Starting phenix.real_space_refine on Sun Aug 24 08:39:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ki9_37255/08_2025/8ki9_37255.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ki9_37255/08_2025/8ki9_37255.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ki9_37255/08_2025/8ki9_37255.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ki9_37255/08_2025/8ki9_37255.map" model { file = "/net/cci-nas-00/data/ceres_data/8ki9_37255/08_2025/8ki9_37255.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ki9_37255/08_2025/8ki9_37255.cif" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.036 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: 4 Type Number sf(0) Gaussians S 121 5.16 5 C 11542 2.51 5 N 2997 2.21 5 O 3422 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 33 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 18082 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 18082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2238, 18082 Classifications: {'peptide': 2238} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 52, 'TRANS': 2185} Chain breaks: 8 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 2, 'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 24 Time building chain proxies: 3.01, per 1000 atoms: 0.17 Number of scatterers: 18082 At special positions: 0 Unit cell: (120.91, 140.17, 167.99, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 121 16.00 O 3422 8.00 N 2997 7.00 C 11542 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.53 Conformation dependent library (CDL) restraints added in 629.9 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4320 Finding SS restraints... Secondary structure from input PDB file: 105 helices and 12 sheets defined 60.5% alpha, 6.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.87 Creating SS restraints... Processing helix chain 'A' and resid 338 through 347 Processing helix chain 'A' and resid 352 through 361 Processing helix chain 'A' and resid 362 through 367 removed outlier: 3.714A pdb=" N CYS A 365 " --> pdb=" O GLY A 362 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N PHE A 366 " --> pdb=" O ASN A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 390 Processing helix chain 'A' and resid 398 through 413 Processing helix chain 'A' and resid 415 through 432 removed outlier: 3.852A pdb=" N LYS A 432 " --> pdb=" O ARG A 428 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 455 Processing helix chain 'A' and resid 483 through 493 Processing helix chain 'A' and resid 509 through 523 removed outlier: 4.278A pdb=" N GLU A 523 " --> pdb=" O LEU A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 554 removed outlier: 3.667A pdb=" N MET A 554 " --> pdb=" O GLY A 550 " (cutoff:3.500A) Processing helix chain 'A' and resid 568 through 585 removed outlier: 3.687A pdb=" N ASN A 585 " --> pdb=" O PHE A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 592 through 603 removed outlier: 3.540A pdb=" N SER A 596 " --> pdb=" O GLY A 592 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N VAL A 597 " --> pdb=" O LYS A 593 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 609 removed outlier: 3.631A pdb=" N LEU A 608 " --> pdb=" O PRO A 605 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 632 Processing helix chain 'A' and resid 633 through 652 Processing helix chain 'A' and resid 692 through 699 removed outlier: 3.705A pdb=" N TYR A 699 " --> pdb=" O PHE A 695 " (cutoff:3.500A) Processing helix chain 'A' and resid 723 through 732 Processing helix chain 'A' and resid 732 through 748 Proline residue: A 738 - end of helix Processing helix chain 'A' and resid 748 through 758 Processing helix chain 'A' and resid 759 through 763 removed outlier: 4.013A pdb=" N VAL A 763 " --> pdb=" O ILE A 760 " (cutoff:3.500A) Processing helix chain 'A' and resid 769 through 788 Processing helix chain 'A' and resid 791 through 804 removed outlier: 3.652A pdb=" N MET A 795 " --> pdb=" O LYS A 791 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 821 Processing helix chain 'A' and resid 832 through 847 Processing helix chain 'A' and resid 871 through 885 removed outlier: 4.013A pdb=" N LEU A 875 " --> pdb=" O THR A 871 " (cutoff:3.500A) Processing helix chain 'A' and resid 892 through 916 removed outlier: 4.402A pdb=" N ASN A 896 " --> pdb=" O ASN A 892 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N THR A 898 " --> pdb=" O VAL A 894 " (cutoff:3.500A) Proline residue: A 904 - end of helix Processing helix chain 'A' and resid 940 through 955 removed outlier: 4.196A pdb=" N VAL A 944 " --> pdb=" O GLY A 940 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LYS A 945 " --> pdb=" O ALA A 941 " (cutoff:3.500A) Processing helix chain 'A' and resid 957 through 969 removed outlier: 3.608A pdb=" N MET A 961 " --> pdb=" O ASN A 957 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLU A 969 " --> pdb=" O ILE A 965 " (cutoff:3.500A) Processing helix chain 'A' and resid 974 through 982 removed outlier: 4.891A pdb=" N SER A 979 " --> pdb=" O TYR A 976 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N THR A 980 " --> pdb=" O LYS A 977 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU A 981 " --> pdb=" O ILE A 978 " (cutoff:3.500A) Processing helix chain 'A' and resid 994 through 1004 removed outlier: 3.969A pdb=" N ILE A 998 " --> pdb=" O SER A 994 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ILE A 999 " --> pdb=" O THR A 995 " (cutoff:3.500A) Processing helix chain 'A' and resid 1006 through 1010 removed outlier: 3.720A pdb=" N ILE A1010 " --> pdb=" O ILE A1007 " (cutoff:3.500A) Processing helix chain 'A' and resid 1015 through 1031 removed outlier: 3.692A pdb=" N ALA A1019 " --> pdb=" O GLY A1015 " (cutoff:3.500A) Processing helix chain 'A' and resid 1031 through 1043 Processing helix chain 'A' and resid 1045 through 1058 Processing helix chain 'A' and resid 1070 through 1075 Processing helix chain 'A' and resid 1077 through 1087 removed outlier: 3.631A pdb=" N VAL A1081 " --> pdb=" O HIS A1077 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N THR A1087 " --> pdb=" O THR A1083 " (cutoff:3.500A) Processing helix chain 'A' and resid 1102 through 1115 removed outlier: 3.684A pdb=" N HIS A1115 " --> pdb=" O VAL A1111 " (cutoff:3.500A) Processing helix chain 'A' and resid 1122 through 1127 removed outlier: 3.703A pdb=" N ASN A1127 " --> pdb=" O ASP A1123 " (cutoff:3.500A) Processing helix chain 'A' and resid 1130 through 1134 removed outlier: 3.733A pdb=" N GLU A1133 " --> pdb=" O LYS A1130 " (cutoff:3.500A) Processing helix chain 'A' and resid 1138 through 1151 removed outlier: 3.599A pdb=" N MET A1142 " --> pdb=" O THR A1138 " (cutoff:3.500A) Processing helix chain 'A' and resid 1167 through 1187 removed outlier: 5.507A pdb=" N HIS A1183 " --> pdb=" O HIS A1179 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N VAL A1184 " --> pdb=" O THR A1180 " (cutoff:3.500A) Processing helix chain 'A' and resid 1198 through 1219 removed outlier: 3.989A pdb=" N ARG A1202 " --> pdb=" O ASP A1198 " (cutoff:3.500A) Processing helix chain 'A' and resid 1237 through 1242 removed outlier: 4.039A pdb=" N ASP A1242 " --> pdb=" O TRP A1238 " (cutoff:3.500A) Processing helix chain 'A' and resid 1244 through 1252 removed outlier: 3.692A pdb=" N VAL A1248 " --> pdb=" O THR A1244 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA A1250 " --> pdb=" O LYS A1246 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N ILE A1252 " --> pdb=" O VAL A1248 " (cutoff:3.500A) Processing helix chain 'A' and resid 1261 through 1274 removed outlier: 3.729A pdb=" N LYS A1274 " --> pdb=" O LEU A1270 " (cutoff:3.500A) Processing helix chain 'A' and resid 1281 through 1295 Processing helix chain 'A' and resid 1300 through 1305 removed outlier: 3.627A pdb=" N LEU A1304 " --> pdb=" O THR A1300 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LEU A1305 " --> pdb=" O ALA A1301 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1300 through 1305' Processing helix chain 'A' and resid 1327 through 1345 Processing helix chain 'A' and resid 1372 through 1380 removed outlier: 3.774A pdb=" N MET A1376 " --> pdb=" O GLU A1372 " (cutoff:3.500A) Processing helix chain 'A' and resid 1384 through 1400 Processing helix chain 'A' and resid 1432 through 1439 Processing helix chain 'A' and resid 1447 through 1465 Processing helix chain 'A' and resid 1470 through 1487 removed outlier: 4.579A pdb=" N PHE A1474 " --> pdb=" O GLU A1470 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N TYR A1487 " --> pdb=" O ALA A1483 " (cutoff:3.500A) Processing helix chain 'A' and resid 1497 through 1505 Processing helix chain 'A' and resid 1509 through 1513 removed outlier: 3.714A pdb=" N GLU A1512 " --> pdb=" O LYS A1509 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ILE A1513 " --> pdb=" O SER A1510 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1509 through 1513' Processing helix chain 'A' and resid 1514 through 1518 removed outlier: 3.711A pdb=" N GLY A1518 " --> pdb=" O THR A1515 " (cutoff:3.500A) Processing helix chain 'A' and resid 1524 through 1531 removed outlier: 3.780A pdb=" N LEU A1528 " --> pdb=" O PRO A1524 " (cutoff:3.500A) Processing helix chain 'A' and resid 1535 through 1549 Processing helix chain 'A' and resid 1553 through 1563 removed outlier: 3.932A pdb=" N ASP A1559 " --> pdb=" O GLU A1555 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N SER A1563 " --> pdb=" O ASP A1559 " (cutoff:3.500A) Processing helix chain 'A' and resid 1565 through 1581 Processing helix chain 'A' and resid 1584 through 1599 Processing helix chain 'A' and resid 1613 through 1620 removed outlier: 4.335A pdb=" N LEU A1618 " --> pdb=" O GLU A1615 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N ASN A1619 " --> pdb=" O ASN A1616 " (cutoff:3.500A) Processing helix chain 'A' and resid 1621 through 1628 removed outlier: 3.699A pdb=" N LYS A1625 " --> pdb=" O MET A1621 " (cutoff:3.500A) Processing helix chain 'A' and resid 1639 through 1654 removed outlier: 3.823A pdb=" N ASN A1654 " --> pdb=" O ILE A1650 " (cutoff:3.500A) Processing helix chain 'A' and resid 1655 through 1660 removed outlier: 4.132A pdb=" N LEU A1659 " --> pdb=" O PRO A1655 " (cutoff:3.500A) Processing helix chain 'A' and resid 1668 through 1674 Processing helix chain 'A' and resid 1681 through 1689 removed outlier: 4.165A pdb=" N LEU A1687 " --> pdb=" O LEU A1683 " (cutoff:3.500A) Processing helix chain 'A' and resid 1699 through 1707 removed outlier: 3.941A pdb=" N ILE A1705 " --> pdb=" O MET A1701 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLU A1707 " --> pdb=" O LYS A1703 " (cutoff:3.500A) Processing helix chain 'A' and resid 1817 through 1828 Processing helix chain 'A' and resid 1830 through 1841 Proline residue: A1837 - end of helix removed outlier: 3.593A pdb=" N SER A1841 " --> pdb=" O PRO A1837 " (cutoff:3.500A) Processing helix chain 'A' and resid 1856 through 1868 removed outlier: 3.628A pdb=" N THR A1860 " --> pdb=" O ARG A1856 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLU A1861 " --> pdb=" O TRP A1857 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N LYS A1862 " --> pdb=" O PHE A1858 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N TRP A1863 " --> pdb=" O GLN A1859 " (cutoff:3.500A) Proline residue: A1865 - end of helix Processing helix chain 'A' and resid 1891 through 1913 removed outlier: 3.781A pdb=" N LEU A1895 " --> pdb=" O LYS A1891 " (cutoff:3.500A) Processing helix chain 'A' and resid 1923 through 1934 Processing helix chain 'A' and resid 1936 through 1945 Processing helix chain 'A' and resid 1957 through 1963 removed outlier: 3.598A pdb=" N PHE A1961 " --> pdb=" O ILE A1957 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ARG A1963 " --> pdb=" O THR A1959 " (cutoff:3.500A) Processing helix chain 'A' and resid 1965 through 1971 removed outlier: 3.601A pdb=" N TYR A1969 " --> pdb=" O SER A1965 " (cutoff:3.500A) Processing helix chain 'A' and resid 1997 through 2028 removed outlier: 3.746A pdb=" N VAL A2001 " --> pdb=" O THR A1997 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N GLU A2011 " --> pdb=" O ASP A2007 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N LYS A2012 " --> pdb=" O MET A2008 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASP A2015 " --> pdb=" O GLU A2011 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N VAL A2018 " --> pdb=" O LEU A2014 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N TYR A2019 " --> pdb=" O ASP A2015 " (cutoff:3.500A) Processing helix chain 'A' and resid 2032 through 2043 Processing helix chain 'A' and resid 2050 through 2067 removed outlier: 3.811A pdb=" N LYS A2057 " --> pdb=" O SER A2053 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N LYS A2060 " --> pdb=" O ASP A2056 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ILE A2061 " --> pdb=" O LYS A2057 " (cutoff:3.500A) Processing helix chain 'A' and resid 2071 through 2076 removed outlier: 3.645A pdb=" N LEU A2076 " --> pdb=" O SER A2072 " (cutoff:3.500A) Processing helix chain 'A' and resid 2078 through 2085 Processing helix chain 'A' and resid 2088 through 2095 removed outlier: 4.004A pdb=" N MET A2095 " --> pdb=" O TRP A2091 " (cutoff:3.500A) Processing helix chain 'A' and resid 2099 through 2110 Processing helix chain 'A' and resid 2153 through 2171 removed outlier: 3.612A pdb=" N ARG A2157 " --> pdb=" O PHE A2153 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N MET A2168 " --> pdb=" O LEU A2164 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N PHE A2169 " --> pdb=" O ALA A2165 " (cutoff:3.500A) Processing helix chain 'A' and resid 2171 through 2176 Processing helix chain 'A' and resid 2239 through 2247 removed outlier: 4.322A pdb=" N ARG A2245 " --> pdb=" O THR A2241 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N MET A2247 " --> pdb=" O LYS A2243 " (cutoff:3.500A) Processing helix chain 'A' and resid 2251 through 2264 removed outlier: 4.240A pdb=" N ALA A2255 " --> pdb=" O THR A2251 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N LYS A2264 " --> pdb=" O SER A2260 " (cutoff:3.500A) Processing helix chain 'A' and resid 2268 through 2290 removed outlier: 3.891A pdb=" N LEU A2279 " --> pdb=" O MET A2275 " (cutoff:3.500A) Processing helix chain 'A' and resid 2297 through 2308 removed outlier: 4.519A pdb=" N GLU A2305 " --> pdb=" O SER A2301 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N ASN A2306 " --> pdb=" O TYR A2302 " (cutoff:3.500A) Processing helix chain 'A' and resid 2311 through 2322 removed outlier: 3.526A pdb=" N ARG A2320 " --> pdb=" O GLU A2316 " (cutoff:3.500A) Processing helix chain 'A' and resid 2329 through 2362 removed outlier: 3.776A pdb=" N LYS A2339 " --> pdb=" O GLU A2335 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N SER A2360 " --> pdb=" O MET A2356 " (cutoff:3.500A) Processing helix chain 'A' and resid 2393 through 2408 removed outlier: 3.973A pdb=" N GLN A2397 " --> pdb=" O LEU A2393 " (cutoff:3.500A) Processing helix chain 'A' and resid 2414 through 2421 removed outlier: 4.307A pdb=" N ASN A2419 " --> pdb=" O SER A2416 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N VAL A2420 " --> pdb=" O LEU A2417 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N LEU A2421 " --> pdb=" O ARG A2418 " (cutoff:3.500A) Processing helix chain 'A' and resid 2442 through 2448 removed outlier: 3.853A pdb=" N MET A2445 " --> pdb=" O ASN A2442 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LYS A2447 " --> pdb=" O LEU A2444 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N SER A2448 " --> pdb=" O MET A2445 " (cutoff:3.500A) Processing helix chain 'A' and resid 2462 through 2472 Processing helix chain 'A' and resid 2497 through 2501 removed outlier: 3.867A pdb=" N ARG A2500 " --> pdb=" O ASN A2497 " (cutoff:3.500A) Processing helix chain 'A' and resid 2502 through 2512 removed outlier: 3.671A pdb=" N ILE A2511 " --> pdb=" O TYR A2507 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LYS A2512 " --> pdb=" O GLU A2508 " (cutoff:3.500A) Processing helix chain 'A' and resid 2525 through 2541 removed outlier: 3.957A pdb=" N GLU A2534 " --> pdb=" O LEU A2530 " (cutoff:3.500A) Processing helix chain 'A' and resid 2546 through 2559 Processing helix chain 'A' and resid 2569 through 2590 Proline residue: A2576 - end of helix removed outlier: 3.928A pdb=" N LYS A2579 " --> pdb=" O VAL A2575 " (cutoff:3.500A) Processing helix chain 'A' and resid 2594 through 2609 Processing helix chain 'A' and resid 2618 through 2631 removed outlier: 3.522A pdb=" N ASP A2631 " --> pdb=" O ILE A2627 " (cutoff:3.500A) Processing helix chain 'A' and resid 2634 through 2652 removed outlier: 3.840A pdb=" N LYS A2638 " --> pdb=" O SER A2634 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU A2639 " --> pdb=" O ARG A2635 " (cutoff:3.500A) Processing helix chain 'A' and resid 2666 through 2689 removed outlier: 3.518A pdb=" N ILE A2670 " --> pdb=" O THR A2666 " (cutoff:3.500A) Processing helix chain 'A' and resid 2698 through 2704 removed outlier: 3.944A pdb=" N SER A2702 " --> pdb=" O ASN A2698 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 498 through 499 removed outlier: 3.524A pdb=" N SER A 705 " --> pdb=" O ILE A 716 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N TYR A 715 " --> pdb=" O HIS A 685 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N HIS A 685 " --> pdb=" O TYR A 715 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N MET A 717 " --> pdb=" O ALA A 683 " (cutoff:3.500A) removed outlier: 5.332A pdb=" N ALA A 683 " --> pdb=" O MET A 717 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N MET A 671 " --> pdb=" O LEU A 684 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LEU A 663 " --> pdb=" O LEU A 672 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 498 through 499 removed outlier: 3.524A pdb=" N SER A 705 " --> pdb=" O ILE A 716 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N TYR A 715 " --> pdb=" O HIS A 685 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N HIS A 685 " --> pdb=" O TYR A 715 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N MET A 717 " --> pdb=" O ALA A 683 " (cutoff:3.500A) removed outlier: 5.332A pdb=" N ALA A 683 " --> pdb=" O MET A 717 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N TYR A 681 " --> pdb=" O GLN A 720 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N GLN A 720 " --> pdb=" O TYR A 681 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 989 through 990 Processing sheet with id=AA4, first strand: chain 'A' and resid 1226 through 1231 removed outlier: 3.597A pdb=" N ARG A1227 " --> pdb=" O ALA A1369 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ALA A1369 " --> pdb=" O ARG A1227 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ALA A1229 " --> pdb=" O LEU A1367 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1278 through 1279 Processing sheet with id=AA6, first strand: chain 'A' and resid 1423 through 1424 Processing sheet with id=AA7, first strand: chain 'A' and resid 1878 through 1879 removed outlier: 3.529A pdb=" N ILE A1989 " --> pdb=" O VAL A1879 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 2044 through 2045 Processing sheet with id=AA9, first strand: chain 'A' and resid 2118 through 2120 removed outlier: 7.958A pdb=" N VAL A2135 " --> pdb=" O LYS A2220 " (cutoff:3.500A) removed outlier: 8.596A pdb=" N LYS A2222 " --> pdb=" O VAL A2135 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N VAL A2137 " --> pdb=" O LYS A2222 " (cutoff:3.500A) removed outlier: 8.143A pdb=" N GLU A2224 " --> pdb=" O VAL A2137 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N LEU A2139 " --> pdb=" O GLU A2224 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LEU A2212 " --> pdb=" O CYS A2182 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N CYS A2182 " --> pdb=" O LEU A2212 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ASN A2214 " --> pdb=" O THR A2180 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N THR A2180 " --> pdb=" O ASN A2214 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 2118 through 2120 removed outlier: 7.958A pdb=" N VAL A2135 " --> pdb=" O LYS A2220 " (cutoff:3.500A) removed outlier: 8.596A pdb=" N LYS A2222 " --> pdb=" O VAL A2135 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N VAL A2137 " --> pdb=" O LYS A2222 " (cutoff:3.500A) removed outlier: 8.143A pdb=" N GLU A2224 " --> pdb=" O VAL A2137 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N LEU A2139 " --> pdb=" O GLU A2224 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N ASN A2214 " --> pdb=" O MET A2193 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N ILE A2191 " --> pdb=" O LYS A2216 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N VAL A2218 " --> pdb=" O SER A2189 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N SER A2189 " --> pdb=" O VAL A2218 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ARG A2188 " --> pdb=" O ASN A2204 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 2390 through 2391 removed outlier: 6.900A pdb=" N GLU A2386 " --> pdb=" O LEU A2434 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 2454 through 2455 894 hydrogen bonds defined for protein. 2586 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: 4.06 Time building geometry restraints manager: 2.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 5034 1.34 - 1.46: 3879 1.46 - 1.58: 9282 1.58 - 1.70: 1 1.70 - 1.83: 198 Bond restraints: 18394 Sorted by residual: bond pdb=" CB ASN A1901 " pdb=" CG ASN A1901 " ideal model delta sigma weight residual 1.516 1.588 -0.072 2.50e-02 1.60e+03 8.33e+00 bond pdb=" C VAL A 679 " pdb=" N PRO A 680 " ideal model delta sigma weight residual 1.334 1.390 -0.056 2.34e-02 1.83e+03 5.78e+00 bond pdb=" C LEU A 807 " pdb=" N PRO A 808 " ideal model delta sigma weight residual 1.334 1.388 -0.054 2.34e-02 1.83e+03 5.37e+00 bond pdb=" CB ASP A1188 " pdb=" CG ASP A1188 " ideal model delta sigma weight residual 1.516 1.564 -0.048 2.50e-02 1.60e+03 3.69e+00 bond pdb=" C ILE A1893 " pdb=" N PRO A1894 " ideal model delta sigma weight residual 1.336 1.359 -0.023 1.20e-02 6.94e+03 3.58e+00 ... (remaining 18389 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.97: 24179 2.97 - 5.93: 481 5.93 - 8.90: 96 8.90 - 11.87: 18 11.87 - 14.84: 6 Bond angle restraints: 24780 Sorted by residual: angle pdb=" C GLU A 567 " pdb=" N ASP A 568 " pdb=" CA ASP A 568 " ideal model delta sigma weight residual 121.54 132.38 -10.84 1.91e+00 2.74e-01 3.22e+01 angle pdb=" CB LYS A 736 " pdb=" CG LYS A 736 " pdb=" CD LYS A 736 " ideal model delta sigma weight residual 111.30 123.83 -12.53 2.30e+00 1.89e-01 2.97e+01 angle pdb=" C GLU A 969 " pdb=" N ASP A 970 " pdb=" CA ASP A 970 " ideal model delta sigma weight residual 121.54 130.71 -9.17 1.91e+00 2.74e-01 2.30e+01 angle pdb=" N GLU A 574 " pdb=" CA GLU A 574 " pdb=" CB GLU A 574 " ideal model delta sigma weight residual 110.28 117.52 -7.24 1.55e+00 4.16e-01 2.18e+01 angle pdb=" C GLU A1914 " pdb=" N ASP A1915 " pdb=" CA ASP A1915 " ideal model delta sigma weight residual 122.82 129.43 -6.61 1.42e+00 4.96e-01 2.17e+01 ... (remaining 24775 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 10027 17.94 - 35.88: 1091 35.88 - 53.82: 135 53.82 - 71.77: 27 71.77 - 89.71: 11 Dihedral angle restraints: 11291 sinusoidal: 4651 harmonic: 6640 Sorted by residual: dihedral pdb=" CA ARG A2485 " pdb=" C ARG A2485 " pdb=" N SER A2486 " pdb=" CA SER A2486 " ideal model delta harmonic sigma weight residual 180.00 125.40 54.60 0 5.00e+00 4.00e-02 1.19e+02 dihedral pdb=" CA VAL A 894 " pdb=" C VAL A 894 " pdb=" N HIS A 895 " pdb=" CA HIS A 895 " ideal model delta harmonic sigma weight residual 180.00 139.24 40.76 0 5.00e+00 4.00e-02 6.65e+01 dihedral pdb=" CA GLU A2488 " pdb=" C GLU A2488 " pdb=" N GLU A2489 " pdb=" CA GLU A2489 " ideal model delta harmonic sigma weight residual 180.00 143.11 36.89 0 5.00e+00 4.00e-02 5.44e+01 ... (remaining 11288 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 2450 0.082 - 0.164: 355 0.164 - 0.246: 30 0.246 - 0.328: 3 0.328 - 0.409: 1 Chirality restraints: 2839 Sorted by residual: chirality pdb=" CB ILE A1607 " pdb=" CA ILE A1607 " pdb=" CG1 ILE A1607 " pdb=" CG2 ILE A1607 " both_signs ideal model delta sigma weight residual False 2.64 2.24 0.41 2.00e-01 2.50e+01 4.19e+00 chirality pdb=" CB VAL A 879 " pdb=" CA VAL A 879 " pdb=" CG1 VAL A 879 " pdb=" CG2 VAL A 879 " both_signs ideal model delta sigma weight residual False -2.63 -2.33 -0.29 2.00e-01 2.50e+01 2.17e+00 chirality pdb=" CG LEU A 881 " pdb=" CB LEU A 881 " pdb=" CD1 LEU A 881 " pdb=" CD2 LEU A 881 " both_signs ideal model delta sigma weight residual False -2.59 -2.30 -0.29 2.00e-01 2.50e+01 2.06e+00 ... (remaining 2836 not shown) Planarity restraints: 3112 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 490 " 0.339 9.50e-02 1.11e+02 1.52e-01 1.55e+01 pdb=" NE ARG A 490 " -0.027 2.00e-02 2.50e+03 pdb=" CZ ARG A 490 " 0.016 2.00e-02 2.50e+03 pdb=" NH1 ARG A 490 " -0.009 2.00e-02 2.50e+03 pdb=" NH2 ARG A 490 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 567 " -0.016 2.00e-02 2.50e+03 3.28e-02 1.08e+01 pdb=" C GLU A 567 " 0.057 2.00e-02 2.50e+03 pdb=" O GLU A 567 " -0.022 2.00e-02 2.50e+03 pdb=" N ASP A 568 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A1410 " 0.016 2.00e-02 2.50e+03 1.98e-02 7.82e+00 pdb=" CG TYR A1410 " -0.044 2.00e-02 2.50e+03 pdb=" CD1 TYR A1410 " 0.024 2.00e-02 2.50e+03 pdb=" CD2 TYR A1410 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR A1410 " -0.011 2.00e-02 2.50e+03 pdb=" CE2 TYR A1410 " 0.012 2.00e-02 2.50e+03 pdb=" CZ TYR A1410 " 0.004 2.00e-02 2.50e+03 pdb=" OH TYR A1410 " -0.002 2.00e-02 2.50e+03 ... (remaining 3109 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 4816 2.80 - 3.33: 17082 3.33 - 3.85: 29582 3.85 - 4.38: 32922 4.38 - 4.90: 55358 Nonbonded interactions: 139760 Sorted by model distance: nonbonded pdb=" O PHE A1176 " pdb=" OG1 THR A1180 " model vdw 2.278 3.040 nonbonded pdb=" O GLU A2265 " pdb=" OH TYR A2329 " model vdw 2.292 3.040 nonbonded pdb=" O GLY A2542 " pdb=" OG1 THR A2660 " model vdw 2.293 3.040 nonbonded pdb=" OH TYR A1247 " pdb=" OG SER A1329 " model vdw 2.293 3.040 nonbonded pdb=" O GLN A1951 " pdb=" NH1 ARG A1953 " model vdw 2.295 3.120 ... (remaining 139755 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.420 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: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 16.040 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 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:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5931 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 18394 Z= 0.226 Angle : 1.060 14.836 24780 Z= 0.552 Chirality : 0.057 0.409 2839 Planarity : 0.006 0.152 3112 Dihedral : 14.344 89.708 6971 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.23 % Allowed : 8.33 % Favored : 91.44 % Rotamer: Outliers : 0.05 % Allowed : 0.63 % Favored : 99.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.28 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.96 (0.15), residues: 2220 helix: -1.40 (0.13), residues: 1215 sheet: -0.68 (0.49), residues: 92 loop : -2.83 (0.18), residues: 913 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG A 490 TYR 0.044 0.002 TYR A1410 PHE 0.040 0.002 PHE A 707 TRP 0.040 0.003 TRP A 907 HIS 0.009 0.001 HIS A1179 Details of bonding type rmsd covalent geometry : bond 0.00459 (18394) covalent geometry : angle 1.06027 (24780) hydrogen bonds : bond 0.13300 ( 877) hydrogen bonds : angle 6.45658 ( 2586) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 414 time to evaluate : 0.644 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 344 ASP cc_start: 0.8060 (m-30) cc_final: 0.7834 (m-30) REVERT: A 355 GLU cc_start: 0.7467 (mm-30) cc_final: 0.6660 (tp30) REVERT: A 364 PHE cc_start: 0.7878 (p90) cc_final: 0.6753 (t80) REVERT: A 392 ILE cc_start: 0.6578 (mm) cc_final: 0.5666 (tp) REVERT: A 450 GLU cc_start: 0.7540 (mt-10) cc_final: 0.7078 (mp0) REVERT: A 452 GLU cc_start: 0.8207 (tm-30) cc_final: 0.7754 (tm-30) REVERT: A 536 MET cc_start: 0.5963 (tpp) cc_final: 0.5157 (tpt) REVERT: A 604 ASN cc_start: 0.7596 (p0) cc_final: 0.7394 (p0) REVERT: A 608 LEU cc_start: 0.8127 (mm) cc_final: 0.7840 (mt) REVERT: A 623 LYS cc_start: 0.8146 (mttt) cc_final: 0.7486 (mmmm) REVERT: A 637 TYR cc_start: 0.6869 (m-10) cc_final: 0.4218 (m-10) REVERT: A 639 GLU cc_start: 0.7558 (tp30) cc_final: 0.7160 (tp30) REVERT: A 642 MET cc_start: 0.7283 (ttt) cc_final: 0.7048 (ttt) REVERT: A 646 LYS cc_start: 0.8809 (ptpt) cc_final: 0.8538 (ptmt) REVERT: A 671 MET cc_start: 0.6434 (ttt) cc_final: 0.5794 (ttt) REVERT: A 691 MET cc_start: 0.7833 (mmm) cc_final: 0.7096 (mtt) REVERT: A 702 GLU cc_start: 0.7083 (pm20) cc_final: 0.6634 (pm20) REVERT: A 770 MET cc_start: 0.7233 (tmm) cc_final: 0.6510 (tmm) REVERT: A 773 LYS cc_start: 0.8907 (tptt) cc_final: 0.8271 (tppt) REVERT: A 785 MET cc_start: 0.5747 (mtp) cc_final: 0.5476 (mmm) REVERT: A 795 MET cc_start: 0.7675 (mtm) cc_final: 0.7050 (mmm) REVERT: A 797 ILE cc_start: 0.7333 (pt) cc_final: 0.6102 (mm) REVERT: A 798 PHE cc_start: 0.7273 (m-10) cc_final: 0.7009 (m-10) REVERT: A 801 MET cc_start: 0.7857 (mtm) cc_final: 0.7624 (mtm) REVERT: A 833 ILE cc_start: 0.8440 (mp) cc_final: 0.8150 (mp) REVERT: A 836 VAL cc_start: 0.8019 (m) cc_final: 0.7783 (p) REVERT: A 842 LEU cc_start: 0.8376 (tp) cc_final: 0.8105 (tp) REVERT: A 873 GLU cc_start: 0.7859 (mt-10) cc_final: 0.7436 (mt-10) REVERT: A 886 MET cc_start: 0.6533 (tpp) cc_final: 0.5633 (tpp) REVERT: A 911 PHE cc_start: 0.5508 (t80) cc_final: 0.4901 (t80) REVERT: A 913 LYS cc_start: 0.8582 (tptt) cc_final: 0.8102 (tppt) REVERT: A 929 MET cc_start: 0.7019 (tpt) cc_final: 0.6447 (tpt) REVERT: A 969 GLU cc_start: 0.7800 (tp30) cc_final: 0.7490 (tp30) REVERT: A 985 LYS cc_start: 0.7790 (tmtt) cc_final: 0.7539 (tmtt) REVERT: A 1106 GLU cc_start: 0.6732 (mm-30) cc_final: 0.6275 (mm-30) REVERT: A 1109 ASP cc_start: 0.7464 (t0) cc_final: 0.6985 (t0) REVERT: A 1126 MET cc_start: 0.7696 (mmm) cc_final: 0.7404 (mmm) REVERT: A 1144 GLU cc_start: 0.7404 (pp20) cc_final: 0.7146 (pp20) REVERT: A 1171 LYS cc_start: 0.7997 (tppt) cc_final: 0.7591 (tppt) REVERT: A 1176 PHE cc_start: 0.7825 (t80) cc_final: 0.7283 (t80) REVERT: A 1193 ILE cc_start: 0.7845 (tp) cc_final: 0.7599 (tp) REVERT: A 1201 ILE cc_start: 0.7089 (mp) cc_final: 0.6880 (mm) REVERT: A 1209 LEU cc_start: 0.8292 (tp) cc_final: 0.8067 (tp) REVERT: A 1217 ASP cc_start: 0.7244 (m-30) cc_final: 0.6936 (m-30) REVERT: A 1237 LYS cc_start: 0.7329 (tptt) cc_final: 0.7044 (mmtt) REVERT: A 1249 LEU cc_start: 0.8007 (tp) cc_final: 0.7784 (tp) REVERT: A 1309 LEU cc_start: 0.5973 (mm) cc_final: 0.5513 (tp) REVERT: A 1320 TRP cc_start: 0.7248 (p-90) cc_final: 0.6441 (p-90) REVERT: A 1321 LEU cc_start: 0.7604 (mt) cc_final: 0.6892 (tt) REVERT: A 1333 HIS cc_start: 0.6773 (t-170) cc_final: 0.6316 (t-170) REVERT: A 1337 MET cc_start: 0.7594 (mmp) cc_final: 0.6805 (mmp) REVERT: A 1338 LYS cc_start: 0.8331 (ptmt) cc_final: 0.8046 (ptmt) REVERT: A 1354 THR cc_start: 0.7474 (p) cc_final: 0.7182 (p) REVERT: A 1363 ASN cc_start: 0.7424 (m-40) cc_final: 0.6768 (m-40) REVERT: A 1385 LEU cc_start: 0.8019 (tt) cc_final: 0.7729 (mp) REVERT: A 1418 PHE cc_start: 0.6765 (t80) cc_final: 0.6457 (t80) REVERT: A 1431 LEU cc_start: 0.7089 (tt) cc_final: 0.6884 (tt) REVERT: A 1435 HIS cc_start: 0.7126 (m90) cc_final: 0.6885 (m90) REVERT: A 1453 MET cc_start: 0.7774 (mmp) cc_final: 0.7519 (mmm) REVERT: A 1457 ILE cc_start: 0.8651 (mt) cc_final: 0.8352 (mt) REVERT: A 1495 ASN cc_start: 0.7426 (t160) cc_final: 0.6488 (t0) REVERT: A 1503 LYS cc_start: 0.8560 (ptpt) cc_final: 0.8324 (ptpt) REVERT: A 1509 LYS cc_start: 0.7869 (mptt) cc_final: 0.7217 (mmtt) REVERT: A 1569 MET cc_start: 0.7359 (ptm) cc_final: 0.6835 (ptm) REVERT: A 1588 LYS cc_start: 0.7625 (tptt) cc_final: 0.7412 (mmmt) REVERT: A 1590 MET cc_start: 0.6845 (tpp) cc_final: 0.6262 (mmp) REVERT: A 1645 GLU cc_start: 0.8303 (pp20) cc_final: 0.7876 (tm-30) REVERT: A 1823 VAL cc_start: 0.7120 (p) cc_final: 0.6866 (t) REVERT: A 1898 ASP cc_start: 0.7819 (m-30) cc_final: 0.7435 (t0) REVERT: A 1912 ILE cc_start: 0.7245 (tt) cc_final: 0.6801 (tt) REVERT: A 1917 LYS cc_start: 0.8439 (tmtt) cc_final: 0.8201 (tptp) REVERT: A 1966 PHE cc_start: 0.6991 (m-80) cc_final: 0.6602 (m-10) REVERT: A 1998 ILE cc_start: 0.7303 (mt) cc_final: 0.6981 (tt) REVERT: A 2009 ASN cc_start: 0.7640 (t0) cc_final: 0.7301 (m-40) REVERT: A 2010 LEU cc_start: 0.8116 (tp) cc_final: 0.7879 (tp) REVERT: A 2033 ARG cc_start: 0.8055 (ttp80) cc_final: 0.7612 (ttp80) REVERT: A 2055 GLU cc_start: 0.7726 (tt0) cc_final: 0.7329 (mm-30) REVERT: A 2057 LYS cc_start: 0.8594 (mmtm) cc_final: 0.8106 (mmmt) REVERT: A 2083 ASN cc_start: 0.8249 (m-40) cc_final: 0.8044 (m110) REVERT: A 2301 SER cc_start: 0.7962 (t) cc_final: 0.7539 (p) REVERT: A 2357 LEU cc_start: 0.7800 (mm) cc_final: 0.7359 (pp) REVERT: A 2395 MET cc_start: 0.6588 (mtt) cc_final: 0.6175 (mmt) REVERT: A 2425 TYR cc_start: 0.4815 (m-10) cc_final: 0.4337 (m-10) REVERT: A 2603 GLU cc_start: 0.8800 (tm-30) cc_final: 0.7967 (tm-30) REVERT: A 2607 LYS cc_start: 0.9045 (mmpt) cc_final: 0.8549 (mmmt) outliers start: 1 outliers final: 0 residues processed: 414 average time/residue: 0.1188 time to fit residues: 74.0198 Evaluate side-chains 392 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 392 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 216 optimal weight: 10.0000 chunk 98 optimal weight: 0.5980 chunk 194 optimal weight: 7.9990 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 0.0980 chunk 103 optimal weight: 4.9990 chunk 200 optimal weight: 9.9990 chunk 212 optimal weight: 9.9990 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 358 HIS ** A 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 407 GLN ** A 419 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 877 ASN ** A 939 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1495 ASN ** A1516 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1605 GLN A1883 ASN ** A1901 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2258 ASN A2528 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4662 r_free = 0.4662 target = 0.199430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.165059 restraints weight = 41414.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.4350 r_free = 0.4350 target = 0.169435 restraints weight = 26385.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.4385 r_free = 0.4385 target = 0.172523 restraints weight = 18573.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.4409 r_free = 0.4409 target = 0.174682 restraints weight = 14084.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.4426 r_free = 0.4426 target = 0.176247 restraints weight = 11376.077| |-----------------------------------------------------------------------------| r_work (final): 0.4400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6044 moved from start: 0.1792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 18394 Z= 0.212 Angle : 0.737 9.792 24780 Z= 0.395 Chirality : 0.046 0.261 2839 Planarity : 0.005 0.055 3112 Dihedral : 5.835 53.390 2411 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 14.62 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.79 % Favored : 91.98 % Rotamer: Outliers : 0.77 % Allowed : 9.43 % Favored : 89.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.97 (0.17), residues: 2220 helix: -0.32 (0.14), residues: 1234 sheet: -0.62 (0.48), residues: 101 loop : -2.85 (0.19), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A1953 TYR 0.032 0.002 TYR A 876 PHE 0.023 0.002 PHE A1400 TRP 0.030 0.002 TRP A1238 HIS 0.013 0.001 HIS A 564 Details of bonding type rmsd covalent geometry : bond 0.00427 (18394) covalent geometry : angle 0.73690 (24780) hydrogen bonds : bond 0.04504 ( 877) hydrogen bonds : angle 5.05718 ( 2586) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 403 time to evaluate : 0.485 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 446 GLN cc_start: 0.7522 (tm-30) cc_final: 0.7244 (tm-30) REVERT: A 536 MET cc_start: 0.6290 (tpp) cc_final: 0.5591 (tpt) REVERT: A 603 LYS cc_start: 0.8349 (tppt) cc_final: 0.8051 (tppt) REVERT: A 604 ASN cc_start: 0.7616 (p0) cc_final: 0.7195 (p0) REVERT: A 608 LEU cc_start: 0.8003 (mm) cc_final: 0.7758 (mt) REVERT: A 623 LYS cc_start: 0.8158 (mttt) cc_final: 0.7463 (mmmm) REVERT: A 637 TYR cc_start: 0.6933 (m-10) cc_final: 0.3685 (m-80) REVERT: A 639 GLU cc_start: 0.7533 (tp30) cc_final: 0.7120 (tp30) REVERT: A 642 MET cc_start: 0.7375 (ttt) cc_final: 0.7021 (ttt) REVERT: A 646 LYS cc_start: 0.8880 (ptpt) cc_final: 0.8558 (ptpp) REVERT: A 670 MET cc_start: 0.6872 (OUTLIER) cc_final: 0.6647 (tmm) REVERT: A 671 MET cc_start: 0.6551 (ttt) cc_final: 0.5815 (ttt) REVERT: A 741 PHE cc_start: 0.6955 (t80) cc_final: 0.6537 (t80) REVERT: A 762 LYS cc_start: 0.7971 (mppt) cc_final: 0.7746 (mppt) REVERT: A 770 MET cc_start: 0.7218 (tmm) cc_final: 0.6669 (tmm) REVERT: A 785 MET cc_start: 0.6098 (mtp) cc_final: 0.5731 (mmm) REVERT: A 802 ARG cc_start: 0.7356 (ttp80) cc_final: 0.7064 (ttp80) REVERT: A 842 LEU cc_start: 0.8480 (tp) cc_final: 0.8268 (tp) REVERT: A 873 GLU cc_start: 0.7903 (mt-10) cc_final: 0.7648 (mt-10) REVERT: A 886 MET cc_start: 0.6180 (tpp) cc_final: 0.5864 (tpp) REVERT: A 911 PHE cc_start: 0.6041 (t80) cc_final: 0.5298 (t80) REVERT: A 913 LYS cc_start: 0.8665 (tptt) cc_final: 0.8208 (tppt) REVERT: A 929 MET cc_start: 0.7066 (tpt) cc_final: 0.6467 (tpt) REVERT: A 969 GLU cc_start: 0.8113 (tp30) cc_final: 0.7828 (tp30) REVERT: A 1102 LYS cc_start: 0.6471 (tptt) cc_final: 0.5969 (tptp) REVERT: A 1106 GLU cc_start: 0.6802 (mm-30) cc_final: 0.6346 (mm-30) REVERT: A 1109 ASP cc_start: 0.7393 (t0) cc_final: 0.7044 (t0) REVERT: A 1112 LYS cc_start: 0.7384 (mtpp) cc_final: 0.7172 (mtpp) REVERT: A 1117 MET cc_start: 0.5781 (tpp) cc_final: 0.5288 (tpt) REVERT: A 1126 MET cc_start: 0.7898 (mmm) cc_final: 0.7680 (mmm) REVERT: A 1171 LYS cc_start: 0.8177 (tppt) cc_final: 0.7741 (tppt) REVERT: A 1176 PHE cc_start: 0.7815 (t80) cc_final: 0.7442 (t80) REVERT: A 1181 PHE cc_start: 0.7694 (t80) cc_final: 0.7403 (t80) REVERT: A 1193 ILE cc_start: 0.7753 (tp) cc_final: 0.7546 (tp) REVERT: A 1201 ILE cc_start: 0.7035 (mp) cc_final: 0.6825 (mm) REVERT: A 1217 ASP cc_start: 0.7378 (m-30) cc_final: 0.7070 (m-30) REVERT: A 1237 LYS cc_start: 0.7168 (tptt) cc_final: 0.6961 (mmtt) REVERT: A 1304 LEU cc_start: 0.8360 (OUTLIER) cc_final: 0.7975 (pp) REVERT: A 1333 HIS cc_start: 0.6643 (t-170) cc_final: 0.6261 (t-170) REVERT: A 1337 MET cc_start: 0.7516 (mmp) cc_final: 0.7128 (mmt) REVERT: A 1376 MET cc_start: 0.7040 (tmm) cc_final: 0.6687 (tmm) REVERT: A 1433 CYS cc_start: 0.6868 (p) cc_final: 0.6411 (p) REVERT: A 1457 ILE cc_start: 0.8725 (mt) cc_final: 0.8453 (mt) REVERT: A 1480 GLN cc_start: 0.7257 (tp40) cc_final: 0.6502 (tp-100) REVERT: A 1495 ASN cc_start: 0.7482 (t0) cc_final: 0.6649 (t0) REVERT: A 1509 LYS cc_start: 0.7887 (mptt) cc_final: 0.7314 (mmtm) REVERT: A 1542 TYR cc_start: 0.7164 (t80) cc_final: 0.6165 (t80) REVERT: A 1569 MET cc_start: 0.7372 (ptm) cc_final: 0.6949 (ptt) REVERT: A 1575 LYS cc_start: 0.8035 (mttp) cc_final: 0.6758 (tptt) REVERT: A 1588 LYS cc_start: 0.7677 (tptt) cc_final: 0.7472 (mmmt) REVERT: A 1645 GLU cc_start: 0.8276 (pp20) cc_final: 0.7963 (tm-30) REVERT: A 1898 ASP cc_start: 0.7771 (m-30) cc_final: 0.7544 (t0) REVERT: A 1917 LYS cc_start: 0.8202 (tmtt) cc_final: 0.7952 (tptp) REVERT: A 1966 PHE cc_start: 0.6906 (m-80) cc_final: 0.6547 (m-10) REVERT: A 1998 ILE cc_start: 0.7531 (mt) cc_final: 0.7233 (tt) REVERT: A 2009 ASN cc_start: 0.7824 (t0) cc_final: 0.7515 (m-40) REVERT: A 2033 ARG cc_start: 0.8055 (ttp80) cc_final: 0.7807 (ttp80) REVERT: A 2057 LYS cc_start: 0.8630 (mmtm) cc_final: 0.8039 (mmmt) REVERT: A 2083 ASN cc_start: 0.8140 (m-40) cc_final: 0.7787 (m110) REVERT: A 2095 MET cc_start: 0.6831 (mpp) cc_final: 0.6631 (mpp) REVERT: A 2301 SER cc_start: 0.8128 (t) cc_final: 0.7662 (p) REVERT: A 2357 LEU cc_start: 0.7749 (mm) cc_final: 0.7507 (pp) REVERT: A 2395 MET cc_start: 0.6772 (mtt) cc_final: 0.6428 (mmt) REVERT: A 2425 TYR cc_start: 0.4929 (m-10) cc_final: 0.4101 (m-80) REVERT: A 2603 GLU cc_start: 0.8771 (tm-30) cc_final: 0.8276 (tm-30) REVERT: A 2607 LYS cc_start: 0.9025 (mmpt) cc_final: 0.8806 (mmmt) outliers start: 16 outliers final: 8 residues processed: 405 average time/residue: 0.1163 time to fit residues: 70.9633 Evaluate side-chains 392 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 382 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 378 ASP Chi-restraints excluded: chain A residue 534 PHE Chi-restraints excluded: chain A residue 670 MET Chi-restraints excluded: chain A residue 765 VAL Chi-restraints excluded: chain A residue 1287 ASN Chi-restraints excluded: chain A residue 1304 LEU Chi-restraints excluded: chain A residue 1328 LEU Chi-restraints excluded: chain A residue 1331 VAL Chi-restraints excluded: chain A residue 1510 SER Chi-restraints excluded: chain A residue 2668 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 6 optimal weight: 2.9990 chunk 175 optimal weight: 4.9990 chunk 3 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 52 optimal weight: 0.9980 chunk 23 optimal weight: 0.9990 chunk 101 optimal weight: 0.9990 chunk 7 optimal weight: 0.9990 chunk 36 optimal weight: 0.9980 chunk 95 optimal weight: 0.0060 chunk 174 optimal weight: 0.8980 overall best weight: 0.7796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 407 GLN ** A 419 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 515 ASN ** A 939 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1901 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2006 GLN A2042 ASN ** A2086 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4684 r_free = 0.4684 target = 0.201439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4329 r_free = 0.4329 target = 0.167151 restraints weight = 41657.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4379 r_free = 0.4379 target = 0.171584 restraints weight = 26690.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4416 r_free = 0.4416 target = 0.174786 restraints weight = 18784.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.4440 r_free = 0.4440 target = 0.177025 restraints weight = 14172.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 56)----------------| | r_work = 0.4457 r_free = 0.4457 target = 0.178639 restraints weight = 11367.154| |-----------------------------------------------------------------------------| r_work (final): 0.4430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5981 moved from start: 0.2030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 18394 Z= 0.134 Angle : 0.671 12.228 24780 Z= 0.348 Chirality : 0.044 0.313 2839 Planarity : 0.004 0.056 3112 Dihedral : 5.469 51.667 2411 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.25 % Favored : 92.57 % Rotamer: Outliers : 1.45 % Allowed : 13.21 % Favored : 85.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.42 (0.17), residues: 2220 helix: 0.21 (0.14), residues: 1233 sheet: -0.53 (0.49), residues: 99 loop : -2.71 (0.20), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 802 TYR 0.044 0.001 TYR A 876 PHE 0.017 0.001 PHE A 644 TRP 0.020 0.002 TRP A1857 HIS 0.006 0.001 HIS A 564 Details of bonding type rmsd covalent geometry : bond 0.00274 (18394) covalent geometry : angle 0.67098 (24780) hydrogen bonds : bond 0.03773 ( 877) hydrogen bonds : angle 4.74958 ( 2586) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 397 time to evaluate : 0.657 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 392 ILE cc_start: 0.6589 (mp) cc_final: 0.5258 (pt) REVERT: A 446 GLN cc_start: 0.7505 (tm-30) cc_final: 0.7189 (tm-30) REVERT: A 475 SER cc_start: 0.6485 (t) cc_final: 0.5790 (p) REVERT: A 536 MET cc_start: 0.6296 (tpp) cc_final: 0.5606 (tpt) REVERT: A 603 LYS cc_start: 0.8378 (tppt) cc_final: 0.8007 (tppt) REVERT: A 604 ASN cc_start: 0.7587 (p0) cc_final: 0.7190 (p0) REVERT: A 623 LYS cc_start: 0.8156 (mttt) cc_final: 0.7523 (mmmm) REVERT: A 637 TYR cc_start: 0.6873 (m-10) cc_final: 0.4042 (m-80) REVERT: A 639 GLU cc_start: 0.7436 (tp30) cc_final: 0.6978 (tp30) REVERT: A 642 MET cc_start: 0.7194 (ttt) cc_final: 0.6861 (ttt) REVERT: A 646 LYS cc_start: 0.8796 (ptpt) cc_final: 0.8492 (ptpp) REVERT: A 671 MET cc_start: 0.6454 (ttt) cc_final: 0.5826 (ttt) REVERT: A 736 LYS cc_start: 0.7718 (mmmm) cc_final: 0.7511 (mmmm) REVERT: A 741 PHE cc_start: 0.6839 (t80) cc_final: 0.6451 (t80) REVERT: A 762 LYS cc_start: 0.8069 (mppt) cc_final: 0.7782 (mppt) REVERT: A 770 MET cc_start: 0.7137 (tmm) cc_final: 0.6561 (tmm) REVERT: A 785 MET cc_start: 0.5824 (mtp) cc_final: 0.5473 (mmm) REVERT: A 802 ARG cc_start: 0.7293 (ttp80) cc_final: 0.7074 (ttp80) REVERT: A 842 LEU cc_start: 0.8386 (tp) cc_final: 0.8177 (tp) REVERT: A 886 MET cc_start: 0.6251 (tpp) cc_final: 0.5947 (tpp) REVERT: A 911 PHE cc_start: 0.5949 (t80) cc_final: 0.5270 (t80) REVERT: A 913 LYS cc_start: 0.8626 (tptt) cc_final: 0.8173 (tppt) REVERT: A 929 MET cc_start: 0.6841 (tpt) cc_final: 0.6351 (tpt) REVERT: A 949 ASP cc_start: 0.8218 (p0) cc_final: 0.7924 (p0) REVERT: A 969 GLU cc_start: 0.8053 (tp30) cc_final: 0.7715 (tp30) REVERT: A 985 LYS cc_start: 0.7319 (tmtt) cc_final: 0.6938 (tptt) REVERT: A 1102 LYS cc_start: 0.6380 (tptt) cc_final: 0.5980 (tptp) REVERT: A 1106 GLU cc_start: 0.6764 (mm-30) cc_final: 0.6332 (mm-30) REVERT: A 1109 ASP cc_start: 0.7287 (t0) cc_final: 0.7024 (t0) REVERT: A 1112 LYS cc_start: 0.7367 (mtpp) cc_final: 0.7055 (mtpp) REVERT: A 1126 MET cc_start: 0.7823 (mmm) cc_final: 0.7591 (mmt) REVERT: A 1171 LYS cc_start: 0.8111 (tppt) cc_final: 0.7656 (tppt) REVERT: A 1176 PHE cc_start: 0.7827 (t80) cc_final: 0.7434 (t80) REVERT: A 1193 ILE cc_start: 0.7778 (tp) cc_final: 0.7561 (tp) REVERT: A 1201 ILE cc_start: 0.7076 (mp) cc_final: 0.6812 (mm) REVERT: A 1304 LEU cc_start: 0.8295 (mm) cc_final: 0.7907 (pp) REVERT: A 1309 LEU cc_start: 0.5979 (mm) cc_final: 0.5534 (pt) REVERT: A 1320 TRP cc_start: 0.7588 (p90) cc_final: 0.7284 (p90) REVERT: A 1333 HIS cc_start: 0.6543 (t-170) cc_final: 0.6219 (t-170) REVERT: A 1337 MET cc_start: 0.7449 (mmp) cc_final: 0.7128 (mmt) REVERT: A 1338 LYS cc_start: 0.8335 (ptmt) cc_final: 0.7932 (pttt) REVERT: A 1376 MET cc_start: 0.6919 (tmm) cc_final: 0.6603 (tmm) REVERT: A 1433 CYS cc_start: 0.6826 (p) cc_final: 0.6418 (p) REVERT: A 1457 ILE cc_start: 0.8643 (mt) cc_final: 0.8337 (mt) REVERT: A 1480 GLN cc_start: 0.7157 (tp40) cc_final: 0.6401 (tp-100) REVERT: A 1482 GLN cc_start: 0.7346 (mm-40) cc_final: 0.7143 (mm110) REVERT: A 1495 ASN cc_start: 0.7464 (t0) cc_final: 0.6573 (t0) REVERT: A 1569 MET cc_start: 0.7399 (ptm) cc_final: 0.6963 (ptt) REVERT: A 1575 LYS cc_start: 0.8007 (mttp) cc_final: 0.6999 (mmmt) REVERT: A 1588 LYS cc_start: 0.7630 (tptt) cc_final: 0.7398 (mmmt) REVERT: A 1645 GLU cc_start: 0.8292 (pp20) cc_final: 0.8021 (tm-30) REVERT: A 1917 LYS cc_start: 0.8223 (tmtt) cc_final: 0.7956 (tptp) REVERT: A 1966 PHE cc_start: 0.6911 (m-80) cc_final: 0.6669 (m-10) REVERT: A 1998 ILE cc_start: 0.7557 (mt) cc_final: 0.7313 (tt) REVERT: A 2009 ASN cc_start: 0.7760 (t0) cc_final: 0.7389 (m-40) REVERT: A 2083 ASN cc_start: 0.8149 (m-40) cc_final: 0.7943 (m110) REVERT: A 2278 PHE cc_start: 0.6536 (m-10) cc_final: 0.6289 (m-80) REVERT: A 2301 SER cc_start: 0.8011 (t) cc_final: 0.7584 (p) REVERT: A 2357 LEU cc_start: 0.7722 (OUTLIER) cc_final: 0.7142 (mt) REVERT: A 2395 MET cc_start: 0.6652 (mtt) cc_final: 0.6317 (mmt) REVERT: A 2603 GLU cc_start: 0.8726 (tm-30) cc_final: 0.8163 (tm-30) REVERT: A 2607 LYS cc_start: 0.9044 (mmpt) cc_final: 0.8743 (mmmt) outliers start: 30 outliers final: 14 residues processed: 410 average time/residue: 0.1131 time to fit residues: 69.7291 Evaluate side-chains 404 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 389 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 534 PHE Chi-restraints excluded: chain A residue 704 TYR Chi-restraints excluded: chain A residue 722 LEU Chi-restraints excluded: chain A residue 729 SER Chi-restraints excluded: chain A residue 766 PHE Chi-restraints excluded: chain A residue 862 CYS Chi-restraints excluded: chain A residue 885 MET Chi-restraints excluded: chain A residue 961 MET Chi-restraints excluded: chain A residue 1287 ASN Chi-restraints excluded: chain A residue 1328 LEU Chi-restraints excluded: chain A residue 1373 VAL Chi-restraints excluded: chain A residue 1510 SER Chi-restraints excluded: chain A residue 1890 LEU Chi-restraints excluded: chain A residue 2357 LEU Chi-restraints excluded: chain A residue 2668 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 13 optimal weight: 4.9990 chunk 133 optimal weight: 2.9990 chunk 135 optimal weight: 0.0970 chunk 201 optimal weight: 30.0000 chunk 189 optimal weight: 5.9990 chunk 193 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 100 optimal weight: 0.8980 chunk 44 optimal weight: 0.7980 chunk 167 optimal weight: 9.9990 overall best weight: 1.3582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 407 GLN ** A 419 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 939 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1480 GLN ** A1482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1901 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2006 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2384 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4664 r_free = 0.4664 target = 0.199381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.164924 restraints weight = 41941.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.4355 r_free = 0.4355 target = 0.169335 restraints weight = 26980.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.4390 r_free = 0.4390 target = 0.172445 restraints weight = 19068.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 63)----------------| | r_work = 0.4415 r_free = 0.4415 target = 0.174638 restraints weight = 14485.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 56)----------------| | r_work = 0.4432 r_free = 0.4432 target = 0.176190 restraints weight = 11667.112| |-----------------------------------------------------------------------------| r_work (final): 0.4402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6045 moved from start: 0.2486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 18394 Z= 0.165 Angle : 0.703 10.358 24780 Z= 0.365 Chirality : 0.045 0.282 2839 Planarity : 0.004 0.056 3112 Dihedral : 5.410 51.342 2411 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 13.66 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.69 % Favored : 91.17 % Rotamer: Outliers : 1.98 % Allowed : 15.58 % Favored : 82.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.27 (0.18), residues: 2220 helix: 0.35 (0.15), residues: 1240 sheet: -0.34 (0.50), residues: 93 loop : -2.70 (0.20), residues: 887 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A2033 TYR 0.042 0.002 TYR A 876 PHE 0.020 0.001 PHE A1400 TRP 0.027 0.002 TRP A1857 HIS 0.008 0.001 HIS A 564 Details of bonding type rmsd covalent geometry : bond 0.00337 (18394) covalent geometry : angle 0.70343 (24780) hydrogen bonds : bond 0.03975 ( 877) hydrogen bonds : angle 4.74292 ( 2586) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 441 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 400 time to evaluate : 0.464 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 421 GLU cc_start: 0.7387 (mm-30) cc_final: 0.7003 (mm-30) REVERT: A 452 GLU cc_start: 0.8089 (tm-30) cc_final: 0.7738 (tm-30) REVERT: A 475 SER cc_start: 0.6661 (t) cc_final: 0.6002 (p) REVERT: A 536 MET cc_start: 0.6434 (tpp) cc_final: 0.5805 (tpt) REVERT: A 558 MET cc_start: 0.1195 (ttt) cc_final: -0.1140 (ttt) REVERT: A 603 LYS cc_start: 0.8429 (tppt) cc_final: 0.8069 (tppt) REVERT: A 604 ASN cc_start: 0.7487 (p0) cc_final: 0.7080 (p0) REVERT: A 623 LYS cc_start: 0.8165 (mttt) cc_final: 0.7553 (mmmm) REVERT: A 637 TYR cc_start: 0.6867 (m-10) cc_final: 0.4888 (m-10) REVERT: A 639 GLU cc_start: 0.7453 (tp30) cc_final: 0.6984 (tp30) REVERT: A 642 MET cc_start: 0.7286 (ttt) cc_final: 0.6933 (ttt) REVERT: A 646 LYS cc_start: 0.8850 (ptpt) cc_final: 0.8546 (ptpp) REVERT: A 671 MET cc_start: 0.6437 (ttt) cc_final: 0.5852 (ttt) REVERT: A 736 LYS cc_start: 0.7910 (mmmm) cc_final: 0.7681 (mmmm) REVERT: A 741 PHE cc_start: 0.6839 (t80) cc_final: 0.6428 (t80) REVERT: A 770 MET cc_start: 0.7135 (tmm) cc_final: 0.6604 (tmm) REVERT: A 785 MET cc_start: 0.5975 (mtp) cc_final: 0.5560 (mmm) REVERT: A 842 LEU cc_start: 0.8402 (tp) cc_final: 0.8164 (tp) REVERT: A 861 LYS cc_start: 0.8705 (mptt) cc_final: 0.8437 (mmtt) REVERT: A 873 GLU cc_start: 0.7806 (mt-10) cc_final: 0.7157 (mp0) REVERT: A 886 MET cc_start: 0.6401 (tpp) cc_final: 0.5954 (tpp) REVERT: A 911 PHE cc_start: 0.6121 (t80) cc_final: 0.5231 (t80) REVERT: A 913 LYS cc_start: 0.8700 (tptt) cc_final: 0.8282 (tppt) REVERT: A 929 MET cc_start: 0.6966 (tpt) cc_final: 0.6517 (tpt) REVERT: A 949 ASP cc_start: 0.8214 (p0) cc_final: 0.7951 (p0) REVERT: A 962 ARG cc_start: 0.7251 (tpt-90) cc_final: 0.6969 (tpt-90) REVERT: A 969 GLU cc_start: 0.7919 (tp30) cc_final: 0.7581 (tp30) REVERT: A 985 LYS cc_start: 0.6795 (tmtt) cc_final: 0.6480 (tptt) REVERT: A 1102 LYS cc_start: 0.6445 (tptt) cc_final: 0.5353 (tptp) REVERT: A 1106 GLU cc_start: 0.6750 (mm-30) cc_final: 0.6340 (mm-30) REVERT: A 1109 ASP cc_start: 0.7306 (t0) cc_final: 0.6826 (t0) REVERT: A 1171 LYS cc_start: 0.8133 (tppt) cc_final: 0.7705 (tppt) REVERT: A 1176 PHE cc_start: 0.7779 (t80) cc_final: 0.7434 (t80) REVERT: A 1181 PHE cc_start: 0.7403 (t80) cc_final: 0.7127 (t80) REVERT: A 1193 ILE cc_start: 0.7738 (tp) cc_final: 0.7533 (tp) REVERT: A 1201 ILE cc_start: 0.7237 (mp) cc_final: 0.6999 (mm) REVERT: A 1309 LEU cc_start: 0.5946 (mm) cc_final: 0.5539 (pt) REVERT: A 1333 HIS cc_start: 0.6754 (t-170) cc_final: 0.6289 (t-170) REVERT: A 1337 MET cc_start: 0.7628 (mmp) cc_final: 0.7288 (mmt) REVERT: A 1338 LYS cc_start: 0.8518 (ptmt) cc_final: 0.8240 (ptmt) REVERT: A 1363 ASN cc_start: 0.7569 (m-40) cc_final: 0.7178 (m-40) REVERT: A 1433 CYS cc_start: 0.6962 (p) cc_final: 0.6475 (p) REVERT: A 1457 ILE cc_start: 0.8685 (mt) cc_final: 0.8442 (mt) REVERT: A 1495 ASN cc_start: 0.7431 (t0) cc_final: 0.6506 (t0) REVERT: A 1509 LYS cc_start: 0.7896 (mptt) cc_final: 0.7374 (mptt) REVERT: A 1528 LEU cc_start: 0.8210 (OUTLIER) cc_final: 0.7970 (tp) REVERT: A 1569 MET cc_start: 0.7408 (ptm) cc_final: 0.6991 (tmm) REVERT: A 1575 LYS cc_start: 0.8080 (mttp) cc_final: 0.7070 (mmmt) REVERT: A 1588 LYS cc_start: 0.7676 (tptt) cc_final: 0.7449 (mmmt) REVERT: A 1621 MET cc_start: 0.5916 (mpp) cc_final: 0.5403 (pmm) REVERT: A 1645 GLU cc_start: 0.8265 (pp20) cc_final: 0.8011 (tm-30) REVERT: A 1704 LYS cc_start: 0.7984 (mmmm) cc_final: 0.7780 (mmmm) REVERT: A 1817 CYS cc_start: 0.6530 (p) cc_final: 0.6275 (t) REVERT: A 1857 TRP cc_start: 0.6946 (t60) cc_final: 0.6721 (t60) REVERT: A 1917 LYS cc_start: 0.8215 (tmtt) cc_final: 0.7947 (tptp) REVERT: A 1966 PHE cc_start: 0.7014 (m-80) cc_final: 0.6781 (m-10) REVERT: A 2009 ASN cc_start: 0.7771 (t0) cc_final: 0.7369 (m-40) REVERT: A 2051 TRP cc_start: 0.5873 (t60) cc_final: 0.5598 (t60) REVERT: A 2057 LYS cc_start: 0.8559 (mmtm) cc_final: 0.8105 (mmmt) REVERT: A 2083 ASN cc_start: 0.8173 (m-40) cc_final: 0.7916 (m110) REVERT: A 2168 MET cc_start: 0.4855 (tpt) cc_final: 0.4271 (mmm) REVERT: A 2278 PHE cc_start: 0.6641 (m-10) cc_final: 0.6367 (m-80) REVERT: A 2301 SER cc_start: 0.8010 (t) cc_final: 0.7559 (p) REVERT: A 2342 GLN cc_start: 0.7178 (mt0) cc_final: 0.6847 (mp10) REVERT: A 2357 LEU cc_start: 0.7739 (OUTLIER) cc_final: 0.7373 (pp) REVERT: A 2395 MET cc_start: 0.6735 (mtt) cc_final: 0.6473 (mmt) REVERT: A 2603 GLU cc_start: 0.8747 (tm-30) cc_final: 0.8121 (tm-30) REVERT: A 2607 LYS cc_start: 0.9021 (mmpt) cc_final: 0.8757 (mmmt) outliers start: 41 outliers final: 26 residues processed: 416 average time/residue: 0.1181 time to fit residues: 73.8190 Evaluate side-chains 420 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 392 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 534 PHE Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain A residue 704 TYR Chi-restraints excluded: chain A residue 722 LEU Chi-restraints excluded: chain A residue 729 SER Chi-restraints excluded: chain A residue 766 PHE Chi-restraints excluded: chain A residue 862 CYS Chi-restraints excluded: chain A residue 885 MET Chi-restraints excluded: chain A residue 961 MET Chi-restraints excluded: chain A residue 1287 ASN Chi-restraints excluded: chain A residue 1304 LEU Chi-restraints excluded: chain A residue 1328 LEU Chi-restraints excluded: chain A residue 1331 VAL Chi-restraints excluded: chain A residue 1345 GLU Chi-restraints excluded: chain A residue 1373 VAL Chi-restraints excluded: chain A residue 1420 SER Chi-restraints excluded: chain A residue 1424 VAL Chi-restraints excluded: chain A residue 1510 SER Chi-restraints excluded: chain A residue 1528 LEU Chi-restraints excluded: chain A residue 1574 LEU Chi-restraints excluded: chain A residue 1836 ILE Chi-restraints excluded: chain A residue 1890 LEU Chi-restraints excluded: chain A residue 1940 LEU Chi-restraints excluded: chain A residue 1953 ARG Chi-restraints excluded: chain A residue 2280 MET Chi-restraints excluded: chain A residue 2357 LEU Chi-restraints excluded: chain A residue 2668 SER Chi-restraints excluded: chain A residue 2675 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 154 optimal weight: 3.9990 chunk 178 optimal weight: 3.9990 chunk 90 optimal weight: 7.9990 chunk 92 optimal weight: 2.9990 chunk 119 optimal weight: 0.0070 chunk 123 optimal weight: 0.6980 chunk 127 optimal weight: 0.9990 chunk 180 optimal weight: 0.9990 chunk 132 optimal weight: 5.9990 chunk 209 optimal weight: 50.0000 chunk 176 optimal weight: 5.9990 overall best weight: 1.1404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 407 GLN ** A 419 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 939 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1324 ASN ** A1901 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2006 GLN ** A2086 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4670 r_free = 0.4670 target = 0.199674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.164893 restraints weight = 41992.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4356 r_free = 0.4356 target = 0.169358 restraints weight = 27145.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 62)----------------| | r_work = 0.4392 r_free = 0.4392 target = 0.172462 restraints weight = 19210.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4416 r_free = 0.4416 target = 0.174561 restraints weight = 14619.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 54)----------------| | r_work = 0.4433 r_free = 0.4433 target = 0.176200 restraints weight = 11850.018| |-----------------------------------------------------------------------------| r_work (final): 0.4408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6039 moved from start: 0.2791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 18394 Z= 0.148 Angle : 0.702 13.576 24780 Z= 0.360 Chirality : 0.044 0.288 2839 Planarity : 0.004 0.052 3112 Dihedral : 5.297 49.683 2411 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 13.39 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.84 % Favored : 92.07 % Rotamer: Outliers : 1.94 % Allowed : 17.46 % Favored : 80.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.10 (0.18), residues: 2220 helix: 0.49 (0.15), residues: 1229 sheet: -0.35 (0.50), residues: 93 loop : -2.59 (0.20), residues: 898 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 802 TYR 0.045 0.001 TYR A 876 PHE 0.017 0.001 PHE A 644 TRP 0.015 0.002 TRP A1857 HIS 0.005 0.001 HIS A 564 Details of bonding type rmsd covalent geometry : bond 0.00307 (18394) covalent geometry : angle 0.70189 (24780) hydrogen bonds : bond 0.03793 ( 877) hydrogen bonds : angle 4.64156 ( 2586) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 398 time to evaluate : 0.551 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 322 THR cc_start: 0.4866 (t) cc_final: 0.4642 (t) REVERT: A 450 GLU cc_start: 0.7798 (mt-10) cc_final: 0.7319 (mt-10) REVERT: A 452 GLU cc_start: 0.8035 (tm-30) cc_final: 0.7667 (tm-30) REVERT: A 475 SER cc_start: 0.6666 (t) cc_final: 0.6019 (p) REVERT: A 536 MET cc_start: 0.6435 (tpp) cc_final: 0.5839 (tpt) REVERT: A 603 LYS cc_start: 0.8377 (tppt) cc_final: 0.8062 (tppt) REVERT: A 604 ASN cc_start: 0.7486 (p0) cc_final: 0.7038 (p0) REVERT: A 623 LYS cc_start: 0.8132 (mttt) cc_final: 0.7558 (mmmm) REVERT: A 637 TYR cc_start: 0.6833 (m-10) cc_final: 0.4748 (m-10) REVERT: A 639 GLU cc_start: 0.7405 (tp30) cc_final: 0.6919 (tp30) REVERT: A 642 MET cc_start: 0.7177 (ttt) cc_final: 0.6829 (ttt) REVERT: A 646 LYS cc_start: 0.8818 (ptpt) cc_final: 0.8524 (ptpp) REVERT: A 671 MET cc_start: 0.6354 (ttt) cc_final: 0.5804 (ttt) REVERT: A 770 MET cc_start: 0.7145 (tmm) cc_final: 0.6579 (tmm) REVERT: A 785 MET cc_start: 0.5869 (mtp) cc_final: 0.5496 (mmm) REVERT: A 842 LEU cc_start: 0.8350 (tp) cc_final: 0.8127 (tp) REVERT: A 861 LYS cc_start: 0.8739 (mptt) cc_final: 0.8298 (mptt) REVERT: A 873 GLU cc_start: 0.7693 (mt-10) cc_final: 0.7115 (mp0) REVERT: A 886 MET cc_start: 0.6292 (tpp) cc_final: 0.5830 (tpp) REVERT: A 892 ASN cc_start: 0.4751 (t0) cc_final: 0.4537 (t0) REVERT: A 911 PHE cc_start: 0.6095 (t80) cc_final: 0.5128 (t80) REVERT: A 913 LYS cc_start: 0.8710 (tptt) cc_final: 0.8314 (tppt) REVERT: A 929 MET cc_start: 0.7028 (tpt) cc_final: 0.6587 (tpt) REVERT: A 962 ARG cc_start: 0.7420 (tpt-90) cc_final: 0.7071 (tpt-90) REVERT: A 969 GLU cc_start: 0.7861 (tp30) cc_final: 0.7469 (tp30) REVERT: A 985 LYS cc_start: 0.6935 (tmtt) cc_final: 0.6549 (tptt) REVERT: A 1102 LYS cc_start: 0.6462 (tptt) cc_final: 0.5512 (tptp) REVERT: A 1106 GLU cc_start: 0.6752 (mm-30) cc_final: 0.6306 (mm-30) REVERT: A 1109 ASP cc_start: 0.7311 (t0) cc_final: 0.6877 (t0) REVERT: A 1171 LYS cc_start: 0.8087 (tppt) cc_final: 0.7730 (tppt) REVERT: A 1176 PHE cc_start: 0.7781 (t80) cc_final: 0.7412 (t80) REVERT: A 1181 PHE cc_start: 0.7323 (t80) cc_final: 0.7101 (t80) REVERT: A 1201 ILE cc_start: 0.7151 (mp) cc_final: 0.6874 (mm) REVERT: A 1304 LEU cc_start: 0.8338 (OUTLIER) cc_final: 0.7957 (pp) REVERT: A 1309 LEU cc_start: 0.5915 (mm) cc_final: 0.5582 (pt) REVERT: A 1333 HIS cc_start: 0.6715 (t-170) cc_final: 0.6221 (t-170) REVERT: A 1338 LYS cc_start: 0.8465 (ptmt) cc_final: 0.8194 (ptmt) REVERT: A 1363 ASN cc_start: 0.7421 (m-40) cc_final: 0.7075 (m-40) REVERT: A 1376 MET cc_start: 0.6902 (tmm) cc_final: 0.6687 (tmm) REVERT: A 1433 CYS cc_start: 0.6899 (p) cc_final: 0.6468 (p) REVERT: A 1457 ILE cc_start: 0.8677 (mt) cc_final: 0.8466 (mt) REVERT: A 1482 GLN cc_start: 0.7363 (tm-30) cc_final: 0.7144 (tm-30) REVERT: A 1489 MET cc_start: 0.5003 (mmm) cc_final: 0.4475 (mmm) REVERT: A 1495 ASN cc_start: 0.7439 (t0) cc_final: 0.6507 (t0) REVERT: A 1528 LEU cc_start: 0.8192 (OUTLIER) cc_final: 0.7970 (tp) REVERT: A 1569 MET cc_start: 0.7358 (ptm) cc_final: 0.6985 (tmm) REVERT: A 1575 LYS cc_start: 0.8054 (mttp) cc_final: 0.7384 (mmmt) REVERT: A 1588 LYS cc_start: 0.7658 (tptt) cc_final: 0.7433 (mmmt) REVERT: A 1645 GLU cc_start: 0.8223 (pp20) cc_final: 0.7983 (tm-30) REVERT: A 1704 LYS cc_start: 0.8051 (mmmm) cc_final: 0.7825 (mmmm) REVERT: A 1817 CYS cc_start: 0.6630 (p) cc_final: 0.6304 (t) REVERT: A 1820 LYS cc_start: 0.8297 (ptpt) cc_final: 0.8069 (ptpt) REVERT: A 1917 LYS cc_start: 0.8160 (tmtt) cc_final: 0.7892 (tptp) REVERT: A 1953 ARG cc_start: 0.6646 (OUTLIER) cc_final: 0.5550 (mmp80) REVERT: A 1966 PHE cc_start: 0.7069 (m-80) cc_final: 0.6734 (m-10) REVERT: A 2009 ASN cc_start: 0.7809 (t0) cc_final: 0.7440 (m-40) REVERT: A 2057 LYS cc_start: 0.8570 (mmtm) cc_final: 0.8064 (mmmt) REVERT: A 2168 MET cc_start: 0.4818 (tpt) cc_final: 0.4327 (mmm) REVERT: A 2301 SER cc_start: 0.8026 (t) cc_final: 0.7588 (p) REVERT: A 2342 GLN cc_start: 0.7250 (mt0) cc_final: 0.6939 (mp10) REVERT: A 2357 LEU cc_start: 0.7659 (OUTLIER) cc_final: 0.7167 (mt) REVERT: A 2395 MET cc_start: 0.6799 (mtt) cc_final: 0.6594 (mmt) REVERT: A 2603 GLU cc_start: 0.8740 (tm-30) cc_final: 0.8101 (tm-30) REVERT: A 2607 LYS cc_start: 0.9026 (mmpt) cc_final: 0.8756 (mmmt) outliers start: 40 outliers final: 26 residues processed: 411 average time/residue: 0.1243 time to fit residues: 76.8947 Evaluate side-chains 415 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 385 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 534 PHE Chi-restraints excluded: chain A residue 704 TYR Chi-restraints excluded: chain A residue 722 LEU Chi-restraints excluded: chain A residue 729 SER Chi-restraints excluded: chain A residue 766 PHE Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 862 CYS Chi-restraints excluded: chain A residue 885 MET Chi-restraints excluded: chain A residue 961 MET Chi-restraints excluded: chain A residue 1287 ASN Chi-restraints excluded: chain A residue 1304 LEU Chi-restraints excluded: chain A residue 1345 GLU Chi-restraints excluded: chain A residue 1373 VAL Chi-restraints excluded: chain A residue 1420 SER Chi-restraints excluded: chain A residue 1424 VAL Chi-restraints excluded: chain A residue 1510 SER Chi-restraints excluded: chain A residue 1528 LEU Chi-restraints excluded: chain A residue 1574 LEU Chi-restraints excluded: chain A residue 1698 GLU Chi-restraints excluded: chain A residue 1832 PHE Chi-restraints excluded: chain A residue 1890 LEU Chi-restraints excluded: chain A residue 1953 ARG Chi-restraints excluded: chain A residue 1997 THR Chi-restraints excluded: chain A residue 1998 ILE Chi-restraints excluded: chain A residue 2039 ILE Chi-restraints excluded: chain A residue 2126 VAL Chi-restraints excluded: chain A residue 2280 MET Chi-restraints excluded: chain A residue 2357 LEU Chi-restraints excluded: chain A residue 2668 SER Chi-restraints excluded: chain A residue 2675 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 213 optimal weight: 6.9990 chunk 187 optimal weight: 5.9990 chunk 7 optimal weight: 6.9990 chunk 110 optimal weight: 0.6980 chunk 98 optimal weight: 0.7980 chunk 32 optimal weight: 2.9990 chunk 163 optimal weight: 0.9990 chunk 189 optimal weight: 0.9980 chunk 90 optimal weight: 4.9990 chunk 138 optimal weight: 0.9990 chunk 204 optimal weight: 10.0000 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 407 GLN ** A 419 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 482 ASN ** A 939 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1901 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2006 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2258 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4678 r_free = 0.4678 target = 0.200403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.165517 restraints weight = 41848.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4364 r_free = 0.4364 target = 0.169976 restraints weight = 27122.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4400 r_free = 0.4400 target = 0.173060 restraints weight = 19245.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4424 r_free = 0.4424 target = 0.175124 restraints weight = 14675.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 65)----------------| | r_work = 0.4441 r_free = 0.4441 target = 0.176794 restraints weight = 11921.056| |-----------------------------------------------------------------------------| r_work (final): 0.4416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6039 moved from start: 0.3004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 18394 Z= 0.135 Angle : 0.693 13.281 24780 Z= 0.354 Chirality : 0.044 0.255 2839 Planarity : 0.004 0.052 3112 Dihedral : 5.159 48.693 2411 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 13.47 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.29 % Favored : 91.62 % Rotamer: Outliers : 2.23 % Allowed : 18.29 % Favored : 79.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.98 (0.18), residues: 2220 helix: 0.63 (0.15), residues: 1221 sheet: -0.33 (0.51), residues: 93 loop : -2.57 (0.20), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 802 TYR 0.043 0.001 TYR A 876 PHE 0.016 0.001 PHE A 644 TRP 0.031 0.002 TRP A2051 HIS 0.004 0.001 HIS A1179 Details of bonding type rmsd covalent geometry : bond 0.00286 (18394) covalent geometry : angle 0.69350 (24780) hydrogen bonds : bond 0.03652 ( 877) hydrogen bonds : angle 4.56343 ( 2586) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 451 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 405 time to evaluate : 0.701 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 450 GLU cc_start: 0.7787 (mt-10) cc_final: 0.7372 (pt0) REVERT: A 452 GLU cc_start: 0.8042 (tm-30) cc_final: 0.7709 (tm-30) REVERT: A 475 SER cc_start: 0.6839 (t) cc_final: 0.6217 (p) REVERT: A 536 MET cc_start: 0.6408 (tpp) cc_final: 0.5819 (tpt) REVERT: A 603 LYS cc_start: 0.8374 (tppt) cc_final: 0.8066 (tppt) REVERT: A 604 ASN cc_start: 0.7426 (p0) cc_final: 0.6995 (p0) REVERT: A 623 LYS cc_start: 0.8115 (mttt) cc_final: 0.7533 (mmmm) REVERT: A 637 TYR cc_start: 0.6833 (m-10) cc_final: 0.4659 (m-10) REVERT: A 639 GLU cc_start: 0.7353 (tp30) cc_final: 0.6861 (tp30) REVERT: A 642 MET cc_start: 0.7126 (ttt) cc_final: 0.6792 (ttt) REVERT: A 646 LYS cc_start: 0.8788 (ptpt) cc_final: 0.8515 (ptpp) REVERT: A 671 MET cc_start: 0.6347 (ttt) cc_final: 0.5759 (ttt) REVERT: A 704 TYR cc_start: 0.4277 (OUTLIER) cc_final: 0.4053 (m-80) REVERT: A 741 PHE cc_start: 0.6774 (t80) cc_final: 0.6359 (t80) REVERT: A 770 MET cc_start: 0.7101 (tmm) cc_final: 0.6531 (tmm) REVERT: A 785 MET cc_start: 0.5824 (mtp) cc_final: 0.5441 (mmm) REVERT: A 791 LYS cc_start: 0.6513 (mtmt) cc_final: 0.6273 (mtmt) REVERT: A 842 LEU cc_start: 0.8334 (tp) cc_final: 0.8064 (tp) REVERT: A 861 LYS cc_start: 0.8707 (mptt) cc_final: 0.8412 (mmtt) REVERT: A 886 MET cc_start: 0.6319 (tpp) cc_final: 0.5873 (tpp) REVERT: A 911 PHE cc_start: 0.6045 (t80) cc_final: 0.5032 (t80) REVERT: A 913 LYS cc_start: 0.8688 (tptt) cc_final: 0.8274 (tppt) REVERT: A 929 MET cc_start: 0.6951 (tpt) cc_final: 0.6502 (tpt) REVERT: A 969 GLU cc_start: 0.7827 (tp30) cc_final: 0.7438 (tp30) REVERT: A 985 LYS cc_start: 0.6936 (tmtt) cc_final: 0.6521 (tptt) REVERT: A 1102 LYS cc_start: 0.6445 (tptt) cc_final: 0.5431 (mmmt) REVERT: A 1106 GLU cc_start: 0.6769 (mm-30) cc_final: 0.6320 (mm-30) REVERT: A 1109 ASP cc_start: 0.7386 (t0) cc_final: 0.6839 (t0) REVERT: A 1142 MET cc_start: 0.6179 (tpt) cc_final: 0.5678 (tpp) REVERT: A 1171 LYS cc_start: 0.8061 (tppt) cc_final: 0.7690 (tppt) REVERT: A 1176 PHE cc_start: 0.7789 (t80) cc_final: 0.7420 (t80) REVERT: A 1181 PHE cc_start: 0.7272 (t80) cc_final: 0.7048 (t80) REVERT: A 1201 ILE cc_start: 0.7197 (mp) cc_final: 0.6903 (mm) REVERT: A 1237 LYS cc_start: 0.6770 (tptt) cc_final: 0.6297 (tptt) REVERT: A 1304 LEU cc_start: 0.8305 (OUTLIER) cc_final: 0.7951 (pp) REVERT: A 1309 LEU cc_start: 0.6070 (mm) cc_final: 0.5652 (pt) REVERT: A 1333 HIS cc_start: 0.6659 (t-170) cc_final: 0.6076 (t-170) REVERT: A 1338 LYS cc_start: 0.8419 (ptmt) cc_final: 0.8166 (ptmt) REVERT: A 1363 ASN cc_start: 0.7356 (m-40) cc_final: 0.6976 (m-40) REVERT: A 1433 CYS cc_start: 0.6828 (p) cc_final: 0.6395 (p) REVERT: A 1482 GLN cc_start: 0.7332 (tm-30) cc_final: 0.7096 (tm-30) REVERT: A 1495 ASN cc_start: 0.7424 (t0) cc_final: 0.6521 (t0) REVERT: A 1566 TYR cc_start: 0.6675 (t80) cc_final: 0.5767 (t80) REVERT: A 1569 MET cc_start: 0.7367 (ptm) cc_final: 0.6987 (tmm) REVERT: A 1575 LYS cc_start: 0.8254 (mttp) cc_final: 0.7309 (mmmt) REVERT: A 1588 LYS cc_start: 0.7638 (tptt) cc_final: 0.7382 (mmmt) REVERT: A 1621 MET cc_start: 0.5905 (mpp) cc_final: 0.5075 (pmm) REVERT: A 1645 GLU cc_start: 0.8223 (pp20) cc_final: 0.7980 (tm-30) REVERT: A 1817 CYS cc_start: 0.6548 (p) cc_final: 0.6231 (t) REVERT: A 1820 LYS cc_start: 0.8275 (ptpt) cc_final: 0.7912 (ptpt) REVERT: A 1898 ASP cc_start: 0.6659 (t0) cc_final: 0.6378 (t0) REVERT: A 1953 ARG cc_start: 0.6690 (OUTLIER) cc_final: 0.6227 (mmt180) REVERT: A 1966 PHE cc_start: 0.7066 (m-80) cc_final: 0.6717 (m-10) REVERT: A 2008 MET cc_start: 0.6957 (ppp) cc_final: 0.6695 (ppp) REVERT: A 2009 ASN cc_start: 0.7809 (t0) cc_final: 0.7490 (m-40) REVERT: A 2057 LYS cc_start: 0.8495 (mmtm) cc_final: 0.8057 (mmmt) REVERT: A 2168 MET cc_start: 0.5111 (tpt) cc_final: 0.4558 (mmm) REVERT: A 2278 PHE cc_start: 0.6462 (m-10) cc_final: 0.6013 (m-80) REVERT: A 2296 VAL cc_start: 0.3486 (OUTLIER) cc_final: 0.2739 (t) REVERT: A 2301 SER cc_start: 0.8028 (t) cc_final: 0.7594 (p) REVERT: A 2342 GLN cc_start: 0.7255 (mt0) cc_final: 0.6936 (mp10) REVERT: A 2357 LEU cc_start: 0.7642 (OUTLIER) cc_final: 0.6988 (mt) REVERT: A 2603 GLU cc_start: 0.8703 (tm-30) cc_final: 0.8052 (tm-30) REVERT: A 2607 LYS cc_start: 0.9017 (mmpt) cc_final: 0.8749 (mmmt) outliers start: 46 outliers final: 30 residues processed: 425 average time/residue: 0.1339 time to fit residues: 85.0594 Evaluate side-chains 426 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 391 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 534 PHE Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain A residue 704 TYR Chi-restraints excluded: chain A residue 729 SER Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 885 MET Chi-restraints excluded: chain A residue 961 MET Chi-restraints excluded: chain A residue 1284 ILE Chi-restraints excluded: chain A residue 1287 ASN Chi-restraints excluded: chain A residue 1304 LEU Chi-restraints excluded: chain A residue 1331 VAL Chi-restraints excluded: chain A residue 1345 GLU Chi-restraints excluded: chain A residue 1373 VAL Chi-restraints excluded: chain A residue 1420 SER Chi-restraints excluded: chain A residue 1424 VAL Chi-restraints excluded: chain A residue 1460 THR Chi-restraints excluded: chain A residue 1510 SER Chi-restraints excluded: chain A residue 1528 LEU Chi-restraints excluded: chain A residue 1537 ASP Chi-restraints excluded: chain A residue 1698 GLU Chi-restraints excluded: chain A residue 1832 PHE Chi-restraints excluded: chain A residue 1836 ILE Chi-restraints excluded: chain A residue 1890 LEU Chi-restraints excluded: chain A residue 1953 ARG Chi-restraints excluded: chain A residue 1997 THR Chi-restraints excluded: chain A residue 1998 ILE Chi-restraints excluded: chain A residue 2037 VAL Chi-restraints excluded: chain A residue 2039 ILE Chi-restraints excluded: chain A residue 2126 VAL Chi-restraints excluded: chain A residue 2280 MET Chi-restraints excluded: chain A residue 2296 VAL Chi-restraints excluded: chain A residue 2357 LEU Chi-restraints excluded: chain A residue 2602 LEU Chi-restraints excluded: chain A residue 2668 SER Chi-restraints excluded: chain A residue 2675 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 98 optimal weight: 0.6980 chunk 110 optimal weight: 0.8980 chunk 43 optimal weight: 0.9980 chunk 161 optimal weight: 6.9990 chunk 104 optimal weight: 3.9990 chunk 221 optimal weight: 10.0000 chunk 112 optimal weight: 0.0870 chunk 16 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 chunk 183 optimal weight: 0.9980 chunk 80 optimal weight: 7.9990 overall best weight: 0.7358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 407 GLN ** A 419 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 446 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 482 ASN ** A 939 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1113 GLN ** A1495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1901 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2006 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4682 r_free = 0.4682 target = 0.200635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.166085 restraints weight = 41862.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4372 r_free = 0.4372 target = 0.170509 restraints weight = 26961.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4407 r_free = 0.4407 target = 0.173531 restraints weight = 19091.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 64)----------------| | r_work = 0.4432 r_free = 0.4432 target = 0.175794 restraints weight = 14538.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4449 r_free = 0.4449 target = 0.177334 restraints weight = 11730.912| |-----------------------------------------------------------------------------| r_work (final): 0.4428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6027 moved from start: 0.3163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 18394 Z= 0.129 Angle : 0.711 12.357 24780 Z= 0.359 Chirality : 0.044 0.300 2839 Planarity : 0.004 0.052 3112 Dihedral : 5.072 47.823 2411 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 13.55 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.84 % Favored : 92.07 % Rotamer: Outliers : 2.13 % Allowed : 19.30 % Favored : 78.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.86 (0.18), residues: 2220 helix: 0.73 (0.15), residues: 1218 sheet: -0.31 (0.50), residues: 93 loop : -2.50 (0.20), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A2033 TYR 0.047 0.001 TYR A 876 PHE 0.019 0.001 PHE A 644 TRP 0.028 0.002 TRP A1857 HIS 0.005 0.001 HIS A 893 Details of bonding type rmsd covalent geometry : bond 0.00277 (18394) covalent geometry : angle 0.71098 (24780) hydrogen bonds : bond 0.03536 ( 877) hydrogen bonds : angle 4.51452 ( 2586) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 394 time to evaluate : 0.619 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 446 GLN cc_start: 0.7770 (pp30) cc_final: 0.7312 (pp30) REVERT: A 450 GLU cc_start: 0.7759 (mt-10) cc_final: 0.7281 (pt0) REVERT: A 475 SER cc_start: 0.6797 (t) cc_final: 0.6177 (p) REVERT: A 536 MET cc_start: 0.6383 (tpp) cc_final: 0.5801 (tpt) REVERT: A 603 LYS cc_start: 0.8365 (tppt) cc_final: 0.8097 (tppt) REVERT: A 604 ASN cc_start: 0.7434 (p0) cc_final: 0.7009 (p0) REVERT: A 620 GLU cc_start: 0.6857 (pm20) cc_final: 0.6614 (pm20) REVERT: A 623 LYS cc_start: 0.8094 (mttt) cc_final: 0.7521 (mmmm) REVERT: A 637 TYR cc_start: 0.6787 (m-10) cc_final: 0.4609 (m-10) REVERT: A 639 GLU cc_start: 0.7343 (tp30) cc_final: 0.6825 (tp30) REVERT: A 671 MET cc_start: 0.6293 (ttt) cc_final: 0.5800 (ttt) REVERT: A 687 VAL cc_start: 0.8099 (t) cc_final: 0.7751 (m) REVERT: A 732 LYS cc_start: 0.7807 (tppp) cc_final: 0.7105 (tppt) REVERT: A 741 PHE cc_start: 0.6746 (t80) cc_final: 0.6352 (t80) REVERT: A 770 MET cc_start: 0.7033 (tmm) cc_final: 0.6482 (tmm) REVERT: A 785 MET cc_start: 0.5832 (mtp) cc_final: 0.5460 (mmm) REVERT: A 842 LEU cc_start: 0.8307 (tp) cc_final: 0.8048 (tp) REVERT: A 873 GLU cc_start: 0.7655 (mt-10) cc_final: 0.7150 (mm-30) REVERT: A 886 MET cc_start: 0.6212 (tpp) cc_final: 0.5790 (tpp) REVERT: A 911 PHE cc_start: 0.6000 (t80) cc_final: 0.5004 (t80) REVERT: A 913 LYS cc_start: 0.8695 (tptt) cc_final: 0.8252 (tppt) REVERT: A 929 MET cc_start: 0.6912 (tpt) cc_final: 0.6470 (tpt) REVERT: A 969 GLU cc_start: 0.7887 (tp30) cc_final: 0.7469 (tp30) REVERT: A 985 LYS cc_start: 0.6931 (tmtt) cc_final: 0.6493 (tptt) REVERT: A 1102 LYS cc_start: 0.6386 (tptt) cc_final: 0.5345 (mmmt) REVERT: A 1106 GLU cc_start: 0.6733 (mm-30) cc_final: 0.6287 (mm-30) REVERT: A 1109 ASP cc_start: 0.7348 (t0) cc_final: 0.6903 (t0) REVERT: A 1142 MET cc_start: 0.6186 (tpt) cc_final: 0.5680 (tpp) REVERT: A 1171 LYS cc_start: 0.8049 (tppt) cc_final: 0.7689 (tppt) REVERT: A 1176 PHE cc_start: 0.7785 (t80) cc_final: 0.7434 (t80) REVERT: A 1181 PHE cc_start: 0.7271 (t80) cc_final: 0.7032 (t80) REVERT: A 1201 ILE cc_start: 0.7159 (mp) cc_final: 0.6741 (mm) REVERT: A 1309 LEU cc_start: 0.5982 (mm) cc_final: 0.5579 (pt) REVERT: A 1333 HIS cc_start: 0.6719 (t-170) cc_final: 0.6278 (t-170) REVERT: A 1338 LYS cc_start: 0.8423 (ptmt) cc_final: 0.8155 (ptmt) REVERT: A 1363 ASN cc_start: 0.7435 (m-40) cc_final: 0.6850 (m-40) REVERT: A 1433 CYS cc_start: 0.6844 (p) cc_final: 0.6481 (p) REVERT: A 1482 GLN cc_start: 0.7268 (tm-30) cc_final: 0.6597 (tm-30) REVERT: A 1495 ASN cc_start: 0.7435 (t0) cc_final: 0.6484 (t0) REVERT: A 1542 TYR cc_start: 0.7033 (t80) cc_final: 0.6067 (t80) REVERT: A 1569 MET cc_start: 0.7401 (ptm) cc_final: 0.6988 (tmm) REVERT: A 1575 LYS cc_start: 0.8280 (mttp) cc_final: 0.7313 (mmmt) REVERT: A 1588 LYS cc_start: 0.7622 (tptt) cc_final: 0.7367 (mmmt) REVERT: A 1621 MET cc_start: 0.5921 (mpp) cc_final: 0.5285 (pmm) REVERT: A 1645 GLU cc_start: 0.8225 (pp20) cc_final: 0.7988 (tm-30) REVERT: A 1673 LEU cc_start: 0.7285 (mm) cc_final: 0.6911 (tp) REVERT: A 1820 LYS cc_start: 0.8251 (ptpt) cc_final: 0.7934 (ptpt) REVERT: A 1827 ILE cc_start: 0.6789 (pt) cc_final: 0.5281 (mt) REVERT: A 1898 ASP cc_start: 0.6631 (t0) cc_final: 0.6395 (t0) REVERT: A 1953 ARG cc_start: 0.6767 (OUTLIER) cc_final: 0.6143 (mmt180) REVERT: A 1966 PHE cc_start: 0.7096 (m-80) cc_final: 0.6755 (m-10) REVERT: A 1971 LYS cc_start: 0.5504 (OUTLIER) cc_final: 0.3509 (mmmt) REVERT: A 2008 MET cc_start: 0.6986 (ppp) cc_final: 0.6677 (ppp) REVERT: A 2009 ASN cc_start: 0.7817 (t0) cc_final: 0.7407 (m-40) REVERT: A 2057 LYS cc_start: 0.8538 (mmtm) cc_final: 0.8069 (mmmt) REVERT: A 2168 MET cc_start: 0.5049 (tpt) cc_final: 0.4519 (mmm) REVERT: A 2278 PHE cc_start: 0.6524 (m-10) cc_final: 0.6314 (m-10) REVERT: A 2296 VAL cc_start: 0.3418 (OUTLIER) cc_final: 0.2634 (t) REVERT: A 2301 SER cc_start: 0.8020 (t) cc_final: 0.7585 (p) REVERT: A 2342 GLN cc_start: 0.7253 (mt0) cc_final: 0.6912 (mp10) REVERT: A 2357 LEU cc_start: 0.7600 (OUTLIER) cc_final: 0.7060 (mt) REVERT: A 2603 GLU cc_start: 0.8668 (tm-30) cc_final: 0.8128 (tm-30) outliers start: 44 outliers final: 30 residues processed: 413 average time/residue: 0.1266 time to fit residues: 79.1665 Evaluate side-chains 419 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 385 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 534 PHE Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain A residue 704 TYR Chi-restraints excluded: chain A residue 722 LEU Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 885 MET Chi-restraints excluded: chain A residue 961 MET Chi-restraints excluded: chain A residue 1284 ILE Chi-restraints excluded: chain A residue 1304 LEU Chi-restraints excluded: chain A residue 1331 VAL Chi-restraints excluded: chain A residue 1345 GLU Chi-restraints excluded: chain A residue 1373 VAL Chi-restraints excluded: chain A residue 1420 SER Chi-restraints excluded: chain A residue 1460 THR Chi-restraints excluded: chain A residue 1510 SER Chi-restraints excluded: chain A residue 1528 LEU Chi-restraints excluded: chain A residue 1537 ASP Chi-restraints excluded: chain A residue 1698 GLU Chi-restraints excluded: chain A residue 1832 PHE Chi-restraints excluded: chain A residue 1836 ILE Chi-restraints excluded: chain A residue 1890 LEU Chi-restraints excluded: chain A residue 1953 ARG Chi-restraints excluded: chain A residue 1971 LYS Chi-restraints excluded: chain A residue 1997 THR Chi-restraints excluded: chain A residue 1998 ILE Chi-restraints excluded: chain A residue 2037 VAL Chi-restraints excluded: chain A residue 2039 ILE Chi-restraints excluded: chain A residue 2280 MET Chi-restraints excluded: chain A residue 2296 VAL Chi-restraints excluded: chain A residue 2357 LEU Chi-restraints excluded: chain A residue 2602 LEU Chi-restraints excluded: chain A residue 2668 SER Chi-restraints excluded: chain A residue 2675 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 206 optimal weight: 7.9990 chunk 15 optimal weight: 0.9990 chunk 67 optimal weight: 9.9990 chunk 118 optimal weight: 1.9990 chunk 140 optimal weight: 1.9990 chunk 119 optimal weight: 0.9980 chunk 137 optimal weight: 4.9990 chunk 78 optimal weight: 3.9990 chunk 129 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 97 optimal weight: 8.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 407 GLN ** A 419 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 482 ASN ** A 939 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1901 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1952 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2006 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4657 r_free = 0.4657 target = 0.198393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4287 r_free = 0.4287 target = 0.163622 restraints weight = 41761.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.168078 restraints weight = 27085.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.4375 r_free = 0.4375 target = 0.171107 restraints weight = 19161.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 60)----------------| | r_work = 0.4399 r_free = 0.4399 target = 0.173287 restraints weight = 14580.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4415 r_free = 0.4415 target = 0.174700 restraints weight = 11767.839| |-----------------------------------------------------------------------------| r_work (final): 0.4392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6089 moved from start: 0.3476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 18394 Z= 0.168 Angle : 0.745 13.038 24780 Z= 0.381 Chirality : 0.045 0.288 2839 Planarity : 0.004 0.052 3112 Dihedral : 5.216 46.854 2411 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 15.28 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.78 % Favored : 91.13 % Rotamer: Outliers : 2.37 % Allowed : 19.98 % Favored : 77.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.09 (0.18), residues: 2220 helix: 0.57 (0.15), residues: 1234 sheet: -0.54 (0.50), residues: 93 loop : -2.69 (0.20), residues: 893 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A2033 TYR 0.047 0.001 TYR A 876 PHE 0.021 0.001 PHE A 707 TRP 0.029 0.002 TRP A1857 HIS 0.004 0.001 HIS A 893 Details of bonding type rmsd covalent geometry : bond 0.00350 (18394) covalent geometry : angle 0.74470 (24780) hydrogen bonds : bond 0.03912 ( 877) hydrogen bonds : angle 4.67239 ( 2586) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 451 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 402 time to evaluate : 0.692 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 322 THR cc_start: 0.4256 (t) cc_final: 0.3977 (t) REVERT: A 446 GLN cc_start: 0.7980 (pp30) cc_final: 0.7379 (pp30) REVERT: A 450 GLU cc_start: 0.7743 (mt-10) cc_final: 0.7463 (mt-10) REVERT: A 475 SER cc_start: 0.6715 (t) cc_final: 0.5909 (p) REVERT: A 482 ASN cc_start: 0.1564 (OUTLIER) cc_final: 0.1311 (p0) REVERT: A 536 MET cc_start: 0.6392 (tpp) cc_final: 0.5944 (tpt) REVERT: A 603 LYS cc_start: 0.8338 (tppt) cc_final: 0.8060 (tppt) REVERT: A 604 ASN cc_start: 0.7381 (p0) cc_final: 0.7131 (p0) REVERT: A 623 LYS cc_start: 0.8124 (mttt) cc_final: 0.7541 (mmmm) REVERT: A 637 TYR cc_start: 0.6808 (m-10) cc_final: 0.4698 (m-10) REVERT: A 639 GLU cc_start: 0.7297 (tp30) cc_final: 0.6871 (tp30) REVERT: A 646 LYS cc_start: 0.8827 (ptpt) cc_final: 0.8601 (ptpp) REVERT: A 671 MET cc_start: 0.6360 (ttt) cc_final: 0.5812 (ttt) REVERT: A 732 LYS cc_start: 0.7791 (tppp) cc_final: 0.7106 (tppt) REVERT: A 741 PHE cc_start: 0.6803 (t80) cc_final: 0.6348 (t80) REVERT: A 770 MET cc_start: 0.7170 (tmm) cc_final: 0.6625 (tmm) REVERT: A 785 MET cc_start: 0.5839 (mtp) cc_final: 0.5466 (mmm) REVERT: A 842 LEU cc_start: 0.8314 (tp) cc_final: 0.8064 (tp) REVERT: A 861 LYS cc_start: 0.8739 (mptt) cc_final: 0.8133 (mmtm) REVERT: A 873 GLU cc_start: 0.7705 (mt-10) cc_final: 0.7159 (mm-30) REVERT: A 886 MET cc_start: 0.6229 (tpp) cc_final: 0.5852 (tpp) REVERT: A 911 PHE cc_start: 0.6166 (t80) cc_final: 0.5086 (t80) REVERT: A 913 LYS cc_start: 0.8729 (tptt) cc_final: 0.8333 (tppt) REVERT: A 929 MET cc_start: 0.6973 (tpt) cc_final: 0.6495 (tpt) REVERT: A 969 GLU cc_start: 0.7922 (tp30) cc_final: 0.7491 (tp30) REVERT: A 985 LYS cc_start: 0.6851 (tmtt) cc_final: 0.6423 (tptt) REVERT: A 1102 LYS cc_start: 0.6547 (tptt) cc_final: 0.6151 (tptm) REVERT: A 1106 GLU cc_start: 0.6732 (mm-30) cc_final: 0.6267 (mm-30) REVERT: A 1109 ASP cc_start: 0.7412 (t0) cc_final: 0.6914 (t0) REVERT: A 1142 MET cc_start: 0.6203 (tpt) cc_final: 0.5662 (tpp) REVERT: A 1171 LYS cc_start: 0.8086 (tppt) cc_final: 0.7705 (tppt) REVERT: A 1176 PHE cc_start: 0.7803 (t80) cc_final: 0.7437 (t80) REVERT: A 1201 ILE cc_start: 0.7115 (mp) cc_final: 0.6696 (mm) REVERT: A 1304 LEU cc_start: 0.8400 (OUTLIER) cc_final: 0.8044 (pp) REVERT: A 1333 HIS cc_start: 0.6534 (t-170) cc_final: 0.6034 (t-170) REVERT: A 1338 LYS cc_start: 0.8584 (ptmt) cc_final: 0.8363 (ptmt) REVERT: A 1363 ASN cc_start: 0.7431 (m-40) cc_final: 0.7157 (m-40) REVERT: A 1433 CYS cc_start: 0.6874 (p) cc_final: 0.6442 (p) REVERT: A 1482 GLN cc_start: 0.7285 (tm-30) cc_final: 0.7026 (tm-30) REVERT: A 1495 ASN cc_start: 0.7244 (t0) cc_final: 0.6238 (t0) REVERT: A 1542 TYR cc_start: 0.7067 (t80) cc_final: 0.6150 (t80) REVERT: A 1569 MET cc_start: 0.7372 (ptm) cc_final: 0.7000 (tmm) REVERT: A 1575 LYS cc_start: 0.8308 (mttp) cc_final: 0.7361 (mmmt) REVERT: A 1588 LYS cc_start: 0.7655 (tptt) cc_final: 0.7440 (mmmt) REVERT: A 1645 GLU cc_start: 0.8223 (pp20) cc_final: 0.8016 (tm-30) REVERT: A 1673 LEU cc_start: 0.7538 (mm) cc_final: 0.7043 (tp) REVERT: A 1820 LYS cc_start: 0.8172 (ptpt) cc_final: 0.7926 (ptpt) REVERT: A 1891 LYS cc_start: 0.8395 (mmtt) cc_final: 0.8072 (mmmt) REVERT: A 1893 ILE cc_start: 0.8169 (OUTLIER) cc_final: 0.7775 (tp) REVERT: A 1898 ASP cc_start: 0.6654 (t0) cc_final: 0.6407 (t0) REVERT: A 1953 ARG cc_start: 0.6781 (OUTLIER) cc_final: 0.6494 (mmt180) REVERT: A 1966 PHE cc_start: 0.7211 (m-80) cc_final: 0.6832 (m-10) REVERT: A 1971 LYS cc_start: 0.5460 (OUTLIER) cc_final: 0.3438 (mmmt) REVERT: A 1978 PHE cc_start: 0.5412 (p90) cc_final: 0.5075 (p90) REVERT: A 2008 MET cc_start: 0.7099 (ppp) cc_final: 0.6673 (ppp) REVERT: A 2009 ASN cc_start: 0.7845 (t0) cc_final: 0.7410 (m-40) REVERT: A 2057 LYS cc_start: 0.8533 (mmtm) cc_final: 0.8048 (mmmt) REVERT: A 2168 MET cc_start: 0.5021 (tpt) cc_final: 0.4506 (mmm) REVERT: A 2296 VAL cc_start: 0.3837 (OUTLIER) cc_final: 0.2866 (t) REVERT: A 2301 SER cc_start: 0.8059 (t) cc_final: 0.7608 (p) REVERT: A 2342 GLN cc_start: 0.6909 (mt0) cc_final: 0.6580 (mp10) REVERT: A 2357 LEU cc_start: 0.7660 (OUTLIER) cc_final: 0.7116 (mt) REVERT: A 2603 GLU cc_start: 0.8682 (tm-30) cc_final: 0.8197 (tm-30) outliers start: 49 outliers final: 31 residues processed: 421 average time/residue: 0.1344 time to fit residues: 85.8405 Evaluate side-chains 428 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 390 time to evaluate : 0.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 482 ASN Chi-restraints excluded: chain A residue 534 PHE Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain A residue 704 TYR Chi-restraints excluded: chain A residue 722 LEU Chi-restraints excluded: chain A residue 729 SER Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 885 MET Chi-restraints excluded: chain A residue 1287 ASN Chi-restraints excluded: chain A residue 1304 LEU Chi-restraints excluded: chain A residue 1331 VAL Chi-restraints excluded: chain A residue 1345 GLU Chi-restraints excluded: chain A residue 1373 VAL Chi-restraints excluded: chain A residue 1420 SER Chi-restraints excluded: chain A residue 1460 THR Chi-restraints excluded: chain A residue 1510 SER Chi-restraints excluded: chain A residue 1528 LEU Chi-restraints excluded: chain A residue 1537 ASP Chi-restraints excluded: chain A residue 1698 GLU Chi-restraints excluded: chain A residue 1832 PHE Chi-restraints excluded: chain A residue 1836 ILE Chi-restraints excluded: chain A residue 1890 LEU Chi-restraints excluded: chain A residue 1893 ILE Chi-restraints excluded: chain A residue 1953 ARG Chi-restraints excluded: chain A residue 1971 LYS Chi-restraints excluded: chain A residue 1997 THR Chi-restraints excluded: chain A residue 1998 ILE Chi-restraints excluded: chain A residue 2039 ILE Chi-restraints excluded: chain A residue 2120 MET Chi-restraints excluded: chain A residue 2126 VAL Chi-restraints excluded: chain A residue 2254 GLU Chi-restraints excluded: chain A residue 2280 MET Chi-restraints excluded: chain A residue 2296 VAL Chi-restraints excluded: chain A residue 2357 LEU Chi-restraints excluded: chain A residue 2602 LEU Chi-restraints excluded: chain A residue 2668 SER Chi-restraints excluded: chain A residue 2675 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 22 optimal weight: 0.6980 chunk 116 optimal weight: 2.9990 chunk 157 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 177 optimal weight: 2.9990 chunk 115 optimal weight: 2.9990 chunk 119 optimal weight: 3.9990 chunk 6 optimal weight: 0.7980 chunk 10 optimal weight: 5.9990 chunk 99 optimal weight: 6.9990 chunk 60 optimal weight: 0.6980 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 407 GLN ** A 419 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 482 ASN ** A 939 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1137 HIS ** A1901 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1952 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2006 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2100 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4642 r_free = 0.4642 target = 0.197221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.162827 restraints weight = 41520.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.4328 r_free = 0.4328 target = 0.167219 restraints weight = 26809.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4364 r_free = 0.4364 target = 0.170236 restraints weight = 18968.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 58)----------------| | r_work = 0.4388 r_free = 0.4388 target = 0.172452 restraints weight = 14410.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4405 r_free = 0.4405 target = 0.174022 restraints weight = 11602.321| |-----------------------------------------------------------------------------| r_work (final): 0.4373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6112 moved from start: 0.3773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 18394 Z= 0.189 Angle : 0.791 12.711 24780 Z= 0.409 Chirality : 0.047 0.290 2839 Planarity : 0.004 0.054 3112 Dihedral : 5.373 45.959 2411 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 16.36 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.78 % Favored : 91.17 % Rotamer: Outliers : 2.23 % Allowed : 20.51 % Favored : 77.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.26 (0.18), residues: 2220 helix: 0.41 (0.15), residues: 1236 sheet: -0.75 (0.51), residues: 93 loop : -2.73 (0.20), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A2033 TYR 0.045 0.002 TYR A 876 PHE 0.054 0.002 PHE A 744 TRP 0.046 0.003 TRP A2051 HIS 0.005 0.001 HIS A 893 Details of bonding type rmsd covalent geometry : bond 0.00394 (18394) covalent geometry : angle 0.79091 (24780) hydrogen bonds : bond 0.04157 ( 877) hydrogen bonds : angle 4.84629 ( 2586) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 453 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 407 time to evaluate : 0.665 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 322 THR cc_start: 0.4381 (t) cc_final: 0.4054 (t) REVERT: A 446 GLN cc_start: 0.8076 (pp30) cc_final: 0.7470 (pp30) REVERT: A 450 GLU cc_start: 0.7741 (mt-10) cc_final: 0.7475 (mt-10) REVERT: A 475 SER cc_start: 0.6652 (t) cc_final: 0.6126 (p) REVERT: A 482 ASN cc_start: 0.1948 (OUTLIER) cc_final: 0.1198 (p0) REVERT: A 491 GLU cc_start: 0.7385 (pp20) cc_final: 0.6944 (pp20) REVERT: A 536 MET cc_start: 0.6425 (tpp) cc_final: 0.5899 (tpt) REVERT: A 603 LYS cc_start: 0.8349 (tppt) cc_final: 0.8131 (tppt) REVERT: A 604 ASN cc_start: 0.7531 (p0) cc_final: 0.6750 (p0) REVERT: A 623 LYS cc_start: 0.8168 (mttt) cc_final: 0.7568 (mmmm) REVERT: A 637 TYR cc_start: 0.6828 (m-10) cc_final: 0.4611 (m-10) REVERT: A 639 GLU cc_start: 0.7256 (tp30) cc_final: 0.6870 (tp30) REVERT: A 642 MET cc_start: 0.7283 (ttt) cc_final: 0.7044 (ttt) REVERT: A 671 MET cc_start: 0.6333 (ttt) cc_final: 0.5758 (ttt) REVERT: A 702 GLU cc_start: 0.7118 (pm20) cc_final: 0.5396 (pm20) REVERT: A 717 MET cc_start: 0.5221 (tpp) cc_final: 0.4681 (tpp) REVERT: A 732 LYS cc_start: 0.7810 (tppp) cc_final: 0.7237 (tppt) REVERT: A 741 PHE cc_start: 0.6981 (t80) cc_final: 0.6546 (t80) REVERT: A 770 MET cc_start: 0.7191 (tmm) cc_final: 0.6698 (tmm) REVERT: A 785 MET cc_start: 0.5810 (mtp) cc_final: 0.5438 (mmm) REVERT: A 791 LYS cc_start: 0.6956 (OUTLIER) cc_final: 0.6705 (ptpp) REVERT: A 836 VAL cc_start: 0.8023 (m) cc_final: 0.7728 (p) REVERT: A 842 LEU cc_start: 0.8297 (tp) cc_final: 0.8053 (tp) REVERT: A 873 GLU cc_start: 0.7728 (mt-10) cc_final: 0.7226 (mm-30) REVERT: A 886 MET cc_start: 0.6291 (tpp) cc_final: 0.5824 (tpp) REVERT: A 913 LYS cc_start: 0.8718 (tptt) cc_final: 0.8337 (tppt) REVERT: A 929 MET cc_start: 0.6979 (tpt) cc_final: 0.6512 (tpt) REVERT: A 969 GLU cc_start: 0.7953 (tp30) cc_final: 0.7504 (tp30) REVERT: A 985 LYS cc_start: 0.6909 (tmtt) cc_final: 0.6522 (tptt) REVERT: A 1102 LYS cc_start: 0.6659 (tptt) cc_final: 0.6293 (tptt) REVERT: A 1106 GLU cc_start: 0.6709 (mm-30) cc_final: 0.6229 (mm-30) REVERT: A 1109 ASP cc_start: 0.7534 (t0) cc_final: 0.7022 (t0) REVERT: A 1142 MET cc_start: 0.6244 (tpt) cc_final: 0.5709 (tpp) REVERT: A 1171 LYS cc_start: 0.8101 (tppt) cc_final: 0.7731 (tppt) REVERT: A 1176 PHE cc_start: 0.7768 (t80) cc_final: 0.7417 (t80) REVERT: A 1201 ILE cc_start: 0.7150 (mp) cc_final: 0.6617 (mm) REVERT: A 1209 LEU cc_start: 0.8202 (tp) cc_final: 0.7977 (tp) REVERT: A 1304 LEU cc_start: 0.8441 (OUTLIER) cc_final: 0.8067 (pp) REVERT: A 1333 HIS cc_start: 0.6395 (t-170) cc_final: 0.5900 (t-170) REVERT: A 1338 LYS cc_start: 0.8618 (ptmt) cc_final: 0.8330 (ptmt) REVERT: A 1363 ASN cc_start: 0.7314 (m-40) cc_final: 0.7073 (m-40) REVERT: A 1433 CYS cc_start: 0.6925 (p) cc_final: 0.6462 (p) REVERT: A 1482 GLN cc_start: 0.7267 (tm-30) cc_final: 0.7056 (tm-30) REVERT: A 1495 ASN cc_start: 0.7083 (t0) cc_final: 0.6117 (t0) REVERT: A 1569 MET cc_start: 0.7397 (ptm) cc_final: 0.6986 (tmm) REVERT: A 1575 LYS cc_start: 0.8371 (mttp) cc_final: 0.7460 (mmmt) REVERT: A 1673 LEU cc_start: 0.7673 (mm) cc_final: 0.7174 (tp) REVERT: A 1820 LYS cc_start: 0.8314 (ptpt) cc_final: 0.7999 (ptpt) REVERT: A 1891 LYS cc_start: 0.8416 (mmtt) cc_final: 0.8112 (mmmt) REVERT: A 1893 ILE cc_start: 0.8190 (OUTLIER) cc_final: 0.7795 (tp) REVERT: A 1953 ARG cc_start: 0.6861 (OUTLIER) cc_final: 0.6241 (mmt180) REVERT: A 1971 LYS cc_start: 0.5483 (OUTLIER) cc_final: 0.3476 (mmmt) REVERT: A 2008 MET cc_start: 0.7081 (ppp) cc_final: 0.6658 (ppp) REVERT: A 2009 ASN cc_start: 0.7951 (t0) cc_final: 0.7491 (m-40) REVERT: A 2057 LYS cc_start: 0.8559 (mmtm) cc_final: 0.8049 (mmmt) REVERT: A 2168 MET cc_start: 0.5129 (tpt) cc_final: 0.4609 (mmm) REVERT: A 2278 PHE cc_start: 0.6523 (m-10) cc_final: 0.6311 (m-10) REVERT: A 2296 VAL cc_start: 0.3651 (OUTLIER) cc_final: 0.2946 (t) REVERT: A 2301 SER cc_start: 0.8063 (t) cc_final: 0.7613 (p) REVERT: A 2342 GLN cc_start: 0.6959 (mt0) cc_final: 0.6690 (mp10) REVERT: A 2357 LEU cc_start: 0.7724 (OUTLIER) cc_final: 0.7211 (mt) REVERT: A 2590 ASN cc_start: 0.4307 (OUTLIER) cc_final: 0.4058 (m-40) REVERT: A 2603 GLU cc_start: 0.8687 (tm-30) cc_final: 0.8253 (tm-30) outliers start: 46 outliers final: 32 residues processed: 425 average time/residue: 0.1280 time to fit residues: 82.4128 Evaluate side-chains 438 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 397 time to evaluate : 0.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 482 ASN Chi-restraints excluded: chain A residue 534 PHE Chi-restraints excluded: chain A residue 704 TYR Chi-restraints excluded: chain A residue 722 LEU Chi-restraints excluded: chain A residue 729 SER Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 791 LYS Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 885 MET Chi-restraints excluded: chain A residue 1228 LEU Chi-restraints excluded: chain A residue 1265 MET Chi-restraints excluded: chain A residue 1287 ASN Chi-restraints excluded: chain A residue 1304 LEU Chi-restraints excluded: chain A residue 1331 VAL Chi-restraints excluded: chain A residue 1345 GLU Chi-restraints excluded: chain A residue 1373 VAL Chi-restraints excluded: chain A residue 1420 SER Chi-restraints excluded: chain A residue 1460 THR Chi-restraints excluded: chain A residue 1510 SER Chi-restraints excluded: chain A residue 1528 LEU Chi-restraints excluded: chain A residue 1537 ASP Chi-restraints excluded: chain A residue 1825 LEU Chi-restraints excluded: chain A residue 1832 PHE Chi-restraints excluded: chain A residue 1836 ILE Chi-restraints excluded: chain A residue 1890 LEU Chi-restraints excluded: chain A residue 1893 ILE Chi-restraints excluded: chain A residue 1953 ARG Chi-restraints excluded: chain A residue 1971 LYS Chi-restraints excluded: chain A residue 1997 THR Chi-restraints excluded: chain A residue 1998 ILE Chi-restraints excluded: chain A residue 2039 ILE Chi-restraints excluded: chain A residue 2120 MET Chi-restraints excluded: chain A residue 2126 VAL Chi-restraints excluded: chain A residue 2254 GLU Chi-restraints excluded: chain A residue 2280 MET Chi-restraints excluded: chain A residue 2296 VAL Chi-restraints excluded: chain A residue 2357 LEU Chi-restraints excluded: chain A residue 2590 ASN Chi-restraints excluded: chain A residue 2602 LEU Chi-restraints excluded: chain A residue 2668 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 120 optimal weight: 1.9990 chunk 90 optimal weight: 6.9990 chunk 160 optimal weight: 0.0870 chunk 158 optimal weight: 4.9990 chunk 73 optimal weight: 10.0000 chunk 185 optimal weight: 7.9990 chunk 137 optimal weight: 0.8980 chunk 23 optimal weight: 0.0570 chunk 204 optimal weight: 50.0000 chunk 67 optimal weight: 7.9990 chunk 207 optimal weight: 0.2980 overall best weight: 0.6678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 419 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 482 ASN ** A 939 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1324 ASN ** A1901 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1952 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4675 r_free = 0.4675 target = 0.200164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.164964 restraints weight = 41750.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4357 r_free = 0.4357 target = 0.169402 restraints weight = 27098.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4393 r_free = 0.4393 target = 0.172493 restraints weight = 19256.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.4417 r_free = 0.4417 target = 0.174667 restraints weight = 14693.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4433 r_free = 0.4433 target = 0.176136 restraints weight = 11935.073| |-----------------------------------------------------------------------------| r_work (final): 0.4409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6068 moved from start: 0.3830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 18394 Z= 0.141 Angle : 0.787 15.228 24780 Z= 0.399 Chirality : 0.046 0.305 2839 Planarity : 0.004 0.053 3112 Dihedral : 5.191 44.964 2411 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 15.37 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.29 % Favored : 91.67 % Rotamer: Outliers : 1.74 % Allowed : 21.43 % Favored : 76.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.07 (0.18), residues: 2220 helix: 0.55 (0.15), residues: 1234 sheet: -0.52 (0.52), residues: 93 loop : -2.63 (0.20), residues: 893 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A2245 TYR 0.047 0.001 TYR A 876 PHE 0.056 0.001 PHE A 744 TRP 0.039 0.002 TRP A1857 HIS 0.006 0.001 HIS A 893 Details of bonding type rmsd covalent geometry : bond 0.00308 (18394) covalent geometry : angle 0.78680 (24780) hydrogen bonds : bond 0.03788 ( 877) hydrogen bonds : angle 4.66225 ( 2586) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 429 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 393 time to evaluate : 0.745 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 322 THR cc_start: 0.4406 (t) cc_final: 0.4163 (t) REVERT: A 407 GLN cc_start: 0.7438 (mm-40) cc_final: 0.6714 (pm20) REVERT: A 446 GLN cc_start: 0.8023 (pp30) cc_final: 0.7325 (pp30) REVERT: A 450 GLU cc_start: 0.7708 (mt-10) cc_final: 0.7438 (mt-10) REVERT: A 452 GLU cc_start: 0.7987 (tm-30) cc_final: 0.7607 (tm-30) REVERT: A 475 SER cc_start: 0.6574 (t) cc_final: 0.5807 (p) REVERT: A 482 ASN cc_start: 0.2117 (OUTLIER) cc_final: 0.1007 (p0) REVERT: A 491 GLU cc_start: 0.7375 (pp20) cc_final: 0.6941 (pp20) REVERT: A 536 MET cc_start: 0.6423 (tpp) cc_final: 0.5895 (tpt) REVERT: A 603 LYS cc_start: 0.8362 (tppt) cc_final: 0.7583 (tppt) REVERT: A 604 ASN cc_start: 0.7469 (p0) cc_final: 0.7055 (p0) REVERT: A 623 LYS cc_start: 0.8132 (mttt) cc_final: 0.7671 (mmmm) REVERT: A 637 TYR cc_start: 0.6854 (m-10) cc_final: 0.4558 (m-10) REVERT: A 639 GLU cc_start: 0.7225 (tp30) cc_final: 0.6903 (tp30) REVERT: A 671 MET cc_start: 0.6261 (ttt) cc_final: 0.5728 (ttt) REVERT: A 702 GLU cc_start: 0.7001 (pm20) cc_final: 0.6337 (pm20) REVERT: A 717 MET cc_start: 0.5034 (tpp) cc_final: 0.4656 (tpp) REVERT: A 732 LYS cc_start: 0.7671 (tppp) cc_final: 0.7073 (tppt) REVERT: A 741 PHE cc_start: 0.6911 (t80) cc_final: 0.6453 (t80) REVERT: A 770 MET cc_start: 0.7189 (tmm) cc_final: 0.6650 (tmm) REVERT: A 785 MET cc_start: 0.5720 (mtp) cc_final: 0.5403 (mmm) REVERT: A 836 VAL cc_start: 0.8021 (m) cc_final: 0.7741 (p) REVERT: A 842 LEU cc_start: 0.8292 (tp) cc_final: 0.8060 (tp) REVERT: A 861 LYS cc_start: 0.8701 (mptt) cc_final: 0.8415 (mmtt) REVERT: A 873 GLU cc_start: 0.7704 (mt-10) cc_final: 0.7221 (mm-30) REVERT: A 886 MET cc_start: 0.6276 (tpp) cc_final: 0.5795 (tpp) REVERT: A 913 LYS cc_start: 0.8698 (tptt) cc_final: 0.8298 (tppt) REVERT: A 929 MET cc_start: 0.6898 (tpt) cc_final: 0.6429 (tpt) REVERT: A 969 GLU cc_start: 0.7924 (tp30) cc_final: 0.7536 (tp30) REVERT: A 985 LYS cc_start: 0.6855 (tmtt) cc_final: 0.6429 (tptt) REVERT: A 1102 LYS cc_start: 0.6480 (tptt) cc_final: 0.6076 (tptm) REVERT: A 1106 GLU cc_start: 0.6748 (mm-30) cc_final: 0.6245 (mm-30) REVERT: A 1109 ASP cc_start: 0.7527 (t0) cc_final: 0.7035 (t0) REVERT: A 1142 MET cc_start: 0.6214 (tpt) cc_final: 0.5640 (tpp) REVERT: A 1171 LYS cc_start: 0.8053 (tppt) cc_final: 0.7708 (tppt) REVERT: A 1176 PHE cc_start: 0.7782 (t80) cc_final: 0.7431 (t80) REVERT: A 1333 HIS cc_start: 0.6414 (t-170) cc_final: 0.5791 (t-170) REVERT: A 1338 LYS cc_start: 0.8512 (ptmt) cc_final: 0.8274 (ptmt) REVERT: A 1363 ASN cc_start: 0.7373 (m-40) cc_final: 0.6884 (m-40) REVERT: A 1408 LYS cc_start: 0.6254 (mttt) cc_final: 0.6003 (mttp) REVERT: A 1433 CYS cc_start: 0.6771 (p) cc_final: 0.6292 (p) REVERT: A 1509 LYS cc_start: 0.7860 (mptt) cc_final: 0.7206 (mptt) REVERT: A 1569 MET cc_start: 0.7399 (ptm) cc_final: 0.6973 (tmm) REVERT: A 1575 LYS cc_start: 0.8277 (mttp) cc_final: 0.7340 (mmmt) REVERT: A 1588 LYS cc_start: 0.7771 (mmmt) cc_final: 0.7533 (mttp) REVERT: A 1618 LEU cc_start: 0.8035 (mt) cc_final: 0.7473 (mp) REVERT: A 1621 MET cc_start: 0.6087 (mpp) cc_final: 0.4830 (pmm) REVERT: A 1673 LEU cc_start: 0.7619 (mm) cc_final: 0.7102 (tp) REVERT: A 1820 LYS cc_start: 0.8193 (ptpt) cc_final: 0.7930 (ptpt) REVERT: A 1834 MET cc_start: 0.3809 (ptt) cc_final: 0.3568 (ptt) REVERT: A 1891 LYS cc_start: 0.8377 (mmtt) cc_final: 0.8050 (mmmt) REVERT: A 1893 ILE cc_start: 0.8143 (OUTLIER) cc_final: 0.7742 (tp) REVERT: A 1953 ARG cc_start: 0.6720 (mmt180) cc_final: 0.6191 (mmt180) REVERT: A 1978 PHE cc_start: 0.5440 (p90) cc_final: 0.5140 (p90) REVERT: A 2057 LYS cc_start: 0.8572 (mmtm) cc_final: 0.8083 (mmmt) REVERT: A 2083 ASN cc_start: 0.8134 (m-40) cc_final: 0.7883 (m110) REVERT: A 2168 MET cc_start: 0.5110 (tpt) cc_final: 0.4597 (mmm) REVERT: A 2296 VAL cc_start: 0.3653 (OUTLIER) cc_final: 0.2665 (t) REVERT: A 2301 SER cc_start: 0.8025 (t) cc_final: 0.7579 (p) REVERT: A 2342 GLN cc_start: 0.6964 (mt0) cc_final: 0.6671 (mp10) REVERT: A 2357 LEU cc_start: 0.7595 (OUTLIER) cc_final: 0.7105 (mt) REVERT: A 2603 GLU cc_start: 0.8672 (tm-30) cc_final: 0.8236 (tm-30) outliers start: 36 outliers final: 25 residues processed: 410 average time/residue: 0.1366 time to fit residues: 85.0489 Evaluate side-chains 416 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 387 time to evaluate : 0.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 482 ASN Chi-restraints excluded: chain A residue 534 PHE Chi-restraints excluded: chain A residue 722 LEU Chi-restraints excluded: chain A residue 729 SER Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 885 MET Chi-restraints excluded: chain A residue 1304 LEU Chi-restraints excluded: chain A residue 1324 ASN Chi-restraints excluded: chain A residue 1331 VAL Chi-restraints excluded: chain A residue 1345 GLU Chi-restraints excluded: chain A residue 1420 SER Chi-restraints excluded: chain A residue 1510 SER Chi-restraints excluded: chain A residue 1537 ASP Chi-restraints excluded: chain A residue 1698 GLU Chi-restraints excluded: chain A residue 1832 PHE Chi-restraints excluded: chain A residue 1836 ILE Chi-restraints excluded: chain A residue 1890 LEU Chi-restraints excluded: chain A residue 1893 ILE Chi-restraints excluded: chain A residue 1997 THR Chi-restraints excluded: chain A residue 1998 ILE Chi-restraints excluded: chain A residue 2039 ILE Chi-restraints excluded: chain A residue 2126 VAL Chi-restraints excluded: chain A residue 2280 MET Chi-restraints excluded: chain A residue 2296 VAL Chi-restraints excluded: chain A residue 2357 LEU Chi-restraints excluded: chain A residue 2414 LEU Chi-restraints excluded: chain A residue 2668 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 57 optimal weight: 0.7980 chunk 200 optimal weight: 40.0000 chunk 205 optimal weight: 9.9990 chunk 20 optimal weight: 0.9990 chunk 198 optimal weight: 5.9990 chunk 81 optimal weight: 1.9990 chunk 181 optimal weight: 0.6980 chunk 140 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 125 optimal weight: 3.9990 chunk 122 optimal weight: 1.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 419 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 482 ASN ** A 939 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1324 ASN A1495 ASN ** A1901 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1938 GLN ** A1952 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2006 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4648 r_free = 0.4648 target = 0.197640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.163027 restraints weight = 42200.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.167461 restraints weight = 27263.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4366 r_free = 0.4366 target = 0.170614 restraints weight = 19208.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.4391 r_free = 0.4391 target = 0.172825 restraints weight = 14598.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4407 r_free = 0.4407 target = 0.174273 restraints weight = 11749.377| |-----------------------------------------------------------------------------| r_work (final): 0.4379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6102 moved from start: 0.3987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 18394 Z= 0.169 Angle : 0.812 14.688 24780 Z= 0.414 Chirality : 0.047 0.269 2839 Planarity : 0.004 0.053 3112 Dihedral : 5.246 44.618 2411 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 16.41 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.10 % Favored : 90.86 % Rotamer: Outliers : 1.50 % Allowed : 22.21 % Favored : 76.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.15 (0.18), residues: 2220 helix: 0.47 (0.15), residues: 1234 sheet: -0.56 (0.52), residues: 93 loop : -2.64 (0.20), residues: 893 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 428 TYR 0.047 0.001 TYR A 876 PHE 0.055 0.002 PHE A 744 TRP 0.064 0.003 TRP A2051 HIS 0.005 0.001 HIS A 893 Details of bonding type rmsd covalent geometry : bond 0.00360 (18394) covalent geometry : angle 0.81238 (24780) hydrogen bonds : bond 0.04032 ( 877) hydrogen bonds : angle 4.80323 ( 2586) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3457.45 seconds wall clock time: 60 minutes 37.26 seconds (3637.26 seconds total)