Starting phenix.real_space_refine on Mon May 19 12:26:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ki9_37255/05_2025/8ki9_37255.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ki9_37255/05_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_37255/05_2025/8ki9_37255.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ki9_37255/05_2025/8ki9_37255.map" model { file = "/net/cci-nas-00/data/ceres_data/8ki9_37255/05_2025/8ki9_37255.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ki9_37255/05_2025/8ki9_37255.cif" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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, 'ARG:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 24 Time building chain proxies: 9.30, per 1000 atoms: 0.51 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: 3.90 Conformation dependent library (CDL) restraints added in 2.3 seconds 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: 2.75 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: 8.86 Time building geometry restraints manager: 4.68 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: 1.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.690 Check model and map are aligned: 0.120 Set scattering table: 0.170 Process input model: 42.410 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.790 ------------------------------------------------------------------------------- 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 : 6.30 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.040 0.003 TRP A 907 HIS 0.009 0.001 HIS A1179 PHE 0.040 0.002 PHE A 707 TYR 0.044 0.002 TYR A1410 ARG 0.020 0.001 ARG A 490 Details of bonding type rmsd hydrogen bonds : bond 0.13300 ( 877) hydrogen bonds : angle 6.45658 ( 2586) covalent geometry : bond 0.00459 (18394) covalent geometry : angle 1.06027 (24780) *********************** 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 : 1.828 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: 0.6661 (tp30) REVERT: A 364 PHE cc_start: 0.7878 (p90) cc_final: 0.6752 (t80) REVERT: A 392 ILE cc_start: 0.6578 (mm) cc_final: 0.5668 (tp) REVERT: A 450 GLU cc_start: 0.7540 (mt-10) cc_final: 0.7077 (mp0) REVERT: A 452 GLU cc_start: 0.8207 (tm-30) cc_final: 0.7755 (tm-30) REVERT: A 536 MET cc_start: 0.5963 (tpp) cc_final: 0.5156 (tpt) REVERT: A 604 ASN cc_start: 0.7596 (p0) cc_final: 0.7393 (p0) REVERT: A 608 LEU cc_start: 0.8127 (mm) cc_final: 0.7838 (mt) REVERT: A 623 LYS cc_start: 0.8146 (mttt) cc_final: 0.7485 (mmmm) REVERT: A 637 TYR cc_start: 0.6869 (m-10) cc_final: 0.4217 (m-10) REVERT: A 639 GLU cc_start: 0.7558 (tp30) cc_final: 0.7158 (tp30) REVERT: A 642 MET cc_start: 0.7283 (ttt) cc_final: 0.7047 (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: 0.5795 (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: 0.6635 (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: 0.8273 (tppt) REVERT: A 785 MET cc_start: 0.5747 (mtp) cc_final: 0.5474 (mmm) REVERT: A 795 MET cc_start: 0.7675 (mtm) cc_final: 0.7098 (mmm) REVERT: A 797 ILE cc_start: 0.7333 (pt) cc_final: 0.6100 (mm) REVERT: A 801 MET cc_start: 0.7857 (mtm) cc_final: 0.7631 (mtm) REVERT: A 833 ILE cc_start: 0.8440 (mp) cc_final: 0.8146 (mp) REVERT: A 836 VAL cc_start: 0.8019 (m) cc_final: 0.7784 (p) REVERT: A 842 LEU cc_start: 0.8376 (tp) cc_final: 0.8107 (tp) REVERT: A 873 GLU cc_start: 0.7859 (mt-10) cc_final: 0.7432 (mt-10) REVERT: A 886 MET cc_start: 0.6533 (tpp) cc_final: 0.5640 (tpp) REVERT: A 911 PHE cc_start: 0.5508 (t80) cc_final: 0.4898 (t80) REVERT: A 913 LYS cc_start: 0.8582 (tptt) cc_final: 0.8101 (tppt) REVERT: A 929 MET cc_start: 0.7019 (tpt) cc_final: 0.6448 (tpt) REVERT: A 969 GLU cc_start: 0.7800 (tp30) cc_final: 0.7488 (tp30) REVERT: A 985 LYS cc_start: 0.7790 (tmtt) cc_final: 0.7536 (tmtt) REVERT: A 1106 GLU cc_start: 0.6732 (mm-30) cc_final: 0.6272 (mm-30) REVERT: A 1109 ASP cc_start: 0.7464 (t0) cc_final: 0.6983 (t0) REVERT: A 1126 MET cc_start: 0.7696 (mmm) cc_final: 0.7403 (mmm) REVERT: A 1144 GLU cc_start: 0.7404 (pp20) cc_final: 0.7171 (pp20) REVERT: A 1171 LYS cc_start: 0.7997 (tppt) cc_final: 0.7588 (tppt) REVERT: A 1176 PHE cc_start: 0.7825 (t80) cc_final: 0.7279 (t80) REVERT: A 1193 ILE cc_start: 0.7845 (tp) cc_final: 0.7591 (tp) REVERT: A 1201 ILE cc_start: 0.7089 (mp) cc_final: 0.6882 (mm) REVERT: A 1209 LEU cc_start: 0.8292 (tp) cc_final: 0.8068 (tp) REVERT: A 1217 ASP cc_start: 0.7244 (m-30) cc_final: 0.6942 (m-30) REVERT: A 1237 LYS cc_start: 0.7329 (tptt) cc_final: 0.7042 (mmtt) REVERT: A 1249 LEU cc_start: 0.8007 (tp) cc_final: 0.7785 (tp) REVERT: A 1309 LEU cc_start: 0.5973 (mm) cc_final: 0.5480 (pt) REVERT: A 1320 TRP cc_start: 0.7248 (p-90) cc_final: 0.6575 (p-90) REVERT: A 1333 HIS cc_start: 0.6773 (t-170) cc_final: 0.6319 (t-170) REVERT: A 1337 MET cc_start: 0.7594 (mmp) cc_final: 0.6807 (mmp) REVERT: A 1338 LYS cc_start: 0.8331 (ptmt) cc_final: 0.8048 (ptmt) REVERT: A 1354 THR cc_start: 0.7474 (p) cc_final: 0.7176 (p) REVERT: A 1363 ASN cc_start: 0.7424 (m-40) cc_final: 0.6770 (m-40) REVERT: A 1373 VAL cc_start: 0.8272 (t) cc_final: 0.7498 (t) REVERT: A 1418 PHE cc_start: 0.6765 (t80) cc_final: 0.6456 (t80) REVERT: A 1431 LEU cc_start: 0.7089 (tt) cc_final: 0.6889 (tt) REVERT: A 1435 HIS cc_start: 0.7126 (m90) cc_final: 0.6882 (m90) REVERT: A 1453 MET cc_start: 0.7774 (mmp) cc_final: 0.7520 (mmm) REVERT: A 1457 ILE cc_start: 0.8651 (mt) cc_final: 0.8353 (mt) REVERT: A 1495 ASN cc_start: 0.7426 (t160) cc_final: 0.6490 (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: 0.7218 (mmtt) REVERT: A 1569 MET cc_start: 0.7359 (ptm) cc_final: 0.6833 (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: 0.6265 (mmp) REVERT: A 1645 GLU cc_start: 0.8303 (pp20) cc_final: 0.7866 (tm-30) REVERT: A 1823 VAL cc_start: 0.7120 (p) cc_final: 0.6865 (t) REVERT: A 1898 ASP cc_start: 0.7819 (m-30) cc_final: 0.7438 (t0) REVERT: A 1912 ILE cc_start: 0.7245 (tt) cc_final: 0.6791 (tt) REVERT: A 1917 LYS cc_start: 0.8439 (tmtt) cc_final: 0.8200 (tptp) REVERT: A 1966 PHE cc_start: 0.6991 (m-80) cc_final: 0.6604 (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: 0.7303 (m-40) REVERT: A 2010 LEU cc_start: 0.8116 (tp) cc_final: 0.7880 (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: 0.8045 (m110) REVERT: A 2301 SER cc_start: 0.7962 (t) cc_final: 0.7538 (p) REVERT: A 2357 LEU cc_start: 0.7800 (mm) cc_final: 0.7360 (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: 0.4339 (m-10) REVERT: A 2603 GLU cc_start: 0.8800 (tm-30) cc_final: 0.7968 (tm-30) REVERT: A 2607 LYS cc_start: 0.9045 (mmpt) cc_final: 0.8550 (mmmt) outliers start: 1 outliers final: 0 residues processed: 414 average time/residue: 0.3133 time to fit residues: 194.0574 Evaluate side-chains 391 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 391 time to evaluate : 1.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 188 optimal weight: 4.9990 chunk 169 optimal weight: 0.4980 chunk 93 optimal weight: 0.8980 chunk 57 optimal weight: 0.7980 chunk 114 optimal weight: 2.9990 chunk 90 optimal weight: 3.9990 chunk 174 optimal weight: 8.9990 chunk 67 optimal weight: 4.9990 chunk 106 optimal weight: 0.8980 chunk 130 optimal weight: 6.9990 chunk 202 optimal weight: 50.0000 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 358 HIS A 407 GLN A 877 ASN ** A 939 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1396 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 ** A1901 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2258 ASN A2397 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4692 r_free = 0.4692 target = 0.202262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.167444 restraints weight = 41508.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4383 r_free = 0.4383 target = 0.171927 restraints weight = 26593.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.4418 r_free = 0.4418 target = 0.175036 restraints weight = 18750.044| |-----------------------------------------------------------------------------| r_work (final): 0.4394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6047 moved from start: 0.1462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 18394 Z= 0.159 Angle : 0.687 9.575 24780 Z= 0.363 Chirality : 0.044 0.252 2839 Planarity : 0.004 0.053 3112 Dihedral : 5.651 53.164 2411 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 12.56 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.25 % Favored : 92.52 % Rotamer: Outliers : 0.68 % Allowed : 8.08 % Favored : 91.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.81 (0.17), residues: 2220 helix: -0.22 (0.14), residues: 1233 sheet: -0.51 (0.48), residues: 101 loop : -2.73 (0.20), residues: 886 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A1238 HIS 0.008 0.001 HIS A 564 PHE 0.019 0.001 PHE A 644 TYR 0.032 0.002 TYR A 876 ARG 0.007 0.000 ARG A 802 Details of bonding type rmsd hydrogen bonds : bond 0.04077 ( 877) hydrogen bonds : angle 4.88246 ( 2586) covalent geometry : bond 0.00322 (18394) covalent geometry : angle 0.68683 (24780) *********************** 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 410 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 396 time to evaluate : 1.851 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 331 THR cc_start: 0.5954 (p) cc_final: 0.5739 (p) REVERT: A 446 GLN cc_start: 0.7533 (tm-30) cc_final: 0.7255 (tm-30) REVERT: A 452 GLU cc_start: 0.8155 (tm-30) cc_final: 0.7737 (tm-30) REVERT: A 465 GLU cc_start: 0.4379 (OUTLIER) cc_final: 0.3930 (tm-30) REVERT: A 536 MET cc_start: 0.6381 (tpp) cc_final: 0.5705 (tpt) REVERT: A 603 LYS cc_start: 0.8342 (tppt) cc_final: 0.7994 (tppt) REVERT: A 604 ASN cc_start: 0.7588 (p0) cc_final: 0.7233 (p0) REVERT: A 608 LEU cc_start: 0.8008 (mm) cc_final: 0.7763 (mt) REVERT: A 618 GLU cc_start: 0.6364 (mp0) cc_final: 0.5932 (mm-30) REVERT: A 623 LYS cc_start: 0.8167 (mttt) cc_final: 0.7423 (mmmm) REVERT: A 637 TYR cc_start: 0.6980 (m-10) cc_final: 0.3797 (m-10) REVERT: A 642 MET cc_start: 0.7220 (ttt) cc_final: 0.6927 (ttt) REVERT: A 646 LYS cc_start: 0.8804 (ptpt) cc_final: 0.8481 (ptpp) REVERT: A 671 MET cc_start: 0.6638 (ttt) cc_final: 0.5938 (ttt) REVERT: A 741 PHE cc_start: 0.6761 (t80) cc_final: 0.6371 (t80) REVERT: A 761 GLU cc_start: 0.7402 (pm20) cc_final: 0.6744 (pm20) REVERT: A 770 MET cc_start: 0.7149 (tmm) cc_final: 0.6525 (tmm) REVERT: A 773 LYS cc_start: 0.9010 (tptt) cc_final: 0.8461 (tptt) REVERT: A 785 MET cc_start: 0.5736 (mtp) cc_final: 0.5481 (mmm) REVERT: A 797 ILE cc_start: 0.7337 (pt) cc_final: 0.6390 (mm) REVERT: A 802 ARG cc_start: 0.7286 (ttp80) cc_final: 0.7085 (ttp80) REVERT: A 842 LEU cc_start: 0.8465 (tp) cc_final: 0.8239 (tp) REVERT: A 861 LYS cc_start: 0.8457 (mmtt) cc_final: 0.8043 (mmtt) REVERT: A 873 GLU cc_start: 0.7843 (mt-10) cc_final: 0.7461 (mt-10) REVERT: A 886 MET cc_start: 0.6198 (tpp) cc_final: 0.5805 (tpp) REVERT: A 911 PHE cc_start: 0.5911 (t80) cc_final: 0.5265 (t80) REVERT: A 913 LYS cc_start: 0.8649 (tptt) cc_final: 0.8135 (tppt) REVERT: A 929 MET cc_start: 0.6931 (tpt) cc_final: 0.6355 (tpt) REVERT: A 969 GLU cc_start: 0.8103 (tp30) cc_final: 0.7825 (tp30) REVERT: A 1102 LYS cc_start: 0.6379 (tptt) cc_final: 0.5821 (tptp) REVERT: A 1106 GLU cc_start: 0.6921 (mm-30) cc_final: 0.6443 (mm-30) REVERT: A 1109 ASP cc_start: 0.7312 (t0) cc_final: 0.6827 (t0) REVERT: A 1171 LYS cc_start: 0.8134 (tppt) cc_final: 0.7683 (tppt) REVERT: A 1176 PHE cc_start: 0.7824 (t80) cc_final: 0.7420 (t80) REVERT: A 1181 PHE cc_start: 0.7628 (t80) cc_final: 0.7327 (t80) REVERT: A 1193 ILE cc_start: 0.7700 (tp) cc_final: 0.7475 (tp) REVERT: A 1201 ILE cc_start: 0.7124 (mp) cc_final: 0.6922 (mm) REVERT: A 1217 ASP cc_start: 0.7370 (m-30) cc_final: 0.7061 (m-30) REVERT: A 1238 TRP cc_start: 0.7201 (t60) cc_final: 0.6875 (t60) REVERT: A 1304 LEU cc_start: 0.8298 (OUTLIER) cc_final: 0.7814 (pp) REVERT: A 1320 TRP cc_start: 0.7504 (p-90) cc_final: 0.6216 (p-90) REVERT: A 1333 HIS cc_start: 0.6565 (t-170) cc_final: 0.6128 (t-170) REVERT: A 1337 MET cc_start: 0.7562 (mmp) cc_final: 0.7232 (mmt) REVERT: A 1433 CYS cc_start: 0.6854 (p) cc_final: 0.6525 (p) REVERT: A 1435 HIS cc_start: 0.7001 (m90) cc_final: 0.6740 (m90) REVERT: A 1453 MET cc_start: 0.7620 (mmp) cc_final: 0.7411 (mmm) REVERT: A 1457 ILE cc_start: 0.8671 (mt) cc_final: 0.8369 (mt) REVERT: A 1480 GLN cc_start: 0.7143 (tp40) cc_final: 0.6383 (tp-100) REVERT: A 1489 MET cc_start: 0.4656 (mmm) cc_final: 0.4084 (mmm) REVERT: A 1495 ASN cc_start: 0.7756 (t0) cc_final: 0.6860 (t0) REVERT: A 1542 TYR cc_start: 0.7164 (t80) cc_final: 0.6260 (t80) REVERT: A 1569 MET cc_start: 0.7398 (ptm) cc_final: 0.6920 (ptt) REVERT: A 1575 LYS cc_start: 0.7984 (mttp) cc_final: 0.6549 (tptt) REVERT: A 1588 LYS cc_start: 0.7624 (tptt) cc_final: 0.7412 (mmmt) REVERT: A 1645 GLU cc_start: 0.8202 (pp20) cc_final: 0.7879 (tm-30) REVERT: A 1917 LYS cc_start: 0.8247 (tmtt) cc_final: 0.7983 (tptp) REVERT: A 1966 PHE cc_start: 0.6808 (m-80) cc_final: 0.6536 (m-10) REVERT: A 1998 ILE cc_start: 0.7400 (mt) cc_final: 0.7087 (tt) REVERT: A 2010 LEU cc_start: 0.8063 (tp) cc_final: 0.7836 (tp) REVERT: A 2033 ARG cc_start: 0.7961 (ttp80) cc_final: 0.7713 (ttp80) REVERT: A 2057 LYS cc_start: 0.8608 (mmtm) cc_final: 0.7987 (mmmt) REVERT: A 2060 LYS cc_start: 0.7697 (ptpp) cc_final: 0.7475 (ptpp) REVERT: A 2083 ASN cc_start: 0.8045 (m-40) cc_final: 0.7732 (m110) REVERT: A 2301 SER cc_start: 0.8054 (t) cc_final: 0.7581 (p) REVERT: A 2357 LEU cc_start: 0.7699 (mm) cc_final: 0.7110 (mt) REVERT: A 2395 MET cc_start: 0.6830 (mtt) cc_final: 0.6411 (mmt) REVERT: A 2425 TYR cc_start: 0.4750 (m-10) cc_final: 0.4083 (m-80) REVERT: A 2603 GLU cc_start: 0.8778 (tm-30) cc_final: 0.8239 (tm-30) REVERT: A 2607 LYS cc_start: 0.9037 (mmpt) cc_final: 0.8806 (mmmt) outliers start: 14 outliers final: 7 residues processed: 399 average time/residue: 0.3080 time to fit residues: 184.1354 Evaluate side-chains 389 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 380 time to evaluate : 1.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 378 ASP Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain A residue 534 PHE Chi-restraints excluded: chain A residue 722 LEU 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 2668 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 158 optimal weight: 3.9990 chunk 166 optimal weight: 3.9990 chunk 153 optimal weight: 2.9990 chunk 84 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 chunk 125 optimal weight: 0.7980 chunk 72 optimal weight: 20.0000 chunk 4 optimal weight: 0.9990 chunk 96 optimal weight: 0.6980 chunk 28 optimal weight: 0.6980 chunk 130 optimal weight: 0.3980 overall best weight: 0.7182 ------------------------------------------------------------------------------- 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 A1141 GLN ** A1482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1883 ASN A2009 ASN A2528 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4702 r_free = 0.4702 target = 0.203334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4351 r_free = 0.4351 target = 0.169006 restraints weight = 41167.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4401 r_free = 0.4401 target = 0.173449 restraints weight = 26473.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4436 r_free = 0.4436 target = 0.176473 restraints weight = 18690.578| |-----------------------------------------------------------------------------| r_work (final): 0.4408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6027 moved from start: 0.1806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 18394 Z= 0.125 Angle : 0.663 11.129 24780 Z= 0.344 Chirality : 0.043 0.270 2839 Planarity : 0.004 0.053 3112 Dihedral : 5.407 52.010 2411 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.98 % Favored : 92.84 % Rotamer: Outliers : 1.50 % Allowed : 11.47 % Favored : 87.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.18), residues: 2220 helix: 0.31 (0.14), residues: 1229 sheet: -0.49 (0.50), residues: 99 loop : -2.64 (0.20), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A1857 HIS 0.005 0.001 HIS A 564 PHE 0.035 0.001 PHE A 744 TYR 0.045 0.001 TYR A 876 ARG 0.007 0.000 ARG A 708 Details of bonding type rmsd hydrogen bonds : bond 0.03621 ( 877) hydrogen bonds : angle 4.65768 ( 2586) covalent geometry : bond 0.00258 (18394) covalent geometry : angle 0.66315 (24780) *********************** 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 426 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 395 time to evaluate : 2.102 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 392 ILE cc_start: 0.6411 (mp) cc_final: 0.4953 (pt) REVERT: A 421 GLU cc_start: 0.7460 (mm-30) cc_final: 0.7109 (mm-30) REVERT: A 450 GLU cc_start: 0.7435 (mt-10) cc_final: 0.7067 (pt0) REVERT: A 452 GLU cc_start: 0.8097 (tm-30) cc_final: 0.7708 (tm-30) REVERT: A 536 MET cc_start: 0.6415 (tpp) cc_final: 0.5760 (tpt) REVERT: A 603 LYS cc_start: 0.8360 (tppt) cc_final: 0.7951 (tppt) REVERT: A 604 ASN cc_start: 0.7569 (p0) cc_final: 0.7189 (p0) REVERT: A 618 GLU cc_start: 0.6255 (mp0) cc_final: 0.5977 (mm-30) REVERT: A 623 LYS cc_start: 0.8131 (mttt) cc_final: 0.7492 (mmmm) REVERT: A 637 TYR cc_start: 0.6909 (m-10) cc_final: 0.4756 (m-10) REVERT: A 639 GLU cc_start: 0.7419 (tp30) cc_final: 0.7030 (tp30) REVERT: A 642 MET cc_start: 0.7095 (ttt) cc_final: 0.6759 (ttt) REVERT: A 646 LYS cc_start: 0.8763 (ptpt) cc_final: 0.8468 (ptpp) REVERT: A 671 MET cc_start: 0.6536 (ttt) cc_final: 0.5867 (ttt) REVERT: A 687 VAL cc_start: 0.7894 (t) cc_final: 0.7597 (m) REVERT: A 741 PHE cc_start: 0.6812 (t80) cc_final: 0.6409 (t80) REVERT: A 770 MET cc_start: 0.7227 (tmm) cc_final: 0.6643 (tmm) REVERT: A 785 MET cc_start: 0.5620 (mtp) cc_final: 0.5372 (mmm) REVERT: A 797 ILE cc_start: 0.6965 (pt) cc_final: 0.6135 (mm) REVERT: A 801 MET cc_start: 0.7743 (mtt) cc_final: 0.7420 (mtm) REVERT: A 842 LEU cc_start: 0.8383 (tp) cc_final: 0.8168 (tp) REVERT: A 873 GLU cc_start: 0.7690 (mt-10) cc_final: 0.7466 (mt-10) REVERT: A 886 MET cc_start: 0.6143 (tpp) cc_final: 0.5882 (tpp) REVERT: A 911 PHE cc_start: 0.5819 (t80) cc_final: 0.5237 (t80) REVERT: A 913 LYS cc_start: 0.8615 (tptt) cc_final: 0.8112 (tppt) REVERT: A 929 MET cc_start: 0.6773 (tpt) cc_final: 0.6329 (tpt) REVERT: A 949 ASP cc_start: 0.8226 (p0) cc_final: 0.7922 (p0) REVERT: A 969 GLU cc_start: 0.7983 (tp30) cc_final: 0.7625 (tp30) REVERT: A 985 LYS cc_start: 0.7326 (tmtt) cc_final: 0.6998 (tptt) REVERT: A 1102 LYS cc_start: 0.6399 (tptt) cc_final: 0.5845 (mmmt) REVERT: A 1106 GLU cc_start: 0.6856 (mm-30) cc_final: 0.6413 (mm-30) REVERT: A 1109 ASP cc_start: 0.7310 (t0) cc_final: 0.7008 (t0) REVERT: A 1112 LYS cc_start: 0.7346 (mtpp) cc_final: 0.7124 (mtpp) REVERT: A 1141 GLN cc_start: 0.6665 (OUTLIER) cc_final: 0.5967 (pp30) REVERT: A 1171 LYS cc_start: 0.8103 (tppt) cc_final: 0.7691 (tppt) REVERT: A 1176 PHE cc_start: 0.7837 (t80) cc_final: 0.7455 (t80) REVERT: A 1193 ILE cc_start: 0.7764 (tp) cc_final: 0.7531 (tp) REVERT: A 1201 ILE cc_start: 0.7098 (mp) cc_final: 0.6864 (mm) REVERT: A 1209 LEU cc_start: 0.8256 (tp) cc_final: 0.8045 (tp) REVERT: A 1217 ASP cc_start: 0.7307 (m-30) cc_final: 0.7003 (m-30) REVERT: A 1238 TRP cc_start: 0.7379 (t60) cc_final: 0.7064 (t60) REVERT: A 1304 LEU cc_start: 0.8275 (mm) cc_final: 0.7786 (pp) REVERT: A 1309 LEU cc_start: 0.6087 (mm) cc_final: 0.5615 (pt) REVERT: A 1320 TRP cc_start: 0.7539 (p-90) cc_final: 0.6346 (p-90) REVERT: A 1333 HIS cc_start: 0.6472 (t-170) cc_final: 0.6113 (t-170) REVERT: A 1337 MET cc_start: 0.7556 (mmp) cc_final: 0.7130 (mmt) REVERT: A 1418 PHE cc_start: 0.6652 (t80) cc_final: 0.6429 (t80) REVERT: A 1433 CYS cc_start: 0.6952 (p) cc_final: 0.6485 (p) REVERT: A 1435 HIS cc_start: 0.6957 (m90) cc_final: 0.6704 (m90) REVERT: A 1457 ILE cc_start: 0.8627 (mt) cc_final: 0.8315 (mt) REVERT: A 1489 MET cc_start: 0.4608 (mmm) cc_final: 0.4262 (mmt) REVERT: A 1495 ASN cc_start: 0.7375 (t0) cc_final: 0.6449 (t0) REVERT: A 1509 LYS cc_start: 0.7753 (mptt) cc_final: 0.7343 (mtmm) REVERT: A 1542 TYR cc_start: 0.7256 (t80) cc_final: 0.6288 (t80) REVERT: A 1569 MET cc_start: 0.7460 (ptm) cc_final: 0.7004 (ptt) REVERT: A 1575 LYS cc_start: 0.7963 (mttp) cc_final: 0.7056 (mmmt) REVERT: A 1588 LYS cc_start: 0.7616 (tptt) cc_final: 0.7348 (mmmt) REVERT: A 1645 GLU cc_start: 0.8247 (pp20) cc_final: 0.7981 (tm-30) REVERT: A 1703 LYS cc_start: 0.6377 (OUTLIER) cc_final: 0.6096 (ptpt) REVERT: A 1704 LYS cc_start: 0.8003 (mmmm) cc_final: 0.7800 (mmmm) REVERT: A 1834 MET cc_start: 0.4364 (ptt) cc_final: 0.4004 (ptt) REVERT: A 1917 LYS cc_start: 0.8291 (tmtt) cc_final: 0.8014 (tptp) REVERT: A 1966 PHE cc_start: 0.6822 (m-80) cc_final: 0.6529 (m-10) REVERT: A 1998 ILE cc_start: 0.7511 (mt) cc_final: 0.7207 (tt) REVERT: A 2009 ASN cc_start: 0.7234 (OUTLIER) cc_final: 0.6694 (m-40) REVERT: A 2010 LEU cc_start: 0.8073 (tp) cc_final: 0.7817 (tp) REVERT: A 2057 LYS cc_start: 0.8593 (mmtm) cc_final: 0.7971 (mmmt) REVERT: A 2168 MET cc_start: 0.4404 (tpt) cc_final: 0.4045 (mmm) REVERT: A 2301 SER cc_start: 0.8047 (t) cc_final: 0.7608 (p) REVERT: A 2357 LEU cc_start: 0.7734 (OUTLIER) cc_final: 0.7118 (mt) REVERT: A 2395 MET cc_start: 0.6796 (mtt) cc_final: 0.6393 (mmt) REVERT: A 2425 TYR cc_start: 0.4731 (m-10) cc_final: 0.3979 (m-80) REVERT: A 2603 GLU cc_start: 0.8768 (tm-30) cc_final: 0.8149 (tm-30) REVERT: A 2607 LYS cc_start: 0.9045 (mmpt) cc_final: 0.8767 (mmmt) outliers start: 31 outliers final: 14 residues processed: 409 average time/residue: 0.3265 time to fit residues: 200.4296 Evaluate side-chains 404 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 386 time to evaluate : 1.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 534 PHE Chi-restraints excluded: chain A residue 722 LEU Chi-restraints excluded: chain A residue 766 PHE Chi-restraints excluded: chain A residue 829 ASN Chi-restraints excluded: chain A residue 862 CYS Chi-restraints excluded: chain A residue 885 MET Chi-restraints excluded: chain A residue 982 LYS Chi-restraints excluded: chain A residue 1141 GLN Chi-restraints excluded: chain A residue 1287 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 1703 LYS Chi-restraints excluded: chain A residue 2009 ASN Chi-restraints excluded: chain A residue 2061 ILE 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 158 optimal weight: 4.9990 chunk 132 optimal weight: 0.0870 chunk 46 optimal weight: 3.9990 chunk 133 optimal weight: 3.9990 chunk 159 optimal weight: 1.9990 chunk 154 optimal weight: 2.9990 chunk 146 optimal weight: 0.5980 chunk 155 optimal weight: 4.9990 chunk 149 optimal weight: 6.9990 chunk 187 optimal weight: 0.8980 chunk 206 optimal weight: 0.9990 overall best weight: 0.9162 ------------------------------------------------------------------------------- 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 939 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2006 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2384 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4696 r_free = 0.4696 target = 0.202537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.168164 restraints weight = 41403.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4391 r_free = 0.4391 target = 0.172565 restraints weight = 26820.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.4425 r_free = 0.4425 target = 0.175545 restraints weight = 19047.623| |-----------------------------------------------------------------------------| r_work (final): 0.4396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6056 moved from start: 0.2139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 18394 Z= 0.135 Angle : 0.667 11.070 24780 Z= 0.346 Chirality : 0.044 0.289 2839 Planarity : 0.004 0.055 3112 Dihedral : 5.269 51.487 2411 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.97 % Favored : 91.89 % Rotamer: Outliers : 1.55 % Allowed : 14.61 % Favored : 83.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.18), residues: 2220 helix: 0.51 (0.15), residues: 1231 sheet: -0.53 (0.48), residues: 99 loop : -2.64 (0.20), residues: 890 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A1857 HIS 0.007 0.001 HIS A 564 PHE 0.028 0.001 PHE A 744 TYR 0.043 0.001 TYR A 876 ARG 0.007 0.000 ARG A2033 Details of bonding type rmsd hydrogen bonds : bond 0.03605 ( 877) hydrogen bonds : angle 4.56591 ( 2586) covalent geometry : bond 0.00277 (18394) covalent geometry : angle 0.66712 (24780) *********************** 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 427 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 395 time to evaluate : 1.847 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 392 ILE cc_start: 0.6461 (mp) cc_final: 0.5093 (pt) REVERT: A 402 LYS cc_start: 0.7472 (mptt) cc_final: 0.7246 (mptt) REVERT: A 450 GLU cc_start: 0.7601 (mt-10) cc_final: 0.7395 (pt0) REVERT: A 452 GLU cc_start: 0.8080 (tm-30) cc_final: 0.7775 (tm-30) REVERT: A 475 SER cc_start: 0.6624 (t) cc_final: 0.6067 (p) REVERT: A 536 MET cc_start: 0.6342 (tpp) cc_final: 0.5726 (tpt) REVERT: A 603 LYS cc_start: 0.8334 (tppt) cc_final: 0.7983 (tppt) REVERT: A 604 ASN cc_start: 0.7490 (p0) cc_final: 0.7076 (p0) REVERT: A 618 GLU cc_start: 0.6145 (mp0) cc_final: 0.5938 (mm-30) REVERT: A 623 LYS cc_start: 0.8103 (mttt) cc_final: 0.7454 (mmmm) REVERT: A 637 TYR cc_start: 0.6916 (m-10) cc_final: 0.5048 (m-10) REVERT: A 639 GLU cc_start: 0.7396 (tp30) cc_final: 0.6964 (tp30) REVERT: A 642 MET cc_start: 0.7092 (ttt) cc_final: 0.6739 (ttt) REVERT: A 646 LYS cc_start: 0.8783 (ptpt) cc_final: 0.8497 (ptpp) REVERT: A 671 MET cc_start: 0.6508 (ttt) cc_final: 0.5891 (ttt) REVERT: A 687 VAL cc_start: 0.7974 (t) cc_final: 0.7656 (m) REVERT: A 741 PHE cc_start: 0.6812 (t80) cc_final: 0.6393 (t80) REVERT: A 770 MET cc_start: 0.7223 (tmm) cc_final: 0.6686 (tmm) REVERT: A 773 LYS cc_start: 0.8973 (tptt) cc_final: 0.8323 (mmtm) REVERT: A 785 MET cc_start: 0.5704 (mtp) cc_final: 0.5419 (mmm) REVERT: A 842 LEU cc_start: 0.8359 (tp) cc_final: 0.8149 (tp) REVERT: A 873 GLU cc_start: 0.7702 (mt-10) cc_final: 0.7478 (mt-10) REVERT: A 886 MET cc_start: 0.6256 (tpp) cc_final: 0.5841 (tpp) REVERT: A 911 PHE cc_start: 0.5979 (t80) cc_final: 0.5402 (t80) REVERT: A 913 LYS cc_start: 0.8630 (tptt) cc_final: 0.8152 (tppt) REVERT: A 929 MET cc_start: 0.6843 (tpt) cc_final: 0.6331 (tpt) REVERT: A 949 ASP cc_start: 0.8228 (p0) cc_final: 0.7970 (p0) REVERT: A 969 GLU cc_start: 0.7915 (tp30) cc_final: 0.7577 (tp30) REVERT: A 985 LYS cc_start: 0.7016 (tmtt) cc_final: 0.6711 (tptt) REVERT: A 1102 LYS cc_start: 0.6271 (tptt) cc_final: 0.5700 (tptp) REVERT: A 1106 GLU cc_start: 0.6798 (mm-30) cc_final: 0.6325 (mm-30) REVERT: A 1109 ASP cc_start: 0.7302 (t0) cc_final: 0.7011 (t0) REVERT: A 1145 PHE cc_start: 0.7486 (t80) cc_final: 0.7275 (t80) REVERT: A 1147 MET cc_start: 0.7649 (tmm) cc_final: 0.7219 (tmm) REVERT: A 1171 LYS cc_start: 0.8057 (tppt) cc_final: 0.7645 (tppt) REVERT: A 1176 PHE cc_start: 0.7787 (t80) cc_final: 0.7461 (t80) REVERT: A 1181 PHE cc_start: 0.7323 (t80) cc_final: 0.7074 (t80) REVERT: A 1193 ILE cc_start: 0.7680 (tp) cc_final: 0.7479 (tp) REVERT: A 1201 ILE cc_start: 0.7147 (mp) cc_final: 0.6877 (mm) REVERT: A 1237 LYS cc_start: 0.5884 (mmtt) cc_final: 0.5596 (mmtm) REVERT: A 1238 TRP cc_start: 0.7480 (t60) cc_final: 0.7187 (t60) REVERT: A 1309 LEU cc_start: 0.6044 (mm) cc_final: 0.5595 (pt) REVERT: A 1320 TRP cc_start: 0.7495 (p-90) cc_final: 0.6389 (p-90) REVERT: A 1333 HIS cc_start: 0.6624 (t-170) cc_final: 0.6253 (t-170) REVERT: A 1337 MET cc_start: 0.7530 (mmp) cc_final: 0.7152 (mmt) REVERT: A 1338 LYS cc_start: 0.8300 (ptmt) cc_final: 0.7833 (pttt) REVERT: A 1363 ASN cc_start: 0.7659 (m-40) cc_final: 0.6936 (m-40) REVERT: A 1433 CYS cc_start: 0.6966 (p) cc_final: 0.6580 (p) REVERT: A 1435 HIS cc_start: 0.6892 (m90) cc_final: 0.6583 (m90) REVERT: A 1457 ILE cc_start: 0.8651 (mt) cc_final: 0.8418 (mt) REVERT: A 1495 ASN cc_start: 0.7319 (t0) cc_final: 0.6392 (t0) REVERT: A 1509 LYS cc_start: 0.7786 (mptt) cc_final: 0.7349 (mtmm) REVERT: A 1542 TYR cc_start: 0.7202 (t80) cc_final: 0.6018 (t80) REVERT: A 1569 MET cc_start: 0.7462 (ptm) cc_final: 0.7038 (tmm) REVERT: A 1575 LYS cc_start: 0.8012 (mttp) cc_final: 0.7026 (mmmt) REVERT: A 1588 LYS cc_start: 0.7637 (tptt) cc_final: 0.7355 (mmmt) REVERT: A 1645 GLU cc_start: 0.8240 (pp20) cc_final: 0.7964 (tm-30) REVERT: A 1703 LYS cc_start: 0.6398 (OUTLIER) cc_final: 0.6129 (ptpt) REVERT: A 1704 LYS cc_start: 0.8015 (mmmm) cc_final: 0.7776 (mmmm) REVERT: A 1917 LYS cc_start: 0.8294 (tmtt) cc_final: 0.8007 (tptp) REVERT: A 1966 PHE cc_start: 0.6976 (m-80) cc_final: 0.6684 (m-10) REVERT: A 1998 ILE cc_start: 0.7557 (mt) cc_final: 0.7288 (tt) REVERT: A 2010 LEU cc_start: 0.8092 (tp) cc_final: 0.7799 (tp) REVERT: A 2022 ASP cc_start: 0.7781 (m-30) cc_final: 0.7425 (p0) REVERT: A 2055 GLU cc_start: 0.7996 (pt0) cc_final: 0.7588 (pt0) REVERT: A 2057 LYS cc_start: 0.8600 (mmtm) cc_final: 0.8056 (mmmt) REVERT: A 2168 MET cc_start: 0.4849 (tpt) cc_final: 0.4291 (mmm) REVERT: A 2278 PHE cc_start: 0.6563 (m-10) cc_final: 0.6298 (m-80) REVERT: A 2301 SER cc_start: 0.8037 (t) cc_final: 0.7607 (p) REVERT: A 2357 LEU cc_start: 0.7749 (OUTLIER) cc_final: 0.7137 (mt) REVERT: A 2386 GLU cc_start: 0.4809 (mt-10) cc_final: 0.4209 (mt-10) REVERT: A 2395 MET cc_start: 0.6746 (mtt) cc_final: 0.6349 (mmt) REVERT: A 2603 GLU cc_start: 0.8719 (tm-30) cc_final: 0.8135 (tm-30) REVERT: A 2607 LYS cc_start: 0.9016 (mmpt) cc_final: 0.8755 (mmmt) outliers start: 32 outliers final: 17 residues processed: 406 average time/residue: 0.3331 time to fit residues: 202.2121 Evaluate side-chains 407 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 388 time to evaluate : 2.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 534 PHE Chi-restraints excluded: chain A residue 722 LEU 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 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 1703 LYS Chi-restraints excluded: chain A residue 1832 PHE Chi-restraints excluded: chain A residue 1890 LEU Chi-restraints excluded: chain A residue 2061 ILE 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 171 optimal weight: 7.9990 chunk 131 optimal weight: 4.9990 chunk 39 optimal weight: 3.9990 chunk 98 optimal weight: 8.9990 chunk 66 optimal weight: 1.9990 chunk 88 optimal weight: 0.7980 chunk 45 optimal weight: 5.9990 chunk 216 optimal weight: 20.0000 chunk 192 optimal weight: 0.6980 chunk 206 optimal weight: 0.7980 chunk 5 optimal weight: 3.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- 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 939 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1333 HIS ** A1445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1516 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1901 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2006 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2009 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2042 ASN ** A2086 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2100 HIS A2397 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4657 r_free = 0.4657 target = 0.198712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.163982 restraints weight = 42370.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.168357 restraints weight = 27233.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.4375 r_free = 0.4375 target = 0.171454 restraints weight = 19266.121| |-----------------------------------------------------------------------------| r_work (final): 0.4347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6138 moved from start: 0.2706 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= 0.188 Angle : 0.722 13.678 24780 Z= 0.378 Chirality : 0.046 0.308 2839 Planarity : 0.004 0.056 3112 Dihedral : 5.417 49.710 2411 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 14.60 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.69 % Favored : 91.22 % Rotamer: Outliers : 1.84 % Allowed : 16.16 % Favored : 82.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.18), residues: 2220 helix: 0.44 (0.15), residues: 1229 sheet: -0.50 (0.49), residues: 93 loop : -2.64 (0.20), residues: 898 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A1857 HIS 0.010 0.001 HIS A 564 PHE 0.026 0.001 PHE A 744 TYR 0.043 0.002 TYR A 876 ARG 0.008 0.001 ARG A 802 Details of bonding type rmsd hydrogen bonds : bond 0.04147 ( 877) hydrogen bonds : angle 4.76317 ( 2586) covalent geometry : bond 0.00380 (18394) covalent geometry : angle 0.72231 (24780) *********************** 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 445 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 407 time to evaluate : 1.848 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 402 LYS cc_start: 0.7477 (mptt) cc_final: 0.7195 (mptt) REVERT: A 446 GLN cc_start: 0.8053 (pp30) cc_final: 0.6736 (pp30) REVERT: A 450 GLU cc_start: 0.7882 (mt-10) cc_final: 0.7463 (pt0) REVERT: A 475 SER cc_start: 0.6820 (t) cc_final: 0.6126 (p) REVERT: A 536 MET cc_start: 0.6455 (tpp) cc_final: 0.5896 (tpt) REVERT: A 570 LEU cc_start: 0.5170 (OUTLIER) cc_final: 0.4686 (pp) REVERT: A 603 LYS cc_start: 0.8365 (tppt) cc_final: 0.8069 (tppt) REVERT: A 604 ASN cc_start: 0.7472 (p0) cc_final: 0.7049 (p0) REVERT: A 623 LYS cc_start: 0.8086 (mttt) cc_final: 0.7439 (mmmm) REVERT: A 637 TYR cc_start: 0.6831 (m-10) cc_final: 0.4880 (m-10) REVERT: A 639 GLU cc_start: 0.7436 (tp30) cc_final: 0.6962 (tp30) REVERT: A 642 MET cc_start: 0.7206 (ttt) cc_final: 0.6833 (ttt) REVERT: A 646 LYS cc_start: 0.8828 (ptpt) cc_final: 0.8548 (ptpp) REVERT: A 671 MET cc_start: 0.6481 (ttt) cc_final: 0.5910 (ttt) REVERT: A 732 LYS cc_start: 0.7582 (mmtt) cc_final: 0.7377 (mmtt) REVERT: A 741 PHE cc_start: 0.6828 (t80) cc_final: 0.6450 (t80) REVERT: A 770 MET cc_start: 0.7151 (tmm) cc_final: 0.6598 (tmm) REVERT: A 785 MET cc_start: 0.5915 (mtp) cc_final: 0.5575 (mmm) REVERT: A 801 MET cc_start: 0.7695 (mtt) cc_final: 0.7457 (mtt) REVERT: A 842 LEU cc_start: 0.8400 (tp) cc_final: 0.8159 (tp) REVERT: A 861 LYS cc_start: 0.8716 (mptt) cc_final: 0.8342 (mptt) REVERT: A 886 MET cc_start: 0.6327 (tpp) cc_final: 0.6038 (tpp) REVERT: A 911 PHE cc_start: 0.6178 (t80) cc_final: 0.5383 (t80) REVERT: A 913 LYS cc_start: 0.8717 (tptt) cc_final: 0.8317 (tppt) REVERT: A 929 MET cc_start: 0.7133 (tpt) cc_final: 0.6645 (tpt) REVERT: A 969 GLU cc_start: 0.7917 (tp30) cc_final: 0.7523 (tp30) REVERT: A 985 LYS cc_start: 0.6978 (tmtt) cc_final: 0.6548 (tptt) REVERT: A 1102 LYS cc_start: 0.6666 (tptt) cc_final: 0.6245 (tptp) REVERT: A 1106 GLU cc_start: 0.6807 (mm-30) cc_final: 0.6347 (mm-30) REVERT: A 1109 ASP cc_start: 0.7381 (t0) cc_final: 0.6919 (t0) REVERT: A 1140 LEU cc_start: 0.8502 (mt) cc_final: 0.8297 (mt) REVERT: A 1142 MET cc_start: 0.6172 (tpt) cc_final: 0.5950 (tpp) REVERT: A 1147 MET cc_start: 0.7774 (tmm) cc_final: 0.7364 (tmm) REVERT: A 1171 LYS cc_start: 0.8133 (tppt) cc_final: 0.7734 (tppt) REVERT: A 1176 PHE cc_start: 0.7775 (t80) cc_final: 0.7407 (t80) REVERT: A 1193 ILE cc_start: 0.7844 (tp) cc_final: 0.7634 (tp) REVERT: A 1201 ILE cc_start: 0.7322 (mp) cc_final: 0.6977 (mm) REVERT: A 1304 LEU cc_start: 0.8419 (OUTLIER) cc_final: 0.8079 (pp) REVERT: A 1309 LEU cc_start: 0.6034 (mm) cc_final: 0.5587 (pt) REVERT: A 1320 TRP cc_start: 0.7421 (p-90) cc_final: 0.6722 (p-90) REVERT: A 1333 HIS cc_start: 0.6388 (t70) cc_final: 0.5946 (t-170) REVERT: A 1338 LYS cc_start: 0.8525 (ptmt) cc_final: 0.8175 (pttt) REVERT: A 1363 ASN cc_start: 0.7569 (m-40) cc_final: 0.7071 (m-40) REVERT: A 1433 CYS cc_start: 0.7000 (p) cc_final: 0.6604 (p) REVERT: A 1453 MET cc_start: 0.7228 (mmm) cc_final: 0.7024 (mmm) REVERT: A 1457 ILE cc_start: 0.8694 (mt) cc_final: 0.8433 (mt) REVERT: A 1489 MET cc_start: 0.4743 (mmt) cc_final: 0.4184 (mmt) REVERT: A 1495 ASN cc_start: 0.7248 (t0) cc_final: 0.6277 (t0) REVERT: A 1542 TYR cc_start: 0.7036 (t80) cc_final: 0.6095 (t80) REVERT: A 1569 MET cc_start: 0.7447 (ptm) cc_final: 0.7044 (tmm) REVERT: A 1575 LYS cc_start: 0.8092 (mttp) cc_final: 0.7419 (mmmt) REVERT: A 1588 LYS cc_start: 0.7685 (tptt) cc_final: 0.7457 (mmmt) REVERT: A 1621 MET cc_start: 0.5864 (mpp) cc_final: 0.5242 (pmm) REVERT: A 1703 LYS cc_start: 0.6349 (OUTLIER) cc_final: 0.6111 (ttmt) REVERT: A 1704 LYS cc_start: 0.8147 (mmmm) cc_final: 0.7932 (mmmm) REVERT: A 1817 CYS cc_start: 0.6694 (p) cc_final: 0.6303 (t) REVERT: A 1857 TRP cc_start: 0.6954 (t60) cc_final: 0.6730 (t60) REVERT: A 1917 LYS cc_start: 0.8298 (tmtt) cc_final: 0.8012 (tptp) REVERT: A 1953 ARG cc_start: 0.6634 (OUTLIER) cc_final: 0.5718 (mmp80) REVERT: A 1966 PHE cc_start: 0.7073 (m-80) cc_final: 0.6805 (m-10) REVERT: A 1998 ILE cc_start: 0.7758 (mt) cc_final: 0.7542 (tt) REVERT: A 2010 LEU cc_start: 0.8099 (tp) cc_final: 0.7841 (tp) REVERT: A 2022 ASP cc_start: 0.7767 (m-30) cc_final: 0.7424 (p0) REVERT: A 2055 GLU cc_start: 0.8092 (pt0) cc_final: 0.6791 (mm-30) REVERT: A 2057 LYS cc_start: 0.8638 (mmtm) cc_final: 0.8177 (mmmt) REVERT: A 2168 MET cc_start: 0.4859 (tpt) cc_final: 0.4373 (mmm) REVERT: A 2301 SER cc_start: 0.8079 (t) cc_final: 0.7608 (p) REVERT: A 2357 LEU cc_start: 0.7713 (OUTLIER) cc_final: 0.7285 (mt) REVERT: A 2395 MET cc_start: 0.6722 (mtt) cc_final: 0.6515 (mmt) REVERT: A 2603 GLU cc_start: 0.8730 (tm-30) cc_final: 0.8177 (tm-30) outliers start: 38 outliers final: 21 residues processed: 422 average time/residue: 0.3084 time to fit residues: 195.2682 Evaluate side-chains 418 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 392 time to evaluate : 1.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 534 PHE Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 722 LEU 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 1111 VAL 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 1420 SER Chi-restraints excluded: chain A residue 1424 VAL Chi-restraints excluded: chain A residue 1510 SER Chi-restraints excluded: chain A residue 1703 LYS 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 2280 MET Chi-restraints excluded: chain A residue 2357 LEU Chi-restraints excluded: chain A residue 2590 ASN 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 185 optimal weight: 2.9990 chunk 7 optimal weight: 0.7980 chunk 15 optimal weight: 0.7980 chunk 9 optimal weight: 5.9990 chunk 160 optimal weight: 0.5980 chunk 145 optimal weight: 0.9980 chunk 76 optimal weight: 5.9990 chunk 47 optimal weight: 4.9990 chunk 148 optimal weight: 3.9990 chunk 176 optimal weight: 0.0980 chunk 64 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 407 GLN ** A 446 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 515 ASN A 877 ASN A1480 GLN ** A1901 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2006 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2009 ASN ** 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 = 0.4685 r_free = 0.4685 target = 0.201331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4327 r_free = 0.4327 target = 0.166841 restraints weight = 41770.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.4379 r_free = 0.4379 target = 0.171262 restraints weight = 26922.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.4414 r_free = 0.4414 target = 0.174357 restraints weight = 19075.217| |-----------------------------------------------------------------------------| r_work (final): 0.4385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6071 moved from start: 0.2825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 18394 Z= 0.127 Angle : 0.692 12.136 24780 Z= 0.354 Chirality : 0.044 0.318 2839 Planarity : 0.004 0.051 3112 Dihedral : 5.189 48.977 2411 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 13.85 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.30 % Favored : 92.61 % Rotamer: Outliers : 1.55 % Allowed : 19.06 % Favored : 79.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.18), residues: 2220 helix: 0.60 (0.15), residues: 1225 sheet: -0.27 (0.50), residues: 93 loop : -2.55 (0.20), residues: 902 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A1238 HIS 0.004 0.001 HIS A 564 PHE 0.020 0.001 PHE A 744 TYR 0.045 0.001 TYR A 876 ARG 0.007 0.000 ARG A2033 Details of bonding type rmsd hydrogen bonds : bond 0.03586 ( 877) hydrogen bonds : angle 4.57552 ( 2586) covalent geometry : bond 0.00274 (18394) covalent geometry : angle 0.69173 (24780) *********************** 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 433 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 401 time to evaluate : 1.967 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: 0.4834 (t) cc_final: 0.4579 (t) REVERT: A 446 GLN cc_start: 0.7993 (pp30) cc_final: 0.7641 (pp30) REVERT: A 450 GLU cc_start: 0.7831 (mt-10) cc_final: 0.7419 (pt0) REVERT: A 452 GLU cc_start: 0.8023 (tm-30) cc_final: 0.7695 (tm-30) REVERT: A 465 GLU cc_start: 0.4040 (OUTLIER) cc_final: 0.3698 (tm-30) REVERT: A 475 SER cc_start: 0.6630 (t) cc_final: 0.6055 (p) REVERT: A 536 MET cc_start: 0.6465 (tpp) cc_final: 0.5901 (tpt) REVERT: A 603 LYS cc_start: 0.8328 (tppt) cc_final: 0.8033 (tppt) REVERT: A 604 ASN cc_start: 0.7468 (p0) cc_final: 0.7073 (p0) REVERT: A 623 LYS cc_start: 0.8102 (mttt) cc_final: 0.7527 (mmmm) REVERT: A 637 TYR cc_start: 0.6805 (m-10) cc_final: 0.4652 (m-10) REVERT: A 639 GLU cc_start: 0.7360 (tp30) cc_final: 0.6886 (tp30) REVERT: A 671 MET cc_start: 0.6459 (ttt) cc_final: 0.5842 (ttt) REVERT: A 741 PHE cc_start: 0.6781 (t80) cc_final: 0.6362 (t80) REVERT: A 770 MET cc_start: 0.7011 (tmm) cc_final: 0.6469 (tmm) REVERT: A 785 MET cc_start: 0.5756 (mtp) cc_final: 0.5402 (mmm) REVERT: A 842 LEU cc_start: 0.8324 (tp) cc_final: 0.8072 (tp) REVERT: A 861 LYS cc_start: 0.8672 (mptt) cc_final: 0.8399 (mmtt) REVERT: A 873 GLU cc_start: 0.7685 (mt-10) cc_final: 0.7164 (mp0) REVERT: A 886 MET cc_start: 0.6221 (tpp) cc_final: 0.5761 (tpp) REVERT: A 911 PHE cc_start: 0.5927 (t80) cc_final: 0.5091 (t80) REVERT: A 913 LYS cc_start: 0.8686 (tptt) cc_final: 0.8255 (tppt) REVERT: A 929 MET cc_start: 0.6968 (tpt) cc_final: 0.6512 (tpt) REVERT: A 969 GLU cc_start: 0.7860 (tp30) cc_final: 0.7442 (tp30) REVERT: A 985 LYS cc_start: 0.7045 (tmtt) cc_final: 0.6647 (tptt) REVERT: A 1102 LYS cc_start: 0.6490 (tptt) cc_final: 0.5439 (tptp) REVERT: A 1106 GLU cc_start: 0.6778 (mm-30) cc_final: 0.6345 (mm-30) REVERT: A 1109 ASP cc_start: 0.7414 (t0) cc_final: 0.6941 (t0) REVERT: A 1147 MET cc_start: 0.7722 (tmm) cc_final: 0.7280 (tmm) REVERT: A 1171 LYS cc_start: 0.8005 (tppt) cc_final: 0.7661 (tppt) REVERT: A 1176 PHE cc_start: 0.7797 (t80) cc_final: 0.7441 (t80) REVERT: A 1181 PHE cc_start: 0.7446 (t80) cc_final: 0.7173 (t80) REVERT: A 1201 ILE cc_start: 0.7199 (mp) cc_final: 0.6953 (mm) REVERT: A 1209 LEU cc_start: 0.8195 (tp) cc_final: 0.7975 (tp) REVERT: A 1309 LEU cc_start: 0.5964 (mm) cc_final: 0.5537 (pt) REVERT: A 1320 TRP cc_start: 0.7628 (p-90) cc_final: 0.6851 (p-90) REVERT: A 1333 HIS cc_start: 0.6222 (t70) cc_final: 0.5744 (t-170) REVERT: A 1338 LYS cc_start: 0.8382 (ptmt) cc_final: 0.7924 (pttt) REVERT: A 1363 ASN cc_start: 0.7461 (m-40) cc_final: 0.7079 (m-40) REVERT: A 1421 GLU cc_start: 0.7586 (mp0) cc_final: 0.7275 (pm20) REVERT: A 1433 CYS cc_start: 0.6890 (p) cc_final: 0.6511 (p) REVERT: A 1453 MET cc_start: 0.7142 (mmm) cc_final: 0.6935 (mmm) REVERT: A 1549 LEU cc_start: 0.7618 (OUTLIER) cc_final: 0.7404 (tp) REVERT: A 1566 TYR cc_start: 0.6576 (t80) cc_final: 0.5710 (t80) REVERT: A 1569 MET cc_start: 0.7397 (ptm) cc_final: 0.7032 (tmm) REVERT: A 1575 LYS cc_start: 0.8249 (mttp) cc_final: 0.7302 (mmmt) REVERT: A 1588 LYS cc_start: 0.7634 (tptt) cc_final: 0.7385 (mmmt) REVERT: A 1621 MET cc_start: 0.5833 (mpp) cc_final: 0.5455 (pmm) REVERT: A 1704 LYS cc_start: 0.8082 (mmmm) cc_final: 0.7796 (mmmm) REVERT: A 1817 CYS cc_start: 0.6626 (p) cc_final: 0.6287 (t) REVERT: A 1820 LYS cc_start: 0.8164 (ptpt) cc_final: 0.7828 (ptpt) REVERT: A 1834 MET cc_start: 0.3727 (ptt) cc_final: 0.3341 (ptt) REVERT: A 1857 TRP cc_start: 0.7022 (t60) cc_final: 0.6801 (t60) REVERT: A 1898 ASP cc_start: 0.6544 (t0) cc_final: 0.6290 (t0) REVERT: A 1953 ARG cc_start: 0.6803 (mmt180) cc_final: 0.6401 (mmt180) REVERT: A 1966 PHE cc_start: 0.7061 (m-80) cc_final: 0.6709 (m-10) REVERT: A 2010 LEU cc_start: 0.8124 (tp) cc_final: 0.7817 (tp) REVERT: A 2022 ASP cc_start: 0.7724 (m-30) cc_final: 0.7436 (p0) REVERT: A 2055 GLU cc_start: 0.8055 (pt0) cc_final: 0.6821 (mm-30) REVERT: A 2057 LYS cc_start: 0.8534 (mmtm) cc_final: 0.8092 (mmmt) REVERT: A 2168 MET cc_start: 0.5039 (tpt) cc_final: 0.4502 (mmm) REVERT: A 2278 PHE cc_start: 0.6506 (m-10) cc_final: 0.6049 (m-80) REVERT: A 2301 SER cc_start: 0.8042 (t) cc_final: 0.7585 (p) REVERT: A 2342 GLN cc_start: 0.7162 (mt0) cc_final: 0.6875 (mp10) REVERT: A 2357 LEU cc_start: 0.7668 (OUTLIER) cc_final: 0.7028 (mt) REVERT: A 2395 MET cc_start: 0.6881 (mtt) cc_final: 0.6650 (mmt) REVERT: A 2603 GLU cc_start: 0.8732 (tm-30) cc_final: 0.8285 (tm-30) outliers start: 32 outliers final: 20 residues processed: 413 average time/residue: 0.3198 time to fit residues: 198.5848 Evaluate side-chains 410 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 387 time to evaluate : 1.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain A residue 534 PHE Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 704 TYR Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 829 ASN 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 1331 VAL Chi-restraints excluded: chain A residue 1345 GLU Chi-restraints excluded: chain A residue 1424 VAL Chi-restraints excluded: chain A residue 1510 SER Chi-restraints excluded: chain A residue 1549 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 2061 ILE 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 3 optimal weight: 5.9990 chunk 153 optimal weight: 0.7980 chunk 24 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 201 optimal weight: 50.0000 chunk 93 optimal weight: 2.9990 chunk 210 optimal weight: 8.9990 chunk 103 optimal weight: 0.9980 chunk 22 optimal weight: 0.5980 chunk 155 optimal weight: 0.9990 chunk 98 optimal weight: 2.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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** ** A2009 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2086 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 = 0.4675 r_free = 0.4675 target = 0.200081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.165303 restraints weight = 41915.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.4363 r_free = 0.4363 target = 0.169771 restraints weight = 27032.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.4398 r_free = 0.4398 target = 0.172872 restraints weight = 19172.111| |-----------------------------------------------------------------------------| r_work (final): 0.4369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6113 moved from start: 0.3066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 18394 Z= 0.146 Angle : 0.710 11.403 24780 Z= 0.364 Chirality : 0.045 0.305 2839 Planarity : 0.004 0.074 3112 Dihedral : 5.177 47.837 2411 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 14.38 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.33 % Favored : 91.58 % Rotamer: Outliers : 1.94 % Allowed : 19.50 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.18), residues: 2220 helix: 0.61 (0.15), residues: 1230 sheet: -0.37 (0.50), residues: 93 loop : -2.54 (0.20), residues: 897 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A1238 HIS 0.005 0.001 HIS A 893 PHE 0.021 0.001 PHE A1548 TYR 0.048 0.001 TYR A 876 ARG 0.021 0.001 ARG A 802 Details of bonding type rmsd hydrogen bonds : bond 0.03749 ( 877) hydrogen bonds : angle 4.61977 ( 2586) covalent geometry : bond 0.00308 (18394) covalent geometry : angle 0.71032 (24780) *********************** 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 441 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 401 time to evaluate : 1.932 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: 0.4927 (t) cc_final: 0.4227 (t) REVERT: A 402 LYS cc_start: 0.7479 (mptt) cc_final: 0.7214 (mptt) REVERT: A 446 GLN cc_start: 0.8014 (pp30) cc_final: 0.7694 (pp30) REVERT: A 450 GLU cc_start: 0.7851 (mt-10) cc_final: 0.7470 (pt0) REVERT: A 475 SER cc_start: 0.6750 (t) cc_final: 0.6037 (p) REVERT: A 536 MET cc_start: 0.6425 (tpp) cc_final: 0.5868 (tpt) REVERT: A 603 LYS cc_start: 0.8351 (tppt) cc_final: 0.8074 (tppt) REVERT: A 604 ASN cc_start: 0.7483 (p0) cc_final: 0.7118 (p0) REVERT: A 618 GLU cc_start: 0.6193 (mp0) cc_final: 0.5873 (mp0) REVERT: A 623 LYS cc_start: 0.8129 (mttt) cc_final: 0.7564 (mmmm) REVERT: A 637 TYR cc_start: 0.6792 (m-10) cc_final: 0.4718 (m-10) REVERT: A 639 GLU cc_start: 0.7289 (tp30) cc_final: 0.6936 (tp30) REVERT: A 671 MET cc_start: 0.6463 (ttt) cc_final: 0.5859 (ttt) REVERT: A 741 PHE cc_start: 0.6725 (t80) cc_final: 0.6329 (t80) REVERT: A 770 MET cc_start: 0.7085 (tmm) cc_final: 0.6540 (tmm) REVERT: A 785 MET cc_start: 0.5844 (mtp) cc_final: 0.5486 (mmm) REVERT: A 817 GLU cc_start: 0.7233 (OUTLIER) cc_final: 0.7013 (pm20) REVERT: A 842 LEU cc_start: 0.8344 (tp) cc_final: 0.8089 (tp) REVERT: A 873 GLU cc_start: 0.7821 (mt-10) cc_final: 0.7234 (mp0) REVERT: A 886 MET cc_start: 0.6281 (tpp) cc_final: 0.5869 (tpp) REVERT: A 911 PHE cc_start: 0.6070 (t80) cc_final: 0.5209 (t80) REVERT: A 913 LYS cc_start: 0.8693 (tptt) cc_final: 0.8268 (tppt) REVERT: A 929 MET cc_start: 0.6990 (tpt) cc_final: 0.6530 (tpt) REVERT: A 969 GLU cc_start: 0.7923 (tp30) cc_final: 0.7492 (tp30) REVERT: A 985 LYS cc_start: 0.6971 (tmtt) cc_final: 0.6519 (tptt) REVERT: A 1102 LYS cc_start: 0.6604 (tptt) cc_final: 0.6035 (mmmt) REVERT: A 1106 GLU cc_start: 0.6782 (mm-30) cc_final: 0.6358 (mm-30) REVERT: A 1109 ASP cc_start: 0.7438 (t0) cc_final: 0.6970 (t0) REVERT: A 1144 GLU cc_start: 0.7252 (pp20) cc_final: 0.6782 (pp20) REVERT: A 1147 MET cc_start: 0.7694 (tmm) cc_final: 0.7288 (tmm) REVERT: A 1171 LYS cc_start: 0.8046 (tppt) cc_final: 0.7686 (tppt) REVERT: A 1176 PHE cc_start: 0.7805 (t80) cc_final: 0.7459 (t80) REVERT: A 1201 ILE cc_start: 0.7182 (mp) cc_final: 0.6903 (mm) REVERT: A 1209 LEU cc_start: 0.8243 (tp) cc_final: 0.7983 (tp) REVERT: A 1237 LYS cc_start: 0.6668 (tptt) cc_final: 0.6181 (tptp) REVERT: A 1309 LEU cc_start: 0.5975 (mm) cc_final: 0.5541 (pt) REVERT: A 1333 HIS cc_start: 0.6386 (t70) cc_final: 0.5992 (t-170) REVERT: A 1338 LYS cc_start: 0.8459 (ptmt) cc_final: 0.8240 (ptmt) REVERT: A 1363 ASN cc_start: 0.7425 (m-40) cc_final: 0.7210 (m-40) REVERT: A 1433 CYS cc_start: 0.6921 (p) cc_final: 0.6511 (p) REVERT: A 1453 MET cc_start: 0.7247 (mmm) cc_final: 0.6983 (mmm) REVERT: A 1509 LYS cc_start: 0.7820 (mptt) cc_final: 0.7200 (mmtt) REVERT: A 1542 TYR cc_start: 0.7006 (t80) cc_final: 0.6028 (t80) REVERT: A 1549 LEU cc_start: 0.7647 (OUTLIER) cc_final: 0.7409 (tp) REVERT: A 1566 TYR cc_start: 0.6664 (t80) cc_final: 0.5738 (t80) REVERT: A 1569 MET cc_start: 0.7419 (ptm) cc_final: 0.7033 (tmm) REVERT: A 1575 LYS cc_start: 0.8288 (mttp) cc_final: 0.7370 (mmmt) REVERT: A 1588 LYS cc_start: 0.7637 (tptt) cc_final: 0.7425 (mmmt) REVERT: A 1820 LYS cc_start: 0.8174 (ptpt) cc_final: 0.7911 (ptpt) REVERT: A 1891 LYS cc_start: 0.8256 (mmtt) cc_final: 0.7919 (mmmt) REVERT: A 1898 ASP cc_start: 0.6644 (t0) cc_final: 0.6364 (t0) REVERT: A 1953 ARG cc_start: 0.6835 (OUTLIER) cc_final: 0.6293 (mmt180) REVERT: A 1966 PHE cc_start: 0.7133 (m-80) cc_final: 0.6744 (m-80) REVERT: A 2010 LEU cc_start: 0.8130 (tp) cc_final: 0.7831 (tp) REVERT: A 2055 GLU cc_start: 0.8093 (pt0) cc_final: 0.6831 (mm-30) REVERT: A 2057 LYS cc_start: 0.8514 (mmtm) cc_final: 0.8078 (mmmt) REVERT: A 2168 MET cc_start: 0.5124 (tpt) cc_final: 0.4590 (mmm) REVERT: A 2278 PHE cc_start: 0.6536 (m-10) cc_final: 0.6077 (m-80) REVERT: A 2301 SER cc_start: 0.8059 (t) cc_final: 0.7576 (p) REVERT: A 2357 LEU cc_start: 0.7651 (OUTLIER) cc_final: 0.7107 (mt) REVERT: A 2386 GLU cc_start: 0.4797 (mt-10) cc_final: 0.4129 (mt-10) REVERT: A 2395 MET cc_start: 0.6763 (mtt) cc_final: 0.6560 (mmt) REVERT: A 2603 GLU cc_start: 0.8693 (tm-30) cc_final: 0.8148 (tm-30) REVERT: A 2607 LYS cc_start: 0.8903 (mmmt) cc_final: 0.8602 (mmmt) outliers start: 40 outliers final: 25 residues processed: 417 average time/residue: 0.3329 time to fit residues: 209.7219 Evaluate side-chains 421 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 392 time to evaluate : 1.856 ------------------------------------------------------------------------------- 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 608 LEU 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 817 GLU Chi-restraints excluded: chain A residue 829 ASN 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 1331 VAL Chi-restraints excluded: chain A residue 1345 GLU Chi-restraints excluded: chain A residue 1424 VAL Chi-restraints excluded: chain A residue 1510 SER Chi-restraints excluded: chain A residue 1549 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 2061 ILE Chi-restraints excluded: chain A residue 2280 MET 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 215 optimal weight: 7.9990 chunk 149 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 19 optimal weight: 5.9990 chunk 180 optimal weight: 3.9990 chunk 127 optimal weight: 0.5980 chunk 0 optimal weight: 7.9990 chunk 206 optimal weight: 10.0000 chunk 86 optimal weight: 0.6980 chunk 207 optimal weight: 6.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- 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** ** A1480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1901 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1952 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2009 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4657 r_free = 0.4657 target = 0.199111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.163662 restraints weight = 41901.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.168145 restraints weight = 27246.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.4370 r_free = 0.4370 target = 0.171252 restraints weight = 19415.676| |-----------------------------------------------------------------------------| r_work (final): 0.4348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6140 moved from start: 0.3343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 18394 Z= 0.159 Angle : 0.735 13.405 24780 Z= 0.377 Chirality : 0.045 0.291 2839 Planarity : 0.004 0.068 3112 Dihedral : 5.219 46.892 2411 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 15.01 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.02 % Favored : 91.89 % Rotamer: Outliers : 1.98 % Allowed : 20.22 % Favored : 77.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.18), residues: 2220 helix: 0.54 (0.15), residues: 1235 sheet: -0.47 (0.50), residues: 93 loop : -2.54 (0.20), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A1857 HIS 0.005 0.001 HIS A 893 PHE 0.021 0.001 PHE A 707 TYR 0.044 0.001 TYR A 876 ARG 0.014 0.001 ARG A 802 Details of bonding type rmsd hydrogen bonds : bond 0.03888 ( 877) hydrogen bonds : angle 4.64973 ( 2586) covalent geometry : bond 0.00335 (18394) covalent geometry : angle 0.73516 (24780) *********************** 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 437 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 396 time to evaluate : 2.522 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: A 322 THR cc_start: 0.4533 (t) cc_final: 0.4296 (t) REVERT: A 402 LYS cc_start: 0.7548 (mptt) cc_final: 0.7253 (mptt) REVERT: A 446 GLN cc_start: 0.8012 (pp30) cc_final: 0.7198 (pp30) REVERT: A 450 GLU cc_start: 0.7857 (mt-10) cc_final: 0.7498 (mt-10) REVERT: A 452 GLU cc_start: 0.8019 (tm-30) cc_final: 0.7668 (tm-30) REVERT: A 475 SER cc_start: 0.6842 (t) cc_final: 0.6136 (p) REVERT: A 482 ASN cc_start: 0.1694 (OUTLIER) cc_final: 0.1202 (p0) REVERT: A 536 MET cc_start: 0.6402 (tpp) cc_final: 0.5878 (tpt) REVERT: A 558 MET cc_start: 0.0882 (ttt) cc_final: -0.1225 (ttt) REVERT: A 603 LYS cc_start: 0.8303 (tppt) cc_final: 0.8070 (tppt) REVERT: A 604 ASN cc_start: 0.7445 (p0) cc_final: 0.7033 (p0) REVERT: A 608 LEU cc_start: 0.7971 (OUTLIER) cc_final: 0.7740 (mt) REVERT: A 623 LYS cc_start: 0.8103 (mttt) cc_final: 0.7538 (mmmm) REVERT: A 637 TYR cc_start: 0.6794 (m-10) cc_final: 0.4625 (m-10) REVERT: A 639 GLU cc_start: 0.7263 (tp30) cc_final: 0.6888 (tp30) REVERT: A 646 LYS cc_start: 0.8809 (ptpt) cc_final: 0.8568 (ptpp) REVERT: A 671 MET cc_start: 0.6404 (ttt) cc_final: 0.5880 (ttt) REVERT: A 732 LYS cc_start: 0.7622 (mmtt) cc_final: 0.7395 (mmtt) REVERT: A 741 PHE cc_start: 0.6734 (t80) cc_final: 0.6357 (t80) REVERT: A 770 MET cc_start: 0.7140 (tmm) cc_final: 0.6604 (tmm) REVERT: A 774 GLN cc_start: 0.7740 (tp40) cc_final: 0.7307 (tp40) REVERT: A 785 MET cc_start: 0.5865 (mtp) cc_final: 0.5503 (mmm) REVERT: A 817 GLU cc_start: 0.7252 (OUTLIER) cc_final: 0.7025 (pm20) REVERT: A 842 LEU cc_start: 0.8352 (tp) cc_final: 0.8104 (tp) REVERT: A 861 LYS cc_start: 0.8703 (mptt) cc_final: 0.8172 (mmtm) REVERT: A 873 GLU cc_start: 0.7753 (mt-10) cc_final: 0.7208 (mp0) REVERT: A 886 MET cc_start: 0.6257 (tpp) cc_final: 0.5808 (tpp) REVERT: A 913 LYS cc_start: 0.8668 (tptt) cc_final: 0.8273 (tppt) REVERT: A 929 MET cc_start: 0.7036 (tpt) cc_final: 0.6573 (tpt) REVERT: A 961 MET cc_start: 0.7527 (OUTLIER) cc_final: 0.6873 (tmm) REVERT: A 969 GLU cc_start: 0.7918 (tp30) cc_final: 0.7473 (tp30) REVERT: A 985 LYS cc_start: 0.6870 (tmtt) cc_final: 0.6435 (tptt) REVERT: A 1102 LYS cc_start: 0.6622 (tptt) cc_final: 0.6064 (mmmt) REVERT: A 1106 GLU cc_start: 0.6746 (mm-30) cc_final: 0.6330 (mm-30) REVERT: A 1109 ASP cc_start: 0.7426 (t0) cc_final: 0.6941 (t0) REVERT: A 1126 MET cc_start: 0.8059 (mmm) cc_final: 0.7794 (mmm) REVERT: A 1142 MET cc_start: 0.6302 (tpt) cc_final: 0.5717 (tpp) REVERT: A 1147 MET cc_start: 0.7723 (tmm) cc_final: 0.7421 (tmm) REVERT: A 1171 LYS cc_start: 0.8041 (tppt) cc_final: 0.7680 (tppt) REVERT: A 1176 PHE cc_start: 0.7784 (t80) cc_final: 0.7444 (t80) REVERT: A 1201 ILE cc_start: 0.7198 (mp) cc_final: 0.6917 (mm) REVERT: A 1209 LEU cc_start: 0.8217 (tp) cc_final: 0.8000 (tp) REVERT: A 1318 MET cc_start: 0.6697 (mmt) cc_final: 0.5240 (tpp) REVERT: A 1333 HIS cc_start: 0.6362 (t70) cc_final: 0.5986 (t-170) REVERT: A 1338 LYS cc_start: 0.8468 (ptmt) cc_final: 0.8253 (ptmt) REVERT: A 1363 ASN cc_start: 0.7375 (m-40) cc_final: 0.7133 (m-40) REVERT: A 1433 CYS cc_start: 0.6934 (p) cc_final: 0.6560 (p) REVERT: A 1482 GLN cc_start: 0.7172 (tm-30) cc_final: 0.6544 (tm-30) REVERT: A 1509 LYS cc_start: 0.7842 (mptt) cc_final: 0.7212 (mptt) REVERT: A 1542 TYR cc_start: 0.7020 (t80) cc_final: 0.6045 (t80) REVERT: A 1549 LEU cc_start: 0.7701 (OUTLIER) cc_final: 0.7312 (tp) REVERT: A 1569 MET cc_start: 0.7433 (ptm) cc_final: 0.7047 (tmm) REVERT: A 1575 LYS cc_start: 0.8340 (mttp) cc_final: 0.7468 (mmmt) REVERT: A 1588 LYS cc_start: 0.7654 (tptt) cc_final: 0.7444 (mmmt) REVERT: A 1621 MET cc_start: 0.5979 (mpp) cc_final: 0.4883 (pmm) REVERT: A 1820 LYS cc_start: 0.8119 (ptpt) cc_final: 0.7877 (ptpt) REVERT: A 1827 ILE cc_start: 0.6629 (pt) cc_final: 0.5296 (mt) REVERT: A 1891 LYS cc_start: 0.8290 (mmtt) cc_final: 0.8019 (mmmt) REVERT: A 1893 ILE cc_start: 0.8210 (OUTLIER) cc_final: 0.7780 (tp) REVERT: A 1898 ASP cc_start: 0.6586 (t0) cc_final: 0.6336 (t0) REVERT: A 1953 ARG cc_start: 0.6849 (OUTLIER) cc_final: 0.6297 (mmt180) REVERT: A 1966 PHE cc_start: 0.7255 (m-80) cc_final: 0.6851 (m-10) REVERT: A 2010 LEU cc_start: 0.8082 (tp) cc_final: 0.7769 (tp) REVERT: A 2055 GLU cc_start: 0.8064 (pt0) cc_final: 0.6744 (mm-30) REVERT: A 2057 LYS cc_start: 0.8563 (mmtm) cc_final: 0.8107 (mmmt) REVERT: A 2168 MET cc_start: 0.5067 (tpt) cc_final: 0.4479 (mmm) REVERT: A 2296 VAL cc_start: 0.3788 (OUTLIER) cc_final: 0.2781 (t) REVERT: A 2301 SER cc_start: 0.8049 (t) cc_final: 0.7591 (p) REVERT: A 2357 LEU cc_start: 0.7704 (OUTLIER) cc_final: 0.7166 (mt) REVERT: A 2603 GLU cc_start: 0.8721 (tm-30) cc_final: 0.8171 (tm-30) REVERT: A 2607 LYS cc_start: 0.8907 (mmmt) cc_final: 0.8534 (mmmt) outliers start: 41 outliers final: 28 residues processed: 412 average time/residue: 0.3044 time to fit residues: 189.1236 Evaluate side-chains 424 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 387 time to evaluate : 2.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 406 ILE 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 608 LEU 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 817 GLU Chi-restraints excluded: chain A residue 829 ASN 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 1510 SER Chi-restraints excluded: chain A residue 1537 ASP Chi-restraints excluded: chain A residue 1549 LEU Chi-restraints excluded: chain A residue 1698 GLU Chi-restraints excluded: chain A residue 1825 LEU Chi-restraints excluded: chain A residue 1832 PHE 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 1997 THR Chi-restraints excluded: chain A residue 2039 ILE Chi-restraints excluded: chain A residue 2061 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 186 optimal weight: 7.9990 chunk 139 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 124 optimal weight: 0.7980 chunk 151 optimal weight: 4.9990 chunk 104 optimal weight: 6.9990 chunk 167 optimal weight: 6.9990 chunk 127 optimal weight: 0.7980 chunk 118 optimal weight: 0.7980 chunk 95 optimal weight: 3.9990 chunk 130 optimal weight: 3.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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** 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** ** A2009 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2309 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 = 0.4656 r_free = 0.4656 target = 0.199077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.163178 restraints weight = 42287.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.4328 r_free = 0.4328 target = 0.167618 restraints weight = 27379.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4364 r_free = 0.4364 target = 0.170673 restraints weight = 19576.987| |-----------------------------------------------------------------------------| r_work (final): 0.4341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6165 moved from start: 0.3532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 18394 Z= 0.161 Angle : 0.759 15.562 24780 Z= 0.387 Chirality : 0.046 0.314 2839 Planarity : 0.004 0.102 3112 Dihedral : 5.240 45.919 2411 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 15.42 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.83 % Favored : 91.13 % Rotamer: Outliers : 2.03 % Allowed : 20.66 % Favored : 77.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.18), residues: 2220 helix: 0.56 (0.15), residues: 1226 sheet: -0.42 (0.51), residues: 93 loop : -2.56 (0.20), residues: 901 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP A1857 HIS 0.005 0.001 HIS A 893 PHE 0.023 0.001 PHE A2278 TYR 0.046 0.002 TYR A 876 ARG 0.013 0.001 ARG A2033 Details of bonding type rmsd hydrogen bonds : bond 0.03939 ( 877) hydrogen bonds : angle 4.68588 ( 2586) covalent geometry : bond 0.00340 (18394) covalent geometry : angle 0.75899 (24780) *********************** 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 441 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 399 time to evaluate : 1.871 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 322 THR cc_start: 0.4534 (t) cc_final: 0.4023 (t) REVERT: A 402 LYS cc_start: 0.7527 (mptt) cc_final: 0.7251 (mptt) REVERT: A 446 GLN cc_start: 0.8022 (pp30) cc_final: 0.7258 (pp30) REVERT: A 450 GLU cc_start: 0.7825 (mt-10) cc_final: 0.7491 (mt-10) REVERT: A 452 GLU cc_start: 0.8022 (tm-30) cc_final: 0.7674 (tm-30) REVERT: A 475 SER cc_start: 0.6678 (t) cc_final: 0.5877 (p) REVERT: A 482 ASN cc_start: 0.2032 (OUTLIER) cc_final: 0.1567 (p0) REVERT: A 536 MET cc_start: 0.6415 (tpp) cc_final: 0.6017 (tpt) REVERT: A 603 LYS cc_start: 0.8263 (tppt) cc_final: 0.8016 (tppt) REVERT: A 604 ASN cc_start: 0.7464 (p0) cc_final: 0.7085 (p0) REVERT: A 623 LYS cc_start: 0.8146 (mttt) cc_final: 0.7614 (mmmm) REVERT: A 637 TYR cc_start: 0.6805 (m-10) cc_final: 0.4575 (m-10) REVERT: A 639 GLU cc_start: 0.7226 (tp30) cc_final: 0.6899 (tp30) REVERT: A 646 LYS cc_start: 0.8811 (ptpt) cc_final: 0.8567 (mtmm) REVERT: A 671 MET cc_start: 0.6396 (ttt) cc_final: 0.5875 (ttt) REVERT: A 702 GLU cc_start: 0.7081 (pm20) cc_final: 0.6758 (pm20) REVERT: A 732 LYS cc_start: 0.7631 (mmtt) cc_final: 0.7389 (mmtt) REVERT: A 741 PHE cc_start: 0.6712 (t80) cc_final: 0.6347 (t80) REVERT: A 770 MET cc_start: 0.7196 (tmm) cc_final: 0.6629 (tmm) REVERT: A 785 MET cc_start: 0.5869 (mtp) cc_final: 0.5485 (mmm) REVERT: A 842 LEU cc_start: 0.8343 (tp) cc_final: 0.8099 (tp) REVERT: A 873 GLU cc_start: 0.7759 (mt-10) cc_final: 0.7193 (mp0) REVERT: A 886 MET cc_start: 0.6244 (tpp) cc_final: 0.5799 (tpp) REVERT: A 911 PHE cc_start: 0.6152 (t80) cc_final: 0.5259 (t80) REVERT: A 913 LYS cc_start: 0.8658 (tptt) cc_final: 0.8262 (tppt) REVERT: A 929 MET cc_start: 0.7086 (tpt) cc_final: 0.6583 (tpt) REVERT: A 961 MET cc_start: 0.7646 (OUTLIER) cc_final: 0.6981 (tmm) REVERT: A 969 GLU cc_start: 0.7936 (tp30) cc_final: 0.7516 (tp30) REVERT: A 985 LYS cc_start: 0.6870 (tmtt) cc_final: 0.6442 (tptt) REVERT: A 1102 LYS cc_start: 0.6607 (tptt) cc_final: 0.6025 (mmmt) REVERT: A 1106 GLU cc_start: 0.6781 (mm-30) cc_final: 0.6350 (mm-30) REVERT: A 1109 ASP cc_start: 0.7443 (t0) cc_final: 0.6923 (t0) REVERT: A 1126 MET cc_start: 0.7966 (mmm) cc_final: 0.7738 (mmm) REVERT: A 1142 MET cc_start: 0.6338 (tpt) cc_final: 0.5759 (tpp) REVERT: A 1147 MET cc_start: 0.7742 (tmm) cc_final: 0.7354 (tmm) REVERT: A 1171 LYS cc_start: 0.8066 (tppt) cc_final: 0.7681 (tppt) REVERT: A 1176 PHE cc_start: 0.7766 (t80) cc_final: 0.7412 (t80) REVERT: A 1201 ILE cc_start: 0.7243 (mp) cc_final: 0.6952 (mm) REVERT: A 1209 LEU cc_start: 0.8300 (tp) cc_final: 0.8032 (tp) REVERT: A 1267 GLU cc_start: 0.7882 (tm-30) cc_final: 0.7557 (tm-30) REVERT: A 1338 LYS cc_start: 0.8478 (ptmt) cc_final: 0.8257 (ptmt) REVERT: A 1433 CYS cc_start: 0.6955 (p) cc_final: 0.6576 (p) REVERT: A 1453 MET cc_start: 0.7323 (mmm) cc_final: 0.7103 (mmm) REVERT: A 1482 GLN cc_start: 0.7165 (tm-30) cc_final: 0.6550 (tm-30) REVERT: A 1509 LYS cc_start: 0.7853 (mptt) cc_final: 0.7205 (mptt) REVERT: A 1542 TYR cc_start: 0.7060 (t80) cc_final: 0.6057 (t80) REVERT: A 1549 LEU cc_start: 0.7700 (OUTLIER) cc_final: 0.7311 (tp) REVERT: A 1569 MET cc_start: 0.7433 (ptm) cc_final: 0.7028 (tmm) REVERT: A 1575 LYS cc_start: 0.8342 (mttp) cc_final: 0.7439 (mmmt) REVERT: A 1588 LYS cc_start: 0.7666 (tptt) cc_final: 0.7458 (mmmt) REVERT: A 1673 LEU cc_start: 0.7277 (mm) cc_final: 0.6667 (tp) REVERT: A 1817 CYS cc_start: 0.6692 (p) cc_final: 0.6491 (t) REVERT: A 1820 LYS cc_start: 0.8175 (ptpt) cc_final: 0.7881 (ptpt) REVERT: A 1827 ILE cc_start: 0.6650 (pt) cc_final: 0.5405 (mt) REVERT: A 1891 LYS cc_start: 0.8287 (mmtt) cc_final: 0.7997 (mmmt) REVERT: A 1893 ILE cc_start: 0.8228 (OUTLIER) cc_final: 0.7808 (tp) REVERT: A 1898 ASP cc_start: 0.6673 (t0) cc_final: 0.6378 (t0) REVERT: A 1953 ARG cc_start: 0.6845 (OUTLIER) cc_final: 0.6218 (mmt180) REVERT: A 1966 PHE cc_start: 0.7297 (m-80) cc_final: 0.6908 (m-80) REVERT: A 1978 PHE cc_start: 0.5605 (p90) cc_final: 0.5188 (p90) REVERT: A 2010 LEU cc_start: 0.8083 (tp) cc_final: 0.7774 (tp) REVERT: A 2034 GLU cc_start: 0.7859 (mp0) cc_final: 0.7387 (mp0) REVERT: A 2055 GLU cc_start: 0.8064 (pt0) cc_final: 0.6762 (mm-30) REVERT: A 2057 LYS cc_start: 0.8584 (mmtm) cc_final: 0.8016 (mmmt) REVERT: A 2168 MET cc_start: 0.5197 (tpt) cc_final: 0.4664 (mmm) REVERT: A 2278 PHE cc_start: 0.6527 (m-10) cc_final: 0.6326 (m-10) REVERT: A 2296 VAL cc_start: 0.3964 (OUTLIER) cc_final: 0.2985 (t) REVERT: A 2301 SER cc_start: 0.8044 (t) cc_final: 0.7579 (p) REVERT: A 2357 LEU cc_start: 0.7716 (OUTLIER) cc_final: 0.7172 (mt) REVERT: A 2603 GLU cc_start: 0.8715 (tm-30) cc_final: 0.8203 (tm-30) REVERT: A 2607 LYS cc_start: 0.8899 (mmmt) cc_final: 0.8635 (mmmt) outliers start: 42 outliers final: 28 residues processed: 416 average time/residue: 0.3199 time to fit residues: 202.1723 Evaluate side-chains 427 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 392 time to evaluate : 2.095 ------------------------------------------------------------------------------- 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 608 LEU 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 829 ASN 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 1420 SER Chi-restraints excluded: chain A residue 1510 SER Chi-restraints excluded: chain A residue 1537 ASP Chi-restraints excluded: chain A residue 1549 LEU Chi-restraints excluded: chain A residue 1698 GLU Chi-restraints excluded: chain A residue 1825 LEU Chi-restraints excluded: chain A residue 1832 PHE 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 1997 THR Chi-restraints excluded: chain A residue 2039 ILE Chi-restraints excluded: chain A residue 2061 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 180 optimal weight: 9.9990 chunk 213 optimal weight: 5.9990 chunk 169 optimal weight: 4.9990 chunk 212 optimal weight: 2.9990 chunk 218 optimal weight: 0.0980 chunk 71 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 chunk 150 optimal weight: 2.9990 chunk 97 optimal weight: 0.5980 chunk 19 optimal weight: 6.9990 chunk 3 optimal weight: 7.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- 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** A1480 GLN ** 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 = 0.4646 r_free = 0.4646 target = 0.197465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.162925 restraints weight = 41768.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.4332 r_free = 0.4332 target = 0.167323 restraints weight = 27030.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.4368 r_free = 0.4368 target = 0.170389 restraints weight = 19213.736| |-----------------------------------------------------------------------------| r_work (final): 0.4338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6166 moved from start: 0.3796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 18394 Z= 0.183 Angle : 0.788 15.409 24780 Z= 0.405 Chirality : 0.047 0.323 2839 Planarity : 0.004 0.101 3112 Dihedral : 5.354 45.359 2411 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 16.85 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.05 % Favored : 90.90 % Rotamer: Outliers : 1.98 % Allowed : 20.80 % Favored : 77.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.23 (0.18), residues: 2220 helix: 0.39 (0.15), residues: 1238 sheet: -0.62 (0.52), residues: 92 loop : -2.65 (0.20), residues: 890 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP A1857 HIS 0.005 0.001 HIS A 893 PHE 0.022 0.001 PHE A 707 TYR 0.045 0.002 TYR A 876 ARG 0.011 0.001 ARG A2033 Details of bonding type rmsd hydrogen bonds : bond 0.04173 ( 877) hydrogen bonds : angle 4.84027 ( 2586) covalent geometry : bond 0.00382 (18394) covalent geometry : angle 0.78806 (24780) ********************** 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 439 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 398 time to evaluate : 1.946 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: A 322 THR cc_start: 0.4502 (t) cc_final: 0.4226 (t) REVERT: A 402 LYS cc_start: 0.7508 (mptt) cc_final: 0.7192 (mptt) REVERT: A 407 GLN cc_start: 0.7382 (mm-40) cc_final: 0.6615 (pm20) REVERT: A 446 GLN cc_start: 0.8052 (pp30) cc_final: 0.7265 (pp30) REVERT: A 450 GLU cc_start: 0.7823 (mt-10) cc_final: 0.7480 (mt-10) REVERT: A 452 GLU cc_start: 0.8056 (tm-30) cc_final: 0.7694 (tm-30) REVERT: A 475 SER cc_start: 0.6687 (t) cc_final: 0.6149 (p) REVERT: A 482 ASN cc_start: 0.2355 (OUTLIER) cc_final: 0.1453 (p0) REVERT: A 536 MET cc_start: 0.6513 (tpp) cc_final: 0.6017 (tpt) REVERT: A 558 MET cc_start: 0.1273 (ttt) cc_final: -0.0936 (ttt) REVERT: A 604 ASN cc_start: 0.7447 (p0) cc_final: 0.6730 (p0) REVERT: A 623 LYS cc_start: 0.8159 (mttt) cc_final: 0.7561 (mmmm) REVERT: A 637 TYR cc_start: 0.6828 (m-10) cc_final: 0.4634 (m-10) REVERT: A 639 GLU cc_start: 0.7280 (tp30) cc_final: 0.6933 (tp30) REVERT: A 642 MET cc_start: 0.7520 (ttt) cc_final: 0.7305 (ttm) REVERT: A 646 LYS cc_start: 0.8829 (ptpt) cc_final: 0.8575 (ptpp) REVERT: A 671 MET cc_start: 0.6431 (ttt) cc_final: 0.5906 (ttt) REVERT: A 702 GLU cc_start: 0.7099 (pm20) cc_final: 0.6350 (pm20) REVERT: A 717 MET cc_start: 0.5131 (tpp) cc_final: 0.4683 (tpt) REVERT: A 741 PHE cc_start: 0.6757 (t80) cc_final: 0.6362 (t80) REVERT: A 770 MET cc_start: 0.7211 (tmm) cc_final: 0.6695 (tmm) REVERT: A 785 MET cc_start: 0.5933 (mtp) cc_final: 0.5505 (mmm) REVERT: A 842 LEU cc_start: 0.8340 (tp) cc_final: 0.8100 (tp) REVERT: A 861 LYS cc_start: 0.8696 (mptt) cc_final: 0.8339 (mmtm) REVERT: A 873 GLU cc_start: 0.7864 (mt-10) cc_final: 0.7301 (mp0) REVERT: A 886 MET cc_start: 0.6218 (tpp) cc_final: 0.5766 (tpp) REVERT: A 913 LYS cc_start: 0.8639 (tptt) cc_final: 0.8257 (tppt) REVERT: A 929 MET cc_start: 0.7129 (tpt) cc_final: 0.6619 (tpt) REVERT: A 961 MET cc_start: 0.7674 (OUTLIER) cc_final: 0.6999 (tmm) REVERT: A 969 GLU cc_start: 0.7943 (tp30) cc_final: 0.7586 (tp30) REVERT: A 985 LYS cc_start: 0.6910 (tmtt) cc_final: 0.6473 (tptt) REVERT: A 1102 LYS cc_start: 0.6703 (tptt) cc_final: 0.6422 (mmmt) REVERT: A 1106 GLU cc_start: 0.6775 (mm-30) cc_final: 0.6336 (mm-30) REVERT: A 1109 ASP cc_start: 0.7422 (t0) cc_final: 0.6942 (t0) REVERT: A 1142 MET cc_start: 0.6349 (tpt) cc_final: 0.5762 (tpp) REVERT: A 1147 MET cc_start: 0.7745 (tmm) cc_final: 0.7329 (tmm) REVERT: A 1171 LYS cc_start: 0.8029 (tppt) cc_final: 0.7618 (tppt) REVERT: A 1176 PHE cc_start: 0.7797 (t80) cc_final: 0.7453 (t80) REVERT: A 1201 ILE cc_start: 0.7187 (mp) cc_final: 0.6883 (mm) REVERT: A 1209 LEU cc_start: 0.8334 (tp) cc_final: 0.8043 (tp) REVERT: A 1267 GLU cc_start: 0.7842 (tm-30) cc_final: 0.7636 (tm-30) REVERT: A 1338 LYS cc_start: 0.8518 (ptmt) cc_final: 0.8281 (ptmt) REVERT: A 1363 ASN cc_start: 0.7686 (m-40) cc_final: 0.7203 (m-40) REVERT: A 1433 CYS cc_start: 0.6978 (p) cc_final: 0.6655 (p) REVERT: A 1453 MET cc_start: 0.7338 (mmm) cc_final: 0.7123 (mmm) REVERT: A 1482 GLN cc_start: 0.7242 (tm-30) cc_final: 0.6622 (tm-30) REVERT: A 1503 LYS cc_start: 0.8396 (ptpt) cc_final: 0.8108 (ptpt) REVERT: A 1509 LYS cc_start: 0.7879 (mptt) cc_final: 0.7233 (mptt) REVERT: A 1549 LEU cc_start: 0.7705 (OUTLIER) cc_final: 0.7361 (tp) REVERT: A 1569 MET cc_start: 0.7434 (ptm) cc_final: 0.7012 (tmm) REVERT: A 1575 LYS cc_start: 0.8324 (mttp) cc_final: 0.7454 (mmmt) REVERT: A 1618 LEU cc_start: 0.8140 (mt) cc_final: 0.7718 (mt) REVERT: A 1621 MET cc_start: 0.6112 (mpp) cc_final: 0.4793 (pmm) REVERT: A 1673 LEU cc_start: 0.7462 (mm) cc_final: 0.6899 (tp) REVERT: A 1820 LYS cc_start: 0.8262 (ptpt) cc_final: 0.7951 (ptpt) REVERT: A 1827 ILE cc_start: 0.6717 (pt) cc_final: 0.5480 (mt) REVERT: A 1891 LYS cc_start: 0.8337 (mmtt) cc_final: 0.8026 (mmmt) REVERT: A 1893 ILE cc_start: 0.8287 (OUTLIER) cc_final: 0.7848 (tp) REVERT: A 1898 ASP cc_start: 0.6747 (t0) cc_final: 0.6450 (t0) REVERT: A 1953 ARG cc_start: 0.6858 (OUTLIER) cc_final: 0.6253 (mmt180) REVERT: A 1966 PHE cc_start: 0.7296 (m-80) cc_final: 0.7062 (m-10) REVERT: A 2010 LEU cc_start: 0.8047 (tp) cc_final: 0.7734 (tp) REVERT: A 2055 GLU cc_start: 0.8060 (pt0) cc_final: 0.6735 (mm-30) REVERT: A 2057 LYS cc_start: 0.8608 (mmtm) cc_final: 0.8045 (mmmt) REVERT: A 2168 MET cc_start: 0.5291 (tpt) cc_final: 0.4707 (mmm) REVERT: A 2296 VAL cc_start: 0.3818 (OUTLIER) cc_final: 0.2858 (t) REVERT: A 2301 SER cc_start: 0.8067 (t) cc_final: 0.7526 (p) REVERT: A 2305 GLU cc_start: 0.6971 (pm20) cc_final: 0.6724 (pm20) REVERT: A 2342 GLN cc_start: 0.7001 (mt0) cc_final: 0.6717 (mp10) REVERT: A 2357 LEU cc_start: 0.7734 (OUTLIER) cc_final: 0.7223 (mt) REVERT: A 2590 ASN cc_start: 0.4361 (OUTLIER) cc_final: 0.4121 (m-40) REVERT: A 2603 GLU cc_start: 0.8693 (tm-30) cc_final: 0.8174 (tm-30) REVERT: A 2607 LYS cc_start: 0.8881 (mmmt) cc_final: 0.8624 (mmmt) outliers start: 41 outliers final: 27 residues processed: 415 average time/residue: 0.3063 time to fit residues: 192.4214 Evaluate side-chains 429 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 394 time to evaluate : 1.918 ------------------------------------------------------------------------------- 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 729 SER Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 829 ASN 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 1420 SER Chi-restraints excluded: chain A residue 1510 SER Chi-restraints excluded: chain A residue 1537 ASP Chi-restraints excluded: chain A residue 1549 LEU Chi-restraints excluded: chain A residue 1698 GLU Chi-restraints excluded: chain A residue 1825 LEU Chi-restraints excluded: chain A residue 1832 PHE 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 1997 THR Chi-restraints excluded: chain A residue 2039 ILE Chi-restraints excluded: chain A residue 2061 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 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 115 optimal weight: 0.3980 chunk 153 optimal weight: 0.5980 chunk 183 optimal weight: 6.9990 chunk 192 optimal weight: 0.7980 chunk 83 optimal weight: 0.0050 chunk 215 optimal weight: 4.9990 chunk 172 optimal weight: 10.0000 chunk 44 optimal weight: 0.9990 chunk 26 optimal weight: 3.9990 chunk 98 optimal weight: 2.9990 chunk 124 optimal weight: 0.7980 overall best weight: 0.5194 ------------------------------------------------------------------------------- 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** A1113 GLN A1141 GLN A1324 ASN ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4674 r_free = 0.4674 target = 0.200282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.165837 restraints weight = 41529.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4366 r_free = 0.4366 target = 0.170342 restraints weight = 26832.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4402 r_free = 0.4402 target = 0.173395 restraints weight = 18956.164| |-----------------------------------------------------------------------------| r_work (final): 0.4378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6089 moved from start: 0.3824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 18394 Z= 0.136 Angle : 0.772 14.912 24780 Z= 0.392 Chirality : 0.045 0.321 2839 Planarity : 0.004 0.074 3112 Dihedral : 5.170 44.124 2411 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 14.54 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.66 % Favored : 92.30 % Rotamer: Outliers : 1.64 % Allowed : 21.53 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.18), residues: 2220 helix: 0.60 (0.15), residues: 1224 sheet: -0.48 (0.51), residues: 94 loop : -2.56 (0.20), residues: 902 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP A1857 HIS 0.005 0.001 HIS A 893 PHE 0.032 0.001 PHE A 707 TYR 0.047 0.001 TYR A 876 ARG 0.012 0.001 ARG A 802 Details of bonding type rmsd hydrogen bonds : bond 0.03684 ( 877) hydrogen bonds : angle 4.57585 ( 2586) covalent geometry : bond 0.00297 (18394) covalent geometry : angle 0.77208 (24780) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6911.27 seconds wall clock time: 121 minutes 53.39 seconds (7313.39 seconds total)