618A 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: 3.515A 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 sheet with id=AA1, first strand: chain 'A' and resid 372 through 373 removed outlier: 3.552A 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: 4.914A 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: 4.914A 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: 6.706A 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 1298 hydrogen bonds defined for protein. 3849 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: 4.96 Time building geometry restraints manager: 1.91 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: 7232 1.36 - 1.51: 6915 1.51 - 1.65: 7043 1.65 - 1.80: 130 1.80 - 1.95: 19 Bond restraints: 21339 Sorted by residual: bond pdb=" C ILE A1084 " pdb=" N PRO A1085 " ideal model delta sigma weight residual 1.337 1.364 -0.027 9.80e-03 1.04e+04 7.68e+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 7.39e+00 bond pdb=" CB THR A2740 " pdb=" CG2 THR A2740 " ideal model delta sigma weight residual 1.521 1.438 0.083 3.30e-02 9.18e+02 6.35e+00 bond pdb=" CB THR A2743 " pdb=" CG2 THR A2743 " ideal model delta sigma weight residual 1.521 1.440 0.081 3.30e-02 9.18e+02 6.02e+00 bond pdb=" CB VAL A2256 " pdb=" CG1 VAL A2256 " ideal model delta sigma weight residual 1.521 1.454 0.067 3.30e-02 9.18e+02 4.08e+00 ... (remaining 21334 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.84: 28553 2.84 - 5.68: 330 5.68 - 8.52: 23 8.52 - 11.36: 2 11.36 - 14.20: 2 Bond angle restraints: 28910 Sorted by residual: angle pdb=" N SER A2007 " pdb=" CA SER A2007 " pdb=" CB SER A2007 " ideal model delta sigma weight residual 110.49 98.97 11.52 1.69e+00 3.50e-01 4.65e+01 angle pdb=" N GLY A 162 " pdb=" CA GLY A 162 " pdb=" C GLY A 162 " ideal model delta sigma weight residual 115.64 107.75 7.89 1.46e+00 4.69e-01 2.92e+01 angle pdb=" C GLY A2006 " pdb=" N SER A2007 " pdb=" CA SER A2007 " ideal model delta sigma weight residual 121.54 128.53 -6.99 1.91e+00 2.74e-01 1.34e+01 angle pdb=" N TYR A1332 " pdb=" CA TYR A1332 " pdb=" C TYR A1332 " ideal model delta sigma weight residual 114.56 110.04 4.52 1.27e+00 6.20e-01 1.27e+01 angle pdb=" C ASP A2005 " pdb=" N GLY A2006 " pdb=" CA GLY A2006 " ideal model delta sigma weight residual 121.41 128.09 -6.68 1.96e+00 2.60e-01 1.16e+01 ... (remaining 28905 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 11686 17.94 - 35.87: 1013 35.87 - 53.81: 245 53.81 - 71.75: 53 71.75 - 89.68: 18 Dihedral angle restraints: 13015 sinusoidal: 5258 harmonic: 7757 Sorted by residual: 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 -144.06 -35.94 0 5.00e+00 4.00e-02 5.17e+01 dihedral pdb=" CA MET A 259 " pdb=" C MET A 259 " pdb=" N LYS A 260 " pdb=" CA LYS A 260 " ideal model delta harmonic sigma weight residual 180.00 -147.20 -32.80 0 5.00e+00 4.00e-02 4.30e+01 dihedral pdb=" CA ALA A 159 " pdb=" C ALA A 159 " pdb=" N LEU A 160 " pdb=" CA LEU A 160 " ideal model delta harmonic sigma weight residual 180.00 -147.59 -32.41 0 5.00e+00 4.00e-02 4.20e+01 ... (remaining 13012 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 1897 0.039 - 0.078: 1081 0.078 - 0.117: 268 0.117 - 0.156: 64 0.156 - 0.196: 5 Chirality restraints: 3315 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 0.20 2.00e-01 2.50e+01 9.56e-01 chirality pdb=" CB ILE A 233 " pdb=" CA ILE A 233 " pdb=" CG1 ILE A 233 " pdb=" CG2 ILE A 233 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.19 2.00e-01 2.50e+01 9.37e-01 chirality pdb=" CA ILE A2004 " pdb=" N ILE A2004 " pdb=" C ILE A2004 " pdb=" CB ILE A2004 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 6.92e-01 ... (remaining 3312 not shown) Planarity restraints: 3686 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A1854 " -0.051 5.00e-02 4.00e+02 7.79e-02 9.70e+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 A 383 " -0.048 5.00e-02 4.00e+02 7.33e-02 8.61e+00 pdb=" N PRO A 384 " 0.127 5.00e-02 4.00e+02 pdb=" CA PRO A 384 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO A 384 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA SER A2007 " 0.013 2.00e-02 2.50e+03 2.54e-02 6.48e+00 pdb=" C SER A2007 " -0.044 2.00e-02 2.50e+03 pdb=" O SER A2007 " 0.016 2.00e-02 2.50e+03 pdb=" N SER A2008 " 0.015 2.00e-02 2.50e+03 ... (remaining 3683 not shown) Histogram of nonbonded interaction distances: 1.87 - 2.48: 106 2.48 - 3.08: 14925 3.08 - 3.69: 30374 3.69 - 4.29: 45146 4.29 - 4.90: 76620 Nonbonded interactions: 167171 Sorted by model distance: nonbonded pdb=" OD1 ASP A2012 " pdb=" OG SER A2034 " model vdw 1.872 3.040 nonbonded pdb=" NZ LYS A1528 " pdb=" OD1 ASN A1573 " model vdw 1.963 3.120 nonbonded pdb=" ND2 ASN A2702 " pdb=" OE1 GLU A2704 " model vdw 1.998 3.120 nonbonded pdb=" OH TYR A 852 " pdb=" OE1 GLN A 934 " model vdw 2.109 3.040 nonbonded pdb=" O SER A1024 " pdb=" OG SER A1029 " model vdw 2.144 3.040 ... (remaining 167166 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.020 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: 0.050 Extract box with map and model: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 20.870 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 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 21340 Z= 0.442 Angle : 0.817 14.198 28912 Z= 0.442 Chirality : 0.048 0.196 3315 Planarity : 0.005 0.078 3686 Dihedral : 14.876 89.682 7948 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.43 % Favored : 92.49 % 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 (0.14), residues: 2596 helix: -1.48 (0.10), residues: 1837 sheet: -0.93 (0.91), residues: 31 loop : -3.27 (0.19), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A2173 TYR 0.026 0.003 TYR A1295 PHE 0.020 0.003 PHE A 791 TRP 0.025 0.003 TRP A2735 HIS 0.007 0.001 HIS A1512 Details of bonding type rmsd covalent geometry : bond 0.01062 (21339) covalent geometry : angle 0.81579 (28910) SS BOND : bond 0.01703 ( 1) SS BOND : angle 4.47344 ( 2) hydrogen bonds : bond 0.14626 ( 1294) hydrogen bonds : angle 6.17005 ( 3849) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5192 Ramachandran restraints generated. 2596 Oldfield, 0 Emsley, 2596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5192 Ramachandran restraints generated. 2596 Oldfield, 0 Emsley, 2596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 538 residues out of total 2281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 415 time to evaluate : 0.722 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: A 293 GLN cc_start: 0.6900 (OUTLIER) cc_final: 0.6336 (mt0) REVERT: A 325 TYR cc_start: 0.7078 (OUTLIER) cc_final: 0.5980 (m-10) REVERT: A 328 ARG cc_start: 0.7308 (ptt180) cc_final: 0.6787 (ptm160) REVERT: A 395 HIS cc_start: 0.8557 (OUTLIER) cc_final: 0.7955 (t-90) REVERT: A 522 LEU cc_start: 0.8068 (OUTLIER) cc_final: 0.7407 (pp) REVERT: A 549 LEU cc_start: 0.8680 (OUTLIER) cc_final: 0.8351 (tt) REVERT: A 607 GLN cc_start: 0.8543 (OUTLIER) cc_final: 0.8121 (mp10) REVERT: A 660 LEU cc_start: 0.8859 (OUTLIER) cc_final: 0.8333 (mt) REVERT: A 826 ILE cc_start: 0.8677 (pt) cc_final: 0.8471 (pt) REVERT: A 1022 LYS cc_start: 0.8043 (ttpt) cc_final: 0.7839 (tptp) REVERT: A 1221 ARG cc_start: 0.7744 (OUTLIER) cc_final: 0.7163 (mtp180) REVERT: A 1342 LYS cc_start: 0.6634 (tttt) cc_final: 0.6182 (mtmt) REVERT: A 1376 TYR cc_start: 0.7491 (OUTLIER) cc_final: 0.4939 (m-80) REVERT: A 1406 HIS cc_start: 0.7957 (OUTLIER) cc_final: 0.7093 (t70) REVERT: A 1708 ASN cc_start: 0.7015 (m-40) cc_final: 0.5878 (t0) REVERT: A 1854 LEU cc_start: 0.8881 (OUTLIER) cc_final: 0.8674 (tm) REVERT: A 1968 ARG cc_start: 0.7756 (ttm-80) cc_final: 0.6483 (mmt-90) REVERT: A 2126 ASP cc_start: 0.7020 (OUTLIER) cc_final: 0.6581 (m-30) REVERT: A 2608 LEU cc_start: 0.8670 (OUTLIER) cc_final: 0.8439 (mt) REVERT: A 2751 MET cc_start: 0.8023 (mmp) cc_final: 0.7381 (mmp) REVERT: A 2826 ASP cc_start: 0.7959 (t0) cc_final: 0.7450 (t0) outliers start: 123 outliers final: 76 residues processed: 524 average time/residue: 0.1672 time to fit residues: 130.1333 Evaluate side-chains 307 residues out of total 2281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 218 time to evaluate : 0.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ILE Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 31 ASP Chi-restraints excluded: chain A residue 56 TYR Chi-restraints excluded: chain A residue 66 CYS Chi-restraints excluded: chain A residue 109 ILE 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 261 ILE Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 293 GLN 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 395 HIS Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 480 GLU Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 502 SER Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 602 PHE 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 658 GLN Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 741 SER Chi-restraints excluded: chain A residue 754 SER Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain A residue 809 ASN Chi-restraints excluded: chain A residue 834 LYS Chi-restraints excluded: chain A residue 855 SER Chi-restraints excluded: chain A residue 896 LEU Chi-restraints excluded: chain A residue 907 THR Chi-restraints excluded: chain A residue 909 LEU Chi-restraints excluded: chain A residue 915 ASP Chi-restraints excluded: chain A residue 916 ILE Chi-restraints excluded: chain A residue 941 GLU Chi-restraints excluded: chain A residue 962 LEU Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 983 CYS Chi-restraints excluded: chain A residue 998 PHE Chi-restraints excluded: chain A residue 1002 TRP Chi-restraints excluded: chain A residue 1009 ILE Chi-restraints excluded: chain A residue 1024 SER Chi-restraints excluded: chain A residue 1065 LEU Chi-restraints excluded: chain A residue 1068 ILE Chi-restraints excluded: chain A residue 1098 ASP Chi-restraints excluded: chain A residue 1104 LEU Chi-restraints excluded: chain A residue 1162 SER Chi-restraints excluded: chain A residue 1200 ASN Chi-restraints excluded: chain A residue 1215 SER Chi-restraints excluded: chain A residue 1221 ARG Chi-restraints excluded: chain A residue 1230 ILE Chi-restraints excluded: chain A residue 1254 LEU Chi-restraints excluded: chain A residue 1255 VAL Chi-restraints excluded: chain A residue 1314 PHE Chi-restraints excluded: chain A residue 1320 ILE Chi-restraints excluded: chain A residue 1324 PHE Chi-restraints excluded: chain A residue 1376 TYR Chi-restraints excluded: chain A residue 1380 ASN Chi-restraints excluded: chain A residue 1397 THR Chi-restraints excluded: chain A residue 1398 ILE Chi-restraints excluded: chain A residue 1399 HIS Chi-restraints excluded: chain A residue 1406 HIS Chi-restraints excluded: chain A residue 1408 CYS Chi-restraints excluded: chain A residue 1410 VAL Chi-restraints excluded: chain A residue 1411 LEU Chi-restraints excluded: chain A residue 1414 ILE Chi-restraints excluded: chain A residue 1427 SER Chi-restraints excluded: chain A residue 1443 VAL Chi-restraints excluded: chain A residue 1568 ASP Chi-restraints excluded: chain A residue 1575 LEU Chi-restraints excluded: chain A residue 1585 LEU Chi-restraints excluded: chain A residue 1608 ASP Chi-restraints excluded: chain A residue 1743 VAL Chi-restraints excluded: chain A residue 1854 LEU Chi-restraints excluded: chain A residue 2126 ASP Chi-restraints excluded: chain A residue 2443 THR Chi-restraints excluded: chain A residue 2465 MET Chi-restraints excluded: chain A residue 2514 SER Chi-restraints excluded: chain A residue 2608 LEU Chi-restraints excluded: chain A residue 2805 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 263 random chunks: chunk 197 optimal weight: 0.9980 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 0.8980 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 0.6980 chunk 244 optimal weight: 0.5980 chunk 183 optimal weight: 1.9990 chunk 111 optimal weight: 6.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 376 ASN A 394 HIS A 395 HIS A 450 HIS A 492 HIS A 519 HIS A 528 GLN A 612 HIS A 632 HIS A 658 GLN A 670 HIS A 934 GLN A1028 ASN A1062 GLN A1096 HIS A1161 HIS A1175 GLN A1242 GLN A1512 HIS A1761 ASN A1764 GLN A2179 GLN A2239 GLN A2255 GLN A2294 GLN A2354 GLN A2356 GLN A2446 GLN A2518 HIS ** A2544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2624 GLN A2678 HIS A2754 HIS A2925 ASN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.144020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.119085 restraints weight = 31558.233| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 1.99 r_work: 0.3257 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3125 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.2241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 21340 Z= 0.152 Angle : 0.608 11.756 28912 Z= 0.314 Chirality : 0.041 0.299 3315 Planarity : 0.005 0.060 3686 Dihedral : 9.303 79.908 3036 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.39 % Favored : 95.57 % Rotamer: Outliers : 4.65 % Allowed : 14.20 % Favored : 81.15 % 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: -0.82 (0.16), residues: 2596 helix: 0.28 (0.12), residues: 1874 sheet: -0.22 (0.96), residues: 31 loop : -2.78 (0.21), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 926 TYR 0.017 0.001 TYR A 145 PHE 0.019 0.002 PHE A 791 TRP 0.015 0.002 TRP A1002 HIS 0.009 0.001 HIS A1512 Details of bonding type rmsd covalent geometry : bond 0.00340 (21339) covalent geometry : angle 0.60789 (28910) SS BOND : bond 0.00188 ( 1) SS BOND : angle 0.19678 ( 2) hydrogen bonds : bond 0.04841 ( 1294) hydrogen bonds : angle 4.29621 ( 3849) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5192 Ramachandran restraints generated. 2596 Oldfield, 0 Emsley, 2596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5192 Ramachandran restraints generated. 2596 Oldfield, 0 Emsley, 2596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 2281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 259 time to evaluate : 0.774 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: A 267 MET cc_start: 0.8111 (mmt) cc_final: 0.7790 (mmt) REVERT: A 325 TYR cc_start: 0.7026 (OUTLIER) cc_final: 0.5466 (m-10) REVERT: A 328 ARG cc_start: 0.7508 (ptt180) cc_final: 0.6900 (ptt90) REVERT: A 415 TYR cc_start: 0.7466 (t80) cc_final: 0.7004 (t80) REVERT: A 522 LEU cc_start: 0.7021 (OUTLIER) cc_final: 0.6405 (pp) REVERT: A 660 LEU cc_start: 0.8792 (OUTLIER) cc_final: 0.8374 (mt) REVERT: A 677 MET cc_start: 0.7487 (ttt) cc_final: 0.7283 (ttp) REVERT: A 842 LYS cc_start: 0.8874 (mtmt) cc_final: 0.8594 (mtmm) REVERT: A 846 LYS cc_start: 0.8424 (mttt) cc_final: 0.7639 (mmtt) REVERT: A 1015 ASP cc_start: 0.7958 (m-30) cc_final: 0.7753 (m-30) REVERT: A 1022 LYS cc_start: 0.8078 (ttpt) cc_final: 0.7546 (tptp) REVERT: A 1122 PHE cc_start: 0.8777 (t80) cc_final: 0.8441 (t80) REVERT: A 1286 MET cc_start: 0.8065 (mmm) cc_final: 0.7581 (tpt) REVERT: A 1342 LYS cc_start: 0.7011 (tttt) cc_final: 0.6316 (mtmt) REVERT: A 1376 TYR cc_start: 0.7026 (OUTLIER) cc_final: 0.4011 (m-80) REVERT: A 1405 LEU cc_start: 0.8156 (OUTLIER) cc_final: 0.7860 (mp) REVERT: A 1406 HIS cc_start: 0.7608 (OUTLIER) cc_final: 0.6721 (t70) REVERT: A 1585 LEU cc_start: 0.8653 (OUTLIER) cc_final: 0.8060 (mp) REVERT: A 1707 ASP cc_start: 0.7976 (m-30) cc_final: 0.7660 (m-30) REVERT: A 1708 ASN cc_start: 0.7435 (m-40) cc_final: 0.6136 (t0) REVERT: A 1854 LEU cc_start: 0.8725 (OUTLIER) cc_final: 0.8475 (tm) REVERT: A 2101 ASP cc_start: 0.8176 (m-30) cc_final: 0.7931 (p0) REVERT: A 2220 MET cc_start: 0.8580 (mtm) cc_final: 0.8166 (mtm) REVERT: A 2239 GLN cc_start: 0.7780 (OUTLIER) cc_final: 0.7565 (pt0) REVERT: A 2751 MET cc_start: 0.8521 (mmp) cc_final: 0.8200 (mmp) REVERT: A 2826 ASP cc_start: 0.8464 (t0) cc_final: 0.8162 (t0) outliers start: 106 outliers final: 65 residues processed: 349 average time/residue: 0.1558 time to fit residues: 84.0080 Evaluate side-chains 279 residues out of total 2281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 205 time to evaluate : 0.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ILE Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 31 ASP Chi-restraints excluded: chain A residue 56 TYR Chi-restraints excluded: chain A residue 69 ILE Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 325 TYR Chi-restraints excluded: chain A residue 362 GLU Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 480 GLU Chi-restraints excluded: chain A residue 502 SER Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 607 GLN Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 658 GLN Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain A residue 793 ILE Chi-restraints excluded: chain A residue 809 ASN Chi-restraints excluded: chain A residue 834 LYS Chi-restraints excluded: chain A residue 896 LEU Chi-restraints excluded: chain A residue 962 LEU Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 998 PHE Chi-restraints excluded: chain A residue 1002 TRP Chi-restraints excluded: chain A residue 1024 SER Chi-restraints excluded: chain A residue 1071 ASP Chi-restraints excluded: chain A residue 1098 ASP Chi-restraints excluded: chain A residue 1104 LEU Chi-restraints excluded: chain A residue 1221 ARG Chi-restraints excluded: chain A residue 1254 LEU Chi-restraints excluded: chain A residue 1255 VAL Chi-restraints excluded: chain A residue 1314 PHE Chi-restraints excluded: chain A residue 1320 ILE Chi-restraints excluded: chain A residue 1324 PHE Chi-restraints excluded: chain A residue 1376 TYR Chi-restraints excluded: chain A residue 1380 ASN Chi-restraints excluded: chain A residue 1397 THR Chi-restraints excluded: chain A residue 1398 ILE Chi-restraints excluded: chain A residue 1399 HIS Chi-restraints excluded: chain A residue 1405 LEU Chi-restraints excluded: chain A residue 1406 HIS Chi-restraints excluded: chain A residue 1410 VAL Chi-restraints excluded: chain A residue 1411 LEU Chi-restraints excluded: chain A residue 1414 ILE Chi-restraints excluded: chain A residue 1568 ASP Chi-restraints excluded: chain A residue 1575 LEU Chi-restraints excluded: chain A residue 1585 LEU Chi-restraints excluded: chain A residue 1591 VAL Chi-restraints excluded: chain A residue 1737 LEU Chi-restraints excluded: chain A residue 1837 GLU Chi-restraints excluded: chain A residue 1854 LEU Chi-restraints excluded: chain A residue 1934 SER Chi-restraints excluded: chain A residue 2052 LEU Chi-restraints excluded: chain A residue 2118 TRP Chi-restraints excluded: chain A residue 2135 GLU Chi-restraints excluded: chain A residue 2234 SER Chi-restraints excluded: chain A residue 2239 GLN Chi-restraints excluded: chain A residue 2247 ASP Chi-restraints excluded: chain A residue 2443 THR Chi-restraints excluded: chain A residue 2482 VAL Chi-restraints excluded: chain A residue 2656 SER Chi-restraints excluded: chain A residue 2792 VAL Chi-restraints excluded: chain A residue 2805 VAL Chi-restraints excluded: chain A residue 2855 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 263 random chunks: chunk 87 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 4 optimal weight: 6.9990 chunk 116 optimal weight: 0.7980 chunk 142 optimal weight: 0.3980 chunk 124 optimal weight: 2.9990 chunk 137 optimal weight: 4.9990 chunk 212 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 143 optimal weight: 1.9990 chunk 147 optimal weight: 0.5980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 120 HIS A 528 GLN A 839 HIS A1000 ASN A1245 GLN A1369 HIS A2239 GLN A2544 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.142937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.118940 restraints weight = 31468.220| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 1.90 r_work: 0.3267 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3143 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.2661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 21340 Z= 0.169 Angle : 0.590 10.035 28912 Z= 0.300 Chirality : 0.040 0.209 3315 Planarity : 0.004 0.050 3686 Dihedral : 8.350 79.271 2976 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.47 % Favored : 95.49 % Rotamer: Outliers : 4.38 % Allowed : 16.22 % Favored : 79.40 % 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: -0.01 (0.17), residues: 2596 helix: 0.90 (0.12), residues: 1868 sheet: -0.32 (0.99), residues: 33 loop : -2.48 (0.22), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A2365 TYR 0.024 0.002 TYR A 145 PHE 0.016 0.001 PHE A 791 TRP 0.014 0.002 TRP A1002 HIS 0.006 0.001 HIS A 824 Details of bonding type rmsd covalent geometry : bond 0.00400 (21339) covalent geometry : angle 0.58968 (28910) SS BOND : bond 0.01667 ( 1) SS BOND : angle 0.37063 ( 2) hydrogen bonds : bond 0.04625 ( 1294) hydrogen bonds : angle 4.09908 ( 3849) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5192 Ramachandran restraints generated. 2596 Oldfield, 0 Emsley, 2596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5192 Ramachandran restraints generated. 2596 Oldfield, 0 Emsley, 2596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 2281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 223 time to evaluate : 0.840 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 36 LEU cc_start: 0.7384 (mm) cc_final: 0.7137 (mt) REVERT: A 325 TYR cc_start: 0.7082 (OUTLIER) cc_final: 0.5385 (m-10) REVERT: A 328 ARG cc_start: 0.7494 (ptt180) cc_final: 0.6960 (ptt90) REVERT: A 415 TYR cc_start: 0.7585 (t80) cc_final: 0.7101 (t80) REVERT: A 522 LEU cc_start: 0.7344 (OUTLIER) cc_final: 0.6769 (pp) REVERT: A 660 LEU cc_start: 0.8831 (OUTLIER) cc_final: 0.8451 (mt) REVERT: A 677 MET cc_start: 0.7774 (ttt) cc_final: 0.7536 (ttp) REVERT: A 755 MET cc_start: 0.7414 (tpp) cc_final: 0.7041 (tpp) REVERT: A 802 LEU cc_start: 0.8218 (OUTLIER) cc_final: 0.7823 (mm) REVERT: A 842 LYS cc_start: 0.8928 (mtmt) cc_final: 0.8680 (mtmm) REVERT: A 846 LYS cc_start: 0.8455 (mttt) cc_final: 0.7740 (mmtt) REVERT: A 1015 ASP cc_start: 0.8029 (m-30) cc_final: 0.7737 (m-30) REVERT: A 1022 LYS cc_start: 0.8115 (ttpt) cc_final: 0.7677 (tptp) REVERT: A 1286 MET cc_start: 0.7967 (mmm) cc_final: 0.7523 (tpt) REVERT: A 1342 LYS cc_start: 0.7011 (tttt) cc_final: 0.6330 (mtmt) REVERT: A 1376 TYR cc_start: 0.7192 (OUTLIER) cc_final: 0.4235 (m-80) REVERT: A 1707 ASP cc_start: 0.7961 (m-30) cc_final: 0.7725 (m-30) REVERT: A 1708 ASN cc_start: 0.7498 (m-40) cc_final: 0.6173 (t0) REVERT: A 1755 ARG cc_start: 0.7778 (mtm110) cc_final: 0.7534 (mtm-85) REVERT: A 1854 LEU cc_start: 0.8850 (OUTLIER) cc_final: 0.8624 (tm) REVERT: A 2104 GLU cc_start: 0.7822 (mt-10) cc_final: 0.7421 (mt-10) REVERT: A 2220 MET cc_start: 0.8610 (mtm) cc_final: 0.8212 (mtm) REVERT: A 2365 ARG cc_start: 0.7655 (ttp80) cc_final: 0.7035 (ttp80) REVERT: A 2751 MET cc_start: 0.8310 (mmp) cc_final: 0.8052 (mmp) REVERT: A 2826 ASP cc_start: 0.8360 (t0) cc_final: 0.8089 (t0) outliers start: 100 outliers final: 67 residues processed: 312 average time/residue: 0.1380 time to fit residues: 67.2964 Evaluate side-chains 275 residues out of total 2281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 202 time to evaluate : 0.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ASP Chi-restraints excluded: chain A residue 56 TYR Chi-restraints excluded: chain A residue 69 ILE Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 325 TYR Chi-restraints excluded: chain A residue 362 GLU Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 480 GLU Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain A residue 607 GLN Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 658 GLN Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain A residue 793 ILE Chi-restraints excluded: chain A residue 802 LEU Chi-restraints excluded: chain A residue 809 ASN Chi-restraints excluded: chain A residue 834 LYS Chi-restraints excluded: chain A residue 896 LEU Chi-restraints excluded: chain A residue 897 SER Chi-restraints excluded: chain A residue 962 LEU Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1002 TRP Chi-restraints excluded: chain A residue 1024 SER Chi-restraints excluded: chain A residue 1068 ILE Chi-restraints excluded: chain A residue 1071 ASP Chi-restraints excluded: chain A residue 1080 ILE Chi-restraints excluded: chain A residue 1104 LEU Chi-restraints excluded: chain A residue 1145 ILE Chi-restraints excluded: chain A residue 1221 ARG Chi-restraints excluded: chain A residue 1232 MET Chi-restraints excluded: chain A residue 1255 VAL Chi-restraints excluded: chain A residue 1314 PHE Chi-restraints excluded: chain A residue 1320 ILE 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 1399 HIS Chi-restraints excluded: chain A residue 1411 LEU Chi-restraints excluded: chain A residue 1414 ILE Chi-restraints excluded: chain A residue 1568 ASP Chi-restraints excluded: chain A residue 1575 LEU Chi-restraints excluded: chain A residue 1591 VAL Chi-restraints excluded: chain A residue 1713 LEU Chi-restraints excluded: chain A residue 1737 LEU Chi-restraints excluded: chain A residue 1779 THR Chi-restraints excluded: chain A residue 1837 GLU Chi-restraints excluded: chain A residue 1854 LEU Chi-restraints excluded: chain A residue 1918 LEU Chi-restraints excluded: chain A residue 1934 SER Chi-restraints excluded: chain A residue 2052 LEU Chi-restraints excluded: chain A residue 2118 TRP Chi-restraints excluded: chain A residue 2234 SER Chi-restraints excluded: chain A residue 2247 ASP Chi-restraints excluded: chain A residue 2318 LEU Chi-restraints excluded: chain A residue 2349 LEU Chi-restraints excluded: chain A residue 2443 THR Chi-restraints excluded: chain A residue 2482 VAL Chi-restraints excluded: chain A residue 2656 SER Chi-restraints excluded: chain A residue 2666 ASN Chi-restraints excluded: chain A residue 2792 VAL Chi-restraints excluded: chain A residue 2805 VAL Chi-restraints excluded: chain A residue 2813 THR Chi-restraints excluded: chain A residue 2855 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 263 random chunks: chunk 31 optimal weight: 2.9990 chunk 192 optimal weight: 0.7980 chunk 110 optimal weight: 0.8980 chunk 82 optimal weight: 6.9990 chunk 162 optimal weight: 0.5980 chunk 214 optimal weight: 0.9980 chunk 145 optimal weight: 0.8980 chunk 36 optimal weight: 3.9990 chunk 225 optimal weight: 3.9990 chunk 72 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 635 HIS A1161 HIS A1245 GLN A1380 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.143964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.119105 restraints weight = 31321.393| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 1.86 r_work: 0.3275 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3151 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.2984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 21340 Z= 0.133 Angle : 0.546 9.452 28912 Z= 0.276 Chirality : 0.039 0.199 3315 Planarity : 0.004 0.046 3686 Dihedral : 7.730 79.788 2957 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.04 % Favored : 95.92 % Rotamer: Outliers : 4.30 % Allowed : 17.01 % Favored : 78.69 % 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: 0.52 (0.17), residues: 2596 helix: 1.28 (0.12), residues: 1878 sheet: -0.27 (0.99), residues: 33 loop : -2.30 (0.22), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A2314 TYR 0.025 0.001 TYR A 145 PHE 0.016 0.001 PHE A1122 TRP 0.014 0.001 TRP A1002 HIS 0.004 0.001 HIS A 839 Details of bonding type rmsd covalent geometry : bond 0.00308 (21339) covalent geometry : angle 0.54601 (28910) SS BOND : bond 0.00697 ( 1) SS BOND : angle 0.02260 ( 2) hydrogen bonds : bond 0.03994 ( 1294) hydrogen bonds : angle 3.88220 ( 3849) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5192 Ramachandran restraints generated. 2596 Oldfield, 0 Emsley, 2596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5192 Ramachandran restraints generated. 2596 Oldfield, 0 Emsley, 2596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 2281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 224 time to evaluate : 0.728 Fit side-chains revert: symmetry clash REVERT: A 325 TYR cc_start: 0.6889 (OUTLIER) cc_final: 0.5199 (m-10) REVERT: A 328 ARG cc_start: 0.7423 (ptt180) cc_final: 0.6532 (ptm160) REVERT: A 415 TYR cc_start: 0.7472 (t80) cc_final: 0.7014 (t80) REVERT: A 522 LEU cc_start: 0.7274 (OUTLIER) cc_final: 0.6720 (pp) REVERT: A 564 LEU cc_start: 0.8064 (OUTLIER) cc_final: 0.7598 (pp) REVERT: A 660 LEU cc_start: 0.8848 (OUTLIER) cc_final: 0.8522 (mt) REVERT: A 682 ARG cc_start: 0.7162 (mtp180) cc_final: 0.6678 (mtt90) REVERT: A 802 LEU cc_start: 0.8085 (OUTLIER) cc_final: 0.7702 (mm) REVERT: A 846 LYS cc_start: 0.8466 (mttt) cc_final: 0.7748 (mmtt) REVERT: A 1015 ASP cc_start: 0.7962 (m-30) cc_final: 0.7505 (m-30) REVERT: A 1022 LYS cc_start: 0.8087 (ttpt) cc_final: 0.7633 (tptp) REVERT: A 1221 ARG cc_start: 0.8130 (OUTLIER) cc_final: 0.7266 (tpp-160) REVERT: A 1242 GLN cc_start: 0.6936 (mm-40) cc_final: 0.6711 (mm-40) REVERT: A 1286 MET cc_start: 0.7878 (mmm) cc_final: 0.7466 (tpt) REVERT: A 1342 LYS cc_start: 0.7052 (tttt) cc_final: 0.6349 (mtmt) REVERT: A 1376 TYR cc_start: 0.7027 (OUTLIER) cc_final: 0.4090 (m-80) REVERT: A 1405 LEU cc_start: 0.8062 (OUTLIER) cc_final: 0.7722 (mp) REVERT: A 1854 LEU cc_start: 0.8741 (OUTLIER) cc_final: 0.8501 (tm) REVERT: A 2104 GLU cc_start: 0.7585 (mt-10) cc_final: 0.7353 (mp0) REVERT: A 2220 MET cc_start: 0.8505 (mtm) cc_final: 0.8147 (mtm) REVERT: A 2365 ARG cc_start: 0.7691 (ttp80) cc_final: 0.7115 (ttp80) REVERT: A 2826 ASP cc_start: 0.8343 (t0) cc_final: 0.8081 (t0) outliers start: 98 outliers final: 63 residues processed: 306 average time/residue: 0.1513 time to fit residues: 71.1517 Evaluate side-chains 280 residues out of total 2281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 208 time to evaluate : 0.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ASP Chi-restraints excluded: chain A residue 56 TYR Chi-restraints excluded: chain A residue 69 ILE Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 325 TYR Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 480 GLU Chi-restraints excluded: chain A residue 492 HIS Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 607 GLN Chi-restraints excluded: chain A residue 637 THR Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 658 GLN Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain A residue 793 ILE Chi-restraints excluded: chain A residue 802 LEU Chi-restraints excluded: chain A residue 894 ILE Chi-restraints excluded: chain A residue 896 LEU Chi-restraints excluded: chain A residue 897 SER Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain A residue 962 LEU Chi-restraints excluded: chain A residue 983 CYS Chi-restraints excluded: chain A residue 1002 TRP Chi-restraints excluded: chain A residue 1025 LEU Chi-restraints excluded: chain A residue 1071 ASP Chi-restraints excluded: chain A residue 1080 ILE Chi-restraints excluded: chain A residue 1104 LEU Chi-restraints excluded: chain A residue 1145 ILE Chi-restraints excluded: chain A residue 1221 ARG Chi-restraints excluded: chain A residue 1232 MET Chi-restraints excluded: chain A residue 1255 VAL Chi-restraints excluded: chain A residue 1314 PHE Chi-restraints excluded: chain A residue 1320 ILE 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 1405 LEU Chi-restraints excluded: chain A residue 1408 CYS Chi-restraints excluded: chain A residue 1414 ILE Chi-restraints excluded: chain A residue 1568 ASP Chi-restraints excluded: chain A residue 1575 LEU Chi-restraints excluded: chain A residue 1591 VAL Chi-restraints excluded: chain A residue 1628 GLU Chi-restraints excluded: chain A residue 1684 SER Chi-restraints excluded: chain A residue 1837 GLU Chi-restraints excluded: chain A residue 1854 LEU Chi-restraints excluded: chain A residue 1918 LEU Chi-restraints excluded: chain A residue 2058 MET Chi-restraints excluded: chain A residue 2096 ILE Chi-restraints excluded: chain A residue 2118 TRP Chi-restraints excluded: chain A residue 2234 SER Chi-restraints excluded: chain A residue 2247 ASP Chi-restraints excluded: chain A residue 2349 LEU Chi-restraints excluded: chain A residue 2443 THR Chi-restraints excluded: chain A residue 2567 ASN Chi-restraints excluded: chain A residue 2656 SER Chi-restraints excluded: chain A residue 2666 ASN Chi-restraints excluded: chain A residue 2715 GLU Chi-restraints excluded: chain A residue 2805 VAL Chi-restraints excluded: chain A residue 2855 VAL Chi-restraints excluded: chain A residue 2917 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 263 random chunks: chunk 226 optimal weight: 5.9990 chunk 78 optimal weight: 4.9990 chunk 143 optimal weight: 1.9990 chunk 186 optimal weight: 3.9990 chunk 144 optimal weight: 1.9990 chunk 212 optimal weight: 3.9990 chunk 215 optimal weight: 0.6980 chunk 240 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 40 optimal weight: 3.9990 chunk 14 optimal weight: 0.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 528 GLN A 664 ASN A1106 HIS A1245 GLN A1380 ASN A1870 ASN A2552 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.142180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.117855 restraints weight = 31362.075| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 2.01 r_work: 0.3240 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3115 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.3102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 21340 Z= 0.176 Angle : 0.576 9.602 28912 Z= 0.289 Chirality : 0.040 0.161 3315 Planarity : 0.004 0.044 3686 Dihedral : 7.311 78.915 2941 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.70 % Favored : 95.26 % Rotamer: Outliers : 4.65 % Allowed : 17.19 % Favored : 78.17 % 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: 0.71 (0.17), residues: 2596 helix: 1.39 (0.12), residues: 1875 sheet: -0.43 (0.94), residues: 33 loop : -2.08 (0.23), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A2524 TYR 0.024 0.002 TYR A 145 PHE 0.015 0.001 PHE A 602 TRP 0.014 0.002 TRP A2118 HIS 0.004 0.001 HIS A 839 Details of bonding type rmsd covalent geometry : bond 0.00421 (21339) covalent geometry : angle 0.57570 (28910) SS BOND : bond 0.00411 ( 1) SS BOND : angle 0.11063 ( 2) hydrogen bonds : bond 0.04372 ( 1294) hydrogen bonds : angle 3.90462 ( 3849) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5192 Ramachandran restraints generated. 2596 Oldfield, 0 Emsley, 2596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5192 Ramachandran restraints generated. 2596 Oldfield, 0 Emsley, 2596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 2281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 217 time to evaluate : 0.822 Fit side-chains revert: symmetry clash REVERT: A 36 LEU cc_start: 0.7570 (mm) cc_final: 0.7271 (mt) REVERT: A 123 GLN cc_start: 0.7460 (tp-100) cc_final: 0.7078 (tm-30) REVERT: A 325 TYR cc_start: 0.6848 (OUTLIER) cc_final: 0.5213 (m-10) REVERT: A 328 ARG cc_start: 0.7405 (ptt180) cc_final: 0.6536 (ptm160) REVERT: A 522 LEU cc_start: 0.7153 (OUTLIER) cc_final: 0.6564 (pp) REVERT: A 528 GLN cc_start: 0.7472 (tt0) cc_final: 0.7126 (tt0) REVERT: A 660 LEU cc_start: 0.8835 (OUTLIER) cc_final: 0.8536 (mt) REVERT: A 682 ARG cc_start: 0.7174 (mtp180) cc_final: 0.6701 (mtt90) REVERT: A 755 MET cc_start: 0.7387 (tpp) cc_final: 0.7136 (tpp) REVERT: A 802 LEU cc_start: 0.8129 (OUTLIER) cc_final: 0.7661 (mm) REVERT: A 846 LYS cc_start: 0.8496 (mttt) cc_final: 0.7769 (mmtt) REVERT: A 1015 ASP cc_start: 0.7975 (m-30) cc_final: 0.7516 (m-30) REVERT: A 1022 LYS cc_start: 0.8157 (ttpt) cc_final: 0.7690 (tptp) REVERT: A 1221 ARG cc_start: 0.8107 (OUTLIER) cc_final: 0.7787 (ptp-170) REVERT: A 1242 GLN cc_start: 0.6937 (mm-40) cc_final: 0.6701 (mm-40) REVERT: A 1253 LYS cc_start: 0.8135 (tttt) cc_final: 0.7783 (ptmt) REVERT: A 1286 MET cc_start: 0.7878 (mmm) cc_final: 0.7502 (tpt) REVERT: A 1313 ILE cc_start: 0.8976 (OUTLIER) cc_final: 0.8716 (pp) REVERT: A 1322 LYS cc_start: 0.6877 (tptt) cc_final: 0.6420 (pptt) REVERT: A 1342 LYS cc_start: 0.7079 (tttt) cc_final: 0.6366 (mtmt) REVERT: A 1376 TYR cc_start: 0.7006 (OUTLIER) cc_final: 0.4091 (m-80) REVERT: A 1405 LEU cc_start: 0.8066 (OUTLIER) cc_final: 0.7720 (mp) REVERT: A 1411 LEU cc_start: 0.9192 (OUTLIER) cc_final: 0.8668 (tt) REVERT: A 1854 LEU cc_start: 0.8789 (OUTLIER) cc_final: 0.8571 (tm) REVERT: A 2220 MET cc_start: 0.8623 (mtm) cc_final: 0.8262 (mtm) REVERT: A 2751 MET cc_start: 0.8333 (mmp) cc_final: 0.7901 (mmp) REVERT: A 2826 ASP cc_start: 0.8404 (t0) cc_final: 0.8144 (t0) outliers start: 106 outliers final: 79 residues processed: 309 average time/residue: 0.1414 time to fit residues: 68.7600 Evaluate side-chains 284 residues out of total 2281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 195 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ASP Chi-restraints excluded: chain A residue 56 TYR Chi-restraints excluded: chain A residue 69 ILE Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 312 MET 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 449 VAL Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 466 GLN Chi-restraints excluded: chain A residue 480 GLU Chi-restraints excluded: chain A residue 492 HIS Chi-restraints excluded: chain A residue 502 SER Chi-restraints excluded: chain A residue 521 SER Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain A residue 566 ASP Chi-restraints excluded: chain A residue 607 GLN Chi-restraints excluded: chain A residue 637 THR Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 658 GLN Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain A residue 793 ILE Chi-restraints excluded: chain A residue 802 LEU Chi-restraints excluded: chain A residue 809 ASN Chi-restraints excluded: chain A residue 894 ILE Chi-restraints excluded: chain A residue 896 LEU Chi-restraints excluded: chain A residue 897 SER Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain A residue 962 LEU Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 983 CYS Chi-restraints excluded: chain A residue 1002 TRP Chi-restraints excluded: chain A residue 1068 ILE Chi-restraints excluded: chain A residue 1071 ASP Chi-restraints excluded: chain A residue 1080 ILE Chi-restraints excluded: chain A residue 1104 LEU Chi-restraints excluded: chain A residue 1145 ILE Chi-restraints excluded: chain A residue 1221 ARG Chi-restraints excluded: chain A residue 1232 MET Chi-restraints excluded: chain A residue 1255 VAL Chi-restraints excluded: chain A residue 1313 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 1397 THR Chi-restraints excluded: chain A residue 1398 ILE Chi-restraints excluded: chain A residue 1405 LEU Chi-restraints excluded: chain A residue 1408 CYS Chi-restraints excluded: chain A residue 1411 LEU Chi-restraints excluded: chain A residue 1414 ILE Chi-restraints excluded: chain A residue 1568 ASP Chi-restraints excluded: chain A residue 1575 LEU Chi-restraints excluded: chain A residue 1591 VAL Chi-restraints excluded: chain A residue 1628 GLU Chi-restraints excluded: chain A residue 1684 SER Chi-restraints excluded: chain A residue 1777 ILE Chi-restraints excluded: chain A residue 1779 THR Chi-restraints excluded: chain A residue 1854 LEU Chi-restraints excluded: chain A residue 1918 LEU Chi-restraints excluded: chain A residue 1934 SER Chi-restraints excluded: chain A residue 2052 LEU Chi-restraints excluded: chain A residue 2058 MET Chi-restraints excluded: chain A residue 2096 ILE Chi-restraints excluded: chain A residue 2118 TRP Chi-restraints excluded: chain A residue 2234 SER Chi-restraints excluded: chain A residue 2244 SER Chi-restraints excluded: chain A residue 2247 ASP Chi-restraints excluded: chain A residue 2349 LEU Chi-restraints excluded: chain A residue 2443 THR Chi-restraints excluded: chain A residue 2516 VAL Chi-restraints excluded: chain A residue 2621 ILE Chi-restraints excluded: chain A residue 2656 SER Chi-restraints excluded: chain A residue 2666 ASN Chi-restraints excluded: chain A residue 2715 GLU Chi-restraints excluded: chain A residue 2792 VAL Chi-restraints excluded: chain A residue 2805 VAL Chi-restraints excluded: chain A residue 2813 THR Chi-restraints excluded: chain A residue 2855 VAL Chi-restraints excluded: chain A residue 2917 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 263 random chunks: chunk 151 optimal weight: 4.9990 chunk 149 optimal weight: 0.2980 chunk 201 optimal weight: 2.9990 chunk 128 optimal weight: 0.8980 chunk 169 optimal weight: 0.4980 chunk 248 optimal weight: 0.7980 chunk 108 optimal weight: 0.7980 chunk 134 optimal weight: 1.9990 chunk 220 optimal weight: 3.9990 chunk 135 optimal weight: 0.7980 chunk 249 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1245 GLN A1380 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.144457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.119709 restraints weight = 31074.940| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 1.86 r_work: 0.3285 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3159 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.3335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 21340 Z= 0.118 Angle : 0.529 9.648 28912 Z= 0.266 Chirality : 0.038 0.159 3315 Planarity : 0.004 0.043 3686 Dihedral : 7.100 79.191 2939 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 4.25 % Allowed : 17.89 % Favored : 77.86 % 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: 1.04 (0.17), residues: 2596 helix: 1.63 (0.12), residues: 1878 sheet: -0.24 (0.96), residues: 33 loop : -1.98 (0.23), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A2314 TYR 0.026 0.001 TYR A 145 PHE 0.018 0.001 PHE A1122 TRP 0.013 0.001 TRP A 301 HIS 0.004 0.001 HIS A 839 Details of bonding type rmsd covalent geometry : bond 0.00270 (21339) covalent geometry : angle 0.52935 (28910) SS BOND : bond 0.00260 ( 1) SS BOND : angle 0.43473 ( 2) hydrogen bonds : bond 0.03712 ( 1294) hydrogen bonds : angle 3.73972 ( 3849) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5192 Ramachandran restraints generated. 2596 Oldfield, 0 Emsley, 2596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5192 Ramachandran restraints generated. 2596 Oldfield, 0 Emsley, 2596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 2281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 233 time to evaluate : 0.805 Fit side-chains revert: symmetry clash REVERT: A 36 LEU cc_start: 0.7560 (mm) cc_final: 0.7246 (mt) REVERT: A 61 GLU cc_start: 0.7547 (pt0) cc_final: 0.7254 (pp20) REVERT: A 123 GLN cc_start: 0.7442 (tp-100) cc_final: 0.7113 (tm-30) REVERT: A 325 TYR cc_start: 0.6783 (OUTLIER) cc_final: 0.5216 (m-10) REVERT: A 328 ARG cc_start: 0.7389 (ptt180) cc_final: 0.6562 (ptm160) REVERT: A 522 LEU cc_start: 0.7172 (OUTLIER) cc_final: 0.6607 (pp) REVERT: A 564 LEU cc_start: 0.8128 (OUTLIER) cc_final: 0.7660 (pp) REVERT: A 660 LEU cc_start: 0.8790 (OUTLIER) cc_final: 0.8526 (mt) REVERT: A 682 ARG cc_start: 0.7186 (mtp180) cc_final: 0.6731 (mtt90) REVERT: A 755 MET cc_start: 0.7551 (tpp) cc_final: 0.7329 (tpp) REVERT: A 802 LEU cc_start: 0.8108 (OUTLIER) cc_final: 0.7679 (mm) REVERT: A 846 LYS cc_start: 0.8474 (mttt) cc_final: 0.7780 (mmtt) REVERT: A 1015 ASP cc_start: 0.7804 (m-30) cc_final: 0.7360 (m-30) REVERT: A 1022 LYS cc_start: 0.8096 (ttpt) cc_final: 0.7636 (tptp) REVERT: A 1221 ARG cc_start: 0.8127 (OUTLIER) cc_final: 0.7399 (tpp-160) REVERT: A 1224 GLN cc_start: 0.8586 (mt0) cc_final: 0.8356 (mt0) REVERT: A 1242 GLN cc_start: 0.6860 (mm-40) cc_final: 0.6628 (mm-40) REVERT: A 1322 LYS cc_start: 0.6840 (tptt) cc_final: 0.6427 (pptt) REVERT: A 1342 LYS cc_start: 0.7029 (tttt) cc_final: 0.6346 (mtmt) REVERT: A 1376 TYR cc_start: 0.6952 (OUTLIER) cc_final: 0.4001 (m-80) REVERT: A 1405 LEU cc_start: 0.8049 (OUTLIER) cc_final: 0.7714 (mp) REVERT: A 1411 LEU cc_start: 0.9197 (OUTLIER) cc_final: 0.8682 (tt) REVERT: A 1854 LEU cc_start: 0.8730 (OUTLIER) cc_final: 0.8482 (tm) REVERT: A 2220 MET cc_start: 0.8487 (mtm) cc_final: 0.8154 (mtm) REVERT: A 2751 MET cc_start: 0.8288 (mmp) cc_final: 0.7845 (mmp) REVERT: A 2826 ASP cc_start: 0.8347 (t0) cc_final: 0.8093 (t0) outliers start: 97 outliers final: 70 residues processed: 315 average time/residue: 0.1456 time to fit residues: 71.2588 Evaluate side-chains 288 residues out of total 2281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 208 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ASP Chi-restraints excluded: chain A residue 56 TYR Chi-restraints excluded: chain A residue 69 ILE Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 325 TYR Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 466 GLN Chi-restraints excluded: chain A residue 480 GLU Chi-restraints excluded: chain A residue 492 HIS Chi-restraints excluded: chain A residue 502 SER Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 566 ASP Chi-restraints excluded: chain A residue 607 GLN Chi-restraints excluded: chain A residue 637 THR Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 658 GLN Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain A residue 793 ILE Chi-restraints excluded: chain A residue 802 LEU Chi-restraints excluded: chain A residue 809 ASN Chi-restraints excluded: chain A residue 896 LEU Chi-restraints excluded: chain A residue 897 SER Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain A residue 962 LEU Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 983 CYS Chi-restraints excluded: chain A residue 1002 TRP Chi-restraints excluded: chain A residue 1025 LEU Chi-restraints excluded: chain A residue 1071 ASP Chi-restraints excluded: chain A residue 1221 ARG Chi-restraints excluded: chain A residue 1232 MET 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 1405 LEU Chi-restraints excluded: chain A residue 1408 CYS Chi-restraints excluded: chain A residue 1411 LEU Chi-restraints excluded: chain A residue 1414 ILE Chi-restraints excluded: chain A residue 1568 ASP Chi-restraints excluded: chain A residue 1575 LEU Chi-restraints excluded: chain A residue 1591 VAL Chi-restraints excluded: chain A residue 1628 GLU Chi-restraints excluded: chain A residue 1684 SER Chi-restraints excluded: chain A residue 1854 LEU Chi-restraints excluded: chain A residue 1918 LEU Chi-restraints excluded: chain A residue 2030 VAL Chi-restraints excluded: chain A residue 2045 SER Chi-restraints excluded: chain A residue 2054 THR Chi-restraints excluded: chain A residue 2058 MET Chi-restraints excluded: chain A residue 2096 ILE Chi-restraints excluded: chain A residue 2118 TRP Chi-restraints excluded: chain A residue 2135 GLU Chi-restraints excluded: chain A residue 2234 SER Chi-restraints excluded: chain A residue 2244 SER Chi-restraints excluded: chain A residue 2247 ASP Chi-restraints excluded: chain A residue 2349 LEU Chi-restraints excluded: chain A residue 2443 THR Chi-restraints excluded: chain A residue 2516 VAL Chi-restraints excluded: chain A residue 2621 ILE Chi-restraints excluded: chain A residue 2656 SER Chi-restraints excluded: chain A residue 2664 VAL Chi-restraints excluded: chain A residue 2666 ASN Chi-restraints excluded: chain A residue 2709 VAL Chi-restraints excluded: chain A residue 2715 GLU Chi-restraints excluded: chain A residue 2805 VAL Chi-restraints excluded: chain A residue 2855 VAL Chi-restraints excluded: chain A residue 2917 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 263 random chunks: chunk 99 optimal weight: 0.0010 chunk 157 optimal weight: 2.9990 chunk 201 optimal weight: 3.9990 chunk 224 optimal weight: 0.7980 chunk 234 optimal weight: 4.9990 chunk 214 optimal weight: 3.9990 chunk 184 optimal weight: 0.6980 chunk 41 optimal weight: 0.8980 chunk 130 optimal weight: 2.9990 chunk 207 optimal weight: 0.8980 chunk 62 optimal weight: 7.9990 overall best weight: 0.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1245 GLN A1380 ASN A1497 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.144270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.119447 restraints weight = 31499.596| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 1.98 r_work: 0.3267 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3138 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.3466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 21340 Z= 0.120 Angle : 0.535 10.244 28912 Z= 0.267 Chirality : 0.038 0.150 3315 Planarity : 0.004 0.042 3686 Dihedral : 6.871 79.275 2936 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 4.08 % Allowed : 18.76 % Favored : 77.16 % 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: 1.22 (0.17), residues: 2596 helix: 1.75 (0.12), residues: 1878 sheet: -0.22 (0.94), residues: 33 loop : -1.88 (0.23), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A2524 TYR 0.027 0.001 TYR A 145 PHE 0.011 0.001 PHE A2724 TRP 0.017 0.001 TRP A 355 HIS 0.004 0.001 HIS A 839 Details of bonding type rmsd covalent geometry : bond 0.00279 (21339) covalent geometry : angle 0.53487 (28910) SS BOND : bond 0.00293 ( 1) SS BOND : angle 0.39426 ( 2) hydrogen bonds : bond 0.03668 ( 1294) hydrogen bonds : angle 3.71042 ( 3849) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5192 Ramachandran restraints generated. 2596 Oldfield, 0 Emsley, 2596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5192 Ramachandran restraints generated. 2596 Oldfield, 0 Emsley, 2596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 2281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 226 time to evaluate : 0.790 Fit side-chains REVERT: A 36 LEU cc_start: 0.7496 (mm) cc_final: 0.7265 (mt) REVERT: A 61 GLU cc_start: 0.7612 (pt0) cc_final: 0.7234 (pp20) REVERT: A 100 LEU cc_start: 0.6899 (mm) cc_final: 0.6695 (mm) REVERT: A 123 GLN cc_start: 0.7425 (tp-100) cc_final: 0.7105 (tm-30) REVERT: A 170 ASP cc_start: 0.7557 (p0) cc_final: 0.7336 (p0) REVERT: A 325 TYR cc_start: 0.6753 (OUTLIER) cc_final: 0.5170 (m-10) REVERT: A 328 ARG cc_start: 0.7372 (ptt180) cc_final: 0.6524 (ptm160) REVERT: A 522 LEU cc_start: 0.7122 (OUTLIER) cc_final: 0.6537 (pp) REVERT: A 564 LEU cc_start: 0.8110 (OUTLIER) cc_final: 0.7626 (pp) REVERT: A 660 LEU cc_start: 0.8777 (OUTLIER) cc_final: 0.8497 (mt) REVERT: A 682 ARG cc_start: 0.7164 (mtp180) cc_final: 0.6713 (mtt90) REVERT: A 802 LEU cc_start: 0.7979 (OUTLIER) cc_final: 0.7572 (mm) REVERT: A 846 LYS cc_start: 0.8503 (mttt) cc_final: 0.7794 (mmtt) REVERT: A 1015 ASP cc_start: 0.7774 (m-30) cc_final: 0.7328 (m-30) REVERT: A 1022 LYS cc_start: 0.8093 (ttpt) cc_final: 0.7651 (tptp) REVERT: A 1221 ARG cc_start: 0.8189 (OUTLIER) cc_final: 0.7422 (tpp-160) REVERT: A 1224 GLN cc_start: 0.8607 (mt0) cc_final: 0.8361 (mt0) REVERT: A 1242 GLN cc_start: 0.6832 (mm-40) cc_final: 0.6588 (mm-40) REVERT: A 1322 LYS cc_start: 0.6790 (tptt) cc_final: 0.6389 (pptt) REVERT: A 1342 LYS cc_start: 0.7079 (tttt) cc_final: 0.6349 (mtmt) REVERT: A 1376 TYR cc_start: 0.6914 (OUTLIER) cc_final: 0.3885 (m-80) REVERT: A 1405 LEU cc_start: 0.8040 (OUTLIER) cc_final: 0.7709 (mp) REVERT: A 1411 LEU cc_start: 0.9194 (OUTLIER) cc_final: 0.8665 (tt) REVERT: A 1854 LEU cc_start: 0.8766 (OUTLIER) cc_final: 0.8511 (tm) REVERT: A 2220 MET cc_start: 0.8587 (mtm) cc_final: 0.8246 (mtm) REVERT: A 2365 ARG cc_start: 0.7679 (ttp80) cc_final: 0.7129 (ttp80) REVERT: A 2751 MET cc_start: 0.8319 (mmp) cc_final: 0.7973 (mmp) REVERT: A 2826 ASP cc_start: 0.8479 (t0) cc_final: 0.8210 (t0) outliers start: 93 outliers final: 77 residues processed: 304 average time/residue: 0.1449 time to fit residues: 68.8039 Evaluate side-chains 295 residues out of total 2281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 208 time to evaluate : 0.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ASP Chi-restraints excluded: chain A residue 56 TYR Chi-restraints excluded: chain A residue 69 ILE Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 325 TYR Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 466 GLN Chi-restraints excluded: chain A residue 480 GLU Chi-restraints excluded: chain A residue 492 HIS Chi-restraints excluded: chain A residue 502 SER Chi-restraints excluded: chain A residue 521 SER Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 566 ASP Chi-restraints excluded: chain A residue 607 GLN 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 658 GLN Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain A residue 793 ILE Chi-restraints excluded: chain A residue 802 LEU Chi-restraints excluded: chain A residue 809 ASN Chi-restraints excluded: chain A residue 896 LEU Chi-restraints excluded: chain A residue 897 SER Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain A residue 962 LEU Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 983 CYS Chi-restraints excluded: chain A residue 1002 TRP Chi-restraints excluded: chain A residue 1025 LEU Chi-restraints excluded: chain A residue 1068 ILE Chi-restraints excluded: chain A residue 1071 ASP Chi-restraints excluded: chain A residue 1160 THR Chi-restraints excluded: chain A residue 1183 GLN Chi-restraints excluded: chain A residue 1221 ARG Chi-restraints excluded: chain A residue 1232 MET 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 1405 LEU Chi-restraints excluded: chain A residue 1408 CYS Chi-restraints excluded: chain A residue 1411 LEU Chi-restraints excluded: chain A residue 1568 ASP Chi-restraints excluded: chain A residue 1575 LEU Chi-restraints excluded: chain A residue 1591 VAL Chi-restraints excluded: chain A residue 1628 GLU Chi-restraints excluded: chain A residue 1684 SER Chi-restraints excluded: chain A residue 1779 THR Chi-restraints excluded: chain A residue 1854 LEU Chi-restraints excluded: chain A residue 1918 LEU Chi-restraints excluded: chain A residue 1934 SER Chi-restraints excluded: chain A residue 2030 VAL Chi-restraints excluded: chain A residue 2045 SER Chi-restraints excluded: chain A residue 2052 LEU Chi-restraints excluded: chain A residue 2054 THR Chi-restraints excluded: chain A residue 2058 MET Chi-restraints excluded: chain A residue 2096 ILE Chi-restraints excluded: chain A residue 2118 TRP Chi-restraints excluded: chain A residue 2234 SER Chi-restraints excluded: chain A residue 2244 SER Chi-restraints excluded: chain A residue 2247 ASP Chi-restraints excluded: chain A residue 2349 LEU Chi-restraints excluded: chain A residue 2443 THR Chi-restraints excluded: chain A residue 2516 VAL Chi-restraints excluded: chain A residue 2621 ILE Chi-restraints excluded: chain A residue 2656 SER Chi-restraints excluded: chain A residue 2664 VAL Chi-restraints excluded: chain A residue 2666 ASN Chi-restraints excluded: chain A residue 2709 VAL Chi-restraints excluded: chain A residue 2715 GLU Chi-restraints excluded: chain A residue 2855 VAL Chi-restraints excluded: chain A residue 2905 VAL Chi-restraints excluded: chain A residue 2917 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 263 random chunks: chunk 34 optimal weight: 1.9990 chunk 246 optimal weight: 0.8980 chunk 165 optimal weight: 0.6980 chunk 51 optimal weight: 0.5980 chunk 69 optimal weight: 4.9990 chunk 158 optimal weight: 0.9990 chunk 133 optimal weight: 0.7980 chunk 111 optimal weight: 0.6980 chunk 70 optimal weight: 0.7980 chunk 124 optimal weight: 3.9990 chunk 60 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 528 GLN A1245 GLN A1380 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.144204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.119169 restraints weight = 31420.436| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 1.89 r_work: 0.3271 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3145 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.3582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 21340 Z= 0.124 Angle : 0.537 10.504 28912 Z= 0.268 Chirality : 0.038 0.148 3315 Planarity : 0.004 0.041 3686 Dihedral : 6.781 79.199 2933 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 4.25 % Allowed : 18.85 % Favored : 76.90 % 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: 1.33 (0.17), residues: 2596 helix: 1.85 (0.12), residues: 1864 sheet: -0.23 (0.93), residues: 33 loop : -1.81 (0.23), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A2524 TYR 0.026 0.001 TYR A 145 PHE 0.018 0.001 PHE A 171 TRP 0.014 0.001 TRP A2355 HIS 0.004 0.001 HIS A 839 Details of bonding type rmsd covalent geometry : bond 0.00291 (21339) covalent geometry : angle 0.53679 (28910) SS BOND : bond 0.00288 ( 1) SS BOND : angle 0.39734 ( 2) hydrogen bonds : bond 0.03663 ( 1294) hydrogen bonds : angle 3.70314 ( 3849) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5192 Ramachandran restraints generated. 2596 Oldfield, 0 Emsley, 2596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5192 Ramachandran restraints generated. 2596 Oldfield, 0 Emsley, 2596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 2281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 214 time to evaluate : 0.796 Fit side-chains revert: symmetry clash REVERT: A 31 ASP cc_start: 0.5731 (OUTLIER) cc_final: 0.5300 (t0) REVERT: A 36 LEU cc_start: 0.7497 (mm) cc_final: 0.7218 (mt) REVERT: A 61 GLU cc_start: 0.7636 (pt0) cc_final: 0.7390 (pp20) REVERT: A 100 LEU cc_start: 0.6857 (mm) cc_final: 0.6654 (mm) REVERT: A 123 GLN cc_start: 0.7427 (tp-100) cc_final: 0.7113 (tm-30) REVERT: A 325 TYR cc_start: 0.6738 (OUTLIER) cc_final: 0.5168 (m-10) REVERT: A 328 ARG cc_start: 0.7332 (ptt180) cc_final: 0.6465 (ptm160) REVERT: A 522 LEU cc_start: 0.7063 (OUTLIER) cc_final: 0.6488 (pp) REVERT: A 564 LEU cc_start: 0.8080 (OUTLIER) cc_final: 0.7583 (pp) REVERT: A 660 LEU cc_start: 0.8751 (OUTLIER) cc_final: 0.8485 (mt) REVERT: A 682 ARG cc_start: 0.7107 (mtp180) cc_final: 0.6812 (mtp85) REVERT: A 802 LEU cc_start: 0.7972 (OUTLIER) cc_final: 0.7584 (mm) REVERT: A 846 LYS cc_start: 0.8492 (mttt) cc_final: 0.7781 (mmtt) REVERT: A 1015 ASP cc_start: 0.7745 (m-30) cc_final: 0.7301 (m-30) REVERT: A 1022 LYS cc_start: 0.8075 (ttpt) cc_final: 0.7618 (tptp) REVERT: A 1221 ARG cc_start: 0.8184 (OUTLIER) cc_final: 0.7406 (tpp-160) REVERT: A 1224 GLN cc_start: 0.8563 (mt0) cc_final: 0.8345 (mt0) REVERT: A 1242 GLN cc_start: 0.6792 (mm-40) cc_final: 0.6568 (mm-40) REVERT: A 1314 PHE cc_start: 0.8361 (OUTLIER) cc_final: 0.7929 (t80) REVERT: A 1320 ILE cc_start: 0.5050 (OUTLIER) cc_final: 0.4605 (pt) REVERT: A 1322 LYS cc_start: 0.6722 (tptt) cc_final: 0.6346 (pptt) REVERT: A 1342 LYS cc_start: 0.7082 (tttt) cc_final: 0.6356 (mtmt) REVERT: A 1376 TYR cc_start: 0.6864 (OUTLIER) cc_final: 0.3816 (m-80) REVERT: A 1405 LEU cc_start: 0.7938 (OUTLIER) cc_final: 0.7615 (mp) REVERT: A 1411 LEU cc_start: 0.9167 (OUTLIER) cc_final: 0.8668 (tt) REVERT: A 1526 GLU cc_start: 0.7577 (mm-30) cc_final: 0.7237 (tp30) REVERT: A 1854 LEU cc_start: 0.8754 (OUTLIER) cc_final: 0.8495 (tm) REVERT: A 2220 MET cc_start: 0.8542 (mtm) cc_final: 0.8207 (mtm) REVERT: A 2751 MET cc_start: 0.8345 (mmp) cc_final: 0.7971 (mmp) REVERT: A 2826 ASP cc_start: 0.8472 (t0) cc_final: 0.8196 (t0) outliers start: 97 outliers final: 76 residues processed: 295 average time/residue: 0.1394 time to fit residues: 65.7042 Evaluate side-chains 294 residues out of total 2281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 205 time to evaluate : 0.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ASP Chi-restraints excluded: chain A residue 56 TYR Chi-restraints excluded: chain A residue 69 ILE Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 325 TYR Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 466 GLN Chi-restraints excluded: chain A residue 480 GLU Chi-restraints excluded: chain A residue 492 HIS Chi-restraints excluded: chain A residue 502 SER Chi-restraints excluded: chain A residue 521 SER Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 566 ASP Chi-restraints excluded: chain A residue 607 GLN 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 658 GLN Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain A residue 793 ILE Chi-restraints excluded: chain A residue 802 LEU Chi-restraints excluded: chain A residue 809 ASN Chi-restraints excluded: chain A residue 896 LEU Chi-restraints excluded: chain A residue 897 SER Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain A residue 962 LEU Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 983 CYS Chi-restraints excluded: chain A residue 1002 TRP Chi-restraints excluded: chain A residue 1025 LEU Chi-restraints excluded: chain A residue 1068 ILE Chi-restraints excluded: chain A residue 1071 ASP Chi-restraints excluded: chain A residue 1104 LEU Chi-restraints excluded: chain A residue 1160 THR Chi-restraints excluded: chain A residue 1221 ARG Chi-restraints excluded: chain A residue 1232 MET Chi-restraints excluded: chain A residue 1314 PHE Chi-restraints excluded: chain A residue 1320 ILE 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 1405 LEU Chi-restraints excluded: chain A residue 1408 CYS Chi-restraints excluded: chain A residue 1411 LEU Chi-restraints excluded: chain A residue 1568 ASP Chi-restraints excluded: chain A residue 1575 LEU Chi-restraints excluded: chain A residue 1591 VAL Chi-restraints excluded: chain A residue 1628 GLU Chi-restraints excluded: chain A residue 1684 SER Chi-restraints excluded: chain A residue 1777 ILE Chi-restraints excluded: chain A residue 1779 THR Chi-restraints excluded: chain A residue 1854 LEU Chi-restraints excluded: chain A residue 1918 LEU Chi-restraints excluded: chain A residue 1934 SER Chi-restraints excluded: chain A residue 2030 VAL Chi-restraints excluded: chain A residue 2045 SER Chi-restraints excluded: chain A residue 2052 LEU Chi-restraints excluded: chain A residue 2058 MET Chi-restraints excluded: chain A residue 2096 ILE Chi-restraints excluded: chain A residue 2118 TRP Chi-restraints excluded: chain A residue 2135 GLU Chi-restraints excluded: chain A residue 2234 SER Chi-restraints excluded: chain A residue 2244 SER Chi-restraints excluded: chain A residue 2247 ASP Chi-restraints excluded: chain A residue 2349 LEU Chi-restraints excluded: chain A residue 2516 VAL Chi-restraints excluded: chain A residue 2621 ILE Chi-restraints excluded: chain A residue 2656 SER Chi-restraints excluded: chain A residue 2664 VAL Chi-restraints excluded: chain A residue 2666 ASN Chi-restraints excluded: chain A residue 2709 VAL Chi-restraints excluded: chain A residue 2715 GLU Chi-restraints excluded: chain A residue 2813 THR Chi-restraints excluded: chain A residue 2855 VAL Chi-restraints excluded: chain A residue 2905 VAL Chi-restraints excluded: chain A residue 2917 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 263 random chunks: chunk 84 optimal weight: 1.9990 chunk 258 optimal weight: 0.9990 chunk 113 optimal weight: 0.4980 chunk 257 optimal weight: 0.8980 chunk 177 optimal weight: 1.9990 chunk 217 optimal weight: 0.8980 chunk 210 optimal weight: 1.9990 chunk 224 optimal weight: 0.9980 chunk 25 optimal weight: 0.8980 chunk 65 optimal weight: 2.9990 chunk 124 optimal weight: 3.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1245 GLN A1380 ASN A1574 GLN A1764 GLN A1844 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.143651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.118949 restraints weight = 31425.132| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 1.92 r_work: 0.3268 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3140 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.3636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 21340 Z= 0.132 Angle : 0.541 10.683 28912 Z= 0.271 Chirality : 0.039 0.488 3315 Planarity : 0.004 0.040 3686 Dihedral : 6.674 78.166 2930 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 4.34 % Allowed : 18.76 % Favored : 76.90 % 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: 1.40 (0.17), residues: 2596 helix: 1.91 (0.12), residues: 1862 sheet: -0.18 (0.93), residues: 33 loop : -1.80 (0.23), residues: 701 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A2524 TYR 0.023 0.001 TYR A 145 PHE 0.012 0.001 PHE A2724 TRP 0.013 0.001 TRP A2118 HIS 0.003 0.001 HIS A 839 Details of bonding type rmsd covalent geometry : bond 0.00312 (21339) covalent geometry : angle 0.54148 (28910) SS BOND : bond 0.00303 ( 1) SS BOND : angle 0.35033 ( 2) hydrogen bonds : bond 0.03758 ( 1294) hydrogen bonds : angle 3.70611 ( 3849) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5192 Ramachandran restraints generated. 2596 Oldfield, 0 Emsley, 2596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5192 Ramachandran restraints generated. 2596 Oldfield, 0 Emsley, 2596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 2281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 209 time to evaluate : 0.841 Fit side-chains REVERT: A 31 ASP cc_start: 0.5835 (OUTLIER) cc_final: 0.5457 (t0) REVERT: A 36 LEU cc_start: 0.7596 (mm) cc_final: 0.7280 (mt) REVERT: A 61 GLU cc_start: 0.7647 (pt0) cc_final: 0.7425 (pp20) REVERT: A 100 LEU cc_start: 0.6888 (mm) cc_final: 0.6674 (mm) REVERT: A 123 GLN cc_start: 0.7551 (tp-100) cc_final: 0.7277 (tm-30) REVERT: A 259 MET cc_start: 0.7544 (mpt) cc_final: 0.6688 (mpp) REVERT: A 325 TYR cc_start: 0.6746 (OUTLIER) cc_final: 0.5203 (m-10) REVERT: A 328 ARG cc_start: 0.7317 (ptt180) cc_final: 0.6431 (ptm160) REVERT: A 522 LEU cc_start: 0.7174 (OUTLIER) cc_final: 0.6590 (pp) REVERT: A 564 LEU cc_start: 0.8180 (OUTLIER) cc_final: 0.7703 (pp) REVERT: A 569 ASN cc_start: 0.8517 (m-40) cc_final: 0.7937 (m-40) REVERT: A 646 ARG cc_start: 0.8373 (mtt-85) cc_final: 0.8071 (mtt-85) REVERT: A 660 LEU cc_start: 0.8762 (OUTLIER) cc_final: 0.8494 (mt) REVERT: A 682 ARG cc_start: 0.7132 (mtp180) cc_final: 0.6832 (mtp85) REVERT: A 802 LEU cc_start: 0.8058 (OUTLIER) cc_final: 0.7674 (mm) REVERT: A 846 LYS cc_start: 0.8499 (mttt) cc_final: 0.7801 (mmtt) REVERT: A 1015 ASP cc_start: 0.7759 (m-30) cc_final: 0.7316 (m-30) REVERT: A 1022 LYS cc_start: 0.8091 (ttpt) cc_final: 0.7650 (tptp) REVERT: A 1209 GLU cc_start: 0.8128 (mm-30) cc_final: 0.7549 (mp0) REVERT: A 1221 ARG cc_start: 0.8198 (OUTLIER) cc_final: 0.7447 (tpp-160) REVERT: A 1224 GLN cc_start: 0.8597 (mt0) cc_final: 0.8396 (mt0) REVERT: A 1242 GLN cc_start: 0.6788 (mm-40) cc_final: 0.6523 (mm-40) REVERT: A 1314 PHE cc_start: 0.8373 (OUTLIER) cc_final: 0.7979 (t80) REVERT: A 1320 ILE cc_start: 0.5067 (OUTLIER) cc_final: 0.4626 (pt) REVERT: A 1322 LYS cc_start: 0.6702 (tptt) cc_final: 0.6374 (pptt) REVERT: A 1342 LYS cc_start: 0.7101 (tttt) cc_final: 0.6352 (mtmt) REVERT: A 1376 TYR cc_start: 0.6910 (OUTLIER) cc_final: 0.3761 (m-80) REVERT: A 1405 LEU cc_start: 0.8003 (OUTLIER) cc_final: 0.7680 (mp) REVERT: A 1411 LEU cc_start: 0.9212 (OUTLIER) cc_final: 0.8724 (tt) REVERT: A 1526 GLU cc_start: 0.7565 (mm-30) cc_final: 0.7226 (tp30) REVERT: A 1854 LEU cc_start: 0.8772 (OUTLIER) cc_final: 0.8520 (tm) REVERT: A 2220 MET cc_start: 0.8561 (mtm) cc_final: 0.8225 (mtm) REVERT: A 2365 ARG cc_start: 0.7691 (ttp80) cc_final: 0.7109 (ttp80) REVERT: A 2751 MET cc_start: 0.8308 (mmp) cc_final: 0.7915 (mmp) REVERT: A 2826 ASP cc_start: 0.8465 (t0) cc_final: 0.8205 (t0) outliers start: 99 outliers final: 78 residues processed: 292 average time/residue: 0.1408 time to fit residues: 65.5212 Evaluate side-chains 291 residues out of total 2281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 200 time to evaluate : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ASP Chi-restraints excluded: chain A residue 56 TYR Chi-restraints excluded: chain A residue 69 ILE Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 325 TYR Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 480 GLU Chi-restraints excluded: chain A residue 492 HIS Chi-restraints excluded: chain A residue 502 SER Chi-restraints excluded: chain A residue 521 SER Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 566 ASP Chi-restraints excluded: chain A residue 607 GLN 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 658 GLN Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain A residue 793 ILE Chi-restraints excluded: chain A residue 802 LEU Chi-restraints excluded: chain A residue 809 ASN Chi-restraints excluded: chain A residue 896 LEU Chi-restraints excluded: chain A residue 897 SER Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain A residue 962 LEU Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 983 CYS Chi-restraints excluded: chain A residue 1002 TRP Chi-restraints excluded: chain A residue 1025 LEU Chi-restraints excluded: chain A residue 1068 ILE Chi-restraints excluded: chain A residue 1071 ASP Chi-restraints excluded: chain A residue 1104 LEU Chi-restraints excluded: chain A residue 1160 THR Chi-restraints excluded: chain A residue 1183 GLN Chi-restraints excluded: chain A residue 1221 ARG Chi-restraints excluded: chain A residue 1232 MET Chi-restraints excluded: chain A residue 1314 PHE Chi-restraints excluded: chain A residue 1320 ILE 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 1405 LEU Chi-restraints excluded: chain A residue 1408 CYS Chi-restraints excluded: chain A residue 1411 LEU Chi-restraints excluded: chain A residue 1568 ASP Chi-restraints excluded: chain A residue 1575 LEU Chi-restraints excluded: chain A residue 1591 VAL Chi-restraints excluded: chain A residue 1628 GLU Chi-restraints excluded: chain A residue 1640 SER Chi-restraints excluded: chain A residue 1684 SER Chi-restraints excluded: chain A residue 1777 ILE Chi-restraints excluded: chain A residue 1779 THR Chi-restraints excluded: chain A residue 1854 LEU Chi-restraints excluded: chain A residue 1918 LEU Chi-restraints excluded: chain A residue 1934 SER Chi-restraints excluded: chain A residue 2030 VAL Chi-restraints excluded: chain A residue 2045 SER Chi-restraints excluded: chain A residue 2052 LEU Chi-restraints excluded: chain A residue 2058 MET Chi-restraints excluded: chain A residue 2096 ILE Chi-restraints excluded: chain A residue 2118 TRP Chi-restraints excluded: chain A residue 2135 GLU Chi-restraints excluded: chain A residue 2234 SER Chi-restraints excluded: chain A residue 2244 SER Chi-restraints excluded: chain A residue 2247 ASP Chi-restraints excluded: chain A residue 2349 LEU Chi-restraints excluded: chain A residue 2443 THR Chi-restraints excluded: chain A residue 2516 VAL Chi-restraints excluded: chain A residue 2621 ILE Chi-restraints excluded: chain A residue 2656 SER Chi-restraints excluded: chain A residue 2664 VAL Chi-restraints excluded: chain A residue 2666 ASN Chi-restraints excluded: chain A residue 2709 VAL Chi-restraints excluded: chain A residue 2715 GLU Chi-restraints excluded: chain A residue 2813 THR Chi-restraints excluded: chain A residue 2855 VAL Chi-restraints excluded: chain A residue 2905 VAL Chi-restraints excluded: chain A residue 2917 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 263 random chunks: chunk 184 optimal weight: 0.7980 chunk 98 optimal weight: 3.9990 chunk 167 optimal weight: 0.9980 chunk 10 optimal weight: 8.9990 chunk 79 optimal weight: 0.0040 chunk 83 optimal weight: 0.9980 chunk 66 optimal weight: 0.3980 chunk 22 optimal weight: 1.9990 chunk 257 optimal weight: 0.5980 chunk 206 optimal weight: 0.9990 chunk 128 optimal weight: 4.9990 overall best weight: 0.5592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1245 GLN A1380 ASN A1497 GLN A2518 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.145014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.120367 restraints weight = 31498.132| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 2.01 r_work: 0.3279 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3150 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.3770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 21340 Z= 0.113 Angle : 0.530 10.738 28912 Z= 0.265 Chirality : 0.038 0.447 3315 Planarity : 0.004 0.041 3686 Dihedral : 6.555 78.178 2930 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 3.99 % Allowed : 19.25 % Favored : 76.76 % 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: 1.56 (0.17), residues: 2596 helix: 2.03 (0.12), residues: 1866 sheet: -0.06 (0.94), residues: 33 loop : -1.77 (0.23), residues: 697 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A2524 TYR 0.025 0.001 TYR A 145 PHE 0.031 0.001 PHE A 171 TRP 0.013 0.001 TRP A 301 HIS 0.003 0.001 HIS A 839 Details of bonding type rmsd covalent geometry : bond 0.00261 (21339) covalent geometry : angle 0.52975 (28910) SS BOND : bond 0.00233 ( 1) SS BOND : angle 0.46438 ( 2) hydrogen bonds : bond 0.03461 ( 1294) hydrogen bonds : angle 3.64469 ( 3849) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5192 Ramachandran restraints generated. 2596 Oldfield, 0 Emsley, 2596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5192 Ramachandran restraints generated. 2596 Oldfield, 0 Emsley, 2596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 2281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 218 time to evaluate : 0.698 Fit side-chains REVERT: A 31 ASP cc_start: 0.5764 (OUTLIER) cc_final: 0.5485 (t0) REVERT: A 36 LEU cc_start: 0.7617 (mm) cc_final: 0.7265 (mt) REVERT: A 123 GLN cc_start: 0.7574 (tp-100) cc_final: 0.7295 (tm-30) REVERT: A 259 MET cc_start: 0.7482 (mpt) cc_final: 0.6645 (mpp) REVERT: A 325 TYR cc_start: 0.6784 (OUTLIER) cc_final: 0.5311 (m-10) REVERT: A 328 ARG cc_start: 0.7312 (ptt180) cc_final: 0.6439 (ptm160) REVERT: A 480 GLU cc_start: 0.7555 (OUTLIER) cc_final: 0.7257 (pm20) REVERT: A 522 LEU cc_start: 0.7131 (OUTLIER) cc_final: 0.6538 (pp) REVERT: A 564 LEU cc_start: 0.8088 (OUTLIER) cc_final: 0.7573 (pp) REVERT: A 569 ASN cc_start: 0.8507 (m-40) cc_final: 0.7931 (m-40) REVERT: A 646 ARG cc_start: 0.8359 (mtt-85) cc_final: 0.8081 (mtt-85) REVERT: A 660 LEU cc_start: 0.8663 (OUTLIER) cc_final: 0.8378 (mt) REVERT: A 682 ARG cc_start: 0.7111 (mtp180) cc_final: 0.6833 (mtp85) REVERT: A 802 LEU cc_start: 0.8031 (OUTLIER) cc_final: 0.7644 (mm) REVERT: A 846 LYS cc_start: 0.8494 (mttt) cc_final: 0.7806 (mmtt) REVERT: A 1015 ASP cc_start: 0.7666 (m-30) cc_final: 0.7231 (m-30) REVERT: A 1022 LYS cc_start: 0.8079 (ttpt) cc_final: 0.7636 (tptp) REVERT: A 1076 LEU cc_start: 0.7995 (tt) cc_final: 0.7565 (tt) REVERT: A 1209 GLU cc_start: 0.8084 (mm-30) cc_final: 0.7522 (mp0) REVERT: A 1221 ARG cc_start: 0.8162 (OUTLIER) cc_final: 0.7403 (tpp-160) REVERT: A 1242 GLN cc_start: 0.6704 (mm-40) cc_final: 0.6436 (mm-40) REVERT: A 1314 PHE cc_start: 0.8317 (OUTLIER) cc_final: 0.8013 (t80) REVERT: A 1322 LYS cc_start: 0.6721 (tptt) cc_final: 0.6383 (pptt) REVERT: A 1342 LYS cc_start: 0.7088 (tttt) cc_final: 0.6339 (mtmt) REVERT: A 1376 TYR cc_start: 0.6800 (OUTLIER) cc_final: 0.3864 (m-80) REVERT: A 1405 LEU cc_start: 0.7923 (OUTLIER) cc_final: 0.7652 (mp) REVERT: A 1411 LEU cc_start: 0.9203 (OUTLIER) cc_final: 0.8706 (tt) REVERT: A 1412 ARG cc_start: 0.8011 (mtt180) cc_final: 0.7784 (ptp-170) REVERT: A 1526 GLU cc_start: 0.7566 (mm-30) cc_final: 0.7225 (tp30) REVERT: A 1587 MET cc_start: 0.9157 (tmm) cc_final: 0.8807 (tmm) REVERT: A 1854 LEU cc_start: 0.8753 (OUTLIER) cc_final: 0.8494 (tm) REVERT: A 2220 MET cc_start: 0.8534 (mtm) cc_final: 0.8209 (mtm) REVERT: A 2583 MET cc_start: 0.7631 (ptp) cc_final: 0.7285 (ptp) REVERT: A 2751 MET cc_start: 0.8330 (mmp) cc_final: 0.7991 (mmp) REVERT: A 2826 ASP cc_start: 0.8493 (t0) cc_final: 0.8223 (t0) outliers start: 91 outliers final: 74 residues processed: 292 average time/residue: 0.1442 time to fit residues: 66.5226 Evaluate side-chains 294 residues out of total 2281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 207 time to evaluate : 0.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ASP Chi-restraints excluded: chain A residue 69 ILE Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 325 TYR Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 480 GLU Chi-restraints excluded: chain A residue 492 HIS Chi-restraints excluded: chain A residue 502 SER Chi-restraints excluded: chain A residue 521 SER Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 566 ASP Chi-restraints excluded: chain A residue 607 GLN 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 658 GLN Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain A residue 793 ILE Chi-restraints excluded: chain A residue 802 LEU Chi-restraints excluded: chain A residue 809 ASN Chi-restraints excluded: chain A residue 896 LEU Chi-restraints excluded: chain A residue 897 SER Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain A residue 962 LEU Chi-restraints excluded: chain A residue 983 CYS Chi-restraints excluded: chain A residue 1002 TRP Chi-restraints excluded: chain A residue 1025 LEU Chi-restraints excluded: chain A residue 1071 ASP Chi-restraints excluded: chain A residue 1104 LEU Chi-restraints excluded: chain A residue 1160 THR Chi-restraints excluded: chain A residue 1183 GLN Chi-restraints excluded: chain A residue 1221 ARG Chi-restraints excluded: chain A residue 1232 MET Chi-restraints excluded: chain A residue 1314 PHE Chi-restraints excluded: chain A residue 1324 PHE Chi-restraints excluded: chain A residue 1343 LEU 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 1405 LEU Chi-restraints excluded: chain A residue 1408 CYS Chi-restraints excluded: chain A residue 1411 LEU Chi-restraints excluded: chain A residue 1414 ILE Chi-restraints excluded: chain A residue 1568 ASP Chi-restraints excluded: chain A residue 1591 VAL Chi-restraints excluded: chain A residue 1628 GLU Chi-restraints excluded: chain A residue 1640 SER Chi-restraints excluded: chain A residue 1684 SER Chi-restraints excluded: chain A residue 1854 LEU Chi-restraints excluded: chain A residue 1918 LEU Chi-restraints excluded: chain A residue 1934 SER Chi-restraints excluded: chain A residue 2030 VAL Chi-restraints excluded: chain A residue 2045 SER Chi-restraints excluded: chain A residue 2054 THR Chi-restraints excluded: chain A residue 2058 MET Chi-restraints excluded: chain A residue 2096 ILE Chi-restraints excluded: chain A residue 2118 TRP Chi-restraints excluded: chain A residue 2135 GLU Chi-restraints excluded: chain A residue 2234 SER Chi-restraints excluded: chain A residue 2244 SER Chi-restraints excluded: chain A residue 2247 ASP Chi-restraints excluded: chain A residue 2349 LEU Chi-restraints excluded: chain A residue 2443 THR Chi-restraints excluded: chain A residue 2516 VAL Chi-restraints excluded: chain A residue 2621 ILE Chi-restraints excluded: chain A residue 2656 SER Chi-restraints excluded: chain A residue 2664 VAL Chi-restraints excluded: chain A residue 2709 VAL Chi-restraints excluded: chain A residue 2715 GLU Chi-restraints excluded: chain A residue 2772 THR Chi-restraints excluded: chain A residue 2813 THR Chi-restraints excluded: chain A residue 2855 VAL Chi-restraints excluded: chain A residue 2905 VAL Chi-restraints excluded: chain A residue 2917 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 263 random chunks: chunk 219 optimal weight: 0.0980 chunk 78 optimal weight: 4.9990 chunk 121 optimal weight: 0.9980 chunk 126 optimal weight: 4.9990 chunk 102 optimal weight: 0.6980 chunk 31 optimal weight: 2.9990 chunk 234 optimal weight: 4.9990 chunk 23 optimal weight: 0.6980 chunk 16 optimal weight: 0.9990 chunk 228 optimal weight: 0.0870 chunk 11 optimal weight: 4.9990 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1245 GLN A1380 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.145325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.120446 restraints weight = 31351.800| |-----------------------------------------------------------------------------| r_work (start): 0.3467 rms_B_bonded: 1.93 r_work: 0.3287 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3157 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.3852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 21340 Z= 0.111 Angle : 0.534 10.733 28912 Z= 0.265 Chirality : 0.038 0.438 3315 Planarity : 0.004 0.040 3686 Dihedral : 6.305 77.895 2926 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 3.73 % Allowed : 19.47 % Favored : 76.81 % 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: 1.65 (0.17), residues: 2596 helix: 2.09 (0.12), residues: 1871 sheet: 0.00 (0.94), residues: 33 loop : -1.76 (0.23), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A2524 TYR 0.021 0.001 TYR A2040 PHE 0.033 0.001 PHE A 171 TRP 0.013 0.001 TRP A1617 HIS 0.003 0.001 HIS A 514 Details of bonding type rmsd covalent geometry : bond 0.00252 (21339) covalent geometry : angle 0.53363 (28910) SS BOND : bond 0.00260 ( 1) SS BOND : angle 0.41492 ( 2) hydrogen bonds : bond 0.03416 ( 1294) hydrogen bonds : angle 3.62076 ( 3849) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5227.78 seconds wall clock time: 90 minutes 2.69 seconds (5402.69 seconds total)